SoySNP618K array: A high-resolution single nucleotide polymorphism platform as a valuable genomic resource for...

Area of Science:

• Plant Genomics
• Crop Science
• Molecular Breeding

Background:

• Genomic innovations enable high-resolution SNP genotyping arrays for crop improvement.
• Soybean (Glycine max) is a vital global crop requiring advanced genomic tools.

Purpose of the Study:

• To develop and validate the SoySNP618K array for soybean research and breeding.
• To assess the array's utility in germplasm management, population genetics, and gene discovery.

Main Methods:

• Selection of 618,888 SNPs from whole-genome resequencing data of 2,214 soybean accessions.
• Analysis of population structure, domestication patterns, and gene bank redundancy.
• Genome-wide association mapping and genomic prediction for key agronomic traits.

Main Results:

• The SoySNP618K array effectively identified redundant accessions and revealed population stratification consistent with previous studies.
• Fine-mapping identified genes influencing flowering time (E2, GmPRR3b) and a novel candidate gene (GmVIP5).
• High accuracy (>0.65) was achieved in genomic prediction of flowering and maturity time in recombinant inbred lines.

Conclusions:

• The SoySNP618K array is a powerful genomic tool for soybean applied breeding and germplasm management.
• It supports basic research by enabling fine-mapping of important agronomic traits.
• The array demonstrates high utility for genomic prediction, accelerating breeding progress.