多位点全基因组关联研究揭示了水稻耐盐性相关的基因组区域。

IF 3.8 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
Manoharan Akilan, Paramasiwam Jeyaprakash, Murugappan Shanmuganathan, Suresh Meena, Venugopal Rajanbabu, Adhimoolam Karthikeyan, Gunasekaran Ariharasutharsan, Kathiresan Pravin Kumar, Palanisamy Savitha, Pulapet Sowmya, Markkandan Kesavan, Chocklingam Vanniarajan
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引用次数: 0

摘要

大米是一种主要的粮食作物,是世界上一半以上人口的主要食物来源,特别是在亚洲。然而,它的种植受到几种非生物胁迫的限制,特别是盐碱化,这大大降低了生产力,预计在不久的将来会恶化。在这项研究中,进行了一项全基因组关联研究(GWAS),以确定与水稻耐盐性相关的基因组区域和候选基因。研究人员利用150个基因型组成的水稻关联图谱,对水稻在4种环境下的耐盐性状和利用测序基因分型(GBS)方法获得的全基因组单核苷酸多态性(snp)进行了评估。结果显示,6个耐盐性状在不同环境下具有较高的表型变异和遗传力。对获得的高质量snp进行连锁不平衡(LD)块构建,得到5,459个标签snp,用于群体结构和GWAS分析。种群结构分析显示面板内有9个不同的亚种群(k = 9)。GWAS利用3个多位点模型,在10条染色体上鉴定了6个耐盐性状的27个一致且稳定的标记-性状关联(mta)。在相应的LD区域内进行候选基因搜索,确定了57个与酸碱耐受性相关的候选基因。此外,对这些候选基因进行了基于基因的单倍型分析,发现编码adp -葡萄糖焦磷酸化酶、酚类外排转运蛋白、DUF1296家族蛋白和F-box结构域蛋白的四个基因在其单倍型组中表现出显著差异。这些候选基因为培育耐盐碱水稻品种提供了宝贵的遗传改良资源。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Multi-locus genome-wide association studies reveal genomic regions associated with sodicity tolerance in rice.

Rice is a major food crop and serves as the primary food source for over half of the world's population, particularly in Asia. However, its cultivation is constrained by several abiotic stresses, notably sodicity, which significantly reduces productivity and is expected to worsen in the near future. In this study, a genome-wide association study (GWAS) was conducted to identify genomic regions and candidate genes associated with sodicity tolerance in rice. A rice association mapping panel consisting of 150 genotypes was evaluated for sodicity tolerance traits across four environments and genome-wide single nucleotide polymorphisms (SNPs) obtained using genotyping-by-sequencing (GBS) approach. The results revealed high phenotypic variation and heritability for six sodicity tolerance traits across the evaluated environments. The high-quality SNPs obtained were subjected to linkage disequilibrium (LD) block construction, resulting in 5,459 tag-SNPs, which were used for population structure and GWAS analyses. Population structure analysis revealed nine distinct sub-populations (k = 9) within the panel. GWAS, using three multi-locus models, identified 27 consistent and stable marker-trait associations (MTAs) for six sodicity tolerance traits across 10 chromosomes. A candidate gene search within the corresponding LD block regions identified 57 putative candidate genes associated with sodicity tolerance. Furthermore, gene-based haplotype analysis was conducted for these candidates and revealed that four genes-encoding ADP-glucose pyrophosphorylase, phenolics efflux transporter, DUF1296 family proteins, and F-box domain-containing proteins-exhibited significant differences among their haplotype groups. These candidate genes may serve as valuable resources for rice genetic improvement programs aimed at developing sodicity-tolerant rice cultivars.

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来源期刊
Plant Molecular Biology
Plant Molecular Biology 生物-生化与分子生物学
自引率
2.00%
发文量
95
审稿时长
1.4 months
期刊介绍: Plant Molecular Biology is an international journal dedicated to rapid publication of original research articles in all areas of plant biology.The Editorial Board welcomes full-length manuscripts that address important biological problems of broad interest, including research in comparative genomics, functional genomics, proteomics, bioinformatics, computational biology, biochemical and regulatory networks, and biotechnology. Because space in the journal is limited, however, preference is given to publication of results that provide significant new insights into biological problems and that advance the understanding of structure, function, mechanisms, or regulation. Authors must ensure that results are of high quality and that manuscripts are written for a broad plant science audience.
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