Genomic adaptation of flowering-time genes during the expansion of rice cultivation area
Genomic adaptation of flowering-time genes during the expansion of rice cultivation area
复制标题
DOI：
10.1111/tpj.13906
复制
发表时间：
2018-06-01
期刊：
影响因子：
7.2
通讯作者：
Izawa, Takeshi
中科院分区：
文献类型：
--
作者：
Itoh, Hironori;Wada, Kaede C.;Izawa, Takeshi
随着自然环境的变化，开花时间的多样化对作物在不同地理区域的传播至关重要。与最近对水稻光周期开花的分子基础的理解相比，人们对水稻亚种内开花时间多样化的结构知之甚少。通过对来自10个分布广泛的水稻种质的429个染色体片段代换系（CSSLs）基因组测序数据的分析，揭示了受体背景中常见花期数量性状位点等位基因变异的不同影响。虽然与少数位点相关的功能变异对应于亚种之间的长期变异，但所鉴定的功能核苷酸多态性是在水稻亚群分化后才出现的，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并不特别相关。对Hd1基因组区域的深入分析发现，在普通粳稻和温带粳稻中，Hd1基因的早期基因渗入具有关键突变的特征。我们的数据表明，在水稻种植面积扩大的过程中，经过这些关键的渗入，新的突变被选择并加速了亚种内开花时间的多样性。这一发现可能意味着开花时间适应的全基因组新变化是建立当地水稻亚群基因组结构的关键决定因素之一。对多种水稻基因组的深入分析，结合大量cssl中遗传证实的表型变化，使我们能够证明在种植面积扩大过程中，水稻基因组动力学是如何与栽培水稻的适应性协调的。
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.