基于全基因组关联分析的大豆发芽期耐寒 SNPs 和候选基因挖掘。

IF 4.4 1区 农林科学 Q1 AGRONOMY Theoretical and Applied Genetics Pub Date : 2024-07-08 DOI:10.1007/s00122-024-04685-y
Yuehan Chen, Zhi Liu, Dezhi Han, Qing Yang, Chenhui Li, Xiaolei Shi, Mengchen Zhang, Chunyan Yang, Lijuan Qiu, Hongchang Jia, Shu Wang, Wencheng Lu, Qian Ma, Long Yan
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引用次数: 0

摘要

关键信息通过全基因组关联分析确定了3个与耐低温相关的QTL,通过单倍型分析和基因表达分析确定了15个候选基因。低温是影响大豆地理分布、生长、发育和产量的关键因素,种子萌发过程中的低温胁迫会导致大量的产量损失。在这项研究中,对由 260 个大豆品种组成的关联面板进行了四种萌发性状和四种耐寒指数性状的评估,结果显示耐寒性存在广泛的变异。全基因组关联研究(GWAS)利用 30,799 个单核苷酸多态性(SNPs)和四个 GWAS 模型确定了与耐寒性相关的 10 个数量性状核苷酸(QTNs)。连锁不平衡(LD)分析将这些 QTNs 定位在三个耐寒数量性状位点(QTL)上,其中 QTL19-1 被三个多焦点模型定位,突出了其作为关键 QTL 的重要性。综合单倍型分析以及转录组分析发现了 15 个候选基因。基因Glyma.18G044200、Glyma.18G044300、Glyma.18G044900、Glyma.18G045100、Glyma.19G222500和Glyma.19G222600中的单倍型表现出显著的表型差异,在不同耐寒性的材料中有不同的表达。本研究鉴定的 QTNs 和候选基因为耐寒大豆育种中的标记辅助选择和基因编辑提供了巨大的潜力,为大豆发芽过程中耐寒性的遗传机制提供了宝贵的见解。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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Cold tolerance SNPs and candidate gene mining in the soybean germination stage based on genome-wide association analysis.

Key message: Three QTLs associated with low-temperature tolerance were identified by genome-wide association analysis, and 15 candidate genes were identified by haplotype analysis and gene expression analyses. Low temperature is a critical factor affecting the geographical distribution, growth, development, and yield of soybeans, with cold stress during seed germination leading to substantial productivity loss. In this study, an association panel comprising 260 soybean accessions was evaluated for four germination traits and four cold tolerance index traits, revealing extensive variation in cold tolerance. Genome-wide association study (GWAS) identified 10 quantitative trait nucleotides (QTNs) associated with cold tolerance, utilizing 30,799 single nucleotide polymorphisms (SNPs) and four GWAS models. Linkage disequilibrium (LD) analysis positioned these QTNs within three cold-tolerance quantitative trait loci (QTL) and, with QTL19-1, was positioned by three multi-locus models, underscoring its importance as a key QTL. Integrative haplotype analysis, supplemented by transcriptome analysis, uncovered 15 candidate genes. The haplotypes within the genes Glyma.18G044200, Glyma.18G044300, Glyma.18G044900, Glyma.18G045100, Glyma.19G222500, and Glyma.19G222600 exhibited significant phenotypic variations, with differential expression in materials with varying cold tolerance. The QTNs and candidate genes identified in this study offer substantial potential for marker-assisted selection and gene editing in breeding cold-tolerant soybeans, providing valuable insights into the genetic mechanisms underlying cold tolerance during soybean germination.

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来源期刊
CiteScore
9.60
自引率
7.40%
发文量
241
审稿时长
2.3 months
期刊介绍: Theoretical and Applied Genetics publishes original research and review articles in all key areas of modern plant genetics, plant genomics and plant biotechnology. All work needs to have a clear genetic component and significant impact on plant breeding. Theoretical considerations are only accepted in combination with new experimental data and/or if they indicate a relevant application in plant genetics or breeding. Emphasizing the practical, the journal focuses on research into leading crop plants and articles presenting innovative approaches.
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