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多数杂草稻的果皮是红色,该特征可用于稻田中杂草稻的早期的初步鉴定,也可用于水稻果皮Rc/rc基因的起源进化研究。本研究利用红色果皮Rc基因第六外显子的In Del标记RID14对来自亚洲不同稻作区的199份杂草稻(O.sativa f.spontanea)、24份栽培稻(O.sativa)和9份野生稻(O.rufipogon)进行基因型鉴定并与表型比对;同时对9份代表性杂草稻Rc-b HLH位点的DNA序列进行测序,并将其与下载的29份栽培稻(籼,粳)和14份野生稻的对应序列进行比对分析。研究结果表明:(1)亚洲杂草稻的果皮颜色的表型多样,多数(84.4%)为红色或褐色(由浅至深)、少数(15.6%)为白色,其基因型与表型鉴定结果高度一致;杂草稻红色果皮Rc基因第六外显子均为无14 bp缺失的类型,仅有一份中国东北杂草稻除外(为14 bp缺失型),揭示用RID14标记可以早期快速的鉴定稻田中红色果皮杂草稻;(2)测试的9份杂草稻其Rc-b HLH位点的DNA序列均较为保守,其中出现4个突变位点;(3)在Rc-b HLH部分区域(1~115 bp),红色果皮的籼型栽培稻、杂草稻和野生稻的DNA序列相同,但红色果皮粳型栽培稻与白色果皮籼型栽培稻和杂草稻在106 bp处存在一个A/G替换;(4)通过对比野生稻和栽培稻,杂草稻在Rc-b HLH位点核苷酸多态性多态性最高,但是野生稻在该位点Tajima’D检验值呈显著,说明Rc-b HLH位点在野生稻中有选择性;通过聚类分析发现分为2个类群,类群1由白色果皮的杂草稻、籼型栽培稻和红/白果皮的粳型栽培稻组成;类群2由红色果皮的栽培稻(籼型)、杂草稻和野生稻组成。该结果暗示:在粳稻区,白色果皮的亚洲杂草稻可能由栽培稻退化返祖而形成的;在籼稻区,红色果皮的亚洲杂草稻可能经由栽培稻及野生稻杂交(如籼籼交或栽野交)演化而来。
The peel of most weedy rice is red, which can be used for the early preliminary identification of weedy rice in paddy field. It can also be used to study the origin and evolution of Rc / rc gene in rice peel. In this study, we used 199 lines of O. sativa f. Sepontanea, 24 species of O. sativa and 9 species of O. sativa from different rice fields in Asia using the In Del marker RID14 of exon 6 of Rc gene of red pericarp. Genotypes were identified and compared with the phenotypes of O. rufipogon. The DNA sequences of the Rc-b HLH loci of 9 representative weedy rice were sequenced and compared with 29 cultivated rice (Indica, japonica) and 14 wild rice corresponding sequences were analyzed. The results showed as follows: (1) The color of pericarp of Asian weedy rice is diverse, most of which (84.4%) are red or brown (from light to dark) and a few (15.6%) are white. The genotype and phenotypic identification Which was highly consistent. The sixth exon of Rc gene of weedy rice red peel was all without the type of 14 bp deletion, except for one weedy paddy in northeastern China (14 bp deletion type), which revealed that the RID14 marker could be used for early and rapid identification (2) The DNA sequences of the Rc-b HLH locus in the 9 weedy rice tested were all relatively conservative with 4 mutation sites; (3) in the Rc-b HLH partial region (1 ~ 115 bp). The DNA sequences of indica cultivated rice, weedy rice and wild rice were the same in red peel, but there was one at 106 bp between red peel japonica rice and white peel indica cultivated rice and weedy rice A / G was replaced by A / G; (4) The nucleotide polymorphisms of Rc-b HLH were the highest in wild rice and cultivated rice by comparison with Tajima’D test Significantly, indicating that the Rc-b HLH locus is selective for wild rice. The cluster analysis revealed that the Rc-b HLH locus was divided into two groups. The group 1 consisted of white peel weedy rice and indica cultivars Rice and red / white peel; group 2 consisted of red peel cultivated rice (indica), weedy rice and wild rice. The results suggest that in the japonica rice area, the white peel of Asian weedy rice may be formed by the degradation and return of cultivated rice; in the indica rice area, the red peel of Asian weedy rice may be crossed by cultivated rice and wild rice (such as indica indica Or planted wild exchange) evolved.