Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 2/11/2008
Publication Date: 3/13/2008
Citation: An, C., Saha, S., Jenkins, J.N., Ma, D., Scheffler, B.E., Kohel, R.J., Yu, J., Stelly, D.M. 2008. Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identification, phylogenomic characterization, chromosome localization and linkage mapping. Theoretical and Applied Genetics. 161:1015-1026. Interpretive Summary: We report single nucleotide polymorphisms (SNP) among six genes involved in fiber information (MYB transcription factors). We found SNP differences among the six genes and located these SNPs on several chromosomes. These markers thus become chromosome specific molecular markers associated with genes that are important in regulating fiber development. Our results indicate that SNP developed independently in the four tetraploid species of cotton. These results confirm that our technique for SNP discovery is reliable in tetraploid cotton species. We suggest that these SNPs may be useful for genetic dissection of economically important fiber and yield traits because of the role of the MYB genes in fiber development.
Technical Abstract: R2R3-MYB transcription factors of plants are involved in the regulation of trichome length and density. Several of them are differentially expressed with initiation and expansion of cotton fibers. We report sequence phylo-genomic 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 was an average one per 77 bases overall, and one per 106 and 30 bases in coding and noncoding regions, respectively. SNP-based multivariate relationships conformed to independent evolution of the six MYB homoeologs 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 variaion in the Dt-D genome comparisons than that in At-A genome comparisons showed no significant bias among synonymous substitution, nonsynonymous substitution, and nucleotide change in noncoding 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. 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.