Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense

Abstract

Gossypium barbadense is widely cultivated because of its extra-long staple cotton with superior luster, silkiness and high yield. These economically important traits were selected during initial domestication of an agronomically inferior wild ancestor, followed by millennia of human-mediated selection. To reveal the effects of this history on the cotton fiber transcriptome, we conducted comparative expression profiling on mechanically isolated fiber cells at three different stages encompassing early, mid, and late fiber elongation in wild (K101) and domesticated (Pima S-7) accessions, using a microarray platform that interrogates 42,429 unigenes. The distribution of differentially expressed genes across developmental stages was different in the two accessions, with a shift toward greater change earlier in cultivated than in wild G. barbadense. Approximately 4200 genes were differentially expressed between wild and domesticated accessions at one or more of the stages studied. Domestication appears to have led to enhanced modulation of cellular redox levels and the avoidance or delay of stress-like processes. Prolonged fiber growth in cultivated relative to wild G. barbadense is associated with upregulation of signal transduction and hormone signaling genes and down-regulation of cell wall maturation genes. Clues are provided into the processes and genes that may unwittingly have been selected by humans during domestication and development of modern elite lines. Several of the transcriptomic differences between wild and domesticated G. barbadense described here appear to have parallels in a second domesticated cotton species, Gossypium hirsutum, suggesting that replicated domestication of two different species has resulted in overlapping, parallel, metabolic transformations.

Effects of Fertilization on Ramie (Boehmeria nivea L.) Growth, Yield and Fiber Quality

“…Aulah and Malhi [15,16] reported that the absorption of N, in the form of NH 4 + , is not affected by K and that the interaction between N and K is the second most important factor after NPK for increasing crop yield, which is not further increased by the increasing concentrations of N and P without the addition of K. Deng et al [13] suggested that several metabolic activities of ramie are affected by N, P, or K deficiency. For instance, the expression of profilin is down regulated under P-deficient conditions, and this affects fiber synthesis [13,17]. Fiber fresh and dry weights were also increased by fertilizer application, particularly NPK, which is consistent with the results reported by Liu et al [18].…”

Parallel up-regulation of the profilin gene family following independent domestication of diploid and allopolyploid cotton ( Gossypium )

“…As a specialized unicellular trichome with a greatly exaggerated length, cotton fiber represents a masterpiece of human domestication, made all the more remarkable by its parallel, independent origin in four cultivated species (three studied here). Little is known about the genetic, genomic, or metabolomic transformations that mediate these independent transformations, although insights are emerging from comparative expression profiling experiments (3)(4)(5)(6). The present study sheds light on one aspect of this general question, implicating the up-regulation of the profilin gene family concomitant with strong directional selection under human domestication.…”

“…With respect to the former, analyses of fiber growth curves reveal that cotton domestication at both the diploid and allopolyploid levels is associated with a prolonged period of fiber elongation (2). As to the genomic underpinnings of fiber evolution, a number of recent studies are generating insights and a rich data set based on comparative transcriptome profiling of fiber development in wild vs. domesticated cotton (3)(4)(5)(6), and from ongoing comparative proteomic analyses (7). Rapp et al (2010), for example, reported thousands of genes that are differentially expressed in developing fiber between wild and domesticated G. hirsutum, many associated with key developmental processes presumed to play important roles in primary and secondary wall synthesis and in modulation of reactive oxygen species (3,5,6).…”

“…As to the genomic underpinnings of fiber evolution, a number of recent studies are generating insights and a rich data set based on comparative transcriptome profiling of fiber development in wild vs. domesticated cotton (3)(4)(5)(6), and from ongoing comparative proteomic analyses (7). Rapp et al (2010), for example, reported thousands of genes that are differentially expressed in developing fiber between wild and domesticated G. hirsutum, many associated with key developmental processes presumed to play important roles in primary and secondary wall synthesis and in modulation of reactive oxygen species (3,5,6). Thus, the evolutionary process associated with strong directional selection practiced by aboriginal domesticators appears to be extraordinarily complex, at least insofar as perturbation of the transcriptional network, especially in the early stages of fiber development (4).…”

MicroRNAs in Cotton

“…Many studies have shown the change in gene expression during cotton fiber initiation and development, and some genes have been studied for their functions during cotton fiber development (Asif et al 2008;Chaudhary et al 2008Chaudhary et al , 2009FeiFei et al 2009;Gao et al 2007;Gou et al 2007;He et al 2008;Hovav et al 2008;Huang et al 2008a, b;Iqbal et al 2008;Li et al 2003Li et al , 2005aLiu et al 2009;Michailidis et al 2009;Schwartz and Smith 2008;Taliercio and Boykin 2007;Tu et al 2007;Wu et al 2008;Xu et al 2008). However, the mechanism of controlling cotton fiber differentiation and development is still unknown.…”