Abstracts - 4th Annual Meeting of the Chickpea Innovation Lab, December 2017


Download the entire program -- includes agenda, overview, abstract and participant list.

Chickpea Innovation Lab Dec 2017 Program Final.pdf


Abstracts listed are in alphabetical order by first author's last name.


Of Chickpeas and Microbes: A Two Pronged Approach for Identifying Bacteria with Plant Growth Promoting Activity

Betsy A. Alford1, Brendan K. Riely1, Ping Song3, Rabia Mufti 2, Douglas R. Cook1

1Department of Plant Pathology, University of California-Davis
2Quaid-i-Azam University, Department of Plant Sciences
3Fujian Agriculture and Forestry University, China

The rhizophere is a complex ecosystem containing microbes that are capable of associating with a plant. Some members of these microbial communities provide services to assist in nutrient acquisition, drought tolerance, and disease resistance.  Here, we use a two-pronged approach to identify microbes with potential beneficial effects on wild plant communities.  First, we used a culture independent, in silico approach based on amplicon sequencing of a 16S rDNA variable region to identify microbes that commonly associate with wild chickpea (Cicer reticulatum and C. echinospermum). Second, we used a baiting approach to culture and identify over 700 individual bacterial isolates from wild origin soils. 

16S analysis identified >8,000 taxonomic bins in wild soils and plant rhizospheres, of which 24 were consistently associated with wild chickpea plants. Interestingly, across 21 wild locations, specific plant compartments (on, in or adjacent to roots or nodules) repeatedly recruited characteristic microbial communities, despite soil type and plant genotype heterogeneity. Soil type was also a factor determining microbial community structure, as revealed in a large common garden experiment, with three genotypes from each of four wild populations (12 genotypes total) reciprocally transplanted into all combinations of their respective home and away soils.

~700 strains were purified from the rhizospheres of plants grown on wild soils. Following taxonomic sequencing, 191 isolates were selected for whole genome sequencing, revealing 19 genera and numerous species spanning all four phyla of the Bacteria. Strains were further characterized by in vitro testing of presumed plant growth promoting properties commonly associated with rhizobacteria: phosphate solubilization, growth on 1-aminocyclopropane carboxylic acid (ACC deamination) or tryptophan (indole acetic acid (IAA) production), and antifungal activity against the chickpea soil borne pathogen Fusarium oxysporum f.sp. ciceris. These results nominate a subset of 14 strains as potential plant growth promoting rhizobacteria (PGPRs): all are effective phosphate solubilizers, 3 have strong antifungal activity, and 2 or 1 strains grow on ACC or IAA as the sole nitrogen source, respectively.

Of the 191 isolates screened for PGPP activity, 188 contained DNA signatures that were also present in the in silico wild chickpea 16S survey, falling into 43 16S taxonomic bins.  Of the 24 taxonomic bins commonly associated with plant tissues, 6 (32 total isolates) are represented in the microbial culture collection. Future work will test the activities of these strains in planta.



Yetsedaw Aynewa1, Addisu Asfaw2, Mohammed Ebrahim2, Temesgen Alene2, Seid Ahmed1 and Zewdie Bishaw1

1 International Center for Agricultural Research in the Dry Areas (ICARDA), Box 5689, Addis Ababa, Ethiopia 

2 International Livestock Research Institute (ILRI), Box 5689, Addis Ababa, Ethiopia

Both Desi and Kabuli chickpea (Cicer arietinum) are important cool-season in wheat-based cropping system of the Ethiopian highlands. The crop is planted mainly on black soil towards the end of the rainy season and suffers from terminal drought. Through changes in planting dates (August), the productivity (over 3t/ha compared to 1.8t/ha national average) and adoption of kabuli chickpea has increased in some portion of the country. The key traits for success of early planting are resistance to Ascochyta blight, wilt/root rot and tolerance to transient waterlogging. Currently many farmers are planting their Kabuli chickpea in August rather than end of September-early October in waterlogged black soil of the mid-highlands. However, there is a need to push chickpea planting dates in early July and early August in moisture stressed areas of the country to break wheat mono-cropping. Five kabuli chickpea cultivars (Ejere=FLIP-97-263; Hora=FLIP-04-9; Habru=FLIP-88-42; Arerti= FLIP 89-84 and DZ-10-4) and one Desi cultivar (Minjar=ICCV-03107) were evaluated as participatory variety trails in South Tigray, Bale, and Hosana zones. Twelve farmers (4 farmers per Zone) participated in hosting the trial. Data on Ascochyta blight (Didymella rabiei) reactions of the cultivars were taken using 1-9 rating scale where 1= highly resistant and 9= highly susceptible. Ascochyta blight was developed from natural inoculum sources and some of the cultivars were killed. The cvs. Arerti and Hora showed good levels of resistance across locations (1-3 rating). The other cultivars showed high susceptibility in some locations but moderately resistance to others. Farmers selected cv. Arerti and Hora in areas where Ascochyta severity of very high and the two cultivars will be promoted in wheat based cropping system where waterlogging is not a major problem. The population of D. rabiei should be studied since some cultivars showed different reactions in different places. Ascochyta blight resistance level in Desi chickpea needs to be improved since inoculum will move from early planted chickpea to the local Desi types which are susceptible to the disease.


Transpiration rate of chickpea wild accessions and cultivars in Turkey

Fatma Basdemir1, Mehmet Yıldırım1, Behiye T. Biçer1, Bekir Bükün1, Vincent Vadez2, Douglas R. Cook3

1Dicle University, Faculty of Agriculture, Diyarbakır, 21280,Turkey

2ICRISAT, Patencheru, 502324,India

3Department of Plant Pathology, University of Californa, Davis, CA 95616, USA

This year VPD experiments were carried out to test transpiration rate (TR mg H20 cm2 min1) at the high vapour pressure deficit (VPD) at two different growing stages (before flowering time at the vegetative stage and middle of pod filling stages). Both experiment were conducted at the Dicle University in the growth chamber. The experimental design was complete randomised block design with 6 replicates. The first TR (for the vegetative growth stage) experiment was conducted during spring season (10 Feb to 16 Apr) and the second TR (for the pod filling growth stage) was conducted 10 Feb to 13 May. Analyses conducted in potted plants acclimated to outdoor conditions, with data collected over the course of an entire day. Potted plants weighed at regular intervals to measure TR, starting from morning to onwards under increasing VPD. Plants were harvested at the end of the TR experiment and total leaf area determined along with shoot and leaf dry weights. VPD conditions varied between 1.84-3.93 kPa, 1.71-3.80 kPa for vegetative stage and pod filling stage, respectively.

At the vegetative stage average transpiration of cultivated genotypes were 54.17 g while wild types 44.42 g. TR of wild genotypes were 3 times higher from cultivated genotypes. However, leaf area of cultivated genotypes were 4 times higher from wild genotypes. There were significant relationship between total transpiration and leaf area.

It is observed that TR sharply declined at the pod filling stage compare to vegetative stage in wild types. TR of wild genotypes was 0,53 at the pod filling stages while was TR 0,76 at the vegetative stages.


Genomics assisted resistance breeding for the development of Fusarium wilt (Fusarium oxysporum f.sp. ciceris) resistant Chickpea (Cicer arietinum L.) genotypes in Ethiopia

Dagnachew Bekele1,2, Kassahun Tesfaye2,3,Asnake Fikre4, Noelia Carrasquilla Garcia5, Douglas Cook5

1Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia.

2Addis Ababa University, Institute of Biotechnology

3Ethiopian Institute of Biotechnology, Addis Ababa, Ethiopia

4International Crop Research Institute for Semi Arid Tropics, Addis Ababa, Ethiopia

5University of California, Davis, USA

Though the potential yield of chickpea exceeds 5t/ha, in Ethiopia the average national yield is below 2t/ha. The wide gap between the average national yield and its genetic potential is mainly due to poor resistance for several biotic and abiotic stresses. Recent advances in next generation sequencing technologies have enabled generation of significant genomic resources that can support the development of biotic and abiotic stresses tolerant varieties. Fusarium wilt caused by Fusarium oxysporum f.sp. ciceris, is one of the most devastating disease of chickpea in Ethiopia that needs very efficient and robust genomic tools to generate resistant varieties. However, only very few incomplete works have been done in Ethiopia and limited information is available to generate Fusarium wilt resistant varieties. To comprehend the existing pathogenic races and their geographical distribution, country wide survey was conducted in 2015 cropping season and diseased plant samples were collected from a total of 217 farmers fields. FOC strains were isolated, purified and spores were used for DNA extraction using a modified phenol chloroform extraction protocol for construction of genomic libraries. A total of 166 representative Fusarium strains were selected and sequenced using WGS. Based on their genomic diversity, pathogenicity test, and geographical distribution a subset of FOC strains will be selected to systematically test wild chickpea introgression populations for Fusarium wilt resistance. Subsequently, chickpea Fusarium wilt resistant genes will be mapped and marker assisted backcrossing will be used for the introgression of the resistant gene into Ethiopian chickpea cultivars.


Scaling of Chickpea Technologies in the Highlands of Ethiopia

Zewdie Bishaw and Adamu Molla

ICARDA, Addis Abeba, Ethiopia

Low national productivity and low adoption of improved technologies of chickpea calls for scaling-up project in making available and accessible improved technologies to the majority of farmers to improve livelihood and nutritional security. Amhara, Oromia and Tigray Regional States are major chickpea producers and target regions of the project. The approach includes demonstration and popularization of improved chickpea varieties and integrated crop management technologies coupled with field days to create awareness and demand; early generation seed (breeder, pre-basic and basic seed) production by NARS; small pack seed distribution through revolving seed fund; rhizobial inoculant pack distribution in partnership with private sector; capacity development of project partners; and forging an effective partnership with private, public and farmer-based actors for sustainability. Achievements: demonstrations proved that improved varieties with improved management packages increased yield by 12-34%, and early planting with improved varieties and management packages increased yield up to three fold; a total of 8639 (1281 female) farmers and 1597 (278 female) staff of stakeholders in chickpea value chain participated in field days; managed to work with 11,024 farmers (1522 female) organized in 19 seed producer and multi-purpose cooperatives; and 4 Unions of cooperatives in seed production, input supply and marketing; distributed 284.8 tons small pack seed, and 20,329 packs of rhizobial inoculants to 43,962 farmers (6,456 female); produced 33.67, 122.34, 782.86 and 1813.15 tons breeder, pre-basic, basic and certified/quality seed in 2015-2016, respectively, benefiting 68,369 farmers; and 465 (53 female) staff of partner NARS and district extension experts trained in training of trainers and in turn trained 9,218 (1,559 females) farmers and 1,474 (248 females) development agents and junior staff of NARS. In conclusion, scaling-up project created awareness and stimulated adoption of improved chickpea technologies. Availability and access to chickpea technologies facilitated through on-farm seed production and marketing. These efforts need to be strengthened to ensure sustainable chickpea production.



Sergey V. Bulyntsev1, Margarita A. Vishnyakova2

1 VIR Kuban Branch, Krasnodar Territory, Russia.

2 Federal Research Centre All-Russian N.I.Vavilov Institute of Plant Genetic Resources (VIR), Saint-Petersburg, Russia,

In recent years, the land under chickpea has been sharply increasing, also in the countries where the acreage has previously been insignificant. It is related to biological properties of the crop, among other things. Chickpea is the second most drought-resistant crop after vetchling, and very often it is the only grain legume represented in crop rotations in the areas with dry climate. As the global climate changes towards warming, and the number of droughty years is increasing, the cultivation area of this crop also tends to increase. Chickpea cultivation was started in the areas where it has never been grown previously.

