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

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Abstract

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 10× 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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Data availability

The datasets generated and/or analyzed during the current study are available from Long Yan on reasonable request.

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Funding

This research was supported by the National Key R & D Project (2021YFD1201602), Natural Science Foundation of Hebei Province (C2020301020), National Natural Science Foundation of China (31871652, 32072092), Modern Agricultural Science and Technology Innovation Project of Hebei Province (2019-4-3), and China Agriculture Research System of MOF and MARA (CARS-04-PS06).

Author information

Author notes

  1. Qing Yang, Jianan Zhang, and Xiaolei Shi contributed equally to this study.

Authors and Affiliations

  1. Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, High-Tech Industrial Development Zone, 162 Hengshan St, Shijiazhuang, 050035, Hebei, People’s Republic of China

    Qing Yang, Xiaolei Shi, Jun Qin, Mengchen Zhang, Chunyan Yang & Long Yan

  2. Mol Breeding Biotechnology Co., Ltd., 136 Huanghe Parkway, Shijiazhuang, 050035, Hebei, People’s Republic of China

    Jianan Zhang

  3. School of Life Sciences, Yantai University, 30# Qingquan Road, Lai Shan District, Yantai, 264005, Shandong, People’s Republic of China

    Lei Chen

  4. Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA

    Qijian Song

Authors
  1. Qing Yang
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  2. Jianan Zhang
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  3. Xiaolei Shi
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  4. Lei Chen
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  5. Jun Qin
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  8. Qijian Song
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  9. Long Yan
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Contributions

Q.J.S., L.Y., C.Y.Y., and M.C.Z. designed the experiments and critically revised the manuscript. Q.Y., J.N.Z., L.C., and L.Y. analyzed the data. Y.Q. wrote the manuscript. L.Y. and X.L.S. carried out the experiments. All authors have read and approved the manuscript.

Corresponding author

Correspondence to Long Yan.

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Tables S1–S4 (XLSX 2831 kb)

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Yang, Q., Zhang, J., Shi, X. et al. Development of SNP marker panels for genotyping by target sequencing (GBTS) and its application in soybean. Mol Breeding 43, 26 (2023). https://doi.org/10.1007/s11032-023-01372-6

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