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.
Highlights
In the past, fundamental researches on increasing shoot biomass and seed yield attracted most attentions of the crop scientists, and the relevance of the root system for food production has often been overlooked [1,2]
Sequence polymorphisms were detected among 73 maize inbred lines across 1279 bp of sequence, which covers a 167 bp 59 untranslated region (UTR), a 735 bp coding region, a 104 bp intron region, and a 273 bp 39 UTR
Among 4 regions of the gene RTCS, the coding region showed much lower nucleotide polymorphism than others, while the intron region had the highest frequency of all sequence variants
Summary
Fundamental researches on increasing shoot biomass and seed yield attracted most attentions of the crop scientists, and the relevance of the root system for food production has often been overlooked [1,2]. Maize (Zea mays L.), one of the most widely grown grain crop in the world, possesses a unique and complex root stock architecture composed of embryonic and postembryonic roots [4,5]. The gene RTCS (rootless concerning crown and seminal roots) was demonstrated to play a central role in the auxin-mediated initiation of seminal and shoot-borne roots in maize [5,9] and the mutant of this gene was impaired in the formation of these roots. Sequence analysis illustrated the maize RTCS gene was composed of 2 exons, separated by a 96-bp intron, and its protein product contained 244 amino acid residues. The maize RTCS gene is preferentially expressed in root tissues [5] and its protein product showed typical features of a transcription factor including nuclear localization, DNA-binding and downstream gene activation [6]
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