棉纤维发育相关基因转录组学、表达谱分析研究
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摘要
陆地棉和海岛棉是目前世界上最具有商业价值的栽培棉种。陆地棉由于产量高和较强的环境适应能力而被广泛种植,占棉花产量的90%。相反,海岛棉仅占棉花产量的5-8%,由于其在长度、强度等方面具有优良纤维品质而价格昂贵。海岛棉(G. barbadense)和陆地棉(G. hirsutum)都是异源四倍体棉花栽培品种,但是他们的纤维品质和发育进程显著不同。虽然科研工作者在揭示棉纤维发育机制上,已经开展了大量的研究,但是目前对于海岛棉优异的纤维品质机理还不清楚,因此,本文对两个棉种胚珠进行转录本测序并进行分析,并对海、陆棉开花后5、10、15、25DPA的棉纤维进行了数字基因表达谱分析,筛选纤维发育各时期表达有差异的基因,以期揭示两个棉种在纤维发育时期的基因组表达差异。获得结果如下：
1.对两个棉种胚珠进行转录本测序并进行分析,从海岛棉和陆地棉中分别获得79,686和67,450个unigenes。将获得的unigenes基因与最近公布的二倍体棉的参考基因组进行比较表明,大约有3/4的胚珠基因与二倍体棉蛋白编码的基因具有高度的同源性,同源性高达90.7%；其次,两个栽培品种胚珠的差异基因主要富集于胚后发育,这与他们纤维发育差异是一致的。最后通过SNPs (single nucleotide polymorphism,单核苷酸多态性)分析表明,两个转录组各有超过200,000个SNPs映射到二倍体基因组。两个四倍体品种间SNP差异可以解释他们间遗传差异。大多数核苷酸变异的基因参与了胚后发育和纤维发育,包括调控细胞大小和表皮毛分化。因此,本研究提供了海岛棉基因的完整列表,揭示数百个新的基因涉及两个棉种之间的不同纤维发育机制。
2.根据棉花同一时期不同棉种之间,以及两种棉种同一时期之间的差异基因分析,两个棉种不同时期差异基因表达数目相似,在5DPA和10DPA,陆地棉和海岛棉共同差异表达基因有1,924个,其中上调的有1,419,下调的505个；在10-15DPA时期,共有936个差异基因,上调的基因只有292个,下调的基因有644个；在15-25DPA时期,共有2,169个差异基因,上调基因1,268个,下调基因901个。
3.找出海岛棉和陆地棉之间的高可信度的差异表达基因,并对差异表达基因进行功能聚类分析(GO),发现海岛棉胚珠发育初期生毛细胞分化基因上调促进其棉纤维发育,海岛棉中纤维细胞的伸长相关基因上调促进其纤维发育,海岛棉纤维伸长期长于陆地棉,这也促进了棉纤维的发育。通过海岛棉和陆地棉纤维相关基因的共性和差异性,发现了海岛棉棉纤维品质优越的决定基因和分子机制。
4.从海岛棉中扩增得到MYB转录因子基因GbMYB25与GbDET2基因,经测序验证、Blast比对与同源性分析,并实时荧光定量PCR分析表明,GbMYB25与GbDET2基因可能参与调控棉花纤维起始发育。
Gossypium hirsutum and Gossypium barbadense are the most commercially cultivated cotton in the world G. hirsutum occupies about90%of the cotton production in the world due to its high yield and strong adaptation to diverse environmental conditions. On the contrary, G. barbadense accounting for only5-8%of the production is much more expensive due to its unprecedented quality of the fiber length, fitness and strength. Gossypium hirsutum and Gossypium barbadense are allotetraploid cotton cultivars differing greatly in their fiber quality and developmental programs. Although a huge number of studies and approaches have been carried out to uncover the cotton fiber developmental mechanisms, it remains unclear how G. barbadense achieves its superior fiber characteristics. Because the transcriptome of the fertilized ovule at the day of anthesis reflects the cotton genome expression at the fiber initiation stage, we sequenced their ovule transcriptomes and analyed the fiber digital gene expression profiling of Gb21and Gh36from5DPA to25DPA (including5,10,15and25DPA). The results were as follows:
1.Here we sequenced and analyzed their ovule transcriptomes, and obtained79,686ovule unigenes for G. hirsutum and67,450for G. barbadense.The confidence of these unigenes was confirmed by three independent analyses. First, comparison with the recently published diploid cotton reference genome showed that90.7%of diploid protein-coding genes are homologous to over three quarters of these ovule unigenes. Second, the ovule unigenes differentially assembled between the two cultivars were strongly enriched in post-embryonic development, consistent with their fiber developmental difference. The two transcriptomes each harbored over0.2million SNPs when mapped onto the diploid genome, consistent with the reported phylogenetic distance. SNPs between the two tetraploid cultivars were recovered to address their genetic difference. Strikingly, the unigenes with most nucleotide variation were those involved in post-embryonic development, and in fiber development including regulation of cell size and trichome differentiation. Therefore, this study provides a comprehensive list of unigenes for G. barbadense, and revealed hundreds of novel unigenes involving in the different fiber developmental mechanisms between the two cultivars.
