Genome-wide association study reveals the genetic basis of amino acids contents variations in Peanut (Arachis hypogaea L.)

Muhammad J Umer; Qing Lu; Lu Huang; Raufa Batool; Hao Liu; Haifen Li; Runfeng Wang; Yu Qianxia; Rajeev K Varshney; Manish K Pandey; Yanbin Hong; Xiaoping Chen

doi:10.1111/ppl.14542

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Genome-wide association study reveals the genetic basis of amino acids contents variations in Peanut (Arachis hypogaea L.)

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Genome-wide association study reveals the genetic basis of amino acids contents variations in Peanut (Arachis hypogaea L.)

Muhammad J Umer, Qing Lu, Lu Huang, Raufa Batool, Hao Liu, Haifen Li, Runfeng Wang, Yu Qianxia, Rajeev K Varshney, Manish K Pandey, …

Physiologia plantarum, Vol.176(5), e14542

2024

DOI: https://doi.org/10.1111/ppl.14542

PMID: 39363145

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Abstract

Amino Acids - metabolism

Arachis - genetics

Arachis - metabolism

Genome-Wide Association Study

Polymorphism, Single Nucleotide - genetics

Seeds - genetics

Seeds - metabolism

Peanut is a significant source of protein for human consumption. One of the primary objectives in peanut breeding is the development of new cultivars with enhanced nutritional values. To further this goal, a genome-wide association study (GWAS) was conducted to analyze seed amino acids contents in 390 diverse peanut accessions collected worldwide, mainly from China, India, and the United States, in 2017 and 2018. These accessions were assessed for their content of 10 different amino acids. Variations in amino acids contents were observed, and arginine (Arg) was found to have the highest average value among all the amino acids quantified. The geographical distribution of the accessions also revealed variations in amino acids contents. High and positive correlation coefficients were observed among the amino acids, suggesting linked metabolic pathways or genetic regulation. A total of 88 single nucleotide polymorphisms (SNPs) spanning various chromosomes were identified, each associated with different amino acids. By using a combination of GWAS, expression anlaysis, and genomic polymorphisim comparisions, the Ahy_A09g041582 (LAC15) gene located on chromrosome A09 was identified as the key candidate which might be involved in plant growth and regulation and may alter amino acids levels. Expression analysis indicated that Ahy_A09g041582 has higher expressions in the shells and seeds than other genes located in the candidate region. This study may help with marker-based breeding of peanuts with higher nutritional value and offers fresh insights into the genetic basis of the amino acids contents of peanuts.

Details

Title: Genome-wide association study reveals the genetic basis of amino acids contents variations in Peanut (Arachis hypogaea L.)
Authors/Creators: Muhammad J Umer - Guangdong Academy of Agricultural Sciences
Qing Lu - Guangdong Academy of Agricultural Sciences
Lu Huang - Guangdong Academy of Agricultural Sciences
Raufa Batool - Ministry of Agriculture and Rural Affairs
Hao Liu - Guangdong Academy of Agricultural Sciences
Haifen Li - Guangdong Academy of Agricultural Sciences
Runfeng Wang - Guangdong Academy of Agricultural Sciences
Yu Qianxia - Guangdong Academy of Agricultural Sciences
Rajeev K Varshney - Murdoch University, Food Futures Institute
Manish K Pandey - International Crops Research Institute for the Semi-Arid Tropics
Yanbin Hong - Guangdong Academy of Agricultural Sciences
Xiaoping Chen - Guangdong Academy of Agricultural Sciences
Publication Details: Physiologia plantarum, Vol.176(5), e14542
Publisher: John Wiley & Sons Ltd on behalf of Scandinavian Plant Physiology Society.
Number of pages: 18
Grant note: 32172051 / National Natural Science Foundation of China R2021PY-QY003 / Special Fund for High Level Academy of Agriculture Science R2020PY-JX004 / Special Fund for High Level Academy of Agriculture Science 2023A04J0776 / Guangzhou Basic and Applied Basic Research Foundation 2023YFD1202800 / National Key Research and Development Program of China 32301869 / National Natural Science Foundation of China R2023PY-JG007 / Special Fund for High Level Academy of Agriculture Science 2022SDZG05 / Open Competition Program of Top Ten Critical Priorities of Agricultural Science and Technology Innovation for the 14th Five-Year Plan in Guangdong Province 2023A1515010098 / Basic and Applied Basic Research Foundation of Guangdong Province CARS-13 / China Agriculture Research System of MOF and MARA
Identifiers: 991005707261707891
Murdoch Affiliation: Centre for Crop and Food Innovation; State Agricultural Biotechnology Centre
Language: English
Resource Type: Journal article

UN Sustainable Development Goals (SDGs)

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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: Plant & Animal Science