Developing an SNP dataset for efficiently evaluating soybean germplasm resources using the genome sequencing data of 3,661 soybean accessions

• Published in: BMC genomics Vol. 25; no. 1; p. 475
• Main Authors: Niu, Yongchao, Yung, Wai-Shing, Sze, Ching-Ching, Wong, Fuk-Ling, Li, Man-Wah, Chung, Gyuhwa, Lam, Hon-Ming
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 14-05-2024; BioMed Central; BMC
• Subjects: Analysis; Arrays; Biomarkers; Biosynthesis; Cultivation; Datasets; Diseases and pests; DNA sequencing; Domestication; Gene Library; Gene mutations; Gene sequencing; Genes; Genetic aspects; Genetics; Genome sequencing; Genome, Plant; Genomes; Genomic libraries; Genomics; Genotype & phenotype; Germplasm; Glycine max - genetics; Growth; Health aspects; InDel marker; INDEL Mutation; Insertion/deletion; Mutants; Mutation; Nucleotide sequencing; Nucleotides; Panels; Plant Breeding; Polymorphism; Polymorphism, Single Nucleotide; Population studies; Populations; Proteins; Single nucleotide polymorphism; Single nucleotide polymorphisms; SNP marker; Soybean; Soybeans; China; Genome sequencing; Germplasm evaluation; InDel marker; Naturally occurring mutant; Single nucleotide polymorphism; Soybean; Insertion/deletion; Large-effect mutation (LEM); SNP marker
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-10382-3

Single nucleotide polymorphism (SNP) markers play significant roles in accelerating breeding and basic crop research. Several soybean SNP panels have been developed. However, there is still a lack of SNP panels for differentiating between wild and cultivated populations, as well as for detecting polymorphisms within both wild and cultivated populations.
This study utilized publicly available resequencing data from over 3,000 soybean accessions to identify differentiating and highly conserved SNP and insertion/deletion (InDel) markers between wild and cultivated soybean populations. Additionally, a naturally occurring mutant gene library was constructed by analyzing large-effect SNPs and InDels in the population.
The markers obtained in this study are associated with numerous genes governing agronomic traits, thus facilitating the evaluation of soybean germplasms and the efficient differentiation between wild and cultivated soybeans. The natural mutant gene library permits the quick identification of individuals with natural mutations in functional genes, providing convenience for accelerating soybean breeding using reverse genetics.