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

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.

FT-IR Examination of the Development of Secondary Cell Wall in Cotton Fibers

“…The development and release of the germplasm line MD 90ne, including fiber quality data and fiber developmental studies, were previously described [15,17,18]. Cotton samples at different developmental stages were obtained by first tagging cotton flowers on DOA, and then harvesting fibers at 18, 20, 24, 28, 32, 36 and 40 days post-anthesis (DPA).…”

“…Cotton samples at different developmental stages were obtained by first tagging cotton flowers on DOA, and then harvesting fibers at 18, 20, 24, 28, 32, 36 and 40 days post-anthesis (DPA). These time periods were chosen since they coincide with secondary cell wall development [1,15]. Beginning with the 20 DPA time points, samples were harvested every 4 days in order to maximize the collected sample sizes.…”

“…Notably, recent cell wall development studies have not included exchange studies [9,10]. The vibrational spectra of cotton fibers harvested between 18 and 40 DPA were examined, a time period during which formation of the secondary cell wall occurs [1,15]. Changes in the regular and D2O-exchanged spectra are highlighted.…”

Cloning and characterization of homeologous cellulose synthase catalytic subunit 2 genes from allotetraploid cotton (Gossypium hirsutum L.)

“…Cotton fiber properties such as bundle strength, fineness, length, and maturity ratio were measured from three biological replications of MD52ne and MD 90ne using a High-Volume Instrumentation (HVI) (USTER Technologies Inc., Charlotte, NC) and an Advanced Fiber Information System (AFIS) (USTER Technologies Inc.) as described in Hinchliffe et al (2010).…”

Cell-Specific Studies of Soybean Resistance to Its Major Pathogen, the Soybean Cyst Nematode as Revealed by Laser Capture Microdissection, Gene Pathway Analyses and Functional Studies

“…The problem with NIL or RIL-based strategies is that even minor differences in the genome that are present can greatly alter gene expression. For example, even in the absence of any pathogen, different NILs have been shown to possess alterations in gene expression in specific cell types (Hinchliffe et al 2010). To circumvent this issue, whole genome sequencing can be performed to understand the genetic and transcriptomic nature of the host.…”