A genomic variation map provides insights into peanut diversity in China and associations with 28 agronomic traits

Lu, Q and Huang, L and Liu, H and Garg, V and Gangurde, S S and Li, H and Chitikineni, A and Guo, D and Pandey, M K and Li, S and Liu, H and Wang, R and Deng, Q and Du, P and Varshney, R K and Liang, X and Hong, Y and Chen, X (2024) A genomic variation map provides insights into peanut diversity in China and associations with 28 agronomic traits. Nature Genetics. pp. 1-16. ISSN 1546-1718

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Abstract

Peanut (Arachis hypogaea L.) is an important allotetraploid oil and food legume crop. China is one of the world’s largest peanut producers and consumers. However, genomic variations underlying the migration and divergence of peanuts in China remain unclear. Here we reported a genome-wide variation map based on the resequencing of 390 peanut accessions, suggesting that peanuts might have been introduced into southern and northern China separately, forming two cultivation centers. Selective sweep analysis highlights asymmetric selection between the two subgenomes during peanut improvement. A classical pedigree from South China offers a context for the examination of the impact of artificial selection on peanut genome. Genome-wide association studies identified 22,309 significant associations with 28 agronomic traits, including candidate genes for plant architecture and oil biosynthesis. Our findings shed light on peanut migration and diversity in China and provide valuable genomic resources for peanut improvement.

Item Type:	Article
Divisions:	Center of Excellence in Genomics and Systems Biology
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Genome-wide association studies, Plant genetics
Subjects:	Mandate crops > Groundnut Others > Genetics and Genomics
Depositing User:	Mr Nagaraju T
Date Deposited:	21 Feb 2024 08:13
Last Modified:	21 Feb 2024 08:13
URI:	http://oar.icrisat.org/id/eprint/12495
Official URL:	https://www.nature.com/articles/s41588-024-01660-7
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	This research was partially supported by the Open Competition Program of Top 10 Critical Priorities of Agricultural Science and Technology Innovation for the 14th Five-Year Plan in Guangdong Province (2022SDZG05 to X.C.), the National Natural Science Foundation of China (32301869 to L.H. and 32172051 to Q.L.), the China Agriculture Research System of MOF and MARA (CARS-13 to X.L.), the Guangdong Provincial Key Research and Development Program-Modern Seed Industry (2020B020219003 to X.C. and 2022B0202060004 to Y.H.), the Guangdong Basic and Applied Basic Research Foundation (2023A1515010098 and 2021A1515010811 to Q.L.), the Guangdong Provincial Department of Science and Technology Project-International Scientific and Technological Cooperation (20200503 to Y.H.), the Special Support Program of Guangdong Province (2021TX06N789 to X.C.), the Agricultural Competitive Industry Discipline Team Building Project of Guangdong Academy of Agricultural Sciences (202104TD to X.C.), the Special Fund for Scientific Innovation Strategy-Construction of High Level Academy of Agriculture Science (R2020PY-JX004 to Q.L., R2020PY-JG005 to X.C. and R2021PY-QY003 to Hao Liu), the Open Fund of Guangdong Provincial Key Laboratory of Crop Genetic Improvement (202101 to Hao Liu and 202201 to Q.L.) and Start-Up grant to R.K.V.
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