Development of SNP marker panels for genotyping by target sequencing (GBTS) and its application in soybean

Authors: YANG, QING - Hebei Academy Of Agriculture & Forestry; ZHANG, JIANAN - Mol Breeding; SHI, XIAOLEI - Hebei Academy Of Agriculture & Forestry; CHEN, LEI - Yantai University; QIN, JUN - Hebei Academy Of Agriculture & Forestry; ZHANG, MENGCHEN - Hebei Academy Of Agriculture & Forestry; YANG, CHUNYAN - Hebei Academy Of Agriculture & Forestry; Song, Qijian; YAN, LONG - Hebei Academy Of Agriculture & Forestry

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/16/2023
Publication Date: 3/29/2023
Citation: Yang, Q., Zhang, J., Shi, X., Chen, L., Qin, J., Zhang, M., Yang, C., Song, Q., Yan, L. 2023. Development of SNP marker panels for genotyping by target sequencing (GBTS) and its application in soybean. Molecular Breeding. 43. Article e26. https://doi.org/10.1007/s11032-023-01372-6.
DOI: https://doi.org/10.1007/s11032-023-01372-6

Interpretive Summary: The two main genotyping platforms, beadchip assay and sequencing, have been widely used to determine DNA variation in soybean genetic studies. Various beadchip assays have been developed, of which the SoySNP50K assay was first developed for 52,041 DNA markers and has been used to genotype all accessions in the USDA Soybean Germplasm Collections and many breeding populations. However, the use of the SoySNP50K assay outside the United States is limited due to lack of genotyping equipment and high cost. Sequencing methods are less expensive than beadchip assays, and sequencers are more easily accessible, but DNA markers in sequencing are random per run, a major problem with genome selection requiring the presence of the same set of markers. Researchers at USDA-ARS and the Hebei Academy of Agriculture and Forestry Sciences in Shijiazhuang, Hebei Province, China have developed soybean genotyping assays by targeting markers in the SoySNP50K beadchip assay using a sequencing approach, so the same set of markers can be genotyped cost-effectively. They also verified that these assays are reliable and accurate. The developed assays provide soybean researchers around the world with a means to acquire SoySNP50K markers and utilize datasets derived from SoySNP50K assays. The low-cost genotyping assays will also facilitate soybean germplasm assessment, genetic linkage map construction, QTL identification, and soybean genome selection.

Technical Abstract: A high-throughput genotyping platform with customization flexibility, high genotyping accuracy, and low cost is critical for marker-assisted selection and genetic mapping in soybean. Three assay sets, 40K, 20K, and 10K, containing 41541, 20748, and 9670 SNP markers, respectively, were selected from SoySNP50K for sequencing-by-target (GBTS) genotyping. Fifteen representative accessions were used to assess the accuracy and consistency of SNP alleles identified by the SNP panel and sequencing platform. SNP alleles were 99.87% identical between technical replicates and 98.86% identical between the 40K SNP GBT panel and 10-fold resequencing analysis. The GBS method was also accurate, the genotype dataset of 15 representative accessions correctly revealed the lineage of the accessions, and the biparental offspring dataset correctly constructed the linkage map of SNPs. A 10K panel was used to genotype two parentally derived populations and analyze QTLs controlling 100 seed weights, resulting in the identification of the stably associated genetic locus Locus_OSW_06 on chromosome 06. Markers flanking the QTL explained 7.05% and 9.83% of the phenotypic variation, respectively. Compared with GBS and DNA chips, the costs of 40K, 20K and 10K were reduced by 5.38% and 139.78%, 27.27% and 189.61%, 55.56% and 253.97%, respectively. Low-cost genotyping panels can facilitate soybean germplasm assessment, genetic linkage map construction, QTL identification, and soybean genome selection.