2.Based on the analysis of differential gene expression between different strains of cotton during the same period and the same period of two strains,the number of differentially expressed genes were similar in different periods of two cotton varieties. At5DPA and10DPA, the differentially expressed genes of Gossypium hirsutum and G. barbadense were1,924, of which1,419were up-regulated,505were down-regulated, During the period of10-15DPA, there were936differential expressed genes, only292up-regulated genes,644down-regulated genes. During the period of15-25DAP, there were2169differential expressed genes, only1,268up-regulated genes,901down-regulated genes.
3. We performed the Gene Ontology (GO) analysis for the highly confidence differentially expressed genes between Gossypium hirsutum and Gossypium barbadense, discoved that the up-regulated hairy cell differentiation genes in the initial stage of ovule development and fiber elongation-related genes promote sea-island cotton fiber development. The fiber elongation stage of sea-island cotton was longer than the upland cotton also facilitates the sea-island cotton fiber development. According to the anlysis of similarities and differences of the sea island fiber related genes, found the genes and molecular mechanisms of sea-island cotton fiber quality superior to upland cotton.
4. Furthermore,one MYB transcription factor GBMYB25and GbDET2were amplified from the sea-island cotton, and verified by sequencing, Blast alignment and homology analysis. By the analysis of real-time fluorescent quantitative PCR showed that the two genes GbMYB25and GbDET2were involved in regulating the fiber developmen.
1.对两个棉种胚珠进行转录本测序并进行分析,从海岛棉和陆地棉中分别获得79,686和67,450个unigenes。将获得的unigenes基因与最近公布的二倍体棉的参考基因组进行比较表明,大约有3/4的胚珠基因与二倍体棉蛋白编码的基因具有高度的同源性,同源性高达90.7%；其次,两个栽培品种胚珠的差异基因主要富集于胚后发育,这与他们纤维发育差异是一致的。最后通过SNPs (single nucleotide polymorphism,单核苷酸多态性)分析表明,两个转录组各有超过200,000个SNPs映射到二倍体基因组。两个四倍体品种间SNP差异可以解释他们间遗传差异。大多数核苷酸变异的基因参与了胚后发育和纤维发育,包括调控细胞大小和表皮毛分化。因此,本研究提供了海岛棉基因的完整列表,揭示数百个新的基因涉及两个棉种之间的不同纤维发育机制。
2.根据棉花同一时期不同棉种之间,以及两种棉种同一时期之间的差异基因分析,两个棉种不同时期差异基因表达数目相似,在5DPA和10DPA,陆地棉和海岛棉共同差异表达基因有1,924个,其中上调的有1,419,下调的505个；在10-15DPA时期,共有936个差异基因,上调的基因只有292个,下调的基因有644个；在15-25DPA时期,共有2,169个差异基因,上调基因1,268个,下调基因901个。
3.找出海岛棉和陆地棉之间的高可信度的差异表达基因,并对差异表达基因进行功能聚类分析(GO),发现海岛棉胚珠发育初期生毛细胞分化基因上调促进其棉纤维发育,海岛棉中纤维细胞的伸长相关基因上调促进其纤维发育,海岛棉纤维伸长期长于陆地棉,这也促进了棉纤维的发育。通过海岛棉和陆地棉纤维相关基因的共性和差异性,发现了海岛棉棉纤维品质优越的决定基因和分子机制。
4.从海岛棉中扩增得到MYB转录因子基因GbMYB25与GbDET2基因,经测序验证、Blast比对与同源性分析,并实时荧光定量PCR分析表明,GbMYB25与GbDET2基因可能参与调控棉花纤维起始发育。
Gossypium hirsutum and Gossypium barbadense are the most commercially cultivated cotton in the world G. hirsutum occupies about90%of the cotton production in the world due to its high yield and strong adaptation to diverse environmental conditions. On the contrary, G. barbadense accounting for only5-8%of the production is much more expensive due to its unprecedented quality of the fiber length, fitness and strength. Gossypium hirsutum and Gossypium barbadense are allotetraploid cotton cultivars differing greatly in their fiber quality and developmental programs. Although a huge number of studies and approaches have been carried out to uncover the cotton fiber developmental mechanisms, it remains unclear how G. barbadense achieves its superior fiber characteristics. Because the transcriptome of the fertilized ovule at the day of anthesis reflects the cotton genome expression at the fiber initiation stage, we sequenced their ovule transcriptomes and analyed the fiber digital gene expression profiling of Gb21and Gh36from5DPA to25DPA (including5,10,15and25DPA). The results were as follows:
