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Transcriptome profiling, sequence characterization, and SNP-based chromosomal assignment of the EXPANSIN genes in cotton

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Abstract

The knowledge of biological significance associated with DNA markers is very limited in cotton. SNPs are potential functional marker to tag genes of biological importance. Plant expansins are a group of extracellular proteins that directly modify the mechanical properties of cell walls, enable turgor-driven cell extension, and likely affect length and quality of cotton fibers. Here, we report the expression profiles of EXPANSIN transcripts during fiber elongation and the discovery of SNP markers, assess the SNP characteristics, and localize six EXPANSIN A genes to chromosomes. Transcriptome profiling of cotton fiber oligonucleotide microarrays revealed that seven EXPANSIN transcripts were differentially expressed when there was parallel polar elongation during morphogenesis at early stage of fiber development, suggesting that major and minor isoforms perform discrete functions during polar elongation and lateral expansion. Ancestral and homoeologous relationships of the six EXPANSIN A genes were revealed by phylogenetic grouping and comparison to extant A- and D-genome relatives of contemporary AD-genome cottons. The average rate of SNP per nucleotide was 2.35% (one SNP per 43 bp), with 1.74 and 3.99% occurring in coding and noncoding regions, respectively, in the selected genotypes. An unequal evolutionary rate of the EXPANSIN A genes at the subgenome level of tetraploid cotton was recorded. Chromosomal locations for each of the six EXPANSIN A genes were established by gene-specific SNP markers. Results revealed a strategy for discovering SNP markers in a polyploidy species like cotton. These markers could be useful to associate candidate genes with the complex fiber traits in MAS.

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Acknowledgments

We gratefully acknowledge the technical help of Mr. Douglas A. Dollar and the suggestions from Dr. Z. T. Burive and Ms. Yufang Guo. We also thank Dr. John Yu for providing G. arboreum and G. raimondii DNA samples.

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  1. Thea A. Wilkins

    Present address: Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA

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

    Brian E. Scheffler

  4. Department of Plant Sciences, University of California, Davis, CA, 95616, USA

    Thea A. Wilkins

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

    David M. Stelly

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Correspondence to Sukumar Saha.

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Communicated by R. Hagemann.

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Mention of trade names or commercial products in this manuscript does not constitute a guarantee or warranty of the product by the 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 EF644199 to EF644335.

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An, C., Saha, S., Jenkins, J.N. et al. Transcriptome profiling, sequence characterization, and SNP-based chromosomal assignment of the EXPANSIN genes in cotton. Mol Genet Genomics 278, 539–553 (2007). https://doi.org/10.1007/s00438-007-0270-9

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