The broadening of the chickpea cultivation area supposes an increase in chickpea breeding activities aimed at creating cultivars fit for cultivation under new soil and climatic conditions, and capable of meeting modern requirements. In this relation, the importance of chickpea collections around the globe as sources of initial breeding material keeps increasing.

Chickpea breeding in the Russian Federation is aimed at creating high-yielding cultivars adapted to the soil and climatic conditions in the cultivation area. Modern chickpea cultivars should be also suitable for the mechanized harvesting. The genotypes to be selected for this aim should feature a compact bush, high level of the lower beans attachment to the plant, as well as high lodging and cracking resistance. The new cultivars should be resistant to droughts and be adapted to high temperatures during the flowering and seed setting. Due to the spread of cultivation to the northern regions, the creation of high-yielding and early ripening cultivars acquires urgency.

A significant requirement to new cultivars is the presence of resistance to the main fungous diseases, such as Ascochyta blight of chickpea and wilt of chickpea. To this end, breeding of resistant forms should be carried out either against the artificial infectious background or in years of epidemics.

In recent years, a lot of damage to chickpeas in the southern regions has been done by the cotton bollworm and the leaf-miner fly. In order to create that would be resistant to these pests, hybridization should employ wild chickpea species which may serve as sources of resistance.

Special requirements are made to seed quality of the newly developed chickpea . The seeds should have good commercial and technological quality, and have a high protein and oil content. Since there is a growing demand for the large-seeded chickpea at the external markets, the creation of with large seeds and 1000 seed weight of 350-450 acquires urgency.


Non-nuclear perspective into the genome of the Cicer genus

Peter L Chang1,2, Gary Molano2, Anupam Singh2, Eric von Wettberg3, Douglas R Cook1, Sergey V Nuzhdin2

1Department of Plant Pathology, University of California, Davis, CA, 95616, USA

2Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA

3Department of Plant and Soil Science, University of Vermont, Burlington, VT, 05405, USA

Chickpea (Cicer arietinum) is one of the oldest crop introduced into human civilization, having been domesticated in the Fertile Crescent ~10,000 years ago. Historically, its importance lies in its capacity for biological nitrogen fixation and as part of the crop rotational system, adding large amounts of nitrogen into the soil and promoting sustainable agriculture. Today, in many regions of the world, its high protein and mineral levels are still important for nutritional security and provides a good source of energy. Within the plant, chloroplasts are the sites of photosynthesis and play a key role in integrating many metabolic pathways essential for growth and development. As such, characterizing the evolution of the chloroplast genome may be critical to understanding changes in seed yield and energy production throughout the domestication period. Non nuclear genomes such as chloroplasts are also transferred from one generation to another maternally. Hence, studying the genome of the chloroplast can reveal new information when compared with the nuclear genome. We analyzed 281 accessions from the cultivated chickpea and its wild ancestors in the Cicer genus to gain insight into genetic diversity, population structure, possible subspeciation and migrational patterns of this cultivated crop using the chloroplast genome.



Pooran M Gaur1, Srinivasan Samineni1, Tsegaye Getahun Bogale1,2 and Douglas Cook3

1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India

2Addis Ababa University, Addis Ababa, Ethiopia

3Department of Plant Pathology, University of California (UC), Davis, CA 95616, USA

The wild Cicer species offer novel sources of variation for various traits, which can be exploited in chickpea improvement. This study was aimed at evaluating interspecific progenies of chickpea for heat tolerance and agronomic traits. A total of 2,703 F3 progenies of C. arietinum x C. reticulatum and C. arietinum x C. echinospermum crosses, received in three batches from UC-Davis, were evaluated at ICRISAT-Patancheru during 2016-17.

The progenies received in the first batch (1,671) and in the second batch (559) were planted on 28 November 2016 and 20 January 2017, respectively, and evaluated for agronomic traits. Observations were recorded on phenological traits (days to flowering and days to maturity), growth habit (SE = semi-erect, SS = semi-spreading and S = spreading) and grain yield. A total of 411 progenies were found uniform for phenological traits (117 Early maturity, 183 medium maturity, 111 late maturity) and growth habit (67 SE, 67, SS and 277 S) and the remaining progenies showed segregation for these traits. The grain yield per plot ranged from 201 to 300 g in 30 progenies, 101 to 200 g in 585 progenies and 0 to 100 g in the remaining progenies. Over 2100 single plants with SE and SS growth habit and early maturity were selected for further evaluation. A uniform early flowering progeny (UCD#1401 9xDerei_072) that flowered in 32 days was selected and crossed with four breeding lines (ICCV 05106, ICCV 03205, ICCIL 01018 and ICCIL 01042) and F1 seeds were harvested. 

A total of 473 progenies received in the third batch along with seven heat tolerant and sensitive genotypes were screened for heat tolerance. The sowing date was advanced (Feb 2017) as to expose the crop to high temperatures during reproductive stage. The experiment was conducted in alpha-lattice design with two replications. Based on visual score and number of filled pods per plant, 249 progenies tolerant to heat stress were identified. In another experiment, 2134 F4 lines developed from single plants selected from non-stress environment along with seven heat tolerant and sensitive genotypes and nine wild parental lines used in development of inter-specific populations were screened for heat tolerance. This experiment was sown in summer on 18 March 2017 using a partial-rep design where 200 plots were replicated twice. The crop in the second experiment received very high temperatures (40-42OC) during reproductive stage. High level of heat tolerance was observed in 149 progenies. These would be evaluated further during summer season 2018.

The findings of these experiments indicate potential of using the wild species C. reticulatum and C. echinospermum in improving heat tolerance and agronomic traits in chickpea. As cultivated chickpea is known to have narrow genetic base, introgression of novel traits and genetic variability from wild species would be helpful in broadening the genetic base of cultivated chickpea and developing climate resilient varieties.


Phenotyping of chickpea (Cicer arietinum L.) F3 Interspecific segregating populations, Land races and Lines for heat stress

1Tsegaye Getahun, 1Kassahun Tesfaye, 2Douglas Cook, 3Pooran M. Gaur and 3Asnake Fikre 

1Addis Ababa University, Institute of Biotechnology, Ethiopia

2University of California Davis, Department of Pathology and Nematology, USA

3International Crop Research Institute for the Semi-Arid Tropics, India and Ethiopia.

High temperatures (≥35 oC) at reproductive stage drastically decrease chickpea potential seed yield (Krishnamurthy et al., 2011). The objective of the present study is to screen heat stress tolerant germplasm of chickpea (Cicer arietinum L.). The temperatures of ICRISAT, Patancheru, India increases rapidly from March onwards and reached the highest maximum (43 OC) and minimum (30 OC) temperatures during February to June, 2017, were ideal for heat screening. Individual plants of F3 interspecific segregation populations were selected and sorted into super-early, early, medium, late and very late phenological classes. Their DFF was from 20-30, 30-40, 40-50, 50-60 and >60 days, respectively. The first two and last two had short (15-30 days) and long (40-61 days) grain filling periods, respectively. Based on average pod set of all phenological classes/family, 9xSavur_063 (58%), 9xKalka_064 (57%) and 9xOyali_084 (53.3%) were found to be heat tolerant families. The largest number of highly heat tolerant (≥70 and/or ≥80 pod set) individual plants were observed in families of 9xSavur_063 (103), 9xKalka_064 (83) and 9xBari1_092 (69). The average total seeds and grain yield/plant/family data showed that 9xOyali_084 (39.3, 4.2), 9xKalka_064 (37.5, 3.9) and 9xBari1_092 (33.6, 3.3) were the most heat tolerant families. Based on the data of the three parameters 9xKalka_064 and 9xOyali_084 were found to be the two best heat tolerant families. From Ethiopian land races and lines, nine heat tolerant and many escaping genotypes were selected from Ethiopia and India. Using the above findings, the adaptation mechanisms and genetic basis of heat stress will be investigated in the near future.



Siva Kumar Golla1, 2, P. Rajasekhar2, Jagdish Jaba1, H.C. Sharma1, 3

1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru- 502324, Telangana, India

2Acharya N.G. Ranga Agricultural University, Guntur- 522509, Andhra Pradesh, India

3Dr. YS Parmar University of Horticulture and Forestry, Nauni, Solan- 173230, Himachal Pradesh, India

The pod borer, Helicoverpa armigera (Hubner) is one of the most important biotic constraints of chickpea production. However, the levels of resistance in the cultivated chickpea are low to moderate, but the wild relatives of chickpea have exhibited high levels of resistance to H. armigera. It is important to identify different components of resistance and their contribution to develop cultivars with high levels of resistance to insect pests. Therefore, we evaluated a diverse array of 15 accessions of wild relatives along with five cultivated genotypes of chickpea for their resistance to H. armigera.

All the wild relatives of chickpea showed high levels of antibiosis to H. armigera ascompared to the cultivated chickpea in terms of lower larval survival, pupation and adult emergence percentage, decreased larval and pupal weights, prolonged larval and pupal developmental periods, and reduced fecundity when the larvae were reared on artificial diet impregnated with lyophilized leaf powder of the genotypes tested. The accessions IG 70018, IG 70012, IG 70022, PI 599046, PI 599066 and IG 70006 (C. bijugum) and ICCW 17148 (C. microphyllum) showed high levels of resistance to H. armigera, followed by PI 568217, PI 599077 (C. judaicum), PI 510663, PI 599109 (C. pinnatifidum), IG 69979 (C. cuneatum) and IG 599076 (C. chrossanicum) as compared to the cultivated chickpea.

The flavonoid compounds such as chlorogenic acid, ferulic acid, naringin, 3, 4- dihydroxy flavones, quercetin, naringenin, genestein, formononetin and biochanin A identified through HPLC finger prints in different genotypes of wild and cultivated chickpea. The flavonoids showed a positive association with larval and pupal period, and a negative association with larval survival, pupation, larval and pupal weights, adult emergence and fecundity. Proteins and phenols showed a negative effect, while tannins and total soluble sugars showed a positive association with survival and development of H. armigera. The wild relatives exhibiting high levels of resistance can be used to increase the levels and diversify the basis of resistance to H. armigera in cultivated chickpea.



Alex Greenspan1, Betsy Alford1, Peter Chang2, Eric Bishop-von Wettberg3, Varma Penmetsa2, Abdullah Kahraman4, Asnake Fikre5 and Douglas R Cook*1

1University of California-Davis, Davis, CA

2University of Southern California, Los Angeles, CA

3University of Vermont, Burlington, VT, 4Harran University, Urfa, AZ, Turkey

5Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia

Legume crops are significant agriculturally and environmentally for their ability to form symbiosis with specific soil bacteria capable of nitrogen fixation. Nitrogen fixation for a given legume in a given soil is limited by the availability of the plant’s bacterial partners, and by variation in the effectiveness of those symbionts. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of nitrogen-fixing bacterial symbionts of the legume crop chickpea. This has been accomplished using culture-dependent and independent approaches to generate over 1,200 draft whole-genome assemblies at the level of bacterial populations, as well as 17 finished-quality genomes using the Pacific Biosciences platform. These strategies reveal that that chickpea’s symbionts across the globe are confined to the genus Mesorhizobium, but a diversity of taxa within the genus. Comparative phylogenomic analysis reveals that despite chickpea’s symbionts within and across regions coming from different taxa, all share almost identical genes for symbiosis. PacBio genome-assemblies reveal that this is due to the horizontal transfer of a 500 kb chromosomal island known as a symbiosis island, between unrelated strains of the genus Mesorhizobium. Analyzing the symbiosis island at the population level reveals that the symbiosis island spreads repeatedly once introduced to a region, suggesting that strains well-adapted to a particular soil climate continue to dominate once the new host (chickpea) has been introduced, through repeated acquisition of the symbiosis island. This dataset provides additional insights into the functional and taxonomic diversity of other bacteria associated with chickpea nodules.



