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

文献类型： 外文期刊

作者： Yang, Qing 1 ; Zhang, Jianan 2 ; Shi, Xiaolei 1 ; Chen, Lei 3 ; Qin, Jun 1 ; Zhang, Mengchen 1 ; Yang, Chunyan 1 ; Song, Qijian 4 ; Yan, Long 1 ;

作者机构： 1.Hebei Acad Agr & Forestry Sci, Minist Agr & Rural Affairs, Inst Cereal & Oil Crops, Natl Soybean Improvement Ctr Shijiazhuang Subctr,H, 162 Hengshan St, Shijiazhuang 050035, Hebei, Peoples R China

2.Mol Breeding Biotechnol Co Ltd, 136 Huanghe Pkwy, Shijiazhuang 050035, Hebei, Peoples R China

3.Yantai Univ, Sch Life Sci, 30 Qingquan Rd, Yantai 264005, Shandong, Peoples R China

4.USDA ARS, Soybean Genom & Improvement Lab, Beltsville, MD USA

关键词： Soybean breeding; Marker-assisted selection (MAS); SNP marker panel; Genotyping by target sequencing (GBTS); Germplasm evaluation; QTL identification

期刊名称：MOLECULAR BREEDING （ 影响因子：3.1； 五年影响因子：3.1 ）

ISSN： 1380-3743

年卷期： 2023 年 43 卷 4 期

页码：

收录情况： SCI

摘要： A high-throughput genotyping platform with customized flexibility, high genotyping accuracy, and low cost is critical for marker-assisted selection and genetic mapping in soybean. Three assay panels were selected from the SoySNP50K, 40K, 20K, and 10K arrays, containing 41,541, 20,748, and 9670 SNP markers, respectively, for genotyping by target sequencing (GBTS). Fifteen representative accessions were used to assess the accuracy and consistency of the SNP alleles identified by the SNP panels and sequencing platform. The SNP alleles were 99.87% identical between technical replicates and 98.86% identical between the 40K SNP GBTS panel and 10x resequencing analysis. The GBTS method was also accurate in the sense that the genotypic dataset of the 15 representative accessions correctly revealed the pedigree of the accessions, and the biparental progeny datasets correctly constructed the linkage maps of the SNPs. The 10K panel was also used to genotype two parent-derived populations and analyze QTLs controlling 100-seed weight, resulting in the identification of the stable associated genetic locus Locus_OSW_06 on chromosome 06. The markers flanking the QTL explained 7.05% and 9.83% of the phenotypic variation, respectively. Compared with GBS and DNA chips, the 40K, 20K, and 10K panels reduced costs by 5.07% and 58.28%, 21.44% and 65.48%, and 35.74% and 71.76%, respectively. Low-cost genotyping panels could facilitate soybean germplasm assessment, genetic linkage map construction, QTL identification, and genomic selection.

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