Near-isogenic cotton germplasm lines that differ in fiber-bundle strength have temporal differences in fiber gene expression patterns as revealed by comparative high-throughput profiling

• Published in: Theoretical and applied genetics Vol. 120; no. 7; pp. 1347 - 1366
• Main Authors: Hinchliffe, Doug J, Meredith, William R, Yeater, Kathleen M, Kim, Hee Jin, Woodward, Andrew W, Chen, Z. Jeffrey, Triplett, Barbara A
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Berlin/Heidelberg : Springer-Verlag 01-05-2010; Springer-Verlag; Springer; Springer Nature B.V
• Subjects: Agriculture; Biochemistry; Biological and medical sciences; Biomedical and Life Sciences; Biotechnology; Cell Wall - genetics; cell wall components; cell walls; Classical genetics, quantitative genetics, hybrids; Computational Biology; Consensus Sequence; Cotton; Cotton Fiber; fiber bundle strength; fiber quality; Fundamental and applied biological sciences. Psychology; Gene expression; Gene Expression Profiling - methods; gene expression regulation; Gene Expression Regulation, Plant; Genes, Plant - genetics; Genetic aspects; Genetics of eukaryotes. Biological and molecular evolution; Gossypium - cytology; Gossypium - genetics; Gossypium - growth & development; Gossypium hirsutum; isogenic lines; Life Sciences; messenger RNA; microarray technology; near-isogenic lines; Oligonucleotide Array Sequence Analysis - methods; Original Paper; Physiological aspects; Physiological research; Plant Biochemistry; Plant Breeding/Biotechnology; plant development; plant fibers; Plant genetics; Plant Genetics and Genomics; Plant physiology; Pteridophyta, spermatophyta; Reproducibility of Results; Reverse Transcriptase Polymerase Chain Reaction; Seasons; secondary cell walls; strength (mechanics); temporal variation; Time Factors; Up-Regulation - genetics; Vegetals; Cotton Fiber; Fiber Development; CesA Gene; Secondary Cell Wall; Fiber Elongation; Malvaceae; Germplasm; Dicotyledones; Angiospermae; Genetics; Spermatophyta; Agriculture; Gossypium hirsutum; Isogenic line; Gene expression; Strength
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-010-1260-6

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.