Jagdish Jaba1, Siva Kumar Golla1 and HC Sharma1,2

1RP-Asia-ICM-Entomology, ICRISAT, Patanchuru, Hyderabad, Telangana, India

2Dr YS Parmar University of Horticulture and Forestry, Nauni, Solan- 173230, Himachal Pradesh, India     

Climate change will have a noteworthy bearing on survival, development, and population dynamics of insect pests. In this manner, we contemplated the survival and development of beet army worm, Spodoptera exigua across a range of temperatures (15, 25, 35, and 45°C), CO2 (350, 550, 750 ppm) and relative humidity (55, 65, 75 and 85 %) regimes. Maximum larval and pupal weights were recorded in insects reared at 25°C. The growth of S. exigua was faster at 35° C (larval period 7.4 days, and pupal period 4.5 days) than at the lower temperatures. At 15 0C, the larval period went on for 61.4 days and the pupae were not develop in the emerge of keeping 90 days. The S. exigua hatchlings did not make due at 45 °C. The larval survival ranged from 31.6 - 57.2%, and maximum survival was recorded at 25°C, and minimum at 45 °C. Maximum adult emergence (84.27%) was recorded in insects reared at 25 °C, the least at 35 °C. Maximum fecundity (384.3 eggs/female) and egg viability (51.97 %) were recorded and in insects reared at 25 °C. Larval and pupal periods increased with an increase in CO2 concentration. Higher pupal weight recorded at CO2 (128.6mg/larva at 550ppm). Highest larval survival (73.5%) was recorded at 550 ppm and minimum at 750 ppm CO2 (37.00%). Fecundity was highest in insects reared at 550 ppm CO2 (657.4 eggs/female), and least in insects reared at 750ppm. Maximum larval and pupal weights were recorded in insects reared at 75 %RH. The growth of S. exigua was faster at 85% RH than at the lower RH. The larval survival ranged between 40.0 - 58.5%. Maximum adult emergence (88.91%) was recorded in insects reared at 75 %RH, the least at 85 %. Maximum fecundity (447.6 eggs/female) at 75 %RH and highest egg viability (72.95 %) were recorded and in insects reared at 65 %. Lifted temperatures and relative moistness will diminish the life cycle, while hoisted CO2 will drag out the life expectancy therefore; there is requirement for top to bottom examinations on the impact of climatic factors on the population dynamics of insect pest, crop losses, and sustainability of crop production.


Differences in transpiration response to progressive soil drying among wild chickpea relatives and elite recurrent parents

Lijalem Korbu1,2, Susan Moenga3, Sivasakthi K4.,Jana Kholova4, Douglas Cook3, Kassahun Tesfaye2 and Vincent Vadez4,5

1Ethiopian Institute of Agricultural Research (EIAR), DebreZeit Research Center, Ethiopia

2Addis Ababa University, Institute of Biotechnology (IoB), Ethiopia

3University of California at Davis (UCD), USA

4International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), India

5Institut de Recherche pour le Développement (IRD), France 

Terminal drought is a major constraint to crop productivity, with yield penalties of 50% and greater possible in the chickpea crop. Physiological adaptation to water limitation is a tradeoff between extracting sufficient water to enable vegetative growth, while ensuring that the crop has adequate water to complete its reproductive phase. One such adaptation involves the regulation of plant water use during vegetative growth in response to soil moisture content.

In order to evaluate genetic differences in sensitivity to soil moisture thresholds, and to assess possible relationships among water-saving traits, we characterized eleven wild chickpea relatives and three elite recurrent parents having contrasting vigor related traits. Methodology for controlled and progressive soil-mediated water deficit was adapted to modulate soil moisture stress.

We observed substantial variation among the tested genotypes (0.2 to 0.64) in the sensitivity of transpiration to declining soil moisture, assessed as the threshold value of fraction of transpirable soil water (FTSW) at which transpiration rates decline. The majority of wild relatives had higher FTSW thresholds than the recurrent cultivated parents, suggesting a more conservative water use strategy in crop wild relatives, but also as a greater range of threshold values. The highest (0.64) FTSW threshold was found in the Bari3-106D wild genotype. By contrast, the lowest FTSW (0.21) was observed in Bari3-072c. We also observed variation in total transpiration and transpiration efficiency (TE) between wild and elite breeding lines. Several wild genotypes, including Kalkan-064, Derei-070, Kayat-077, Sarik-067 and Savur-063, had higher FTSW thresholds, higher TE and higher biomass under stress conditions than did elite parents, including the drought tolerant check ICC 14778. Remarkably, some wild accessions can withstand consecutive days at close to zero FTSW. These results identify water saving characteristics of wild relatives. These same wild genotypes are genetic donors in a large pre-breeding population, and thus can provide the basis to expand the genetic capacity to breed for novel, drought tolerant cultivated varieties of chickpea.



Lijalem Korbu1, Brian Machovina2, Ellen Garcia2, and Eric von Wettberg3

1Ethiopian Institute of Agricultural Research, Debre Zeit, Ethiopia

2Department of Biological Sciences, Florida International University, Miami FL 33199 USA

3Department of Plant and Soil Science, University of Vermont, Burlington VT 05401, USA

Determining the degree to which agriculturally viable areas will change with climate change is a key task to understanding the challenges we will face in coming years. Here, we examine predicted shifts in suitable production areas for eight leading crops in Ethiopia based on raw climate data associated with occurrence points and ecological niche models (ENMs) developed with Maxent. Our results suggest that production area will decline from 25-100% for crops ranging from teff, wheat, barley, sorghum, chickpea, lentils, grasspea, and coffee based on different projects of expected climate change in the year 2070. Models of more aggressive reduction in climate change lead to less loss of suitable area, as expected. Although most crops may gain some areas that are currently unsuitable in the Ethiopian highlands, these gains are more than offset by loss of suitable areas at lower elevation. Coupled with developmental trends that area leading to increased meat consumption, challenges to food security in Ethiopia are likely to increase substantially due to climate change.


Phenotyping Wild Chickpea Crosses by Team Canada

Donna L. Lindsay, Waliur Rahman, and Bunyamin Tar’an

Crop Development Centre (CDC)/Department of Plant Sciences, University of Saskatchewan, SK, Canada

Twenty populations were developed from crosses between CDC Leader (kabuli) with the newly collected 20 accessions of Cicer reticulatum. In 2015, over 4,000 F2 seeds were screened for homozygous cultivated alleles at FTa and GH loci. Selected F2 plants were crossed to each other within the same population (‘intra crosses’) and across different populations (‘inter crosses’). Progeny from the later crosses were selfed to F3 (F2:3) and grown under field conditions and under high disease pressure in 2016. The surviving F2:4 (498 lines) were tested under field conditions at two locations in Saskatchewan in 2017. Morphological and physiological characteristics, including those closely associated with yield potential, were recorded. Selected F2:5 were tested for their response to low temperature under controlled conditions. Promising lines with juvenile frost tolerance were identified. The next step is to observe these lines under field conditions. Preliminary screening of the progeny also showed higher iron and zinc levels in several lines relative to cultivars. RAD-GBS based genotyping on the F2:5 from ‘intra’ and F2:4 from ‘inter’ crosses is underway. Also, selected diverse progeny of the ‘interspecific’ crosses, with acceptable visual seed quality, were integrated into the CDC chickpea breeding program to further diversify the germplasm base in the breeding program.



Edward Marques1, Irshad Ahmed2, Reyaz Mir Rouf2, Pooran Gaur3, Vincent Vadez3, Eric von Wettberg1, R. Varma Penmetsa4, Jana Kholova 

1Department of Plant and Soil Science, University of Vermont, Burlington VT 05401, USA

2Sher-E-Kashmir University of Science and Technology, INDIA       

3International Crops Research Institute for the Semi-Arid Tropics, INDIA

4Department of Plant Pathology, University of California, Davis, CA 95616 USA

Chickpea is the second most grown pulse legume worldwide and is a primary source of plant protein for 15% of the world’s population living in semi-arid tropical (SAT) regions. In these regions, fluctuations in chickpea production and consumption threaten the nutritional and economic status of the subsistent farming communities. In many of these SAT regions, chickpea crops are typically grown during the low-income post-rainy season under variable rain-fed conditions, which largely affects its production. Thus, finding and introducing chickpea adapted to these conditions is a practical strategy to enhance chickpea production value chains of the semi-arid tropics. One viable option to overcome this post-rain season and limited irrigation environment is “cosmetic” stay-green chickpea technology. This stay-green chickpea type carries a deleterious mutation of the StGR1 gene that inhibits enzymes of the chlorophyll catabolism pathway, which leads to extended chlorophyll retention in seeds and leaves. Consequently, elevated levels of chlorophyll may extend the lifespan of light harvesting antennae (and increases production of reactive oxygen species (ROS)) in plant tissues, which in turn, requires additional maintenance in the form of higher carotenoid levels, the ROS scavengers. Higher levels of carotenoids involved in photo-oxidative protection are very likely to enhance the nutritional value of the crop since these are also precursors of vitamin A. Therefore, the goal of this study is to investigate the effect of this trait on key agronomic parameters and response to growth in SAT (drought-prone) regions. With the use of the introgressed StGR1 gene (from donor parent ICC16340) on the background of two cultivars (KAK2, JGK1) fixed for phenology and harvest index. We assessed the StGR1 mutation effect on basic agronomy traits, plant water use-related traits, responsiveness to soil and atmospheric drought, chlorophyll contents, and carotenoid concentrations. The current status of the study will be presented, but ultimately the data gathered will allow us to determine the potential of stay-green technology to enhance crop production and nutrition for small-hold farmers in the semi-arid tropics.



Edward Marques1, Chris Krieg3, Manny Dacosta2, Camilo Soares2, Joe Rahm2, Annie Mazor2, Rebecca Valls2, Christina Currais2, Shelby Rosten1, Giovanna Carlson1, Erika Bueno1, Eric von Wettberg1

1Department of Plant and Soil Science, University of Vermont, Burlington, VT 05401, USA

2Department of Biology, Florida International University, Miami, FL 33199, USA

3Department of Biology, University of Florida, Gainesville, FL 32609, USA

It has been widely observed that nitrogen fertilizer applications on legumes positively affect grain and forage yields as well as negatively affect symbiotic relationships with nitrogen-fixing rhizobial bacteria. Domestication likely impacted plant responses to nitrogen, as wild taxa were introduced from nitrogen-limited environments to deeper agronomic soils and were possibly fertilized by human and animal manures. We test this possibility in chickpea (Cicer arietinum) and its wild progenitors, by growing 7 cultivated and 20 wild lines at four nitrogen levels (1, 10, 50, 100g N m−2) without rhizobial partners. We measured root system architecture (WinRHIZO), isotopic fractionation, photosynthetic rate, leaf dentition and morphology, and biomass. The current status of this study will be presented, however, preliminary results suggest that domestication and post-domestication diversification greatly altered responses to nitrogen in chickpea.


