The Composition and Origins of Genomic Variation among Individuals of the Soybean Reference Cultivar Williams 82
The Composition and Origins of Genomic Variation among Individuals of the Soybean Reference Cultivar Williams 82
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DOI：
10.1104/pp.110.166736
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发表时间：
2011-02-01
期刊：
影响因子：
7.4
通讯作者：
Stupar, Robert M.
中科院分区：
文献类型：
--
作者：
Haun, William J.;Hyten, David L.;Stupar, Robert M.
大豆（Glycine max）是一种自花授粉物种，与其他作物物种相比，其核苷酸多态性率相对较低。尽管核苷酸多态性发生率较低，但仍存在多种可遗传的表型变异。甚至有证据表明某些品种的个体之间存在可遗传的表型变异。 Williams 82 是用于产生参考基因组序列的大豆品种，源自供体亲本 Kingwa 的疫霉根腐病抗性基因座与轮回亲本 Williams 的回交。为了探索品种内变异的遗传基础，我们研究了不同 Williams 82 个体的核苷酸、结构和基因含量变异。 Williams 82 个体表现出渗入 Kingwa 基因座的数量和大小的变化。在这些基因组异质性区域中，参考 Williams 82 基因组序列由 Williams 和 Kingwa 单倍型的嵌合体组成。 Williams 和 Kingwa 之间的基因组结构变异在异质性区域内的 Williams 82 个体之间保持不变。此外，异质性区域在 Williams 82 个体之间表现出基因含量差异。这些发现表明，Williams 82 的遗传异质性主要源于育种过程中回交和单种子传代后多态性染色体区域的差异分离。我们的结论是，大豆单倍型可以具有高比例的结构和基因内容变异，并且品种内遗传异质性的影响可能是显着的。这种详细的表征将有助于解释大豆基因组数据集，并强调了正在开发或利用参考基因组序列的研究团体的重要考虑因素。
Soybean (Glycine max) is a self-pollinating species that has relatively low nucleotide polymorphism rates compared with other crop species. Despite the low rate of nucleotide polymorphisms, a wide range of heritable phenotypic variation exists. There is even evidence for heritable phenotypic variation among individuals within some cultivars. Williams 82, the soybean cultivar used to produce the reference genome sequence, was derived from backcrossing a Phytophthora root rot resistance locus from the donor parent Kingwa into the recurrent parent Williams. To explore the genetic basis of intracultivar variation, we investigated the nucleotide, structural, and gene content variation of different Williams 82 individuals. Williams 82 individuals exhibited variation in the number and size of introgressed Kingwa loci. In these regions of genomic heterogeneity, the reference Williams 82 genome sequence consists of a mosaic of Williams and Kingwa haplotypes. Genomic structural variation between Williams and Kingwa was maintained between the Williams 82 individuals within the regions of heterogeneity. Additionally, the regions of heterogeneity exhibited gene content differences between Williams 82 individuals. These findings show that genetic heterogeneity in Williams 82 primarily originated from the differential segregation of polymorphic chromosomal regions following the backcross and single-seed descent generations of the breeding process. We conclude that soybean haplotypes can possess a high rate of structural and gene content variation, and the impact of intracultivar genetic heterogeneity may be significant. This detailed characterization will be useful for interpreting soybean genomic data sets and highlights important considerations for research communities that are developing or utilizing a reference genome sequence.