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An international initiative to conduct comprehensive genome-wide association studies (GWAS) for an array of agronomic traits in peanut
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An international initiative to conduct comprehensive genome-wide association studies (GWAS) for an array of agronomic traits in peanut

  1. Inclusive Market-Oriented Development (IMOD) – our approach to bringing prosperity in the drylands. ICRISAT is a member of the CGIAR Consortium. RK Varshney1*, L Froencike2, MK Pandey1, SN Nayak1, HD Upadhyaya1, A Rathore1, B Liao3, N Barkley4, B Guo5, MVC Gowda6, C Holbrook7, TB Brenneman8, RS Bhat6, C Chen9, J Damicone10, MD Burrow11, T Isleib12, L Dean12, ML Wang4, V Vadez1, S Jackson13, RW Michelmore2 1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; 2University of California, Davis, USA; 3CAAS Oil Crops Research Institute, Wuhan, China; 4USDA-Plant Genetic Resources Conservation Unit, Griffin, USA; 5Crop Protection and Management Research Unit, USDA-ARS, Tifton, USA; 6University of Agricultural Sciences, Dharwad, India; 7Crop Breeding, USDA-ARS, Tifton, USA; 8Coastal Plain Experiment Station, UGA, Tifton, USA; 9Auburn University, Auburn, USA; 10Oklahoma State University, Stillwater, USA; 11Texas AgriLife Research, Texas A & M System, Lubbock, USA; 12North Carolina State University, Raleigh, USA; 13University of Georgia, Athens, USA; *Address for correspondence: r.k.varshney@cgiar.org Financial support from the Peanut Foundation and the CGIAR Generation Challenge Programme (GCP) is gratefully acknowledged. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes. An international initiative to conduct comprehensive genome-wide association studies (GWAS) for an array of agronomic traits in peanut  Compiling, curating and analyzing scattered phenotyping data on three important collections of the world (ICRISAT, USA and China)  Population structure and linkage disequilibrium decay using GBS genotyping data  Genome-wide association analysis for identification of marker-trait associations (MTAs)  Data, results and molecular tools made available to peanut research community An international initiative has been started to undertake a comprehensive genome-wide association studies (GWAS) in three different germplasm sets i.e. the reference set (300 genotypes) consisting of global mini core collection (184 accessions) of ICRISAT, the US mini-core collection (112 accessions) and the Chinese mini-core collection (298 accessions). The phenotypic data have been collected for 22 to 50 traits including resistance to diseases, aflatoxin contamination, tolerance to drought and salinity, and several agronomic (yield, 100-seed weight) and nutritional quality traits in several seasons at multiple locations. This initiative plans to compile and curate available phenotypic data, generate high-density genotyping data based on sequencing, conduct comprehensive statistical analysis, estimate diversity features and undertake GWAS for traits of importance to breeders using all three germplasm sets. In summary, this initiative is expected to provide: (i) sequence-based markers and haplotypes associated with traits of agronomic importance, (ii) accessions with superior alleles for their use as donors in breeding programmes, and (iii) breeders-friendly databases for phenotyping and genotyping data. Besides, the collaborative spirit of peanut research community will add momentum to peanut improvement. Abstract Acknowledgements Summary Distribution of genotypes of global peanut reference collection from 48 countries GWAS analysis for marker-trait associations Germplasm sets and traits characterized Collections Traits characterized US minicore collection Disease resistance Early leaf spot, late leaf spot, tomato spotted wilt virus, nematode and preharvest aflatoxin contamination, Sclerotinia and pepper spot, Rhizoctonia limb rot Morphological descriptors Above and below ground descriptor data, U.S. descriptors, percent shell out Abiotic stress Tolerance to heat stress and drought stress Fatty acid components Oil content, fatty acids, flavonoid, resveratrol, amino acids, tocopherols, folic acid Global minicore collection/ reference set (ICRISAT) Disease resistance Aspergillus, early leaf spot, late leaf spot, rust resistance, groundnut rosette disease Oil and nutritional quality Oil content, oleic acid, oleic/linoleic acid ratio, protein content, zinc content, iron content Physiological traits Emergence, first flowering, D13C, leaf dry weight, leaf area, specific leaf area, total leaf area, total leaf weight, SPAD chlorophyll meter reading, leaf length, leaf weight, leaf width, R/S ratio, rate of water loss, root length, root volume, root weight, shelling percentage, shoot length, shoot weight, total dry matter, total dry mass/leaf area, SMK percentage, harvest index, haulm weight, days to flower, days to mature Yield and components traits Plant number, plant height, pod length, pod width, pods / plant, primary branching, pod weight, seed length, seed weight, seed width, test weight, yield /plant, plot yield Chinese mini-core collection Morphological descriptors Plant height, length of first branch, total branching number, number of branches with pods, leaflet length, leaflet width, distance between apical and basilar leaflets, petiole length Yield and component traits Number of primary, secondary and tertiary branches, pods / plant, pod length, pod width, seed length, seed width, 100-pod weight, seed weight of 100-pod, 100-seed weight, shelling percentage and pod yield / plant Expected outcome GWAS Linked markers Molecular breeding Peanut improvement
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