Molecular Genetic Analysis for Genes Underlying Cold Tolerance and Nutritional Traits in Chickpea


Reyazul Rouf Mir


Division of Genetics & Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-Kashmir), Wadura Campus, Sopore-193201, Kashmir


Chickpea (Cicer arietinum L.) is the second most important cool season food legume in the world after dry beans. For the development of nutrient dense, high-yielding cold tolerant chickpea cultivars, efforts have been made by us to procure/collect a set of 500 chickpea genotypes which include cultivated Cicer aretinum, primary gene pool species Cicer reticulatum, secondary gene pool species Cicer echinospermum and cold tolerant tertiary gene pool species Cicer microphyllum (collected from various hot spots in Ladakh). All the 500 genotypes have been sown on raised beds in the field (in the month of October, 2017) as well as in the green-house. Under field conditions data will be recorded on percent survival and cold tolerance (in the scale of 1-9) and under controlled conditions data will be recorded on LT50 calculated by either re-growth, electrolyte leakage, browning or chlorophyll fluorescence, after plants have been subjected to standardized cold /freezing treatment. Based on preliminary trait evaluations, a set of 100 diverse lines including lines from wild gene pools have been selected and subjected to micronutrient analysis (including Fe, Zn, Mn, Cu, K and Ca) using ICP-OES and AAS and nutrient dense lines have been identified. In addition, superior candidate lines (for cold tolerance, nutritional traits and extra early maturity) already identified have been also utilized in crossing program and a set of ~37 F1 seeds have been obtained. The F1 will be raised by sowing them in the month of April 2018. The trait evaluation for cold tolerance and micronutrients and high-throughput genotyping data to be generated using 50K SNP array will be utilized for the study of marker-trait associations (MTAs). The useful MTAs will be utilized in marker-assisted breeding (MAB) programs for developing new chickpea cultivars with enhanced nutrient density and cold tolerance.



Interspecific Cicer transcriptome divergence under drought


Susan Moenga, Laura Perilla, Yunpeng Gai, Noelia Carrasquilla, Douglas Cook


University of California at Davis (UCD), USA


Cicer reticulatum has over 100-fold genetic variation relative to the cultivated Cicer arietinum with the variants potentially contributing to divergent, adaptive responses to drought, the most limiting stress to chickpea production. Here, we characterize drought response strategies in wild cultivated chickpea and associated transcriptome profiles. Two Cicer reticulatum accessions, Savur_063 and Kalkan_064 and two chickpea cultivars with contrasting water-use capacities under stress, ICC14778 (drought tolerant) and ICC8058 (drought sensitive) were assayed for early physiological and transcriptional responses to mild and severe drought. After four weeks at ~80% available soil water (ASW), each accession was subjected to mild (40% ASW), severe (20% ASW) or left at 80%ASW as non-stressed controls. Both wild accessions were more conservative in water use as inferred from temporal and cumulative transpiration under both stressed and non-stressed conditions. Savur_063 maintained transpiration at 38% and 10% relative to the control at medium and severe stress respectively, being significantly lower than both cultivars and Kalkan_064.


To identify the genomic loci and underlying networks that are perturbed under drought stress, RNAseq libraries from leaf RNA at 1 week after stress imposition were prepared for single end read sequencing on Hiseq4000. Transcript abundance and differential gene expression was estimated using the cufflinks pipeline and CummeRbund package respectively, utilizing Kabuli v.2.63 as a mapping reference. Clusters of genes that are up/downregulated under stress are distinct between the two Cicer species, implying diverged mechanisms in early responses to drought. The top differentially expressed genes are similar in all four accessions, albeit at varying folds across treatments. Among the set of highly induced genes common to all accessions under drought stress, protein synthesis and post-translational modification are the most enriched GeneOntology categories, followed by transcription, potentially indicating the activation of specific processes in response to reduced plant water supply. Among down-regulated genes, the signal transduction category was the most enriched among the annotated loci, followed by secondary metabolite synthesis and carbohydrate metabolism. Outcomes from accession specific assays of the most affected pathways will be presented.




Genomic Diversity of Chickpea Wilt Pathogen (Fusarium oxysporium f.sp ciceris) in Ethiopia


Sultan Mohammed 1,2, Anandkumar Surendrarao2,3, Peter Chang2,3, Brendan K. Riely2, Noelia Carrasquilla-Garcia2, Negussie Tadesse4, Aladdin Hamwieh4, Chemeda Fininsa5, Seid Ahmed4,

Douglas Cook2


1Woldia University, Woldia, Ethiopia

2University of California Davis, USA

3University of Southern California, USA

4International Center for Agricultural Research in the Dry Areas (ICARDA)

5Haramaya University, Haramaya, Ethiopia.


Chickpea (Cicer arietinum) is the third most important grain legume grown in the arid and semi-arid regions of the world. However, its productivity is limited by a range of biotic and abiotic stresses, includingFusarium wilt caused by Fusarium oxysporum f. sp. ciceris (FOC). Under conditions favorable to the pathogen, losses due to wilt can approach 100%. To better understand geographic patterns of genomic variation of FOC in Ethiopia, a GPS-based survey was conducted during the 2014/2015 cropping seasons. 150 Fusaria were isolated from symptomatic tissues and pure strains were derived from single spore isolation. Purified strains were assessed for virulence on susceptible chickpea genotypes. After DNA extraction and library development we sequenced 119 Foc isolates using a whole genome sequence (WGS) approach to an average depth of 56X coverage (Illumina HiSeq 4000 at the UC Davis Genome Center). Draft genome assemblies were obtained using the A5 pipeline and gene prediction was conducted using Fgenesh, yielding a majority of genomes with sizes of 51-55 Mbp and gene content of ~16,800 genes. The estimation of genome completeness based on presence/absence of 3725 highly conserved genes across Sordariomyceta genes revealed that 50% of strains are >99% complete. Polymorphismsweredetected among strains by mapping individual reads to Fusarium oxysporum f. sp. lycopersici strain 4287 as a reference. Structure analyses nominated 6 genetic groups, with further subdivision into 15 groups possible based on Nei's standard genetic distance. Similarly, catenation of 2,900 conserved genes across the 66 highest coverage genomes allowed detailed phylogenetic analysis, from which 19 well-supported phylogenetic groups were identified. Eight of these phylogenetic groups contain the majority of sampled isolates and define a core of related strains. The geographic pattern of genomic diversity indicates the existence of multiple, broadly distributed phylotypes, with no relationship between geographic and genetic distance. This complex biogeography is consistent with known difficulty in developing stable FOC host resistance. WGS of Ethiopian Foc isolates will facilitate the identification of pathogenicity mechanisms which will help to develop effective methods for managing chickpea vascular wilt disease, including improvement of disease resistance in chickpea.





Zehara Mohammed1,2, Eddie Maqrues6, Brendan Riely4, Noelia Carrasquilla4, Eric von Wettberg5,6 Alex Greenspan4, Asnake Fikre3, Fassil Assefa2 and Douglas Cook4


1Ethiopian Institute of Agricultural Research Debre Zeit Center, Ethiopia

2Department of Microbial, Cellular and Molecular Biology Addis Ababa University Ethiopia

3International Crops Research Institute for the Semi-Arid Tropics, Ethiopia

4Department of Plant Pathology, University of California, Davis, USA

5University of Vermont, USA

6Department of Biology, Florida International University, Miami, USA.


Chickpea (Cicer arietinum L.) is a major legume crop in Ethiopia and provide multiple benefits, due to high nutritive value as well as the ability of the crop to enrich nitrogen poor soils and saves fertilizer costs in subsequent crops. In spite of its yield potential this legume depends on the rhizobial association. Thus, this study investigates the efficiency of its symbionts to accomplish its nitrogen requirements for effective growth and production not yet extensively addressed previously. Various sample of root nodule, soil, questioner survey including GPS based location points were collected from138 farmers field representing 4 regions. Isolation of 106 pure strains, phenotypic characterization, DNA extraction, 16S and nodC sequence were performed. Subsequently, libraries development, whole genome sequencing and classification of strains related to phylogenetic diversity were developed. Initial authentication and second phase greenhouse screening of symbiotic performance was done on Natoli and Arerti genotypes. Thus, ten high performing strains from the greenhouse experiment were evaluated at field conditions on the same genotypes. Ten species and numerous distinct phylotypes of Mesorhizobium were identified. Most strains are closely related to symbionts of other legume species like Mesorhizobium plurifarium, a species originally isolated from Acacia species. The rest of the strains distributed in six new clades: M.sp1 and 2, M. gobiense, M. ciceri, M. opportunistum, farther resolved Rhizobium groups and majority of these new strains are previously unrecognized in chickpea. Higher symbiotic effectiveness than current commercial chickpea inoculants in greenhouse experiment and significant host genotype variation between Mesorhizobium species was observed. Therefore, improving the nitrogen fixation ability among phylogenetically diverse bacteria for better symbiotic nitrogen fixation will be expected to maximize chickpea productivity for smallholder farmers of Ethiopia.



Heat Tolerance Responses of Chickpea (Cicer arietinum L.) Genotypes in the Thermal Zone of Ethiopia, a Case of Werer Station


Tesfashbamlak Mola1, Shimelis Alemayehu2,Asnake Fikre1, Chris Ojiewo1,Ketema Alemu1,   Tullu Leta3


1International Crops Research Institute for Semi-Arid Tropics

2Ethiopian Institute of Agricultural Research

3 Science and Technology University, Adama


Chickpea (Cicer arietinum L.) is an important cool season food legumes with indeterminate growth habit.  The crop is valued for its nutritive seeds and use as animal feed in many developing countries. The productivity of the crop is constrained by several abiotic stresses, among which high temperature is one of the key determinants of crop. The present study was conducted to screen, evaluate and select Chickpea genotypes possessing high yield potential under heat stress condition at Werer Agricultural Research Center. The experiment was laid in RCBD of three replications using eighteen early maturing chickpea genotypes of ICRISAT in 2015. Two times planting ie 23 Jan and 24 February was done each on 4.8m2   plot with 30cm and 10 cm spacing, and data was determined on the two central rows. Growth period maximum temperature of >35OC, considered threshold for heat assessment, was sufficiently interfaced in both planting days. Combined analysis of variance revealed existence of highly significant differences among the tested genotypes for most of the agronomic traits. The top 3 best performing lines with extra early phenology were ICCV 09309 (1187 kg/ha), ICCV 10103 (1035 kg/ha) and ICCV 10108 (1014 kg/ha). Delayed planting posed more stress on the crop and yield, possibly the increasingly progressing temperature interfered beyond physiological adjustment of the crop. Heat tolerance indices like STI, TOL, SSI, MP and GMP calculated on the basis of grain yield, and genotypes ICCV-10102, ICCV-09309, DZ-2012-CK-0034 and DZ-2012-CK-0041 showed lower TOL and higher STI values indicating as tolerant genotypes relative to others.






Arpan Mukherjee1,2, Richa Raghuwanshi1, Birinchi K. Sarma2


1Department of Botany, Faculty of Science, Banaras Hindu University, Varanasi-221005

2Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi-221005


Chickpea have a great nutritional value as well as economic importance among all pulses. It contains a high amount of protein, vitamins, minerals, etc. Several biotic and abiotic factors are responsible for decreased production of chickpea, among them plant pathogens greatly affects the production. Seed biopriming with beneficial microbes has well defined role in plant growth promotion and biotic stress management. Here we analyzed the biocontrol activity and plant growth-promoting effects of some freshly isolated rhizospheric bacterial strains. The bacterial strains of fluorescent Pseudomonas were identified based on their 16S rDNA gene sequencing. The bacterial strains PsD1 and S11 showed very high degree of antagonistic activities against the chickpea pathogens Sclerotinia, Phoma and Rhizoctonia spp. during dual culture assays. Seed biopriming of chickpea with Pseudomonas strains namely PsD1 and S11 significantly increased the total biomass of root (96.34 % and 135.2%) and shoot (11.36% and 50.1%), number of leaflet (32.31% and 36.58%), plant length (86.36% and 93.18 %), chlorophyll (15.6 % and 17.02%) and micronutrients status to that of non-bioprimed control plants, respectively. Interestingly, the root hairs of bioprimed seeds are also surprisingly increased compared to the untreated seedlings. The isolates were also able to inhibit the pathogen growth as well as promote the plant growth by production of some important metabolites like siderophores, proteases, phosphatase, amylase, HCN and indole-3-acetic acid. We concluded that seed biopriming with these Pseudomonas strains promoted plant growth and demonstrated antagonistic activities against some chickpea pathogens.





