Abstract
Cotton (Gossypium spp.) is an important crop plant that is widely grown to produce both natural textile fibers and cottonseed oil. Cotton fibers, the economically more important product of the cotton plant, are seed trichomes derived from individual cells of the epidermal layer of the seed coat. It has been known for a long time that large numbers of genes determine the development of cotton fiber, and more recently it has been determined that these genes are distributed across At and Dt subgenomes of tetraploid AD cottons. In the present study, the organization and evolution of the fiber development genes were investigated through the construction of an integrated genetic and physical map of fiber development genes whose functions have been verified and confirmed. A total of 535 cotton fiber development genes, including 103 fiber transcription factors, 259 fiber development genes, and 173 SSR-contained fiber ESTs, were analyzed at the subgenome level. A total of 499 fiber related contigs were selected and assembled. Together these contigs covered about 151 Mb in physical length, or about 6.7% of the tetraploid cotton genome. Among the 499 contigs, 397 were anchored onto individual chromosomes. Results from our studies on the distribution patterns of the fiber development genes and transcription factors between the At and Dt subgenomes showed that more transcription factors were from Dt subgenome than At, whereas more fiber development genes were from At subgenome than Dt. Combining our mapping results with previous reports that more fiber QTLs were mapped in Dt subgenome than At subgenome, the results suggested a new functional hypothesis for tetraploid cotton. After the merging of the two diploid Gossypium genomes, the At subgenome has provided most of the genes for fiber development, because it continues to function similar to its fiber producing diploid A genome ancestor. On the other hand, the Dt subgenome, with its non-fiber producing D genome ancestor, provides more transcription factors that regulate the expression of the fiber genes in the At subgenome. This hypothesis would explain previously published mapping results. At the same time, this integrated map of fiber development genes would provide a framework to clone individual full-length fiber genes, to elucidate the physiological mechanisms of the fiber differentiation, elongation, and maturation, and to systematically study the functional network of these genes that interact during the process of fiber development in the tetraploid cottons.
Highlights
Gossypium, composed of 50 species including 45 diploid and 5 allopolyploid species[1], is an excellent system for studying many fundamental questions relating to genome evolution, plant development, polyploidization, and crop productivity
Individual genes were assembled into sequence contigs for three main reasons: the first was to remove redundancy of all the sequences for the subsequent Overgo primer design; the second was to crosscheck the functions of the assembled genes in each contig; and the third was to further link assembled contigs/singletons with other sequence-tagged-sites (STS), which included bacterial artificial chromosome (BAC)-end sequences, BAC sub-clone sequences, and mapped genetic marker sequences in the integrated genetic and physical map of tetraploid cotton
None of the D genome diploids, including the presumed Dt subgenome donor, are cultivated because they do not produce spinnable fibers, even though their seeds are pubescent [54]. Both A genome diploid and AD tetraploid Gossypium taxa produce spinnable fibers, and both of them are still planted for fibers by farmers, the yield and quality from domesticated A genome diploids (G. arboreum and G. herbaceum) are lower than that from AD tetraploid cottons (G. hirsutum and G. barbadense)
Summary
Gossypium, composed of 50 species including 45 diploid and 5 allopolyploid species[1], is an excellent system for studying many fundamental questions relating to genome evolution, plant development, polyploidization, and crop productivity. A better understanding of the genetic processes that regulate which and how many epidermal cells become fibers and the genetic processes that regulate fiber elongation would allow us to biologically manipulate the single cells to increase yield and improve fiber length and uniformity for a higher quality fiber. Both cotton scientists and other plant biologists have focused on the isolation, characterization, and evaluation of genes related to fiber development [25]
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