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

Content Provider	Springer Nature Link
Author	An, Chuanfu Saha, Sukumar Jenkins, Johnie N. Scheffler, Brian E. Wilkins, Thea A. Stelly, David M.
Copyright Year	2007
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.
Starting Page	539
Ending Page	553
Page Count	15
File Format	PDF
ISSN	16174615
Journal	Molecular and General Genetics MGG
Volume Number	278
Issue Number	5
e-ISSN	16174623
Language	English
Publisher	Springer-Verlag
Publisher Date	2007-08-28
Publisher Place	Berlin/Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Gossypium spp. EXPANSIN Transcriptome profiling Single-nucleotide polymorphism Chromosomal assignment Microbial Genetics and Genomics Biochemistry Cell Biology
Content Type	Text
Resource Type	Article
Subject	Genetics Medicine Molecular Biology

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