Atsede Muleta1, 2, Fasil Assefa1, Kassahun Tesfaye1, Douglas R. Cook3, Brendan K. Reily3, Noelia Carrasquilla-Garcia3, Alex Greenspan3, Yunpeng Gai3


1Addis Ababa University, College of Natural and Computational science, Department of Microbial, Cellular and Molecular Biology, Addis Ababa, Ethiopia

2University of Gondar, College of Natural and Computational science, Department of Biology, Gondar, Ethiopia

3University of California Davis, Department of Plant Pathology, Davis, United States.



In general, nitrogen and phosphorus deficiency are the two most limiting factors in crop production and that of chickpea in particular. This is because nitrogen fixing process requires P and P deficiency is aggravated under acidic soils. Therefore, this study was aimed at to study the genetic diversity and evaluation of biological nitrogen fixing and phosphate solubilizing rhizobia of chickpea from acidic soil of Ethiopia.


A total of 68 Mesorhizobium strains were isolated from root nodules of chickpea collected from central, western and northern part of Ethiopia. The isolates were checked for some presumptive cultural test and screened based on grown at low pH medium and solubilize insoluble phosphate on tri calcium phosphate source on sold medium. Then, total genomic DNA extracted from each culture, libraries were prepared and sequenced. The phylogenetic relationships investigated based on 16S rRNA, protein coding gene (recA, atpD, glnA and gyrB) and symbiotic gene (nifH, nodC). The strains showed wide diversity in their different C and N-sources utilization pattern and tolerance to acidic pH, salinity, high temperatures, heavy metals, antibiotics. Moreover, phosphate solubilizing efficiency of the strain showed variation in solubilizing three different phosphate sources and among the strains, AtACR-64 released maximum 22.6mg/ml amount of P from tri calcium phosphate (Ca3(PO4)2). Sixty six percent of the strain was found to be indole-3-acetic acid (IAA) producer. Furthermore, 55.9% tested strains showed antagonistic activity against Fusarium oxysporum cicer in dual culture assay. Green house and field experiments our next activity plan and will be presented in the near future.





Hawi Negusse1, Kassahun Tesfaye1, 2, Teklehaimanot Haileselassie1


1Institute of Biotechnology, AAU, P.O. Box 1176, Addis Ababa, Ethiopia

2Department of Microbial, Cellular and Molecular Biology, CNS, AAU, Addis Ababa, Ethiopia


Soil acidity reduces the average productivity of major crop plants by more than 50% and aluminum is a commonly toxic metal pollutant worldwide limiting crop productivity in acidic soils. In Ethiopia, vast areas of land in the western, southern and central highlands which receive high rainfall are thought to be affected by soil acidity. It is also a major productivity problem that has not been addressed in depth. Information regarding aluminum tolerant chickpea genotypes in Ethiopia is lacking. Hence, this study is aimed to fill the above gap.


A total of 29 chickpea genotypes: 24 nationally released varieties, four advanced lines and one local variety from Wollega zone were screened under hydroponic condition at 0 and 120 μM Al3+concentration. Phenotypic parameters: tap root length, shoot length, root fresh weight and shoot fresh weight were collected. The phenotypic data was analyzed using Genestat computer packages and Ryan–Einot–Gabriel–Welsch (REGW) Multiple Range Test was used to rank the genotypes based on Al tolerance. ANOVA revealed a highly significant difference (P<0.001) among genotypes for all phenotypic traits measured. DZ-2012-ck-20113-2-0042 was the most tolerant genotype with respect to the trait tap root length followed by DZ-2012-ck-0233 while yelebe was the most susceptible genotype followed by Akaki.



Computational analysis of diversity and evolution of Type III secretion system (TTSS) from Chickpea (Cicer reticulatum) symbionts


Hien P. Nguyen1, Alex Greenspan2 and Douglas Cook2  


1Tokyo University of Agriculture and Technology, Tokyo, Japan. United Graduate School of Agricultural Science

2University of California, Davis, USA, Department of Plant Pathology.


The Type III secretion system (TTSS) is a molecular machine by which Gram-negative bacteria introduce virulence factors (known as “T3 effectors”) into eukaryotic host cells. In many plant and animal pathogens, TTSS is a key determinant of serious disease. Recently TTSS has been identified in beneficial, symbiotic bacteria that “fix” nitrogen in association with legume plants. Instead of causing disease, these symbiotic T3 effectors control host-range by augmenting the host response. Although many studies have been done to understand the role of TTSS in symbiosis, we still have a relatively crude understanding of this aspect of symbiotic function. We hypothesize that TTSS is a key factor determining the efficiency of nodulation and nitrogen fixation in chickpea; if true, then knowledge of TTSS function may enable development of more efficient nitrogen fixation in agricultural systems. The Chickpea Innovation Lab has previously sequenced 100’s of genomes of chickpea’s symbiotic Mesorhizobium, providing an opportunity to identify and study the evolution of TTSS genes important to chickpea nitrogen fixation.


TTSS genes are typically organized in clusters within genomes. By computational analysis, we searched for TTSS clusters among fourteen chickpea symbiont genomes assembled from Pacific Biosciences (PacBio) sequencing. All fourteen genomes contain a primary TTSS (designated TTSS1), while five also possess a second TTSS (designated TTSS2). Based on the distribution of known TTSS homologs we delimited each TTSS cluster to region of approximately 31 Kb. Annotation of transcriptional cis-elements (termed tts, nod and hrp boxes) supported the boundaries of these clusters. In each genome the TTSS1 cluster occurs within a previously defined “symbiosis island”, containing numerous genes required for symbiosis (e.g., Nod factor biosynthesis and nitrogenase enzymes). All TTSS1 clusters contain a transcriptional regulator, ttsI, preceded by a nod box. nod boxes typically confer symbiosis-specific transcription, indicating that TTSS1 is regulated in concert with other symbiosis genes. Similar organization is observed in the well-characterized M. loti MAFF303099, suggesting their similar function. Conversely TTSS2 clusters are always external to the symbiosis island, and none contained the ttsI regulatory gene. TTSS1 and TTSS2 also differ in that TTSS1 clusters contain numerous tts boxes known to regulate symbiotic gene expression, while TTSS2 clusters are devoid of both tts and nod boxes. Interestingly, two of the genomes contain a second full symbiosis island, including a number of nod boxes identified adjacent to nodulation genes. Several hrp boxes were found in both TTSS1 and TTSS2, but less conserved than tts or nod boxes. The combination of tts, nod and hrp boxes hint at complex regulatory inputs that are characteristic and different between TTSS1 and TTSS2. Phylogenetic analyses with a set of 9 genes conserved between TTSS1 and TTSS2 reveal two well resolved clades corresponding to TTSS1 and TTSS2, demonstrating distinct histories for these gene clusters and supporting our inference of distinct regulatory patterns and potentially distinct functions in chickpea symbiosis. These findings provide a basis for evaluating the bacterium’s role in symbiotic efficiency, which may have direct practical application to strain selection for agricultural use. 





Laura M. Perilla1, Yang Zhao2, Emily Bergman1, Joanne Chung1, Ramya Immaredy1, Douglas R. Cook1


1Department of Plant Pathology, University of California, Davis, CA 95616, USA

2The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, China


Chickpea (Cicer arietinum) is one of the most important legumes worldwide. Plant breeding programs and modern cultivation have focused on much needed yield, agronomic, or pathogen resistance traits. However, the natural nitrogen fixation capacity and efficiency of chickpea and its close wild relatives has not been incorporated in breeding programs. With compatible symbiotic partner, biological nitrogen fixation provides highly limiting nitrogen as plant biomass. The mechanisms that control efficient nitrogen fixation in crop legumes are poorly understood, and the interactions among Mesorhizobium and chickpea species offers a model system in which to address such questions.


The main objective of this work was to characterize the phenotypic response of wild and cultivated chickpea for nitrogen fixation capacity and quality of interaction. We evaluated symbiotic efficiency of two species of Mesorhizobium bacterial species that nodulate Cicer species in wild environments in Turkey. All assayed plant genotypes have full genome sequences and genetic resources of segregating populations, including the domesticated (C. arietinum) cultivar ICCV96029 and the wild genotype Oyali_84 of chickpea (C. reticulatum). Plants were inoculated with M. ciceri (Kar-203) and M. mediterraneum (B2O3/Rse19) and harvested at different growth stages over a plant developmental time course. We documented the biomass of shoots, roots, and nodules; the numbers of nodules, nodule size, and morphology. The most significant differences were observed at 50% pod stage in the early flowering cultivar ICCV96029, while the wild Oyali_84 showed significant biomass differences at first open flower stage. Domesticated C. arietinum (ICCV96029) and wild C. reticulatum (Oyali) differ in biomass allocation to roots versus shoots depending on the symbiont species. Wild increased biomass was nearly proportionally to above and below ground organs, while domesticated increase shoot but not root biomass. Interestingly, there were striking differences in both nodule number and nodule size depending on the bacterial strain. To evaluate whether this response is extended across C. reticulatum wild genotypes, we expanded the analysis using eight C. reticulatum genotypes, two C. echinospermum genotypes and two C. arietinum genotypes. We also increase the amount of strains from each Mesorhizobium species, testing three M. ciceri and three M. mediterraneum with each plant genotype. Preliminary analyses reveal that Mesorhizobium symbionts induced changes in total biomass and biomass allocation, with significant differences depending on the strain and host genotype. The greater effect among Mesorhizobium fixation efficiency is dependent on the wild species (C. reticulatum vs C. echinospermun). Further assays will be carried out to explore the mechanisms underlying the observed differences.





Hatice Polatbilek1, Ayse Anay2, Canan Can1


1Department of Biology, University Gaziantep, 27310, Turkey

2Agricultural Quarantine Directorate, Mersin, Turkey


Legumes are traditional crop species in Turkey and the grain legumes are cultivated in almost every province, covering 7.098.000 ha of area in the 2016 growing season. Among them chickpea and lentils are the main grain legumes that have economic importance. Origin of legume (chickpea, lentil) domestication occurred in the Fertile Crescent including Southeastern region of Turkey and the co-evolution of Ascochyta complex with Cicer spp is well documented. Therefore, Turkey has an important resource for both grain legume diversity and their phytopathogens like Fusarium spp and Ascochyta spp to study plant pathogen interactions.


The main reason of reduced yield in chickpea is biotic stress factors generated by Fusarium wilt and Ascochyta blight that together may result complete yield loss. Plant breeding efforts against these devastating diseases in chickpea are being conducted in 10 research institutes and 15 universities in Turkey but resistance/tolerance is broken every 4-5 years in chickpea genotypes. Fusarium wilt of chickpea steadily increases its population especially in the Central, Mediterranean and Aegean regions of Turkey that hold major chickpea growing areas. In order to breed resistant/tolerant varieties in lentil and chickpea against Fusarium wilt, further analyses on population characterization is needed.


