Identification of candidate genes and genomic prediction of soybean fatty acid components in two soybean populations.

IF 4.4 1区 农林科学 Q1 AGRONOMY Theoretical and Applied Genetics Pub Date : 2024-08-29 DOI:10.1007/s00122-024-04716-8
Fengmin Wang, Tiantian Zhao, Yan Feng, Zengfa Ji, Qingsong Zhao, Qingmin Meng, Bingqiang Liu, Luping Liu, Qiang Chen, Jin Qi, Zhengge Zhu, Chunyan Yang, Jun Qin
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Abstract

Soybean, a source of plant-derived lipids, contains an array of fatty acids essential for health. A comprehensive understanding of the fatty acid profiles in soybean is crucial for enhancing soybean cultivars and augmenting their qualitative attributes. Here, 180 F10 generation recombinant inbred lines (RILs), derived from the cross-breeding of the cultivated soybean variety 'Jidou 12' and the wild soybean 'Y9,' were used as primary experimental subjects. Using inclusive composite interval mapping (ICIM), this study undertook a quantitative trait locus (QTL) analysis on five distinct fatty acid components in the RIL population from 2019 to 2021. Concurrently, a genome-wide association study (GWAS) was conducted on 290 samples from a genetically diverse natural population to scrutinize the five fatty acid components during the same timeframe, thereby aiming to identify loci closely associated with fatty acid profiles. In addition, haplotype analysis and the Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed to predict candidate genes. The QTL analysis elucidated 23 stable QTLs intricately associated with the five fatty acid components, exhibiting phenotypic contribution rates ranging from 2.78% to 25.37%. In addition, GWAS of the natural population unveiled 102 significant loci associated with these fatty acid components. The haplotype analysis of the colocalized loci revealed that Glyma.06G221400 on chromosome 6 exhibited a significant correlation with stearic acid content, with Hap1 showing a markedly elevated stearic acid level compared with Hap2 and Hap3. Similarly, Glyma.12G075100 on chromosome 12 was significantly associated with the contents of oleic, linoleic, and linolenic acids, suggesting its involvement in fatty acid biosynthesis. In the natural population, candidate genes associated with the contents of palmitic and linolenic acids were predominantly from the fatty acid metabolic pathway, indicating their potential role as pivotal genes in the critical steps of fatty acid metabolism. Furthermore, genomic selection (GS) for fatty acid components was conducted using ridge regression best linear unbiased prediction based on both random single nucleotide polymorphisms (SNPs) and SNPs significantly associated with fatty acid components identified by GWAS. GS accuracy was contingent upon the SNP set used. Notably, GS efficiency was enhanced when using SNPs derived from QTL mapping analysis and GWAS compared with random SNPs, and reached a plateau when the number of SNP markers exceeded 3,000. This study thus indicates that Glyma.06G221400 and Glyma.12G075100 are genes integral to the synthesis and regulatory mechanisms of fatty acids. It provides insights into the complex biosynthesis and regulation of fatty acids, with significant implications for the directed improvement of soybean oil quality and the selection of superior soybean varieties. The SNP markers delineated in this study can be instrumental in establishing an efficacious pipeline for marker-assisted selection and GS aimed at improving soybean fatty acid components.

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在两个大豆种群中鉴定候选基因并对大豆脂肪酸成分进行基因组预测。
大豆是植物源脂类的一种来源,含有一系列对健康至关重要的脂肪酸。全面了解大豆中的脂肪酸谱对于改良大豆品种和提高其品质属性至关重要。本文以栽培大豆品种'吉豆 12'和野生大豆'Y9'杂交产生的 180 个 F10 代重组近交系(RIL)为主要实验对象。本研究利用包容性复合间隔图谱(ICIM),在2019年至2021年期间对RIL群体中的五种不同脂肪酸组分进行了数量性状位点(QTL)分析。与此同时,在同一时间段内,还对来自遗传多样性自然群体的290个样本进行了全基因组关联研究(GWAS),对这五种脂肪酸成分进行了仔细研究,旨在找出与脂肪酸特征密切相关的位点。此外,还进行了单倍型分析和京都基因和基因组百科全书通路分析,以预测候选基因。QTL分析阐明了23个与五种脂肪酸组分密切相关的稳定QTL,其表型贡献率从2.78%到25.37%不等。此外,对自然群体的 GWAS 分析还发现了 102 个与这些脂肪酸成分相关的重要基因位点。对共定位位点的单倍型分析表明,6号染色体上的Glyma.06G221400与硬脂酸含量有显著相关性,与Hap2和Hap3相比,Hap1的硬脂酸含量明显升高。同样,第 12 号染色体上的 Glyma.12G075100 与油酸、亚油酸和亚麻酸的含量显著相关,表明它参与了脂肪酸的生物合成。在自然群体中,与棕榈酸和亚麻酸含量相关的候选基因主要来自脂肪酸代谢途径,表明它们可能是脂肪酸代谢关键步骤中的关键基因。此外,利用基于随机单核苷酸多态性(SNPs)和通过全球基因组研究发现的与脂肪酸成分显著相关的 SNPs 的脊回归最佳线性无偏预测,对脂肪酸成分进行了基因组选择(GS)。GS的准确性取决于所使用的SNP集。值得注意的是,与随机 SNP 相比,当使用 QTL 图谱分析和 GWAS 得出的 SNP 时,GS 效率有所提高,当 SNP 标记的数量超过 3,000 个时,GS 效率达到顶峰。因此,这项研究表明,Glyma.06G221400 和 Glyma.12G075100 是脂肪酸合成和调控机制中不可或缺的基因。该研究深入揭示了脂肪酸复杂的生物合成和调控机制,对定向改善大豆油品质和选育优良大豆品种具有重要意义。本研究中划定的 SNP 标记有助于建立一个有效的标记辅助选择和基因组学管道,以改善大豆的脂肪酸成分。
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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.
期刊最新文献
Leveraging genomic prediction to surpass current yield gains in spring barley. Fine mapping of QGPC.caas-7AL for grain protein content in bread wheat. Genetic loci associated with sorghum drought tolerance in multiple environments and their sensitivity to environmental covariables. Correction to: Identification and development of functional markers for purple grain genes in durum wheat (Triticum durum Desf.). Correction to: Identification and map‑based cloning of an EMS‑induced mutation in wheat gene TaSP1 related to spike architecture.
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