Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 27, 2009
Publication Date: January 20, 2010
Citation: Hinchliffe, D.J., Meredith Jr, W.R., Yeater, K.M., Kim, H. 2010. Near-Isogenic Cotton Germplasm Lines that Differ in Fiber-Bundle Strength have Temporal Differences in Fiber Gene Expression Pattern as Revealed by Comparative High-Throughput Profiling. Theoretical and Applied Genetics. 120:1347-1366. Interpretive Summary: Cotton fiber quality measurements, such as fiber strength and fiber length, are used worldwide to dictate the final value of raw cotton fiber. In order to remain competitive in the global marketplace, US cotton producers must grow cotton varieties that produce fibers with superior quality characteristics that are desirable to textile mills and can compete with synthetic fibers. Textile mills typically use high-speed spinning equipment that requires high levels of fiber strength for efficient processing of cotton fibers into yarns. Therefore, the ability to increase the fiber strength of new cotton varieties, while not adversely affecting other fiber quality measurements or fiber yield, is of great benefit to cotton producers and the textile industry. In this manuscript, we have evaluated two lines of cotton that are very closely related but differ in fiber strength. Using a technique in molecular biology called microarray analysis with appropriate statistical analyses, we have analyzed fibers of the two cotton lines and identified genes that may be responsible for the observed difference in fiber strength. The main finding of the work indicates that the high fiber strength line begins synthesizing cellulose, the major component of the fiber, earlier than the lower strength line. Further analysis of the identified genes and their functions is currently underway with the aim of transferring this genomic information into useful strategies for plant breeders to develop cotton with improved fiber strength.
Technical Abstract: Gene expression profiles of developing cotton (Gossypium hirsutum L.) fibers from two near-isogenic lines (NILs) that differ in fiber-bundle strength, short-fiber content, and in fewer than two genetic loci were compared using an oligonucleotide microarray. Fiber gene expression was compared at five time-points spanning fiber elongation and secondary cell wall (SCW) biosynthesis. Fiber samples were collected from field plots in a randomized, complete-block design, with three spatially-distinct biological replications for each NIL at each time-point. Microarray hybridizations were performed in a loop experimental design that allowed comparisons of fiber gene expression profiles as a function of time between the two NILs. Overall, developmental expression patterns revealed by the microarray experiment agreed with previously reported cotton-fiber gene-expression patterns for specific genes. Additionally, genes expressed coordinately with the onset of SCW biosynthesis in cotton fiber correlated with gene expression patterns of other SCW-producing plant tissues. Functional classification and enrichment analysis of differentially expressed genes between the two NILs revealed that genes associated with SCW biosynthesis were significantly up-regulated in fibers of the high fiber-quality line at the transition stage of cotton fiber development. For independent corroboration of the microarray results, 15 genes were selected for quantitative reverse-transcription PCR analysis of fiber gene expression. These analyses, conducted over multiple field-years, confirmed the temporal difference in fiber gene expression between the two NILs. We hypothesize that the loci conferring temporal differences in fiber gene expression between the NILs are important regulatory sequences that offer the potential for more targeted manipulation of cotton fiber quality.