An Chuanfu, Saha Sukumar, Jenkins Johnie N, Ma Din-Pow, Scheffler Brian E, Kohel Russell J, Yu John Z, Stelly David M
Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA.
Theor Appl Genet. 2008 May;116(7):1015-26. doi: 10.1007/s00122-008-0732-4. Epub 2008 Mar 13.
R2R3-MYB transcription factors of plants are involved in the regulation of trichome length and density. Several of them are differentially expressed during initiation and elongation of cotton fibers. We report sequence phylogenomic characterization of the six MYB genes, their chromosomal localization, and linkage mapping via SNP marker in AD-genome cotton (2n = 52). Phylogenetic grouping and comparison to At- and Dt-genome putative ancestral diploid species of allotetraploid cotton facilitated differentiation between genome-specific polymorphisms (GSPs) and marker-suitable locus-specific polymorphisms (LSPs). The SNP frequency averaged one per 77 bases overall, and one per 106 and 30 bases in coding and non-coding regions, respectively. SNP-based multivariate relationships conformed to independent evolution of the six MYB homoeologous loci in the four tetraploid species. Nucleotide diversity analysis indicated that the six MYB loci evolved more quickly in the Dt- than At-genome. The greater variation in the Dt-D genome comparisons than that in At-A genome comparisons showed no significant bias among synonymous substitution, non-synonymous substitution, and nucleotide change in non-coding regions. SNPs were concordantly mapped by deletion analysis and linkage mapping, which confirmed their value as candidate gene markers and indicated the reliability of the SNP discovery strategy in tetraploid cotton species. We consider that these SNPs may be useful for genetic dissection of economically important fiber and yield traits because of the role of these genes in fiber development.
植物的R2R3-MYB转录因子参与了表皮毛长度和密度的调控。其中一些在棉纤维起始和伸长过程中差异表达。我们报道了六个MYB基因的序列系统基因组特征、它们的染色体定位以及通过AD基因组棉花（2n = 52）中的SNP标记进行的连锁作图。系统发育分组以及与异源四倍体棉花的At和Dt基因组假定祖先二倍体物种的比较，有助于区分基因组特异性多态性（GSP）和适合标记的位点特异性多态性（LSP）。SNP频率总体上平均每77个碱基出现一个，在编码区和非编码区分别为每106个和30个碱基出现一个。基于SNP的多变量关系符合四个四倍体物种中六个MYB同源位点的独立进化。核苷酸多样性分析表明，六个MYB位点在Dt基因组中比在At基因组中进化得更快。Dt-D基因组比较中的变异大于At-A基因组比较中的变异，在同义替换、非同义替换和非编码区核苷酸变化之间没有显示出明显的偏差。通过缺失分析和连锁作图对SNP进行了一致的定位，这证实了它们作为候选基因标记的价值，并表明了四倍体棉花物种中SNP发现策略的可靠性。我们认为，由于这些基因在纤维发育中的作用，这些SNP可能对经济上重要的纤维和产量性状的遗传剖析有用。
