Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan.
Kazusa DNA Research Institute, Chiba 292-0818, Japan.
DNA Res. 2023 Oct 1;30(5). doi: 10.1093/dnares/dsad015.
Frequent polyploidization events in plants have led to the establishment of many lineage-specific traits representing each species. Little is known about the genetic bases for these specific traits in polyploids, presumably due to plant genomic complexity and their difficulties in applying genetic approaches. Hexaploid Oriental persimmon (Diospyros kaki) has evolved specific fruit characteristics, including wide variations in fruit shapes and astringency. In this study, using whole-genome diploidized/quantitative genotypes from ddRAD-Seq data of 173 persimmon cultivars, we examined their population structures and potential correlations between their structural transitions and variations in nine fruit traits. The population structures of persimmon cultivars were highly randomized and not substantially correlated with the representative fruit traits focused on in this study, except for fruit astringency. With genome-wide association analytic tools considering polyploid alleles, we identified the loci associated with the nine fruit traits; we mainly focused on fruit-shape variations, which have been numerically characterized by principal component analysis of elliptic Fourier descriptors. The genomic regions that putatively underwent selective sweep exhibited no overlap with the loci associated with these persimmon-specific fruit traits. These insights will contribute to understanding the genetic mechanisms by which fruit traits are independently established, possibly due to polyploidization events.
植物中频繁的多倍化事件导致了许多代表每个物种的谱系特异性特征的建立。对于多倍体中这些特定特征的遗传基础知之甚少，这可能是由于植物基因组的复杂性及其在应用遗传方法方面的困难。六倍体东方柿（Diospyros kaki）已经进化出了特定的果实特征，包括果实形状和涩味的广泛变化。在这项研究中，我们使用了来自 173 个柿品种的 ddRAD-Seq 数据的全基因组二倍体/定量基因型，研究了它们的群体结构以及结构转变与九个果实特征之间的潜在相关性。柿品种的群体结构高度随机化，与本研究重点关注的代表性果实特征没有实质性相关性，除了果实涩味。我们使用考虑多倍体等位基因的全基因组关联分析工具，鉴定了与九个果实特征相关的基因座；我们主要关注果实形状的变化，这些变化已经通过椭圆傅里叶描述符的主成分分析进行了数值特征化。推测经历了选择清除的基因组区域与与这些柿特异性果实特征相关的基因座没有重叠。这些见解将有助于理解果实特征独立建立的遗传机制，这可能是由于多倍化事件。
