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Molecular Genetics and Genomics

, Volume 278, Issue 5, pp 539–553 | Cite as

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

  • Chuanfu An
  • Sukumar SahaEmail author
  • Johnie N. Jenkins
  • Brian E. Scheffler
  • Thea A. Wilkins
  • David M. Stelly
Original Paper

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.

Keywords

Gossypium spp. EXPANSIN Transcriptome profiling Single-nucleotide polymorphism Chromosomal assignment 

Notes

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.

Supplementary material

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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Chuanfu An
    • 1
  • Sukumar Saha
    • 2
    Email author
  • Johnie N. Jenkins
    • 2
  • Brian E. Scheffler
    • 3
  • Thea A. Wilkins
    • 4
    • 5
  • David M. Stelly
    • 6
  1. 1.Department of Plant and Soil Sciences Mississippi State UniversityMississippi StateUSA
  2. 2.USDA-ARS, Crop Science Research LaboratoryMississippi StateUSA
  3. 3.USDA-ARS-CGRUStonevilleUSA
  4. 4.Department of Plant SciencesUniversity of CaliforniaDavisUSA
  5. 5.Department of Plant and Soil ScienceTexas Tech UniversityLubbockUSA
  6. 6.Department of Soil and Crop SciencesTexas A&M UniversityCollege StationUSA

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