全基因组关联研究和多亲本群体热带玉米种质穗重预测。

Genome-Wide Association Study and Prediction of Tassel Weight of Tropical Maize Germplasm in Multi-Parent Population.

机构信息

School of Agriculture, Yunnan University, Kunming 650500, China.

Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China.

出版信息

Int J Mol Sci. 2024 Feb 1;25(3):1756. doi: 10.3390/ijms25031756.

Abstract

Tassel weight (TW) is a crucial agronomic trait that significantly affects pollen supply and grain yield development in maize breeding. To improve maize yield and develop new varieties, a comprehensive understanding of the genetic mechanisms underlying tassel weight is essential. In this study, tropical maize inbred lines, namely CML312, CML373, CML444, and YML46, were selected as female parents and crossed with the elite maize inbred line Ye107, which served as the common male parent, to develop a multi-parent population comprising four F8 recombinant inbred line (RIL) subpopulations. Using 6616 high-quality single nucleotide polymorphism (SNP) markers, we conducted genome-wide association analysis (GWAS) and genomic selection (GS) on 642 F8 RILs in four subpopulations across three different environments. Through GWAS, we identified 16 SNPs that were significantly associated with TW, encompassing two stable loci expressed across multiple environments. Furthermore, within the candidate regions of these SNPs, we discovered four novel candidate genes related to TW, namely , , , and distributed on chromosomes 1, 3, and 8, which have not been previously reported. These genes are involved in processes such as signal transduction, growth and development, protein splicing, and pollen development, all of which play crucial roles in inflorescence meristem development, directly affecting TW. The co-localized SNP, S8_137379725, on chromosome 8 was situated within a 16.569 kb long terminal repeat retrotransposon (LTR-RT), located 22.819 kb upstream and 26.428 kb downstream of the candidate genes ( and ). When comparing three distinct GS models, the BayesB model demonstrated the highest accuracy in predicting TW. This study establishes the theoretical foundation for future research into the genetic mechanisms underlying maize TW and the efficient breeding of high-yielding varieties with desired tassel weight through GS.

摘要

穗重(TW)是一个重要的农艺性状,对玉米育种中的花粉供应和籽粒产量发育有显著影响。为了提高玉米产量和培育新品种,全面了解穗重的遗传机制至关重要。在这项研究中,选择了热带玉米自交系 CML312、CML373、CML444 和 YML46 作为母本,与优良玉米自交系 Ye107 杂交,作为共同的父本,开发了一个由四个 F8 重组自交系(RIL)亚群组成的多亲本群体。利用 6616 个高质量的单核苷酸多态性(SNP)标记,我们对四个亚群的 642 个 F8 RIL 在三个不同环境下进行了全基因组关联分析(GWAS)和基因组选择(GS)。通过 GWAS,我们鉴定出 16 个与 TW 显著相关的 SNP,包含两个在多个环境中表达稳定的位点。此外,在这些 SNP 的候选区域内,我们发现了四个与 TW 相关的新的候选基因,分别为、、和 ,分布在 1、3 和 8 号染色体上,这些基因以前没有报道过。这些基因参与信号转导、生长发育、蛋白质剪接和花粉发育等过程,它们都在花序分生组织发育中发挥着关键作用,直接影响 TW。在 8 号染色体上,共定位 SNP 为 S8_137379725,位于一个 16.569 kb 的长末端重复反转录转座子(LTR-RT)内,位于候选基因(和 )上游 22.819 kb 和下游 26.428 kb。在比较三种不同的 GS 模型时,BayesB 模型在预测 TW 方面表现出最高的准确性。这项研究为未来研究玉米 TW 的遗传机制以及通过 GS 高效培育具有理想穗重的高产品种奠定了理论基础。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b256/10855296/d2ef72e63982/ijms-25-01756-g001.jpg

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