J Integr Plant Biol. ›› 2022, Vol. 64 ›› Issue (3): 632-648.DOI: 10.1111/jipb.13202

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SoySNP618K array: A high-resolution single nucleotide polymorphism platform as a valuable genomic resource for soybean genetics and breeding

Yan‐Fei Li1†, Ying‐Hui Li1†, Shan‐Shan Su2, Jochen C. Reif3, Zhao‐Ming Qi4, Xiao‐Bo Wang5, Xing Wang6, Yu Tian1, De‐Lin Li1,7, Ru‐Jian Sun1,4,8, Zhang‐Xiong Liu1, Ze‐Jun Xu6, Guang‐Hui Fu9, Ya‐Liang Ji2, Qing‐Shan Chen4, Ji‐Qiang Liu2 and Li‐Juan Qiu1*   

  1. 1 The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    2 Beijing Compass Biotechnology Co. Ltd, Beijing 102206, China
    3 Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
    4 Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China
    5 School of Agronomy, Anhui Agricultural University, Hefei 230036, China
    6 Xuzhou Institute of Agricultural Sciences of Xu‐huai Region of Jiangsu, Xuzhou 221131, China
    7 Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
    8 Hulun Buir Institution of Agricultural Sciences, ZhalantunInner Mongolia 021000, China
    9 Suzhou Academy of Agricultural Sciences, Suzhou 234000, China

    These authors contributed equally to this work.
    *Correspondence: Li-Juan Qiu (qiulijuan@caas.cn)
  • Received:2021-10-05 Accepted:2021-12-05 Online:2021-12-16 Published:2022-03-01

Abstract: Innovations in genomics have enabled the development of low-cost, high-resolution, single nucleotide polymorphism (SNP) genotyping arrays that accelerate breeding progress and support basic research in crop science. Here, we developed and validated the SoySNP618K array (618,888 SNPs) for the important crop soybean. The SNPs were selected from whole-genome resequencing data containing 2,214 diverse soybean accessions; 29.34% of the SNPs mapped to genic regions representing 86.85% of the 56,044 annotated high-confidence genes. Identity-by-state analyses of 318 soybeans revealed 17 redundant accessions, highlighting the potential of the SoySNP618K array in supporting gene bank management. The patterns of population stratification and genomic regions enriched through domestication were highly consistent with previous findings based on resequencing data, suggesting that the ascertainment bias in the SoySNP618K array was largely compensated for. Genome-wide association mapping in combination with reported quantitative trait loci enabled fine-mapping of genes known to influence flowering time, E2 and GmPRR3b, and of a new candidate gene, GmVIP5. Moreover, genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate (>0.65). Thus, the SoySNP618K array is a valuable genomic tool that can be used to address many questions in applied breeding, germplasm management, and basic crop research.

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