Identification of superior haplotypes and candidate gene for seed size-related traits in soybean (Glycine max L.)

Ye Zhang; Xinjing Yang; Javaid Akhter Bhat; Yaohua Zhang; Moran Bu; Beifang Zhao; Suxin Yang

doi:10.1007/s11032-024-01525-1

Identification of superior haplotypes and candidate gene for seed size-related traits in soybean (Glycine max L.)

Mol Breed. 2024 Dec 22;45(1):3. doi: 10.1007/s11032-024-01525-1. eCollection 2025 Jan.

Authors

Ye Zhang^{1

2}, Xinjing Yang^{1

2}, Javaid Akhter Bhat³, Yaohua Zhang¹, Moran Bu^{1

2}, Beifang Zhao¹, Suxin Yang^{1

2}

Affiliations

¹ Key Laboratory of Soybean Molecular Design Breeding, National Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102 China.
² College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
³ Zhejiang Lab, Research Institute of Intelligent Computing, Hangzhou, 310012 China.

Abstract

Seed size is an economically important trait that directly determines the seed yield in soybean. In the current investigation, we used an integrated strategy of linkage mapping, association mapping, haplotype analysis and candidate gene analysis to determine the genetic makeup of four seed size-related traits viz., 100-seed weight (HSW), seed area (SA), seed length (SL), and seed width (SW) in soybean. Linkage mapping identified a total of 23 quantitative trait loci (QTL) associated with four seed size-related traits in the F₂ population; among them, 17 were detected as novel QTLs, whereas the remaining six viz., qHSW3-1, qHSW4-1, qHSW18-1, qHSW19-1, qSL4-1 and qSW6-1 have been previously identified. Six out of 23 QTLs were major possessing phenotypic variation explained (PVE) ≥ 10%. Besides, the four QTL Clusters/QTL Hotspots harboring multiple QTLs for different seed size-related traits were identified on Chr.04, Chr.16, Chr.19 and Chr.20. Genome-wide association study (GWAS) identified a total of 62 SNPs significantly associated with the four seed size-related traits. Interestingly, the QTL viz., qHSW18-1 was identified by both linkage mapping and GWAS, and was regarded as the most stable loci regulating HSW in soybean. In-silico, sequencing and qRT-PCR analysis identified the Glyma.18G242400 as the most potential candidate gene underlying the qHSW18-1 for regulating HSW. Moreover, three haplotype blocks viz., Hap2, Hap6A and Hap6B were identified for the SW trait, and one haplotype was identified within the Glyma.18G242400 for the HSW. These four haplotypes harbor three to seven haplotype alleles across the association mapping panel of 350 soybean accessions, regulating the seed size from lowest to highest through intermediate phenotypes. Hence, the outcome of the current investigation can be utilized as a potential genetic and genomic resource for breeding the improved seed size in soybean.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01525-1.

Keywords: Genetic mapping; Haplotype analysis; QTL; Seed size; Soybean.