Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identification, phylogenomic characterization, chromosome localization, and linkage mapping
Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identification, phylogenomic characterization, chromosome localization, and linkage mapping
复制标题
DOI：
10.1007/s00122-008-0732-4
复制
发表时间：
2008-05-01
影响因子：
5.4
通讯作者：
Stelly, David M.
中科院分区：
文献类型：
--
作者：
An, Chuanfu;Saha, Sukumar;Stelly, David M.
R2 R3-MYB转录因子参与植物毛状体长度和密度的调控。其中一些在棉纤维的起始和伸长过程中差异表达。我们报告了6个MYB基因的序列分析、染色体定位和通过SNP标记在AD基因组棉花（2n = 52）中的连锁图谱。系统发育分组和比较，在和DT-基因组推定的祖先二倍体物种的异源四倍体棉花促进基因组特异性多态性（GSPs）和标记合适的位点特异性多态性（LSPs）之间的分化。SNP频率平均为每77个碱基一个，编码区和非编码区分别为每106个和30个碱基一个。基于SNP的多变量关系符合4个四倍体物种中6个MYB同源基因座的独立进化。核苷酸多样性分析表明，6个MYB基因座在Dt-比At-基因组中进化更快。Dt-D基因组比较的变异性大于At-A基因组比较的变异性，表明同义替换、非同义替换和非编码区核苷酸变化之间无显著偏倚。通过缺失分析和连锁作图对SNP进行了一致性定位，证实了SNP作为候选基因标记的价值，表明SNP发现策略在四倍体棉花中的可靠性。我们认为，这些SNPs可能是有用的经济上重要的纤维和产量性状的遗传解剖，因为这些基因在纤维发育的作用。
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.