1.Here we sequenced and analyzed their ovule transcriptomes, and obtained79,686ovule unigenes for G. hirsutum and67,450for G. barbadense.The confidence of these unigenes was confirmed by three independent analyses. First, comparison with the recently published diploid cotton reference genome showed that90.7%of diploid protein-coding genes are homologous to over three quarters of these ovule unigenes. Second, the ovule unigenes differentially assembled between the two cultivars were strongly enriched in post-embryonic development, consistent with their fiber developmental difference. The two transcriptomes each harbored over0.2million SNPs when mapped onto the diploid genome, consistent with the reported phylogenetic distance. SNPs between the two tetraploid cultivars were recovered to address their genetic difference. Strikingly, the unigenes with most nucleotide variation were those involved in post-embryonic development, and in fiber development including regulation of cell size and trichome differentiation. Therefore, this study provides a comprehensive list of unigenes for G. barbadense, and revealed hundreds of novel unigenes involving in the different fiber developmental mechanisms between the two cultivars.
2.Based on the analysis of differential gene expression between different strains of cotton during the same period and the same period of two strains,the number of differentially expressed genes were similar in different periods of two cotton varieties. At5DPA and10DPA, the differentially expressed genes of Gossypium hirsutum and G. barbadense were1,924, of which1,419were up-regulated,505were down-regulated, During the period of10-15DPA, there were936differential expressed genes, only292up-regulated genes,644down-regulated genes. During the period of15-25DAP, there were2169differential expressed genes, only1,268up-regulated genes,901down-regulated genes.
3. We performed the Gene Ontology (GO) analysis for the highly confidence differentially expressed genes between Gossypium hirsutum and Gossypium barbadense, discoved that the up-regulated hairy cell differentiation genes in the initial stage of ovule development and fiber elongation-related genes promote sea-island cotton fiber development. The fiber elongation stage of sea-island cotton was longer than the upland cotton also facilitates the sea-island cotton fiber development. According to the anlysis of similarities and differences of the sea island fiber related genes, found the genes and molecular mechanisms of sea-island cotton fiber quality superior to upland cotton.
4. Furthermore,one MYB transcription factor GBMYB25and GbDET2were amplified from the sea-island cotton, and verified by sequencing, Blast alignment and homology analysis. By the analysis of real-time fluorescent quantitative PCR showed that the two genes GbMYB25and GbDET2were involved in regulating the fiber developmen.
