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Molecular cloning and characterization of genomic sequence tags (GSTs) from the PHYA, PHYB, and HY5 gene families of cotton (Gossypium species)
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The goals of this research project were to identify and characterize the cotton orthologs and paralogs of the Arabidopsis phytochrome genes and the cell elongation factor HY5. Based on close evolutionary relatedness between cotton and Arabidopsis, the similar genes to PHYA, PHYB and HY5 genes from Gossypium species have been identified. GSTs for two paralogous PHYA genes (PHYA1 and PHYA2) from diploid cottons have been cloned, sequenced and characterized. At least four PHYA genes: two PHYA1 and two PHYA2 genes (A&D-genome specific) have been determined in tetraploid cottons that were acquired from diploid ancestors. Cotton PHYA genes share 60-65% nucleotide identity with Arabidopsis PHYA gene. Approximately 80% nucleotide similarity between cotton PHYA1 and PHYA2 has been observed. Both cotton PHYA genes were actively expressed. The expression of A-genome PHYA1 and D-genome PHYA2 has been observed in G. hirsutum seedlings. A CAPS marker (BbvI) has been developed for PHYA1 gene, and a QTL locus that is closely linked (LOD = 4.13) to fiber length has been identified using the PHYA1 CAPS marker. In addition, GST for cotton PHYB gene has been cloned using the similar approach. Cloned cotton PHYB gene shows remarkable conservation within cotton species and shares 85% and 78% nucleotide sequence similarity with Arabidopsis PHYB and PHYD genes, respectively. GSTs for cotton HY5 gene have been cloned and characterized. Tetraploid cottons G. hirsutum and G. barbadense have two genes for HY5: HY5-A and HY5-B, which were acquired from wild diploid ancestors through polyploidization. The D-genome contributed HY5-A gene while the A-genome contributed HY5-B gene. Approximately 50-60% structural similarity between cotton and Arabidopsis HY5 loci has been observed. HY5-A gene was expressed in cotton seedlings while the expression of HY5-B was not observed. Using polymorphic sites in HY5-B genes, CAPS marker (RsaI) has been developed for HY5-B loci. However, no significant linkage was determined in QTL-mapping of an F₂ fiber length cotton population using HY5-B CAPS. Gossypium derived phytochrome and HY5 genes have the potential to be useful as molecular markers in marker-assisted cotton breeding, to improve cotton fiber quality, resistance to pathogens and insects, and tolerance to environmental adversities.
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Includes bibliographical references (leaves 72-80).
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Abdurakhmonov, Ibrokhim Yulchievich (2001). Molecular cloning and characterization of genomic sequence tags (GSTs) from the PHYA, PHYB, and HY5 gene families of cotton (Gossypium species). Master's thesis, Texas A&M University. Available electronically from
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