title: Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identification, phylogenomic characterization, chromosome localization, and linkage mapping.
abstract: 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.
authors.affiliation: Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA.
authors.forename: Chuanfu
authors.initials: C
authors.lastname: An
authors.forename: Sukumar
authors.initials: S
authors.lastname: Saha
authors.forename: Johnie N
authors.initials: JN
authors.lastname: Jenkins
authors.forename: Din-Pow
authors.initials: DP
authors.lastname: Ma
authors.forename: Brian E
authors.initials: BE
authors.lastname: Scheffler
authors.forename: Russell J
authors.initials: RJ
authors.lastname: Kohel
authors.forename: John Z
authors.initials: JZ
authors.lastname: Yu
authors.forename: David M
authors.initials: DM
authors.lastname: Stelly
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D020570:Genes, myb / Q000235:genetics*; D018745:Genome, Plant; D003368:Gossypium / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D014157:Transcription Factors