Abhishek Rathore

Genetic Dissection of Drought and Heat Tolerance in Chickpea through Genome-Wide and Candidate Gene-Based Association Mapping Approaches

To understand the genetic basis of tolerance to drought and heat stresses in chickpea, a comprehensive association mapping approach has been undertaken. Phenotypic data were generated on the reference set (300 accessions, including 211 mini-core collection accessions) for drought tolerance related root traits, heat tolerance, yield and yield component traits from 1–7 seasons and 1–3 locations in India (Patancheru, Kanpur, Bangalore) and three locations in Africa (Nairobi, Egerton in Kenya and Debre Zeit in Ethiopia). Diversity Array Technology (DArT) markers equally distributed across chickpea genome were used to determine population structure and three sub-populations were identified using admixture model in STRUCTURE. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations (r2; when r2<0.20) was found to decay rapidly with the genetic distance of 5 cM. For establishing marker-trait associations (MTAs), both genome-wide and candidate gene-sequencing based association mapping approaches were conducted using 1,872 markers (1,072 DArTs, 651 single nucleotide polymorphisms [SNPs], 113 gene-based SNPs and 36 simple sequence repeats [SSRs]) and phenotyping data mentioned above employing mixed linear model (MLM) analysis with optimum compression with P3D method and kinship matrix. As a result, 312 significant MTAs were identified and a maximum number of MTAs (70) was identified for 100-seed weight. A total of 18 SNPs from 5 genes (ERECTA, 11 SNPs; ASR, 4 SNPs; DREB, 1 SNP; CAP2 promoter, 1 SNP and AMDH, 1SNP) were significantly associated with different traits. This study provides significant MTAs for drought and heat tolerance in chickpea that can be used, after validation, in molecular breeding for developing superior varieties with enhanced drought and heat tolerance.

Large genetic variation for heat tolerance in the reference collection of chickpea (Cicer arietinum L.) germplasm

Chickpea is the third most important pulse crop worldwide. Changes in cropping system that necessitate late planting, scope for expansion in rice fallows and the global warming are pushing chickpeas to relatively warmer growing environment. Such changes demand identification of varieties resilient to warmer temperature. Therefore, the reference collection of chickpea germplasm, defined based on molecular characterization of global composite collection, was screened for high temperature tolerance at two locations in India (Patancheru and Kanpur) by delayed sowing and synchronizing the reproductive phase of the crop with the occurrence of higher temperatures (

Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects

358C). A heat tolerance index (HTI) was calculated using a multiple regression approach where grain yield under heat stress is considered as a function of yield potential and time to 50% flowering. There were large and significant variations for HTI, phenology, yield and yield components at both the locations. There were highly significant genotypic effects and equally significant G £ E interactions for all the traits studied. A cluster analysis of the HTI of the two locations yielded five cluster groups as stable tolerant (n ¼ 18), tolerant only at Patancheru (n ¼ 34), tolerant only at Kanpur (n ¼ 23), moderately tolerant (n ¼ 120) and stable sensitive (n ¼ 82). The pod number per plant and the harvest index explained

Plant growth-promoting activities of Streptomyces spp. in sorghum and rice

60% of the variation in seed yield and

New sources of resistance to Fusarium wilt and sterility mosaic disease in a mini-core collection of pigeonpea germplasm

49% of HTI at Kanpur and

Genomewide Association Studies for 50 Agronomic Traits in Peanut Using the ‘Reference Set’ Comprising 300 Genotypes from 48 Countries of the Semi-Arid Tropics of the World

80% of the seed yield and

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

35% of HTI at Patancheru, indicating that partitioning as a consequence of poor pod set is the most affected trait under heat stress. A large number of heat-tolerant genotypes also happened to be drought tolerant.

Novel cross linked guar gum-g-poly(acrylate) porous superabsorbent hydrogels: Characterization and swelling behaviour in different environments

Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gains is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last 5 years. The availability of the draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale genomic resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seems appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries.

Genomics-assisted breeding for boosting crop improvement in pigeonpea (Cajanus cajan)

Five strains of Streptomyces (CAI-24, CAI-121, CAI-127, KAI-32 and KAI-90) were earlier reported by us as biological control agents against Fusarium wilt of chickpea caused by Fusarium oxysporum f. sp. ciceri (FOC). In the present study, the Streptomyces were characterized for enzymatic activities, physiological traits and further evaluated in greenhouse and field for their plant growth promotion (PGP) of sorghum and rice. All the Streptomyces produced lipase, β-1-3-glucanase and chitinase (except CAI-121 and CAI-127), grew in NaCl concentrations of up to 6%, at pH values between 5 and 13 and temperatures between 20 and 40°C and were highly sensitive to Thiram, Benlate, Captan, Benomyl and Radonil at field application level. When the Streptomyces were evaluated in the greenhouse on sorghum all the isolates significantly enhanced all the agronomic traits over the control. In the field, on rice, the Streptomyces significantly enhanced stover yield (up to 25%; except CAI-24), grain yield (up to 10%), total dry matter (up to 18%; except CAI-24) and root length, volume and dry weight (up to 15%, 36% and 55%, respectively, except CAI-24) over the control. In the rhizosphere soil, the Streptomyces significantly enhanced microbial biomass carbon (except CAI-24), nitrogen, dehydrogenase (except CAI-24), total N, available P and organic carbon (up to 41%, 52%, 75%, 122%, 53% and 13%, respectively) over the control. This study demonstrates that the selected Streptomyces which were antagonistic to FOC also have PGP properties.

Plant growth-promoting traits of biocontrol potential bacteria isolated from rice rhizosphere

Fusarium wilt (FW) and Sterility mosaic disease (SMD) are important biotic constraints to pigeonpea production worldwide. Host plant resistance is the most durable and economical way to manage these diseases. A pigeonpea mini-core collection consisting of 146 germplasm accessions developed from a core collection of 1290 accessions from 53 countries was evaluated to identify sources of resistance to FW and SMD under artificial field epiphytotic conditions during 2007–08 and 2008–09 crop seasons. Resistant sources identified in the field were confirmed in the greenhouse using a root dip screening technique for FW and a leaf stapling technique for SMD. Six accessions (originated from India and Italy were found resistant to FW (<10% mean disease incidence). High level of resistance to SMD was found in 24 accessions (mean incidence <10%). These SMD resistant accessions originated from India, Italy, Kenya, Nepal, Nigeria, Philippines and United Kingdom. Combined resistance to FW and SMD was found in five accessions (ICPs 6739, 8860, 11015, 13304 and 14819). These diverse accessions that are resistant to FW or SMD will be useful to the pigeonpea resistance breeding program.