Department of Agricultural and Environmental Biology, Laboratory of Plant Breeding & Genetics, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan.
Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka Setagaya-Ku, Tokyo, 156-8502, Japan.
BMC Genomics. 2023 Jun 24;24(1):348. doi: 10.1186/s12864-023-09428-9.
Moso bamboo (Phyllostachys edulis) is a typical East Asian bamboo that does not flower for > 60 years and propagates without seed reproduction. Thus, Moso bamboo can be propagated vegetatively, possibly resulting in highly heterozygous genetic inheritance. Recently, a draft genome of Moso bamboo was reported, followed by whole genome single nucleotide polymorphisms (SNP) analysis, which showed that the genome of Moso bamboo in China has regional characteristics. Moso bamboo in Japan is thought to have been introduced from China over the sea in 1736. However, it is unclear where and how Moso bamboo was introduced in Japan from China. Here, based on detailed analysis of heterozygosity in genome diversity, we estimate the spread of genome diversity and its pedigree of Moso bamboo.
We sequenced the whole genome of Moso bamboo in Japan and compared them with data reported previously from 15 regions of China. Only 4.1 million loci (0.37% of the analyzed genomic region) were identified as polymorphic loci. We next narrowed down the number of polymorphic loci using several filters and extracted more reliable SNPs. Among the 414,952 high-quality SNPs, 319,431 (77%) loci were identified as heterozygous common to all tested samples. The result suggested that all tested samples were clones via vegetative reproduction. Somatic mutations may accumulate in a heterozygous manner within a single clone. We examined common heterozygous loci between samples from Japan and elsewhere, from which we inferred that an individual closely related to the sample from Fujian, China, was introduced to Japan across the sea without seed reproduction. In addition, we collected 16 samples from four nearby bamboo forests in Japan and performed SNP and insertion/deletion analyses using a genotyping by sequencing (GBS) method. The results suggested that a small number of somatic mutations would spread within and between bamboo groves.
High heterozygosity in the genome-wide diversity of Moso bamboo implies the vegetative propagation of Moso bamboo from China to Japan, the pedigree of Moso bamboo in Japan, and becomes a useful marker to approach the spread of genome diversity in clonal plants.
毛竹（Phyllostachys edulis）是一种典型的东亚竹种，其开花周期超过 60 年，且不通过种子繁殖。因此，毛竹可以通过营养繁殖，可能导致高度杂合的遗传继承。最近，报道了毛竹的基因组草案，随后进行了全基因组单核苷酸多态性（SNP）分析，结果表明中国毛竹的基因组具有区域特征。日本的毛竹被认为是在 1736 年从中国通过海路传入的。然而，尚不清楚毛竹是从中国的哪个地方以及如何传入日本的。在这里，我们基于对基因组多样性杂合性的详细分析，估计了毛竹基因组多样性的传播及其谱系。
我们对日本的毛竹进行了全基因组测序，并与之前从中国 15 个地区报告的数据进行了比较。仅鉴定出 410 万个（分析基因组区域的 0.37%）作为多态性位点的基因座。接下来，我们使用几个筛选器缩小了多态性基因座的数量，并提取了更可靠的 SNP。在 414,952 个高质量 SNP 中，有 319,431（77%）个基因座被鉴定为所有测试样本的杂合常见。结果表明，所有测试样本均通过营养繁殖产生克隆。体细胞突变可能在单个克隆内以杂合方式积累。我们检查了来自日本和其他地方的样本之间的常见杂合基因座，由此推断，一个与中国福建样本密切相关的个体是通过无种子繁殖从中国传入日本的。此外，我们从日本附近的四个竹林中收集了 16 个样本，并使用基于测序的基因分型（GBS）方法进行了 SNP 和插入/缺失分析。结果表明，少数体细胞突变会在竹林内和竹林之间传播。
毛竹全基因组多样性的高杂合性暗示了毛竹从中国到日本的营养繁殖、日本毛竹的谱系，并且成为一种有用的标记，可用于研究克隆植物基因组多样性的传播。