This study was undertaken to assign distribution of Fusarium wilt and yellowing in chickpea growing areas in Turkey. Survey studies were conducted during 2015-2016 growing season covering 7 regions. The survey area covered 1049 ha in 36 provinces and out of 880 Fusarium spp, 416 isolates were determined as F. oxysporum fsp ciceris through pathogenicity assay. The wilting isolates were assigned to a single VCG. The yellowing form of the F. oxysporum f.sp. ciceris was isolated from all the regions while wilting form was observed in the Mediterranean and Central Anatolia regions.






Raju Pushpavalli, Christiane Ludwig, Kelley Whisson, Sylvia Osterrieder, Andrew Fletcher, Jens Berger


Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat 6014, Western Australia


Chickpea (Cicer arietinum L.) ranks second among the world’s pulses. Chickpea is affected by a range of biotic and abiotic stresses, and a narrow genetic and adaptive base limits where the crop can be grown Terminal drought reduces chickpea yield across much of its production range in Mediterranean climates and the Indian subcontinent.


Recent collection wild genetic resources (Cicer echinospermum, Cicer reticulatum) has dramatically increased the genetic variation available for chickpea improvement. Here we ask whether this genetic variation among wild Cicer may provide useful water conservation related traits. In its natural distribution, wild Cicer tends to mature later than other sympatric annuals, suggestion either greater water acquisition, reduced rates of water use, or both. Moreover, wild Cicer habitats vary in terms of rainfall, temperature and soil depth, and therefore water acquisition/use might also be expected to vary across collection sites.


In the present study we focus on diurnal water use. 132 wild Cicer genotypes (four replications) were evaluated for their response to changing vapor pressure deficit. There were significant differences across wild genotypes for diurnal transpiration patterns (P<0.001) that were not explained by habitat: responses varied both within and between collection sites. Thus some wild Cicer genotypes conserve water at high VPD, while others do not; collection sites typically contain a wide range of responses. This result is important as water conserving wild Cicer lines can be further exploited for the development of elite drought tolerant chickpea cultivars.



Climate Resilient Chickpea project rhizobia isolates: exploring their potential as commercial inoculants


Guido M. Ramirez Cáceres1, Alejandro O. Rossi1, Luisina Andriolo1, Maria L. Maneiro1, Brendan K. Riely2, Douglas R. Cook2


1Rizobacter, Pergamino, Buenos Aires, Argentina.

2Department of Plant Pathology, University of California, Davis, CA 95616, USA.


Nitrogen fixation contribution to total nutrient requirement in chickpea varies within the range of 41 to 90% (Unkovich et al 2010). Wild chickpea progenitors and their microbiome were collected in the species’ area of origin as part of the global Climate Resilient Chickpea initiative. Nitrogen-fixing symbionts were isolated, characterized and some of them, sequenced. As part of a Research Collaboration between UC-Davis and Rizobacter, an inoculant company, a set of the most promising chickpea rhizobia species were shipped to the laboratories of the firm. Broths and liquid osmo-protected inoculant formulations were prepared for a selected group of these strains. On-package bacteria survival, pH and purity were evaluated periodically. At the same time, a growth chamber trial was established to check the nodulation efficacy of these experimental formulations and compare their performance with a commercial check when applied to a local Kabuli type variety. Pre-sowing treatment at 0, 7 and 14 days before planting were employed to assess performance variation through time. On-package survival data showed 5 out of 10 strains were within commercial standards (>108 cfu/ml, pure) after 5 months from elaboration. Growth chamber trial results showed no significant difference in nodulation between the commercial formulation and 2 of the experimental ones, based on isolates from Ethiopia and Turkey. Field trials are to be carried out to support these initial results. Data shows the potential of some of the strains to be used as commercial inoculant formulations to enhance nitrogen fixation.





Resistance to root-lesion nematode (Pratylenchus thornei) in a new collection of wild species of chickpea


Roslyn Reen, Hannah Rostad and John Thompson


Centre for Crop Health, University of Southern Queensland, Toowoomba, Australia.


Root-lesion nematode (RLN) Pratylenchus thornei, known as the legume and cereal nematode, is a microscopic eel-like plant parasite that feeds and reproduces in chickpea (Cicer arietinum) roots. It is widespread in Europe, Asia and Australia causing yield losses up to ~25% in intolerant Australian chickpea cultivars. We have screened a recent collection of wild Cicer from 19 sites within five provinces of Turkey to identify better sources of resistance to RLN than in current Australian cultivars. Plants were grown in a controlled glasshouse environment (20-25°C) in a randomised block design. Accessions comprised 151 wild Cicer (119 C. reticulatum, 32 C. echinospermum) plus 25 check cultivars (15 domestic chickpea, 4 other wild Cicer accessions, 5 wheat cultivars and one unplanted control). Pots of 330 g pasteurised vertisol received a solution of NPK, and a 10 mL suspension of P. thornei equivalent to 10 nematodes/g soil. After 18 weeks plant growth, P. thornei were extracted from a 150-g subsample of soil and roots using the Whitehead tray method. Roots were recovered from each nematode extraction sample and oven dried to determine any correlations between root mass and final P. thornei numbers. Pratylenchus thornei were quantified under a compound microscope and counts were log transformed and expressed as P. thornei/kg soil and roots, or as P. thornei/g dry weight root. Data were analysed using a linear mixed model with the level of significance set at P=0.05.


Results showed significant differences between accessions for resistance to P. thornei. Accessions of the wild species C. reticulatum and C. echinospermum were more resistant than cultivars of domestic chickpea C. arietinum. Twenty nine accessions (7 C. echinospermum, 22 C. reticulatum) had high levels of resistance with lower P. thornei numbers than the unplanted check. Four of these accessions two each of C. reticulatum, and C. echinospermum are part of a subset of 25 crossed with cultivar PBA HatTrick for a Nested Association Mapping (NAM) population (L. Kamphuis, pers comm). Of the new wild Cicer accessions 16% were significantly more resistant than PBA Seamer, the most resistant commercial cultivar in this experiment. Clustering of resistance in provinces was not evident, with Adiyaman having the most resistant accessions (6 C. reticulatum, 2 C. echinospermum) and the Oyali site within this province, having the two most resistant accessions both C. reticulatums. No significant correlations were found between root mass and P. thornei numbers, however, there was a strong correlation (R2=0.663 P<0.001)) between P. thornei/kg soil and P. thornei/g dry weight root, indicating either term showed similar levels of resistance. Overall the results indicate high levels of RLN resistance exist within this collection of wild Cicer. Of interest are the 25 lines of the NAM population tested in this experiment with four showing high RLN resistance making them valuable for future genetic studies. Currently a second screening of all accessions is being processed. The resulting information will allow selection of the most resistant accessions for future germplasm development for chickpea breeding and genetic studies that will ultimately benefit chickpea industries on a national and international level.





Brendan K. Riely1, Yunpeng Gai1, Ana V. Palacios2, Harun-or Rashid3,4, Michael Wink4, Kirstin E. Bett2, Douglas R. Cook1


1Department of Plant Pathology, University of California, Davis, CA 95616, USA

2Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
3Bangladesh Institute of Nuclear Agriculture, Mymensingh, Bangladesh

4Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Heidelberg, Germany


The pulse legume Lentil (Lens culinaris ssp culinaris) was first domesticated ~8000 years ago in the Middle East. Today, it is an important source of protein for millions of people worldwide. Lentil’s high protein content is a bi-product of its ability to form a symbiotic relationship with several species of nitrogen fixing bacteria from the genus Rhizobium. Rhizobium isolates vary in the efficiency with which they fix nitrogen and consequently bacterial genes and genomes can impact both the vigor and yield potential of the host. The identification of efficient nitrogen fixing strains that are adapted to different agro-ecological environments may enhance lentil production in a sustainable manner.


As part of the AGILE (Application of Genomics to Innovation in the Lentil Economy) project, we have established a collection of diverse, lentil-nodulating bacteria and sequenced their genomes in order to determine the level of genetic and genomic diversity present within our collection. To date, we have sequenced approximately 300 genomes from strains originating from eleven different countries. Phylogenetic analyses indicate that the European strains are primarily R. leguminosarum whereas our South-Asian isolates are closely related to R. phaseoli and R. etli. Pairwise Average Nucleotide Identity (ANI) analyses suggest that several isolates from New Zealand and Nepal may represent new species. These data have allowed us to rationally select strains representing the breadth of the genetic diversity reflective of the different agro-ecological niches from which the bacteria evolved and were isolated. We are testing these strains in greenhouse and field experiments to assess the efficacy of their plant growth promoting activities. Our preliminary results suggest that our selected isolates differ in their ability to enhance lentil yield with some strains proving greater benefits than commercially available inoculant.



CHICKPEA RESPONSES TO Fusarium oxysporum f. sp. cicerisVIA MEDIATION OF Trichoderma asperellum T42: A PROTEOMIC VIEW


Birinchi K. Sarma and Jai Singh Patel


Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005


Proteome gives a true insight of the physiological responses of a plant in a given situation. In the current study, we treated chickpea seeds (cv. Radhey) with Trichoderma asperellum T42 and subsequently challenged with the wilt pathogen Fusarium oxysporum f.sp. ciceris (Foc). We then analysed the proteome of chickpea seedlings after 48 h of pathogen challenge and compared the results of each treatment (only T42, only Foc and T42 + Foc) with control (C). Analysis of proteomics results showed that 317 proteins were common in all treatments. In only T42 treatment without Foc challenge, expression of defensin, PR-5, NADPH oxidase, glucanase, peroxidase, calmodulin, NBS-LRR, NAC transcription family, WRKY transcription family, PAL, Rubisco and Thaumatin were more than doubled compared to control. Similarly, in only Foc treatment expression of the proteins such as Thaumatin, glucanase, peroxidase, NBS-LRR, NADPH quinine oxidoreductase, NAC family transcription factors, superoxide dismutase, MAP Kinase, chitinase, autophagy, lipoxygenase, multidrug resistance protein, and WRKY were more than doubled. Further, in the T42 + Foc treated plants it was observed that in addition to some of the already mentioned genes there was increase in expression levels of NBS-LRR, glycolate oxidase, ascorbate peroxidase, peroxidase, and NADPH oxidase. Expression of NADPH quinine oxidoreductase was highest in T42 + Foc followed by T42 and C, which is known for production of ROS (Reactive oxygen species). Calmodulin protein related to calcium ion signaling showed highest 2.9 fold increase in T42 followed by 1.87 in Foc and 0.49 in T42 + Foc compared to C. Peroxidase showed highest 3.0 folds increase in expression level in T42 followed by 2.0 in Foc. Highest fold change 2.27 in cysteine protease was observed in Foc followed by 1.3 fold in T42 compared to C. From the results, it can be concluded that Trichoderma increases activities of antioxidant enzymes, calcium signaling, defense protein synthesis and structural integrity through lignifications. However, Foc enhances the activities of cysteine protease, autophagy, antioxidant enzymes and multidrug resistance proteins. Interestingly, in the co-inoculated treatment (T42 + Foc) there was enhanced expression of NBS-LRR proteins, glycolate oxidase, ascorbate peroxidase, peroxidase, and NADPH oxidase.





