全基因组关联研究揭示了狐尾黍(Setaria italica)中十种微量元素的遗传位点。

IF 4.4 1区 农林科学 Q1 AGRONOMY Theoretical and Applied Genetics Pub Date : 2024-07-17 DOI:10.1007/s00122-024-04690-1
Hanxiao Liu, Xin Zhang, Yuping Shang, Shaoxing Zhao, Yingjia Li, Xutao Zhou, Xiaoyu Huo, Pengfei Qiao, Xin Wang, Keli Dai, Huixia Li, Jie Guo, Weiping Shi
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引用次数: 0

摘要

关键信息通过全基因组关联研究发现了155个狐尾粟微量元素浓度的QTL,并发现了一个与镍-钴-铬浓度相关的候选基因。狐尾黍(Setaria italica)是一种重要的地区性作物,以其丰富的矿物质营养成分而闻名,对人类健康有益。我们评估了 408 个狐尾粟品种谷粒中 10 种微量元素(钡、钴、铬、铜、铁、锰、镍、铅、锶和锌)的浓度。在春播和夏播狐尾黍两个亚群之间,五种元素(钡、钴、镍、锶和锌)的浓度存在显著差异。此外,84.4%的元素对表现出显著的相关性。为了确定影响微量元素积累的遗传因素,研究人员进行了一项全面的全基因组关联研究,在三种不同环境中确定了 155 个十种微量元素的数量性状位点(QTL)。其中,10个QTL在多个环境中被一致检测到,包括qZn2.1、qZn4.4、qCr4.1、qFe6.3、qFe6.5、qCo6.1、qPb7.3、qPb7.5、qBa9.1和qNi9.1。检测到 13 个多元素 QTL 簇,这部分解释了元素之间的相关性。此外,狐尾粟亚群之间五种元素的浓度不同是由于与重要标记-性状关联相关的高浓度等位基因频率不同造成的。单倍型分析发现了一个与镍积累相关的候选基因 SETIT_036676mg,其 GG 单倍型可显著提高狐尾黍中镍-钴-铬的浓度。基于 SETIT_036676mg 的两个单倍型,开发并验证了裂解扩增多态性序列标记(cNi6676)。研究结果为狐尾粟微量元素含量的遗传研究和改良提供了有价值的参考信息。
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Genome-wide association study reveals genetic loci for ten trace elements in foxtail millet (Setaria italica).

Key message: One hundred and fifty-five QTL for trace element concentrations in foxtail millet were identified using a genome-wide association study, and a candidate gene associated with Ni-Co-Cr concentrations was detected. Foxtail millet (Setaria italica) is an important regional crop known for its rich mineral nutrient content, which has beneficial effects on human health. We assessed the concentrations of ten trace elements (Ba, Co, Cr, Cu, Fe, Mn, Ni, Pb, Sr, and Zn) in the grain of 408 foxtail millet accessions. Significant differences in the concentrations of five elements (Ba, Co, Ni, Sr, and Zn) were observed between two subpopulations of spring- and summer-sown foxtail millet varieties. Moreover, 84.4% of the element pairs exhibited significant correlations. To identify the genetic factors influencing trace element accumulation, a comprehensive genome-wide association study was conducted, identifying 155 quantitative trait locus (QTL) for the ten trace elements across three different environments. Among them, ten QTL were consistently detected in multiple environments, including qZn2.1, qZn4.4, qCr4.1, qFe6.3, qFe6.5, qCo6.1, qPb7.3, qPb7.5, qBa9.1, and qNi9.1. Thirteen QTL clusters were detected for multiple elements, which partially explained the correlations between elements. Additionally, the different concentrations of five elements between foxtail millet subpopulations were caused by the different frequencies of high-concentration alleles associated with important marker-trait associations. Haplotype analysis identified a candidate gene SETIT_036676mg associated with Ni accumulation, with the GG haplotype significantly increasing Ni-Co-Cr concentrations in foxtail millet. A cleaved amplified polymorphic sequence marker (cNi6676) based on the two haplotypes of SETIT_036676mg was developed and validated. Results of this study provide valuable reference information for the genetic research and improvement of trace element content in foxtail millet.

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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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