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

Pandey, M K and Upadhyaya, H D and Rathore, A and Vadez, V and Sheshshayee, M S and Sriswathi, M and Govil, M and Kumar, A and Gowda, M V and Sharma, S and Hamidou, F and Kumar, V A and Khera, P and Bhat, R S and Khan, A W and Singh, S and Li, H and Monyo, E and Nadaf, H L and Mukri, G and Jackson, S A and Guo, B and Liang, X and Varshney, R K (2014) 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, 9 (8). pp. 1-14. ISSN 1932-6203

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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.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Agronomic Traits; Peanut; Semi-Arid Tropics; Genome analysis; Genotyping; Phenotypes; Quantitative trait loci; Alleles; Variant genotypes; Genomics; Groundnut
Subjects: Mandate crops > Groundnut
Depositing User: Mr Ramesh K
Date Deposited: 17 Jul 2015 07:44
Last Modified: 17 Jul 2015 07:45
URI: http://oar.icrisat.org/id/eprint/8871
Official URL: http://dx.doi.org/10.1371/journal.pone.0105228
Projects: UNSPECIFIED
Funders: 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
Acknowledgement: UNSPECIFIED
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