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Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identification, phylogenomic characterization, chromosome localization, and linkage mapping

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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.

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Acknowledgments

The authors grateful acknowledge the initial works on MYB genes by Drs. T.A. Wilkins, Texas Tech University, TX and J.F. Wendel, Iowa State University, IA. We also thank Drs. I.Y. Abdurakhmonov, Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan, Uzbekistan, J. Li, and J. Wilkinson, Mississippi State University, MS for their valuable suggestions in this paper.

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Authors and Affiliations

  1. Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, 39762, USA

    Chuanfu An

  2. USDA-ARS, Crop Science Research Laboratory, P.O. Box 5367, Mississippi State, MS, 39762, USA

    Sukumar Saha & Johnie N. Jenkins

  3. Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, MS, 39762, USA

    Din-Pow Ma

  4. USDA-ARS-CGRU, Stoneville, MS, 38776, USA

    Brian E. Scheffler

  5. USDA-ARS, Crop Germplasm Research Unit, 2765 F&B Road, College Station, TX, 77845, USA

    Russell J. Kohel & John Z. Yu

  6. Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA

    David M. Stelly

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  1. Chuanfu An
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Correspondence to Sukumar Saha.

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Communicated by D. Lightfoot.

Disclaimer: Mention of trade names or commercial products does not constitute a guarantee or warranty of the product by US Department of Agriculture and does not imply its approval to the exclusion of other products that may also be suitable.

Nucleotide sequence data reported are available in GenBank database under the accession numbers EU249397 to EU249456.

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An, C., Saha, S., Jenkins, J.N. et al. Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identification, phylogenomic characterization, chromosome localization, and linkage mapping. Theor Appl Genet 116, 1015–1026 (2008). https://doi.org/10.1007/s00122-008-0732-4

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