Functional Plant Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, 305-8602, Tsukuba, Japan.
National Agriculture and Food Research Organization, Institute of Crop Science, NARO (NICS), Kannondai 2-1-2, 305-8518, Tsukuba, Japan.
Plant J. 2018 Jun;94(5):895-909. doi: 10.1111/tpj.13906. Epub 2018 Apr 21.
The diversification of flowering time in response to natural environments is critical for the spread of crops to diverse geographic regions. In contrast with recent advances in understanding the molecular basis of photoperiodic flowering in rice (Oryza sativa), little is known about how flowering-time diversification is structured within rice subspecies. By analyzing genome sequencing data and a set of 429 chromosome segment substitution lines (CSSLs) originating from 10 diverse rice accessions with wide distributions, we revealed diverse effects of allelic variations for common flowering-time quantitative trait loci in the recipient's background. Although functional variations associated with a few loci corresponded to standing variations among subspecies, the identified functional nucleotide polymorphisms occurred recently after rice subgroup differentiation, indicating that the functional diversity of flowering-time gene sequences was not particularly associated with phylogenetic relationship between rice subspecies. Intensive analysis of the Hd1 genomic region identified the signature of an early introgression of the Hd1 with key mutation(s) in aus and temperate japonica accessions. Our data suggested that, after such key introgressions, new mutations were selected and accelerated the flowering-time diversity within subspecies during the expansion of rice cultivation area. This finding may imply that new genome-wide changes for flowering-time adaptation are one of the critical determinants for establishing genomic architecture of local rice subgroups. In-depth analyses of various rice genomes coupling with the genetically confirmed phenotypic changes in a large set of CSSLs enabled us to demonstrate how rice genome dynamics has coordinated with the adaptation of cultivated rice during the expansion of cultivation area.
开花时间的多样化是作物向不同地理区域传播的关键，以适应自然环境。与近年来对水稻（Oryza sativa）光周期开花分子基础的理解进展相比，对于水稻亚种内开花时间多样化的结构知之甚少。通过分析基因组测序数据和一组源自 10 个分布广泛的不同水稻品种的 429 个染色体片段替换系（CSSL），我们揭示了在受体背景下常见开花时间数量性状基因座的等位变异的多样化影响。尽管与少数几个基因座相关的功能变异对应于亚种之间的固定变异，但鉴定出的功能核苷酸多态性是在水稻亚群分化后不久发生的，这表明开花时间基因序列的功能多样性与水稻亚种之间的系统发育关系没有特别关联。对 Hd1 基因组区域的深入分析确定了 Hd1 与 aus 和温带粳稻品种中的关键突变一起早期渗入的特征。我们的数据表明，在这些关键基因渗入之后，新的突变被选择并在水稻种植面积扩大过程中加速了亚种内的开花时间多样性。这一发现可能意味着，新的全基因组开花时间适应变化是建立本地水稻亚群基因组结构的关键决定因素之一。对各种水稻基因组的深入分析以及在大量 CSSL 中证实的遗传表型变化，使我们能够展示在种植面积扩大过程中，水稻基因组动态是如何与栽培水稻的适应相协调的。