Exploration of bioactive metabolites from Streptomyces as natural insecticides against chickpea pod borer Helicoverpa armigera


Sathya A1, S. Gopalakrishnan1, Vijayabharathi R1, Sharma HC1, Srinivas V1, Ratna Kumari B1, Gonzalez SV2, Melø TM3, Simic N2


1ICRISAT, Patancheru, India

2Department of Chemistry, Norwegian University of Science and Technology (NTNU), Trondheim, Norway

3Department of Biotechnology, NTNU, Trondheim, Norway


Microorganisms produce a range of metabolites that play key roles in agriculture including pest control properties. With this concept, 15 Streptomyces strains with insecticidal activity against the chickpea pod borer Helicoverpa armigera were identified. Based on the activity units, S. griseoplanus SAI-25 and Streptomyces sp., CAI-155 were further studied to identify the key insecticidal metabolites against H. armigera. An insecticidal compound called cyclo(Trp-Phe) belongs to the diketopiperazine class was purified from SAI-25 with antifeedant (70%), larvicidal (67%), and pupicidal (59%) activity. The LD50 and LD90 values were observed to be 619 and 2750 ppm, respectively. In the context of Streptomyces sp., CAI-155, a novel fatty acid amide derivative called N-(1-(2,2-dimethyl-5-undecyl-1,3-dioxolan-4-yl)-2-hydroxyethyl) stearamide with insecticidal activity of 70–78% was identified. The LD50 and LD90 valueswere found to be 627 and 2276 ppm respectively. Further characterization of these metabolites in the field conditions, will bring out the potentiality of microbial metabolites for the pod borer management.






Mamta Sharma, Raju Ghosh, Avijit Tarafdar, andRajeev Varshney


International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, PO 502324, Hyderabad, Telangana, India.


Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. ciceris (Foc), is a major factor limiting chickpea production worldwide. The pathogen long survival in soil and high pathogenic variability, with eight races 0, 1A, 1B/C, 2, 3, 4, 5, and 6 identified so far, are key elements in the development and management of the disease. Use of high-yielding cultivars resistant to the prevalent pathogen race(s) in a given area is the most practical and cost-efficient disease control measure for management of the disease. We have summarized here recent developments in Foc, with respect to host plant resistance and pathogenic variability.


Considerable progress has been made in the past in developing FW resistance screening techniques, identifying resistance sources and transferring resistance genes into high yielding, improved and agronomically superior genetic background. Well standardized field (sick plots) and controlled environment screening techniques are available for reliable and repeatable screening for FW. Stable and broad based sources of resistance has been identified through multi-location and multi-year testing at hot spot locations in India. Genotype and G × E analyses allowed the selection of few genotypes (ICCV 05527, ICCV 05528, ICCV 96818 and ICC 11322) with stable performance across the environments.


Recent advances made in the area of whole genome sequencing and transcriptomics of Foc provide greater insights to understand lineage-specific genes involved in host-specific pathogenicity. Comparative genomic studies of Foc, Fom (f. sp. medicaginis) and Fop (f. sp. pisi) have revealed that the host-specific pathogenicity of the F. oxysporum species complex was determined by distinct sets of supernumerary chromosomes. The whole genome sequence varied in length from ~51.1 Mb (Fom), ~54.8 Mb (Foc) and 55.1 Mb (Fop). Legume-infecting isolates didn’t share large genomic regions of pathogenicity-related content, smaller regions and candidate effector proteins were highly conserved, suggesting that they may play specific roles in inducing disease on legume hosts. Efforts are underway to decipher the races of Foc through re-sequencing of isolates.


Genome-wide expression profiling of Foc during various stages of conidial germination revealed that genes linked to fungal development are transcribed in successive ways. Analysis showed that Foc have large sets of germination-related genes and families of genes encoding secreted effectors, cell wall/pectin-degrading enzymes, metabolism related enzymes, transporters and peptidases. We found that metabolism related enzymes are up-regulated at early time points whereas most transporters and secondary metabolites important for tissue colonization and pathogenicity are up-regulated later as evident from the qRT-PCR. The study demonstrated that early conidial germination in Foc is accompanied by rapid shifts in gene expression that prepare the fungus for germ tube outgrowth, host cell invasion and pathogenesis. This work lays the foundation for facilitating further research towards understanding this host-pathogen interaction. These advances in host plant resistance and genomics will serve as an additional resource to augment the existing systems to assist crop improvement efforts and disease management practices for this pathogen.

A genome-wide association study identifies alleles associated with seed coat color regulation of Chickpea


Min-Gyoung Shin1, Susan Moenga2, Peter L. Chang1, Douglas R. Cook2, Sergey V. Nuzhdin1


1Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA

2Department of Plant Pathology, University of California, Davis, CA 95616, USA


Chickpea is one of the most highly-produced crops cultivated in over 50 countries. The global demand for chickpea has been growing due to its nutritional benefits. Among other properties, seed coat color of chickpea has been a key market factor because of consumer preference toward light-colored chickpeas. We investigated the underlying mechanisms of determination of chickpea seed coat colors by using genome-wide association approaches. Two species with high genetic variation, Cicer echinospermum and C. reticulatum, were used for both combined and individual analyses. In order to effectively control for population structure of the samples, analyses based upon a linear mixed model was used. To address associations derived from genetic variations that are specific to one of the chickpea species and common to the both, combined and separated datasets were analyzed. We identified candidate loci and genes that regulate variation of seed coat colors. The identified genes include genes that have been reported to be related to seed coat color traits in Arabidopsis thaliana in earlier studies. We propose that the identified genes are important genetic resources for the future chickpea breeding.









Anupam Singh1, Min-Gyoung Shin1, Peter L. Chang1,2, Bilal Aydin1, ​Ahmet Cakmak1, Christiane Ludwig1, ​Kelley Whisson1, Abdulkadir Aydogan3, Abdullah Kahraman4, Jens Berger5, Douglas R. Cook2, Sergey V. Nuzhdin1


1Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA

2Department of Plant Pathology, University of California, Davis, CA, 95616, USA

3Central Research Institute for Field Crops (CRIFC), Ankara, Turkey

4Department of Field Crops, Faculty of Agriculture, Harran University, Şanlıurfa, Turkey

5Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, Perth, WA, Australia


Adaptation and yield of chickpea is dependent on its flowering time. Apart from being an easily monitored trait, it serves as an indicator for the phenological status of the plant. Temperature, photoperiod, amount of moisture in the soil, altitude and the latitude of the region in which chickpea is grown cause alteration in this highly variable trait of flowering. Studies have identified markers associated with flowering genes (including efl-1 and efl-2) in the cultivated species, Cicer arietinum. In this study, we aim to identify many more genes and markers from two wild species (Cicer reticulatum and Cicer echinospermum) using whole genome sequencing of 249 genotypes.


Seeds were planted in Turkey and Australia under five different treatment conditions in the span of three years. On testing for the significance of variables associated with the experimental design, we found site, year and treatment to be important factors that affect time to first flowering. In a genome-wide association analysis for flowering time in Mt. Barker site of Australia, we identified numerous hits, identifying potential markers associated with flowering time in the wild Cicer ancestry of chickpea.





Plant vigour and water saving traits contributes to water stress adaptation in chickpea: Use of advanced phenotyping facilities and QTL analysis to assist chickpea breeding programs


Kaliamoorthy Sivasakthi1,2, Mahendar Thudi1, Murugesan Tharanya1, 2, Sandip M Kale1, Bingi P. Mallikarjuna1, Jana Kholová1, Mahamat Hissene Halime1, Deepa Jaganathan1, Rekha Baddam1, Thiyagarajan Thirunalasundari2, Pooran M. Gaur1, Rajeev K. Varshney1, Vincent Vadez1


1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India

2Bharathidasan University, Tiruchirappalli, Tamil Nadu, India        


Terminal drought stress leads to substantial annual yield losses in chickpea (Cicer arietinum L.). Adaptation to water limitation is a matter of matching water supply to water demand by the crop and harnessing the genetics of traits contributing to plant water use, i.e. transpiration rate and canopy development dynamics, is important to design crop ideotypes suited to a varying range of water limited environments. With an aim of identifying and validating of genomic regions for plant vigor and water saving traits recombinant inbred lines ßwere phenotyped using two mapping populations. i.e. 232 recombinant inbred lines, derived from a cross between ICC 4958 and ICC 1882 (Bi-Parental mapping population) and 279 chickpea reference set lines (association mapping panel). Both bi-parental and association mapping panel were phenotyped at vegetative stage under well water conditions using a high throughput phenotyping platform (LeasyScan) during 2015 and 2016 in post-rainy season. Different density genetic maps (241-SSR-Low density, 1007-SSR+SNPs-High density and 1557-SNPs-Ultra high density) were developed earlier and used for the identification of quantitative trait locus (QTL). To conduct, genome wide association study (GWAS) 1872 markers were used. Results revealed that several major QTLs (M-QTLs) and marker trait associations (MTAs) for plant vigor related traits (Vigor, 3D-leaf area, Leaf area index, shoot biomass, plant height and growth related traits) were identified on CaLG04. These traits co-mapped with a previously identified major drought tolerance QTL-hotspot region on CaLG04 (~300Kb). One SNP marker showed a significant marker-trait association with plant vigor and its related traits. Importantly, loci for most of the plant vigor related traits from GWAS showed that they were located within the CaLG04 genomic regions, co-mapping with previously reported QTLs for these traits. In addition, identified MTAs were also successfully validated by QTL mapping in a bi-parental population. Once the markers for vigor related traits (e.g., vigor score) are re-validated using large germplasm, vigor being a critical trait in chickpea breeding, these could be used as a diagnostic marker in breeding programs to develop varieties with improved drought adaptation.



Reference Sequences of the genomes of cultivated and wild Cicer species


Vasantika Suryawanshi1, Peter L. Chang2, Asif Zubair1, Eric J von Wettberg3, Noelia Carrasquilla-Garcia2, R Varma Penmetsa2, Sergey Nuzhdin1, Douglas R. Cook2


1Molecular and Computational Biology Dept., University of Southern California, Los Angeles, CA 90089, USA

2Department of Plant Pathology, University of California, Davis, CA 95616, USA

3Florida International University, Dept of Biological Sciences, Miami, FL 33199


The aim of this work is to improve and generate reference sequences for the genomes of chickpea species - Cicer arietinum, it's wild progenitor - Cicer reticulatum and another closely related wild annual species - Cicer echinospermum. The Cicer arietinum genome is moderately sized at ~750Mbp and the two wild Cicer genomes are estimated to be about 10% larger, largely attributable to increase in repetitive DNA content. To assemble the highly repetitive genomes, integration of complementary data sources – short reads long reads (~30x coverage), genetic maps and optical maps was considered imperative. The HiSeq 2500 whole-genome shotgun reads (125-150bp) were produced at >100x coverage, long reads from PacBio (median length 8-12Kbp) at ~30x coverage. To validate the assembled contigs and assist with the construction of pseudomolecules, we constructed optical BioNano genome (BNG) maps of all three accessions at ~100x coverage.


To generate draft genome assemblies, two approaches were implemented. First, the PacBio-only strategy utilized only the long-reads to assemble the genomes using Canuv1.4 assembler. Second, the Hybrid strategy combined both long and short reads to assemble the genomes using MaSuRCA-LR assembler. The assemblies from both approaches were then merged to yield final assembled genome sizes of 647Mb, 645Mb and 716Mb for the C. arietinum, C. echinospermum and C. reticulatum respectively. Less than 1200 contigs of min. size ~230Kb constituted over half of the assembled genome sizes. Over 98% of the short reads were successfully mapped back to the assemblies. CEGMA results suggested that approximately 98% of the gene-space has been covered in the present assemblies, with almost 90% genes at full coverage.