引文
[1]Adams M D, Moreno R F, Kerlavage A R,et al. Complementary DNA Sequencing:Expressed Sequence Tags and Human Genome Project[J]. Science,1991,252(5013):1651-1656.
[2]Al-Ghazi Y, Bourot S, Arioli T, et al. Transcript profiling during fiber development identifies pathways in secondary metabolism and cell wall structure that may contribute to cotton fiber quality[J]. Plant Cell Physiol,2009,50(7):1364-1381.
[3]Ansorge W J. Next-generation DNA sequencing techniques[J]. New biotechnology,2009, 25(4):195-203.
[4]Arioli T, Birch R, Cork A, et al. Molecular Analysis of Cellulose Biosynthesis in Arabidopsis[J]. Science,1998,279(5351):717-720.
[5]Arpat A B, Wilkins T A, Waugh M, et al. Functional genomics of cell elongation in developing cotton fibers[J]. Plant molecular biology,2004,54(6):911-929.
[6]Arpat A, Waugh M, Sullivan J P, et al. Functional genomics of cell elongation in developing cotton fibers[J]. Plant molecular biology,2004,54(6):911-929.
[7]Bannigan A, Baskin T I. Directional cell expansion--turning toward actin[J]. Curr Opin Plant Biol, 2005,8(6):619-624.
[8]Basra A S, Malik C P. Development of the cotton fiber[J]. Int Rev Cytol,1984,89(1):65-113.
[9]Byers R L, Harker D B, Yourstone S M, et al. Development and mapping of SNP assays in allotetraploid cotton[J]. Theor Appl Genet,2012,124(7):1201-1214.
[10]Chee P W, Draye X, Jiang C, et al. Molecular dissection of phenotypic variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach:Ⅲ. Fiber length[J]. Theoretical and applied genetics,2005,111(4):772-781.
[11]Chen X, Guo W, Liu B, et al. Molecular mechanisms of fiber differential development between G. barbadense and G. hirsutum revealed by genetical genomics[J]. PloS one,2012,7(1):e30056.
[12]Chory, Li. Gibberellins, brassinosteroids and light-regulated development[J]. Plant, Cell and Environment,1997,20(6):801-806.
[13]Cosgrove D J. Wall structure and wall loosening. A look backwards and forwards[J]. Plant Physiology,2001,125(1):131-134.
[14]Cosgrove D J. Loosening of plant cell walls by expansins[J]. Nature,2000,407(6802):321-326.
[15]Delmer D P, Pear J R, Andrawis A, et al. Genes encoding small GTP-binding proteins analogous to mammalian rac are preferentially expressed in developing cotton fibers[J]. MGG Molecular & General Genetics,1995,248(1):43-51.
[16]Diatchenko L, Sverdlov E D, Siebert P D, et al. Suppression subtractive hybridization:a method for generating differentially regulated or tissue-specific cDNA probes and libraries[J]. Proceedings of the National Academy of Sciences of the United States of America,1996, 93(12):6025-6030.
[17]Fujioka S, Chory J, Sakurai A, et al. The Arabidopsis deetiolated2 mutant is blocked early in brassinosteroid biosynthesis [J]. The Plant cell,1997,9(11):1951-1962.
[18]Fujioka S, Yokota T. Biosynthesis and metabolism of brassinosteroids[J]. Annual Review of Plant Biology,2003,54(1):137-164.
[19]Gou J Y, Wang L J, Chen S P, et al.. Gene expression and metabolite profiles of cotton fiber during cell elongation and secondary cell wall synthesis[J]. Cell Res,2007,17(5):422-434.
[20]Gou J, Wang L, Chen S, et al. Gene expression and metabolite profiles of cotton fiber during cell elongation and secondary cell wall synthesis[J]. Cell research,2007,17(5):422-434.
[21]Grabherr M G, Zeng Q, Chen Z, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome[J]. Nature biotechnology,2011,29(7):644-652.
[22]Graves D A, Stewart J M. Chronology of the differentiation of cotton (Gossypium hirsutum L.) fiber cells[J]. Planta,1988,175(2):254-258.
