Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identification, phylogenomic.pdf

Theor Appl Genet (2008) 116:1015–1026 DOI 10.1007/s00122-008-0732-4 ORIGINAL PAPER Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identiWcation, phylogenomic characterization, chromosome localization, and linkage mapping Chuanfu An · Sukumar Saha · Johnie N. Jenkins · Din-Pow Ma · Brian E. ScheZer · Russell J. Kohel · John Z. Yu · David M. Stelly Received: 6 August 2007 / Accepted: 11 February 2008 / Published online: 13 March 2008 ? Springer-Verlag 2008 Abstract R2R3-MYB transcription factors of plants are involved in the regulation of trichome length and density. Several of them are diVerentially expressed during initiation and elongation of cotton Wbers. We report sequence phyloge- nomic characterization of the six MYB genes, their chromo- somal localization, and linkage mapping via SNP marker in AD-genome cotton (2n = 52). Phylogenetic grouping and comparison to At- and Dt-genome putative ancestral dip- loid species of allotetraploid cotton facilitated diVerentia- tion between genome-speciWc polymorphisms (GSPs) and marker-suitable locus-speciWc 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 signiWcant 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 conWrmed their value as candidate gene markers and indicated the reliability of the SNP discovery strategy in tetraploid cotton species. We con- sider that these SNPs may be useful for genetic dissection of economical