Genotypic variations and inoculation response in chickpea after rice cultivation


Karivaradharajan Swarnalakshmi, Shubham Gambhir, Vandana Yadav, Shailesh Tripati and Kannepalli Annapurna


ICAR-Indian Agricultural Research Institute (IARI), New Delhi-110012, India


In India, vast area under Rainfed Rice Fallow Lands (RRFL) remains fallow after rainfed rice cultivation during kharif season. Pulses particularly, chickpea grown after rice harvest can improve the soil fertility as well as sustainable rice production in subsequent Kharif season. Although improved chickpea varieties suitable for RRFL have been established, crop productivity is very low. A number of abiotic factors related to soil and water lead to stagnated production in rice-chickpea cropping systems. Nutrient constraints after rice-crop affect symbiotic performance, growth and yield of chickpea grown during rabi season. In this context, seed inoculation with efficient Mesorhizobium along with beneficial microorganism such as Arbuscular mycorrhiza is known to increase nodulation, nitrogen fixation and plant growth in chickpea. A field experiment was conducted to evaluate the response of chickpea genotypes (BGD-72, GNG-1581, PUSA-256, PUSA-362, PUSA-372, PUSA-547 and PUSA 1103) with and without inoculation of Mesorhizobium + Arbuscular mycorrhiza for symbiotic potential, plant growth and yield after rice cultivation. The Mesorhizobial count of rice field soil showed nil population. The inoculation with Mesorhizobium + Arbuscular mycorrhiza showed increased nodulation ranging from 12.67 % to 82% and shoot growth (2.27 to 32%) over uninoculated control at vegetative stage. There is a remarkable increment in seed yield as compared to uninoculated plants at harvest stage. Our study suggests that the selected inoculation had a positive effect on the growth and yield of chickpea genotypes suitable for late-sown conditions under RRFL. Since continuous use of chemical fertilizers decrease crop productivity, the research on agro-ecosystems based plant and micro-organisms mediated nutrient management strategies are required to attain higher nutrient use efficiencies in rice-chickpea cropping systems.







Kassahun Tesfaye (PhD) and Paulos Asrat (PhD Fellow)


Addis Ababa University, Addis Ababa, Ethiopia


Chickpea is one of the main annual crops in Ethiopia both in terms of its share of the total cropped area and its direct consumption and marketing role. Improvement in its productivity, marketing and subsequent value chain can be a major milestone in the fight against poverty in the country. In this regard, the present study has three major components including chickpea seed system; chickpea marketing and chickpea value chain analysis in the central highland of Ethiopian. A sample of 834 randomly selected households was interviewed using a structured questionnaire complemented by intensive focus group discussions and secondary data. Descriptive, method, econometric method and integrated value chain approach were used to analyze the data.


The empirical evidence suggests that improving smallholder farmers’ awareness for the uptake of improved chickpea technologies would improve farm-gate net returns to smallholder producers. The marketable surplus will also be improved if farmers switch to production of improved varieties. The study, further ascertains that smallholder farmers need to know how to identify preferable potential buyers that will enhance competitiveness of chickpea market. In this regard, the study revealed inadequate horizontal and vertical linkages among chickpea market participants. Limited participation in valued addition, limited access to information, credit and related business services also continue to stifle the marketing system.


Therefore, addressing these issues along the chickpea value chain requires collaborative efforts to introduce appropriate technologies and market information systems that improve productivity and that help to meet quality and quantity requirements of different end-users in both domestic and international markets. Based on the study result, establishing quality-based marketing systems that create self-enforcing incentives for producers to supply high quality produce is possible through reducing asymmetric information that prevents farmers from receiving better prices for their produce. Moreover, there is a need for increased participation of the private sector in strengthening business support services to traders along the value chain. The strength of market linkages between farmers and traders operating at the upper end of the value chain needs to be enhanced through better market linkages and development of mutually beneficial contractual arrangements. More importantly, there is a need for institutional innovations to reduce transaction costs through better coordination of marketing activities of smallholder farmers and increased exchange of information along the value chain.



Identifying low pH TOLERANCE IN WILD Cicer


Wendy H Vance, Scott R Strachan, and Richard W Bell


School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia


Soil acidity restricts plant growth mainly due to the toxicity effects of Al and Mn. Deficiencies of Mo, N, P, Ca and Mg can also occur in acid soils. In Western Australia, Al toxicity is most prevalent on acid soils, whilst in Eastern Australia acid soils more commonly cause Mn toxicity in crops. Insoluble Al is abundant in most soils, but under acid conditions (pHCaCl2) less than 4.5) some forms of aluminium are solubilized to release Al3+ and Al(OH)2+, ions that are highly toxic to roots and bacteria. Aluminium toxicity inhibits cell division and reduces root elongation of plants. Severe symptoms of aluminium toxicity include brown stubby roots and decreased fine branching roots. Such effects on root growth not only impair nutrient acquisition by crops but may also exacerbate drought by restricting access of roots to soil-soil water storage. The objective of this research is to determine if there are wild relatives of chickpea (Cicer arietinum L.) that are tolerant to low pH, high Al conditions. Initial experiments were completed on C. arietinum L. to test screening procedures and determine the tolerance of C. arietinum L. to low pH and high Al.


The response of C. arietinum L. cultivars (5 cv’s) to pH (3 to 6.5) in solution culture without Al suggests that at a pH of 4.2, there is some differentiation between sensitive and more tolerant cultivars. When C. arietinum L. accessions were screened at different solution pH, there was a reduction in length of the longest root (LLR) of 44% in a solution of pH 4.2, 57% at pH 3.8, and 90% for pH 3.4 compared to the control (pH 6.5). There was an interaction between treatment pH and cultivar.


Thirteen domesticated chickpea varieties were tested in dose response experiments (low pH 4.2 and +/- Al 0 to 90 μMol). In an initial experiment with 5 cv’s there was no effect of the treatment by cultivar interaction. There were significant differences in root and shoot weight with increasing Al concentration from 15 to 90 µM.  The lowest Al concentration that showed a significant decline in root and shoot growth was at the 30 and 45 µM Al levels. In a second dose experiment on 8 additional C. arietinum L. cultivars there were significant differences in root and shoot weights, and LLR, with each increase in Al concentration from 0 to 15 to 30 µMol. There was no difference in seedling growth between the 30 and 60 µMol treatments. PBA Pistol was the cultivar that had the greatest LLR, and root weight. Within the treatment by cultivar interaction, PBA Pistol had a greater LLR at 15 µMol Al than all other cultivars and was similar to the LLR of some of the cultivars with no Al in solution.


Screening of 118 wild Cicer accessions in solution culture has been completed at pH 4.2 with 15 and 60 uMol Al. Within these accessions there is variation in LLR, root tolerance index and root and shoot weights that indicate there is some differentiation in tolerance of wild Cicer accessions to low pH, high Al conditions.




ChIckpea collection in the vavilov institute: diversity and use


Margarita Vishnyakova1,Sergey Bulyntsev2


1Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), Saint-Petersburg, Russia,

2VIR Kuban Branch, Krasnodar Territory, Russia.


The first introductions of chickpea accessions in the VIR collection date back to 1916. These were landraces collected by N.I. Vavilov in Iran (former Persia). Now the collection contains 3567 accessions originating from 71 countries. More than a half of the collection is represented by old landraces. Many of them were introduced in the collection about one hundred years ago from the centers of origin and diversity of the crop, that is, from Western Asia, Mediterranean Region, Ethiopia and India.


Phenotyping of the collection is systematically carried out in various environments at the Astrakhan, Kuban and Central Russia branches of VIR. The Tambov Region in a new site for chickpea cultivation as the most northern region of this crop production in the Russian Federation. The results of evaluation performed in this environment for several years revealed a gene pool adaptive to these latitudes. The main aim of the annual evaluation of the collection is the identification of the elite germplasm that can be taken as the sources of valuable traits for breeding programs in different regions of chickpea production. Accessions of some wild species conserved in the collection are sources of resistance to abiotic and biotic stressors and thus can be involved in introgressive breeding. All Russian chickpea varieties and many others in the former USSR have been bred on the basis of the VIR collection.





Sudheer K. Yadav1, Surendra Singh1, Birinchi K. Sarma2 and Harikesh B. Singh2


1Department of Botany, Faculty of Science, Banaras Hindu University, Varanasi-221005

2Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi-221005


In the present scenario of pulses, chickpea is a very essential crop and considered to be a good source of proteins. Chickpea consumption may also lower blood cholesterol level. Further reports also prove that chickpea leaves have higher mineral content than cabbage and spinach. The present study evaluates the effect of beneficial microbial inoculation on enhancing the nutritional values in edible parts of chickpea. Two rhizosphere-competent compatible microbes (Pseudomonas fluorescens OKC and Trichoderma asperellum T42) were selected and used either individually or in combination for biopriming the seeds of chickpea before sowing. The three different parts (seed, foliage and pericarp) of chickpea plants were selected for nutritional quality evaluation after harvesting. Chickpea seeds primed with the microbes showed enhanced plant growth [88.93% shoot length at 60 days after sowing (DAS)] and biomass accumulation (21.37% at 120 DAS). Notably, the uptake of mineral nutrients, viz., N (90.27, 91.45, and 142.64%), P (14.13, 58.73, and 56.84%), K (20.5, 9.23, and 35.98%), Na (91.98, 101.66, and 36.46%), Ca (16.61, 29.46, and 16%), and organic carbon (28.54, 17.09, and 18.54%), was found in the seed, foliage, and pericarp of the chickpea plants, respectively. Additionally, nutritional quality, viz., total phenolic (59.7, 2.8, and 17.25%), protein (9.78, 18.53, and 7.68%), carbohydrate content (26.22, 30.21, and 26.63%), total flavonoid content (3.11, 9.15, and 7.81%), and reducing power (112.98, 75.42, and 111.75%), was also found in the seed, foliage, and pericarp of the chickpea plants. Most importantly, the microbial consortium-treated plants showed the maximum increase of nutrient accumulation and enhancement in nutritional quality in all edible parts of chickpea. The mentioned parameters are capable of increasing plant and their consumer’s health as well. The expression of nitrate transporter gene (NRT1) was also checked after 7, 14 and 21 days of sowing. The plants arisen from seeds primed with microbial consortium have prolonged up-regulated NRT1 expression to that of un-primed control. The up-regulation of NRT1 enhances the better nitrate uptake, ultimately resulting the good plant growth and health. Thus, it is clear that microbial consortium of PGPR and biocontrol agents in the form of P. fluorescens OKC and T. asperellum T42 have the capability to reduce the requirement of chemical fertilizer to achieve the better yield, plant health and nutritional quality of food.




Nested Association Mapping (NAM) analysis for Chickpea hybrid populations


Asif Zubair1, Peter L. Chang1, Douglas R. Cook2, Sergey V. Nuzhdin1


1Department of Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90007, USA

2Department of Plant Pathology, University of California, Davis, CA 95616, USA


NAM populations utilize the framework of common reference design to produce synthetic mapping populations that take advantage of both historic and recent recombination events such that marker density requirement is kept low while having higher allelic richness and statistical power. Pursuant of this aim, and keeping in mind that our goal is to introgress favourable alleles from wild populations into cultivated varieties, crosses of two wild chickpea species, C. echinospermum and C. reticulatum, called wild founders, were made with three different elite cultivars.


In the present analysis, we examine hybrid crosses of wild founders with the elite cultivar, ICCV96029. Limiting ourselves to species divergent markers, we conduct an association study with six continuous phenotypes including important traits like yield and shattering index. This reveals important features of the genomic architecture underlying these traits. Additionally, by breaking down the association analysis by population, we locate markers that may be active in a population specific manner. Finally, by conducting a PCA-based selection scan, we identify distortion regions that may indicate potential incompatibility loci.