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

Nature Genetics volume 56, pages 530–540 (2024)Cite this article

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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.

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Fig. 1: Geographic distribution, population structure and LD decay of 390 peanut accessions.
Fig. 2: Summary of gene linkage or pleiotropy.
Fig. 3: Genome-wide screening of selective sweep regions and GWAS signals.
Fig. 4: Pedigree of Yueyou7hao and GWAS for yield-related traits.
Fig. 5: GWAS for branching habit and AhBSK1 identification.
Fig. 6: GWAS for oil traits and AhWRI1 identification.

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Data availability

All the 390 genomic sequence data for GWAS analysis have been deposited in the National Center for Biotechnology Information (NCBI) database under BioProject number PRJNA776707. All the 11 varieties of genomic sequence data for IBD analysis have been deposited in the NCBI database under BioProject number PRJNA1031811. The SNP and InDel genotypes have been deposited in Zenodo81 (https://doi.org/10.5281/zenodo.10054109). The published transcriptomic datasets for candidate gene expression analysis can be downloaded from the NCBI Sequence Read Archive under accession numbers SRP167797 and SRP033292 mentioned in the corresponding original literature. Source data are provided with this paper.

Code availability

Custom scripts for calculating the coverage of the aligned sequence are available at Zenodo82 (https://doi.org/10.5281/zenodo.10023694).

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Acknowledgements

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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  1. These authors contributed equally: Qing Lu, Lu Huang, Hao Liu.

Authors and Affiliations

  1. Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China

    Qing Lu, Lu Huang, Hao Liu, Haifen Li, Dandan Guo, Shaoxiong Li, Haiyan Liu, Runfeng Wang, Quanqing Deng, Puxuan Du, Xuanqiang Liang, Yanbin Hong & Xiaoping Chen

  2. WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia

    Vanika Garg, Annapurna Chitikineni & Rajeev K. Varshney

  3. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India

    Sunil S. Gangurde & Manish K. Pandey

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Contributions

Q.L., X.C., Y.H., X.L. and R.K.V. conceived and designed the study. Q.L., Hao Liu, H. Li, D.G., L.H. and S.L. performed data analysis. Haiyan Liu and R.W. prepared the samples. Q.D. and P.D. measured the agronomic traits. Q.L. wrote the manuscript. R.K.V., V.G., A.C., M.K.P. and S.S.G. revised the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Qing Lu, Rajeev K. Varshney, Xuanqiang Liang, Yanbin Hong or Xiaoping Chen.

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Lu, Q., Huang, L., Liu, H. et al. A genomic variation map provides insights into peanut diversity in China and associations with 28 agronomic traits. Nat Genet 56, 530–540 (2024). https://doi.org/10.1038/s41588-024-01660-7

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