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

IF 2.6 3区农林科学 Q1 AGRONOMY

Molecular Breeding Pub Date : 2024-12-22 eCollection Date: 2025-01-01 DOI:10.1007/s11032-024-01525-1

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

{"title":"Identification of superior haplotypes and candidate gene for seed size-related traits in soybean (Glycine max L.).","authors":"Ye Zhang, Xinjing Yang, Javaid Akhter Bhat, Yaohua Zhang, Moran Bu, Beifang Zhao, Suxin Yang","doi":"10.1007/s11032-024-01525-1","DOIUrl":null,"url":null,"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.","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"45 1","pages":"3"},"PeriodicalIF":2.6000,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11663835/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Breeding","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1007/s11032-024-01525-1","RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"Q1","JCRName":"AGRONOMY","Score":null,"Total":0}

引用次数: 0

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.

查看原文本刊更多论文

大豆种子大小相关性状优良单倍型及候选基因的鉴定。

大豆种子大小是一项重要的经济性状，直接决定大豆种子产量。本研究采用连锁作图、关联作图、单倍型分析和候选基因分析等综合策略，确定了大豆百粒重（HSW）、种子面积（SA）、种子长（SL）和种子宽（SW） 4个与种子大小相关性状的遗传组成。连锁定位鉴定出F2群体中与4个种子大小相关性状相关的23个QTL；其中17个为新发现的qtl，其余6个为qHSW3-1、qHSW4-1、qHSW18-1、qHSW19-1、qSL4-1和qSW6-1。23个qtl中有6个主要qtl的表型变异解释率(PVE)≥10%。此外，还鉴定出4个QTL集群/QTL热点，这些QTL集群/QTL热点分别位于Chr.04、Chr.16、Chr.19和Chr.20上，包含多个不同种子大小相关性状的QTL。全基因组关联研究（GWAS）共鉴定出62个snp与4个种子大小相关性状显著相关。有趣的是，qHSW18-1 QTL通过连锁定位和GWAS鉴定，被认为是大豆中调控HSW最稳定的位点。通过测序和qRT-PCR分析，Glyma.18G242400是qHSW18-1调控HSW的潜在候选基因。此外，在Glyma.18G242400中鉴定出了HSW的1个单倍型，分别为Hap2、Hap6A和Hap6B。这四种单倍型在350份大豆材料的关联图谱中包含3 - 7个单倍型等位基因，通过中间表型从低到高调节种子大小。因此，本研究结果可作为大豆种子大小改良育种的潜在遗传和基因组资源。补充资料：在线版本提供补充资料，网址为10.1007/s11032-024-01525-1。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Molecular Breeding 农林科学-农艺学

CiteScore

5.60

自引率

6.50%

发文量

审稿时长

1.5 months

期刊介绍： Molecular Breeding is an international journal publishing papers on applications of plant molecular biology, i.e., research most likely leading to practical applications. The practical applications might relate to the Developing as well as the industrialised World and have demonstrable benefits for the seed industry, farmers, processing industry, the environment and the consumer. All papers published should contribute to the understanding and progress of modern plant breeding, encompassing the scientific disciplines of molecular biology, biochemistry, genetics, physiology, pathology, plant breeding, and ecology among others. Molecular Breeding welcomes the following categories of papers: full papers, short communications, papers describing novel methods and review papers. All submission will be subject to peer review ensuring the highest possible scientific quality standards. Molecular Breeding core areas: Molecular Breeding will consider manuscripts describing contemporary methods of molecular genetics and genomic analysis, structural and functional genomics in crops, proteomics and metabolic profiling, abiotic stress and field evaluation of transgenic crops containing particular traits. Manuscripts on marker assisted breeding are also of major interest, in particular novel approaches and new results of marker assisted breeding, QTL cloning, integration of conventional and marker assisted breeding, and QTL studies in crop plants.