大豆（L.）种子大小相关性状的优良单倍型及候选基因鉴定

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

作者信息

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

机构信息

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.

College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.

出版信息

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

DOI:10.1007/s11032-024-01525-1

PMID:39717350

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11663835/

Abstract

UNLABELLED

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 F population; among them, 17 were detected as novel QTLs, whereas the remaining six viz., , , , , and 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., was identified by both linkage mapping and GWAS, and was regarded as the most stable loci regulating HSW in soybean. , sequencing and qRT-PCR analysis identified the as the most potential candidate gene underlying the 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 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.

摘要

未标记

种子大小是大豆中一个重要的经济性状，直接决定大豆的种子产量。在本研究中，我们采用连锁图谱构建、关联图谱分析、单倍型分析和候选基因分析的综合策略，来确定大豆中四个与种子大小相关性状的遗传组成，即百粒重（HSW）、种子面积（SA）、种子长度（SL）和种子宽度（SW）。连锁图谱分析在F群体中鉴定出总共23个与四个种子大小相关性状相关的数量性状位点（QTL）；其中，17个被检测为新的QTL，而其余6个，即、、、、和先前已被鉴定。23个QTL中有6个是主效QTL，其表型变异解释率（PVE）≥10%。此外，在第4号、第16号、第19号和第20号染色体上鉴定出四个包含多个与不同种子大小相关性状的QTL的QTL簇/QTL热点区域。全基因组关联研究（GWAS）鉴定出总共62个与四个种子大小相关性状显著相关的单核苷酸多态性（SNP）。有趣的是，QTL ，即通过连锁图谱分析和GWAS均被鉴定出来，并被认为是调控大豆百粒重最稳定的位点。测序和qRT-PCR分析确定是调控百粒重的最具潜力的候选基因。此外，针对种子宽度性状鉴定出三个单倍型块，即Hap2、Hap6A和Hap6B，针对百粒重性状在内鉴定出一个单倍型。在350份大豆种质的关联分析群体中，这四个单倍型包含三到七个单倍型等位基因，通过中间表型将种子大小从最低调节到最高。因此，本研究结果可作为培育大豆改良种子大小的潜在遗传和基因组资源。