Identification and molecular mapping of the semi-dwarf locus (sdf-1) in soybean by SLAF-seq method

Abstract

Plant height is one of the most important agronomic traits in soybean. The semi-dwarf soybean cultivars could improve lodging resistance and solar radiation use efficiency so as to increase soybean yield. However, the inheritance of semi-dwarf traits has not been intensively studied and few semi-dwarf genes have been isolated in soybean. In this study, we use specific-length amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) to map the semi-dwarf gene in soybean. Plant height of 213 F2:3 families, derived from a cross between ‘Jimidou-1’ (semi-dwarf) and ‘Gongjiao9112’ (tall), was evaluated under field conditions. Genetic analysis indicated that the semi-dwarf trait was controlled by one single recessive gene. Associated with the semi-dwarf trait, SLAF-seq combined with BSA was used to develop polymorphic SLAF markers and identify a 1.04 Mb genomic region, which was designated as sdf-1. The sdf-1 locus was delimited to 80.72 kb region on chromosome 19 by KASP SNP markers developed from the SLAF markers and 6 K SNP chip. There were 14 putative genes in the associated region. From annotation information, three genes (Glyma.19g194800, Glyma.19g194500 and Glyma.19g195200) might be interesting candidate genes that are highly related to plant height growth or semi-dwarf trait. The successful identification and localization of sdf-1 could help reveal molecular mechanisms underlying soybean semi-dwarfism and to indirectly improve total yield.

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Acknowledgements

This project is supported by National Key Research and Development Plan (No. 2017YFD0101304) and National Natural Science Foundation of China (No. 31301347). The development of SNP marker by 6 K SNP chip and genotype identification by KASP SNP were conducted in the lab of the soybean genetics and breeding lab in Michigan State University, USA. We thank all staff work in the labs. We especially thank Dechun Wang, Zhixiang Wen and Wenyan Du for helping in marker development by 6 K SNP chip and the synthesis of KASP SNP primers.

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ZD and BL designed and directed the project. ZD performed the association analysis and KASP SNP marker development. ZD and NL analysed the sequencing data. LC constructed the genetic linkage map. ZD and LC wrote the manuscript with input from all authors. SZ performed the genotype analysis in the mapping population. ZL and JL developed the BC1, F2 and F2:3 mapping population, and performed the genetics analysis of dwarf phenotype. ZL designed the figures and tables in the manuscript. BL helped supervise the project. All authors discussed the results and contributed to the final manuscript.

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Correspondence to Baoquan Liu.

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Zhimin Dong and Liang Chen are co-first authors.

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Dong, Z., Chen, L., Li, Z. et al. Identification and molecular mapping of the semi-dwarf locus (sdf-1) in soybean by SLAF-seq method. Euphytica 216, 103 (2020). https://doi.org/10.1007/s10681-020-02633-7

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Keywords

  • Candidate genes
  • High-throughput sequencing
  • Semi-dwarfism
  • SNP