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Naturally colored cotton is cotton fiber contains natural pigments, pigment material and its related genes but not yet conclusive, the pigment formation mechanism is not yet clear. In this study, to the fiber color shades varying degrees of colored cotton varieties for materials, different colored cotton fiber pigment synthesis gene expression differences by cDNA microarray technology, real-time quantitative PCR and technology research, and the CHI gene depth research. To study colored cotton pigment type, and pigment synthesis and accumulation of a critical period and the molecular mechanism, fully articulated and lay a good foundation with pigment related genes, using genetic engineering technology to cultivate color stability, good quality, high yield colored cotton varieties have greater significance. The main results are as follows: 1) in brown cotton varieties brown 128 with two white cotton varieties Kuqa T94-4 and Liao 96-23-30 for the test material, pigment synthesis genes using cDNA microarray technology system. The final total of 821 differentially expressed genes, and 821 differentially expressed genes, Bioinformatics, KEGG (Kyoto Encyclopedia of Genes and Genomes) biological pathway analysis, these genes can be divided into a total of 64 biological pathways, which flavonoid biosynthesis 7 ways to match the number of genes (F3H, LDOX, TT7, ATCHS/CHS/TT4, AT5G66220, BAN, All/CFI/TT5) and ribosomal pathway followed by starch and sucrose metabolism phenylpropionic acid bio synthesis, matching the number of genes for five. Another brown cotton differentially expressed genes include photosynthesis antenna protein, the glycolytic pathway, fixed carbon, and other biological pathways. Colored cotton fiber development and the development of white cotton fiber has many different ways. GO (Gene Ontology) analysis showed that the same gene is not just participate in a biological process, but involved in several biological processes, which not only reflects the versatility of a gene, also reflects the in vivo biological processes the regulation and role. 2) We selected cDNA microarray relates 6 gene maximum number, the highest match rates of the flavonoid biosynthetic pathway gene (CHS, CHI and F3H, F3'H, LDOX, ANR), as the goal of our research gene while the other three on the flavonoid biosynthetic pathway related the gene (F3'5'H DFR, LAR) by real-time PCR technology in these nine target gene expression differences in six different color fiber germplasm conducted a study of the system. The results showed that the pigment genes may be related with brown cotton flavonoid biosynthetic pathway, and finally the formation of condensed tannins, thus the formation of oxidized tannins, and thus the performance of the brown fiber, but the the green cotton pigment synthesis and proanthocyanidin biosynthesis pathway relations are not large. Related genes in brown cotton pigment formed when 5DPA begin to express 10DPA peaked, some genes 15DPA higher expression levels. 3) the use of PCR and chromosome walking technique of gene fragments obtained by the CHI gene of the DNA total length of 4781bp, wherein the 5 'flanking promoter region of 1442bp, by GENSCAN software analysis, 684bp ORF (open reading frame), a total of encoding 227 amino acids. 4) using the DNAstar software analysis of the amino acid sequence of the CHI gene, predict the secondary structure of the sequence can form a plurality of α-helix, β-sheet, the corner and curling, and using software Mega4.1 on the gene in other species The protein sequence clustering analysis results show that the relationship of the CHI genes with leguminous far a large class of poly with dicotyledonous plants. 5) the use of various regulatory elements PLANTCARE software CHI gene promoter portion was predicted and analyzed, the found MYSI and MRE regulatory elements, it is the binding sites of the MYB and light response MYB binding sites, MYB is the regulation of the gene encoding transcription factor, This shows that the CHI genes may be regulated by the MYB gene, and thus the impact of flavonoid synthesis of the substance.
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