Transcriptome profiling, sequence characterization, and assignment to chromosomes of SNP markers for EXPANSIN genes in cotton

Authors: AN, CHUANFU - MISSISSIPPI STATE UNIV; Saha, Sukumar; Jenkins, Johnie; Scheffler, Brian; WILKINS, THEA - UNIVERSITY OF CALIFORNIA; STELLY, DAVID - TEXAS A&M UNIVERSITY

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/15/2007
Publication Date: 12/1/2007
Citation: An, C., Saha, S., Jenkins, J.N., Scheffler, B.E., Wilkins, T.A., Stelly, D.M. 2007. Transcriptome profiling, sequence characterization, and SNP-based chromosomal assignment of the EXPANSIN genes in cotton. Molecular Genetics and Genomics. 278:539-553.

Interpretive Summary: Plant expansins are a group of extracellular proteins that directly modify the mechanical properties of cell walls, leading to turgor-driven cell wall extensions and hence likely play an important role in determining fiber properties in cotton. The objectives of this study were to: 1) investigate the expression of EXPANSIN transcripts accumulated at fiber elongation phase, 2) develop a strategy to identify SNP markers associated with six EXPANSIN genes in allotetraploid cotton, and 3) discover their chromosome location using SNP markers. Results revealed that seven EXPANSIN transcripts were differentially expressed and parallel polar elongation during fiber morphogenesis, suggesting major and minor isoforms perform discrete functions during polar elongation and lateral expansion during fiber growth. Separation between the homoeologous loci of the six EXPANSIN A genes was accomplished based on phylogenetic grouping and comparison with the two ancestral diploid genome species of allotetraploid cotton. A total of 223 SNP’s including 119 single-bae changes and 104 indels, were identified by SNP discovery approach. The average rate of SNP per nucleotide was 0.42% (1 SNP per 238 bp of sequence), with 0.35% and 0.54% occurring in coding and non-coding regions, respectively. Chromosome location for each of six EXPANSIN A genes was discovered by gene-specific SNP markers. Homoeologous loci for GhEXPA2 were assigned to the long arm of chromosomes 10 and 20, while GhEXPA1, GhEXPA3, GhEXPA4, GhEXPA5, and GhEXPA6 were assigned to the long arm of chromosomes 20, 10, 9, 1, and 3, respectively. The agreement of chromosomal locations and previously reported fiber quality QTL for fiber length and elongation indicated some EXPANSIN A genes might play an important role in these QTL. SNP markers associated with EXPANSIN genes are useful tools for basic and applied research to elucidate the developmental and regulatory processes of cotton fiber development. Their value is increased with knowledge of their location in the genome.

Technical Abstract: Plant expansins are a group of extracellular proteins that directly modify the mechanical properties of cell walls, leading to turgor-driven cell extension and hence are likely play an important role in determining fiber properties. The objectives of this study were to investigate the expression profiling of EXPANSIN transcripts accumulated at fiber elongation phase, to develop a strategy for allotetraploid cotton SNP discovery, to assess SNP characteristics of six EXPANSIN A genes, and to determine the chromosomal locations of the SNP markers. Transcriptome profiling of cotton fiber oligonucleotide microarrays revealed that seven EXPANSIN transcripts were differentially expressed and they parallel polar elongation during fiber morphogenesis, suggesting major and minor isoforms perform discrete functions during polar elongation and lateral expansion. Discrimination of homoeologous loci of the six EXPANSIN A genes was accomplished by phylogentic grouping and comparison to the two progenitor diploid genome species of allotetraploid cotton. A total of 223 SNPs, including 119 single-base changes and 104 indels, were identified by in vitro SNP discovery approach. The average rate of SNP per nucleotide was 0.42% (1 SNP per 238 bp of sequence), with 0.35% and 0.54% occurring in coding and noncoding regions, respectively. The frequency of total SNP, nonsynonymous changes, and nucleotide diversity were higher in the Dt-genome compared to the At-genome suggesting an unequal evolutionary rate of the EXPANSIN A genes in tetraploid cotton species. Chromosomal locations for each of six EXPANSIN A genes were established by gene-specific SNP markers. Homoeologous loci for GhEXPA2 were assigned to the long arm of chromosomes 10 and 20, while GhEXPA1, GhEXPA3, GhEXPA4, GhEXPA5, and GhEXPA6 were assigned to the long arm of chromosomes 20, 10, 9, 1, and 3, respectively. The agreement of chromosomal locations with previously reported fiber quality QTL (quantitative trait loci) for fiber length and elongation indicated some EXPANSIN A genes may have an important role in these QTLs.