title: Nucleotide polymorphisms and haplotype diversity of RTCS gene in China elite maize inbred lines.
abstract: 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.
authors: Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, College of Agriculture, Yangzhou University, Yangzhou, China.
authors: Enying
authors: E
authors: Zhang
authors: Zefeng
authors: Z
authors: Yang
authors: Yifan
authors: Y
authors: Wang
authors: Yunyun
authors: Y
authors: Hu
authors: Xiyun
authors: X
authors: Song
authors: Chenwu
authors: C
authors: Xu
mesh_terms: D029681:Arabidopsis Proteins / Q000235:genetics; D001947:Breeding; D014644:Genetic Variation; D006239:Haplotypes; D007438:Introns / Q000235:genetics; D015810:Linkage Disequilibrium; D010940:Plant Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017434:Protein Structure, Tertiary; D014157:Transcription Factors / Q000235:genetics*; D020506:Untranslated Regions / Q000235:genetics; D003313:Zea mays / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; C464510:LOB protein, Arabidopsis; D010940:Plant Proteins; D014157:Transcription Factors; D020506:Untranslated Regions