Zhao Xiangqian, Yang Long, Zheng Yan, Xu Zhaohua, Wu Weiren
Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China.
J Genet Genomics. 2009 Jul;36(7):435-42. doi: 10.1016/S1673-8527(08)60133-2.
It is generally accepted that Oryza rufipogon is the progenitor of Asian cultivated rice (O. sativa). However, how the two subspecies of O. sativa (indica and japonica) were domesticated has long been debated. To investigate the genetic differentiation in O. rufipogon in relation to the domestication of O. sativa, we developed 57 subspecies-specific intron length polymorphism (SSILP) markers by comparison between 10 indica cultivars and 10 japonica cultivars and defined a standard indica rice and a standard japonica rice based on these SSILP markers. Using these SSILP markers to genotype 73 O. rufipogon accessions, we found that the indica alleles and japonica alleles of the SSILP markers were predominant in the O. rufipogon accessions, suggesting that SSILPs were highly conserved during the evolution of O. sativa. Cluster analysis based on these markers yielded a dendrogram consisting of two distinct groups: one group (Group I) comprises all the O. rufipogon accesions from tropical (South and Southeast) Asia as well as the standard indica rice; the other group (Group II) comprises all the O. rufipogon accessions from Southern China as well as the standard japonica rice. Further analysis showed that the two groups have significantly higher frequencies of indica alleles and japonica alleles, respectively. These results support the hypothesis that indica rice and japonica rice were domesticated from the O. rufipogon of tropical Asia and from that of Southern China, respectively, and suggest that the indica-japonica differentiation should have formed in O. rufipogon long before the beginning of domestication. Furthermore, with an O. glaberrima accession as an outgroup, it is suggested that the indica-japonica differentiation in O. rufipogon might occur after its speciation from other AA-genome species.
一般认为，野生稻是亚洲栽培稻（水稻）的祖先。然而，水稻的两个亚种（籼稻和粳稻）是如何被驯化的，长期以来一直存在争议。为了研究与水稻驯化相关的野生稻遗传分化，我们通过比较10个籼稻品种和10个粳稻品种，开发了57个亚种特异性内含子长度多态性（SSILP）标记，并基于这些SSILP标记定义了一个标准籼稻和一个标准粳稻。利用这些SSILP标记对73份野生稻材料进行基因分型，我们发现SSILP标记的籼稻等位基因和粳稻等位基因在野生稻材料中占主导地位，这表明SSILP在水稻进化过程中高度保守。基于这些标记的聚类分析产生了一个由两个不同组组成的树状图：一组（第一组）包括来自热带（南亚和东南亚）亚洲的所有野生稻材料以及标准籼稻；另一组（第二组）包括来自中国南方的所有野生稻材料以及标准粳稻。进一步分析表明，这两组分别具有显著更高频率的籼稻等位基因和粳稻等位基因。这些结果支持了以下假设：籼稻和粳稻分别是从热带亚洲的野生稻和中国南方的野生稻驯化而来的，并表明籼粳分化应该在驯化开始之前很久就在野生稻中形成了。此外，以一份非洲栽培稻材料作为外类群，表明野生稻中的籼粳分化可能发生在其与其他AA基因组物种形成物种之后。
