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

M.K. Pandey; H.D. Upadhyaya; A. Rathore; V. Vadez; M.S. Sheshshayee; M. Sriswathi; M. Govil; A. Kumar; M.V.C. Gowda; S. Sharma; F. Hamidou; V.A. Kumar; P. Khera; R.S. Bhat; A.W. Khan; S. Singh; H. Li; E. Monyo; H.L. Nadaf; G. Mukri; S.A. Jackson; B. Guo; X. Liang; R.K. Varshney

doi:10.1371/journal.pone.0105228

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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

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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

M.K. Pandey, H.D. Upadhyaya, A. Rathore, V. Vadez, M.S. Sheshshayee, M. Sriswathi, M. Govil, A. Kumar, M.V.C. Gowda, S. Sharma, …

PLoS ONE, Vol.9(8), Art. e105228

2014

DOI: https://doi.org/10.1371/journal.pone.0105228

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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 (pvalue >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.

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Title: 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
Authors/Creators: M.K. Pandey (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
H.D. Upadhyaya (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
A. Rathore (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
V. Vadez (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
M.S. Sheshshayee (Author/Creator) - University of Agricultural Sciences, Bangalore
M. Sriswathi (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
M. Govil (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
A. Kumar (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
M.V.C. Gowda (Author/Creator) - University of Agricultural Sciences, Dharwad
S. Sharma (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
F. Hamidou (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
V.A. Kumar (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
P. Khera (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
R.S. Bhat (Author/Creator) - University of Agricultural Sciences, Dharwad
A.W. Khan (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
S. Singh (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
H. Li (Author/Creator) - ShanDong Shofine Seed Technology Co Ltd, Jining, Shandong, China.
E. Monyo (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
H.L. Nadaf (Author/Creator) - University of Agricultural Sciences, Dharwad
G. Mukri (Author/Creator) - University of Agricultural Sciences, Dharwad
S.A. Jackson (Author/Creator) - Applied Genetic Technologies (United States)
B. Guo (Author/Creator) - United States Department of Agriculture
X. Liang (Author/Creator) - Guangdong Academy of Agricultural Sciences
R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
Publication Details: PLoS ONE, Vol.9(8), Art. e105228
Publisher: Public Library of Science
Identifiers: 991005542846807891
Copyright: © 2021 The Authors.
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Plant Sciences
ESI research areas: Agricultural Sciences