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

PLoS One. 2014 Aug 20;9(8):e105228. doi: 10.1371/journal.pone.0105228. eCollection 2014.

Abstract

Peanut is an important and nutritious agricultural commodity and a livelihood of many small-holder farmers in the semi-arid tropics (SAT) of world which are facing serious production threats. Integration of genomics tools with on-going genetic improvement approaches is expected to facilitate accelerated development of improved cultivars. Therefore, high-resolution genotyping and multiple season phenotyping data for 50 important agronomic, disease and quality traits were generated on the 'reference set' of peanut. This study reports comprehensive analyses of allelic diversity, population structure, linkage disequilibrium (LD) decay and marker-trait association (MTA) in peanut. Distinctness of all the genotypes can be established by using either an unique allele detected by a single SSR or a combination of unique alleles by two or more than two SSR markers. As expected, DArT features (2.0 alleles/locus, 0.125 PIC) showed lower allele frequency and polymorphic information content (PIC) than SSRs (22.21 alleles /locus, 0.715 PIC). Both marker types clearly differentiated the genotypes of diploids from tetraploids. Multi-allelic SSRs identified three sub-groups (K = 3) while the LD simulation trend line based on squared-allele frequency correlations (r2) predicted LD decay of 15-20 cM in peanut genome. Detailed analysis identified a total of 524 highly significant MTAs (p value > 2.1 × 10-6) with wide phenotypic variance (PV) range (5.81-90.09%) for 36 traits. These MTAs after validation may be deployed in improving biotic resistance, oil/ seed/ nutritional quality, drought tolerance related traits, and yield/ yield components.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arachis / genetics*
  • Cluster Analysis
  • Crops, Agricultural / genetics
  • Genes, Plant
  • Genetic Enhancement
  • Genome-Wide Association Study / standards*
  • Genotype
  • Hybridization, Genetic
  • Linkage Disequilibrium
  • Microsatellite Repeats
  • Reference Standards
  • Tropical Climate

Grants and funding

This study was undertaken as a part of Tropical Legumes I (TLI- Objective 1: Groundnut) funded by Bill & Melinda Gates Foundation (BMGF) through CGIAR Generation Challenge Programme (http://www.generationcp.org/) and The Peanut Foundation, USA (http://www.peanutfoundation.org/). This work has been undertaken as part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of CGIAR Consortium. ShanDong Shofine Seed Technology Co Ltd, Jining, Shandong, China provided support in the form of a salary for author HL who participated in data analysis using analytical tools, but did not have any additional role in the study design and data collection, decision to publish, or preparation of the manuscript. The specific roles of the authors are articulated in the “author contributions” section. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.