Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut

Pushpesh Joshi; Pooja Soni; Vinay Sharma; Surendra S Manohar; Sampath Kumar; Shailendra Sharma; Janila Pasupuleti; Vincent Vadez; Rajeev K Varshney; Manish K Pandey; Naveen Puppala

doi:10.3390/genes15020140

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Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut

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Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut

Pushpesh Joshi, Pooja Soni, Vinay Sharma, Surendra S Manohar, Sampath Kumar, Shailendra Sharma, Janila Pasupuleti, Vincent Vadez, Rajeev K Varshney, Manish K Pandey, …

Genes, Vol.15(2), 140

2024

DOI: https://doi.org/10.3390/genes15020140

PMID: 38397130

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Abstract

Arachis - genetics

Chromosome Mapping

Phenotype

Plant Breeding

Quantitative Trait Loci

Peanuts (Arachis hypogaea L.) are important high-protein and oil-containing legume crops adapted to arid to semi-arid regions. The yield and quality of peanuts are complex quantitative traits that show high environmental influence. In this study, a recombinant inbred line population (RIL) (Valencia-C × JUG-03) was developed and phenotyped for nine traits under two environments. A genetic map was constructed using 1323 SNP markers spanning a map distance of 2003.13 cM. Quantitative trait loci (QTL) analysis using this genetic map and phenotyping data identified seventeen QTLs for nine traits. Intriguingly, a total of four QTLs, two each for 100-seed weight (HSW) and shelling percentage (SP), showed major and consistent effects, explaining 10.98% to 14.65% phenotypic variation. The major QTLs for HSW and SP harbored genes associated with seed and pod development such as the seed maturation protein-encoding gene, serine-threonine phosphatase gene, TIR-NBS-LRR gene, protein kinase superfamily gene, bHLH transcription factor-encoding gene, isopentyl transferase gene, ethylene-responsive transcription factor-encoding gene and cytochrome P450 superfamily gene. Additionally, the identification of 76 major epistatic QTLs, with PVE ranging from 11.63% to 72.61%, highlighted their significant role in determining the yield- and quality-related traits. The significant G × E interaction revealed the existence of the major role of the environment in determining the phenotype of yield-attributing traits. Notably, the seed maturation protein-coding gene in the vicinity of major QTLs for HSW can be further investigated to develop a diagnostic marker for HSW in peanut breeding. This study provides understanding of the genetic factor governing peanut traits and valuable insights for future breeding efforts aimed at improving yield and quality.

Details

Title: Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut
Authors/Creators: Pushpesh Joshi - International Crops Research Institute for the Semi-Arid Tropics
Pooja Soni - International Crops Research Institute for the Semi-Arid Tropics
Vinay Sharma - International Crops Research Institute for the Semi-Arid Tropics
Surendra S Manohar - International Crops Research Institute for the Semi-Arid Tropics
Sampath Kumar - Agricultural Research Station, Andhra Pradesh Agricultural University, Anantapur 515591, India
Shailendra Sharma - Chaudhary Charan Singh University
Janila Pasupuleti - International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
Vincent Vadez - Diversity Adaptation plant Development
Rajeev K Varshney - Murdoch University, Food Futures Institute
Manish K Pandey - International Crops Research Institute for the Semi-Arid Tropics
Naveen Puppala - New Mexico State University
Publication Details: Genes, Vol.15(2), 140
Publisher: MDPI
Grant note: 2023 / the New Mexico Peanut Research Board, National Peanut Research Board, and was supported [in part] by the intramural research program of the U.S. Department of Agriculture, National Institute of Food and Agriculture, Hatch Capacity funds. PR18251 / National Agricultural Science Fund, Indian Council of Agricultural Research (ICAR), India; DBT-BioCARe (PR18251) of the Department of Biotechnology, India,
Identifiers: 991005642770007891
Murdoch Affiliation: Centre for Crop and Food Innovation
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: Genetics & Heredity
ESI research areas: Molecular Biology & Genetics