Nucleotide polymorphisms and haplotype diversity of RTCS gene in China elite maize inbred lines.
Nucleotide polymorphisms and haplotype diversity of RTCS gene in China elite maize inbred lines.
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中国优良玉米自交系RTCS基因核苷酸多态性及单倍型多样性
DOI：
10.1371/journal.pone.0056495
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Xu C
中科院分区：
文献类型：
--
作者：
Zhang E;Yang Z;Wang Y;Hu Y;Song X;Xu C
玉米RTCS基因编码一个LOB结构域的转录因子，在胚性种子和胚后茎生根的发生中起着重要的作用。本研究获得了73份中国优良自交系的基因组序列，包括5个温带杂交群的63个自交系和10个热带种质，并对其核苷酸多态性和单倍型多样性进行了分析。共检测到63个序列变异，包括44个SNPs和19个Indels，其中大部分位于非编码区和内含子区域。在所有供试自交系中，该基因编码区携带14种单倍型，编码7种延迟RTCS蛋白。对多态位点的分析表明，至少发生了6次重组事件。在供试的6个群体中，只有P优势群体的核苷酸多样性远低于整个群体，选择分析也表明只有这个群体处于较强的负选择。但黄早寺及其衍生品系的核苷酸多样性高于全系，没有发现选择信号。
The maize RTCS gene, encoding a LOB domain transcription factor, plays important roles in the initiation of embryonic seminal and postembryonic shoot-borne root. In this study, the genomic sequences of this gene in 73 China elite inbred lines, including 63 lines from 5 temperate heteroric groups and 10 tropic germplasms, were obtained, and the nucleotide polymorphisms and haplotype diversity were detected. A total of 63 sequence variants, including 44 SNPs and 19 indels, were identified at this locus, and most of them were found to be located in the regions of UTR and intron. The coding region of this gene in all tested inbred lines carried 14 haplotypes, which encoding 7 deferring RTCS proteins. Analysis of the polymorphism sites revealed that at least 6 recombination events have occurred. Among all 6 groups tested, only the P heterotic group had a much lower nucleotide diversity than the whole set, and selection analysis also revealed that only this group was under strong negative selection. However, the set of Huangzaosi and its derived lines possessed a higher nucleotide diversity than the whole set, and no selection signal were identified.
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DOI：
10.1007/978-1-59745-251-9_17
发表时间：
2009-01-01
期刊：
BIOINFORMATICS FOR DNA SEQUENCE ANALYSIS
影响因子：
--
作者：
Rozas, Julio
通讯作者：
Rozas, Julio
影响因子：
0.4
作者：
Berilli, A. P. C. G.;Pereira, M. G.;do Amaral Junior, A. T.
通讯作者：
do Amaral Junior, A. T.
影响因子：
2.3
作者：
Hammer, Graeme L.;Dong, Zhanshan;Cooper, Mark
通讯作者：
Cooper, Mark
影响因子：
1.5
作者：
Li, Liang;Hao, Zhuanfang;Zhang, Shihuang
通讯作者：
Zhang, Shihuang
影响因子：
5.8
作者：
Larkin, M. A.;Blackshields, G.;Higgins, D. G.
通讯作者：
Higgins, D. G.