Genome-wide association studies (GWAS) of gene-rich regions associated with target traits for peanut breeding using diverse global germplasm collections
Duration: 01/Jul/2013 - 31/Dec/2015
Project contact: Dr Rajeev K Varshney (R.K.Varshney@CGIAR.ORG)
Donor: Foundation or Trust
CGIAR Research Program: Grain Legumes
Genome-wide association studies (GWAS) exploit historical recombination to provide marker-trait associations of high genetic resolution and require diverse germplasm panels, precise phenotyping data, and high-density genotyping data. Three high-quality diverse germplasm panels exist for peanut: the ICRISAT reference set of 300 accessions based on a global germplasm collection of Arachis species, the US mini-core collection of 112 accessions based on US peanut germplasm, and the Chinese mini-core of 298 accessions based on Chinese germplasm. Multiple-season data on ICRISATs reference set are available for 51 traits (467 environments) while the US and Chinese mini-core collections contain data on 22 to 35 traits including resistance to many diseases, oil/seed/nutritional quality, physiological/drought tolerance, and yield/yield components. In parallel, UC-Davis (RWM group) is embarking on generating high density genotype data for these panels. This project will compile and curate the phenotypic data, conduct comprehensive statistical analyses on the curated datasets, estimate diversity features based on genotyping data, and undertake GWAS for traits of importance to breeders. Identified marker-trait associations will be integrated with the existing QTL data as well as new QTL data generated with extant recombinant inbred line (RIL) populations. The project will provide sequence-based markers and haplotypes associated with traits of agronomic importance as well as identify accessions with superior alleles that can be used as donors in breeding programs to develop peanut varieties relevant to the peanut industry in the USA and national programs in India and China.