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首页> 外文期刊>PLoS One >Major Soybean Maturity Gene Haplotypes Revealed by SNPViz Analysis of 72 Sequenced Soybean Genomes
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Major Soybean Maturity Gene Haplotypes Revealed by SNPViz Analysis of 72 Sequenced Soybean Genomes

机译：SNPViz分析揭示的72个测序大豆基因组的主要大豆成熟度基因单倍型

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In this Genomics Era, vast amounts of next-generation sequencing data have become publicly available for multiple genomes across hundreds of species. Analyses of these large-scale datasets can become cumbersome, especially when comparing nucleotide polymorphisms across many samples within a dataset and among different datasets or organisms. To facilitate the exploration of allelic variation and diversity, we have developed and deployed an in-house computer software to categorize and visualize these haplotypes. The SNPViz software enables users to analyze region-specific haplotypes from single nucleotide polymorphism (SNP) datasets for different sequenced genomes. The examination of allelic variation and diversity of important soybean [Glycine max (L.) Merr.] flowering time and maturity genes may provide additional insight into flowering time regulation and enhance researchers' ability to target soybean breeding for particular environments. For this study, we utilized two available soybean genomic datasets for a total of 72 soybean genotypes encompassing cultivars, landraces, and the wild species Glycine soja. The major soybean maturity genes E1, E2, E3, and E4 along with the Dt1 gene for plant growth architecture were analyzed in an effort to determine the number of major haplotypes for each gene, to evaluate the consistency of the haplotypes with characterized variant alleles, and to identify evidence of artificial selection. The results indicated classification of a small number of predominant haplogroups for each gene and important insights into possible allelic diversity for each gene within the context of known causative mutations. The software has both a stand-alone and web-based version and can be used to analyze other genes, examine additional soybean datasets, and view similar genome sequence and SNP datasets from other species.
机译：在这个基因组学时代，大量的下一代测序数据已公开提供给数百个物种的多个基因组。这些大型数据集的分析可能变得麻烦，尤其是在比较数据集内多个样本之间以及不同数据集或生物之间的核苷酸多态性时。为了促进对等位基因变异和多样性的探索，我们开发并部署了内部计算机软件来对这些单倍型进行分类和可视化。 SNPViz软件使用户能够从单核苷酸多态性（SNP）数据集中分析不同测序基因组的区域特定单倍型。重要大豆[Glycine max（L.）Merr。]开花时间和成熟基因的等位基因变异和多样性的检查可以提供对开花时间调控的更多见解，并增强研究人员针对特定环境进行大豆育种的能力。在这项研究中，我们利用了两个可用的大豆基因组数据集，获得了72个大豆基因型，包括栽培品种，地方品种和野生大豆。分析了主要的大豆成熟基因E1，E2，E3和E4以及用于植物生长结构的Dt1基因，以确定每个基因的主要单倍型数量，以评估具有特征性变异等位基因的单倍型的一致性，并找出人为选择的证据。结果表明，每个基因的少数主要单倍群的分类，以及在已知致病突变背景下对每个基因可能的等位基因多样性的重要见解。该软件具有独立版本和基于Web的版本，可用于分析其他基因，检查其他大豆数据集以及查看其他物种的相似基因组序列和SNP数据集。

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