Functional genomics of cell elongation in developing cotton fibers

Abstract

Cotton fibers are single-celled seed trichomes of major economic importance. Factors that regulate the rate and duration of cell expansion control fiber morphology and important agronomic traits. For genetic characterization of rapid cell elongation in cotton fibers, approximately 14,000 unique genes were assembled from 46,603 expressed sequence tags (ESTs) from developmentally staged fiber cDNAs of a cultivated diploid species ( Gossypium arboreum L.). Conservatively, the fiber transcriptome represents 35-40% of the genes in the cotton genome. In silico expression analysis revealed that rapidly elongating fiber cells exhibit significant metabolic activity, with the bulk of gene transcripts, represented by three major functional groups - cell wall structure and biogenesis, the cytoskeleton and energy/carbohydrate metabolism. Oligonucleotide microarrays revealed dynamic changes in gene expression between primary and secondary cell wall biogenesis showing that fiber genes in the dbEST are highly stage-specific for cell expansion - a conclusion supported by the absence of known secondary cell wall-specific genes from our fiber dbEST. During the developmental switch from primary to secondary cell wall syntheses, 2553 "expansion-associated" fiber genes are significantly down regulated. Genes (81) significantly up-regulated during secondary cell wall synthesis are involved in cell wall biogenesis and energy/carbohydrate metabolism, which is consistent with the stage of cellulose synthesis during secondary cell wall modification in developing fibers. This work provides the first in-depth view of the genetic complexity of the transcriptome of an expanding cell, and lays the groundwork for studying fundamental biological processes in plant biology with applications in agricultural biotechnology.

Toward Sequencing Cotton (Gossypium) Genomes: Figure 1.

“…As of July 18, 2007, 356,889 Gossypium sequences were in GenBank, including 40,069 ESTs from G. arboreum (A), 67,098 from G. raimondii (D), 232,006 from G. hirsutum (AD tetraploid), and a few from other Gossypium members (Arpat et al, 2004;Udall et al, 2006;Yang et al, 2006;Taliercio and Boykin, 2007). Among these ESTs, many are from developing fiber and are enriched in putative MYB and WRKY transcription factors and phytohormone regulators .…”

“…Moreover, A subgenome ESTs of all functional classifications are dramatically enriched in G. hirsutum fiber , a result consistent with the production of long lint fibers in A genome species. Some ESTs have been used to develop sequence-specific markers in breeding and to construct microarrays, leading to the identification of many candidate genes involved in fiber cell initiation and elongation (Arpat et al, 2004;Lee et al, 2006;Shi et al, 2006;Wu et al, 2006;Udall et al, 2007).…”

Gene copy number evolution during tetraploid cotton radiation

“…The amplified PCR products were run in 1% agarose gel and the bands were cut and cleaned with a Qiagen kit. A subset (39) of cotton unigenes from G. arboreum immature fiber (Arpat et al, 2004) was selected randomly as a control for comparison with the candidate DR genes.…”

Types, levels and patterns of low-copy DNA sequence divergence, and phylogenetic implications, for Gossypium genome types

“…For example, between two diploid A genome species, Gate3AE04, from a fiber related EST library (Arpat et al, 2004) has 1.8 SNP/100 bp and 2.6 polymorphic sites/100 bp including three extended indels with one spanning 58 base pairs. However, many sequences from the same library do not have any polymorphisms between A1 and A2 species.…”