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

Yan Fei Li, Ying Hui Li, Shan Shan Su, Jochen C. Reif, Zhao Ming Qi, Xiao Bo Wang, Xing Wang, Yu Tian, De Lin Li, Ru Jian Sun, Zhang Xiong Liu, Ze Jun Xu, Guang Hui Fu, Ya Liang Ji, Qing Shan Chen, Ji Qiang Liu, Li Juan Qiu

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)632-648
Number of pages17
JournalJournal of Integrative Plant Biology
Issue number3
StatePublished - Mar 2022
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2021 Institute of Botany, Chinese Academy of Sciences


  • functional single nucleotide polymorphism array
  • gene discovery
  • genome-wide association studies
  • genomic selection
  • marker-assisted selection
  • soybean

ASJC Scopus subject areas

  • Biochemistry
  • General Biochemistry, Genetics and Molecular Biology
  • Plant Science


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