[23]Huang G Q, Gong S Y, Xu W L, et al. A fasciclin-like arabinogalactan protein, GhFLAl, is involved in fiber initiation and elongation of cotton[J]. Plant Physiol,2013,161(3):1278-1290.
[24]Iseli C, Jongeneel C V, Bucher P. ESTScan:a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences[J]. Proc Int Conf Intell Syst Mol Biol, 1999:138-148.
[25]Ji S, Lu Y, Feng J, et al. Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and cDNA array [J]. Nucleic acids research,2003, 31(10):2534-2543.
[26]Jin X, Li Q, Xiao G, et al.. Using Genome-Referenced Expressed Sequence Tag Assembly to Analyze the Origin and Expression Patterns of Gossypium hirsutum Transcripts[J]. Journal of integrative plant biology,2013,55(7):576-585.
[27]John M E. Tissue-Specific and Developmental Regulation of Cotton Gene FbL2A:Demonstration of Promoter Activity in Transgenic Plants[J]. Plant Physiology,1996,112(3):1331-1341.
[28]John, Keller. Characterization of mRNA for apraline-rich protein of cotton fiber[J]. Plant Physiol, 1995,108:669-676.
[29]John, L C. Gene Expression in Cotton (Gossypium hirsutum L.) Fiber:Cloning of the mRNAs[J], Proceedings of the National Academy of Sciences of the United States of America,1992, 89(13):5769-5773.
[30]Joshi P C, Wadhwani A M, Johri B M. Morphological and embryological studies of Gossypium L[C],1967.
[31]Kasukabe Y, Fujisawa K, Nishiguchi S, et al.. Production of cotton fiber with improved fiber characteristics[Z]. Google Patents,2003.
[32]Kim D, Pertea G, Trapnell C, et al. TopHat2:accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions[J]. Genome Biology (Online Edition),2013,14:R36.
[33]Kim H J, Triplett B A. Cotton fiber growth in planta and in vitro. Models for plant cell elongation and cell wall biogenesis[J]. Plant Physiology,2001,127(4):1361-1366.
[34]Kwak P B, Wang Q Q, Chen X S, et al. Enrichment of a set of microRNAs during the cotton fiber development[J]. BMC genomics,2009,10(1):457.
[35]Lacape J, Claverie M, Vidal R O, et al. Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton[J]. PloS one,2012,7(11):e48855.
[36]Langmead B, Trapnell C, Pop M, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome[J]. Genome Biol,2009,10(3):R25.
[37]Laosinchai W, Cui X, Brown R M. A full cDNA of cotton cellulose synthase has high homology with the Arabidopsis RSW1 gene and cotton CelA1 (Accession No. AF 200453)(PGR 00-002)[J]. Plant Physiol,2000,122:291.
[38]Lee J J, Chen Z J, Hassan O S S, et al. Developmental and gene expression analyses of a cotton naked seed mutant[J]. Planta,2006,223(3):418-432.
[39]Lee J J, Woodward A W, Chen Z J. Gene expression changes and early events in cotton fibre development[J]. Annals of botany,2007a,100(7):1391-1401.
[40]Lee J J, Woodward A W, Chen Z J. Gene Expression Changes and Early Events in Cotton Fibre Development[J]. Annals of Botany,2007b,100(7):1391-1401.
[41]Lee Y, Choi D, Kende H. Expansins:ever-expanding numbers and functions [J]. Current opinion in plant biology,2001,4(6):527-532.
[42]Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools[J]. Bioinformatics,2009,25(16):2078-2079.
[43]Li L, Wang X, Huang G, et al. Molecular characterization of cotton GhTUA9 gene specifically expressed in fibre and involved in cell elongation[J]. Journal of experimental botany,2007a, 58(12):3227-3238.
[44]Li L, Wang X, Huang G, et al. Molecular characterization of cotton GhTUA9 gene specifically expressed in fibre and involved in cell elongation[J]. Journal of experimental botany,2007b, 58(12):3227-3238.
[45]Li X B, Fan X P, Wang X L, et al. The cotton ACTIN1 gene is functionally expressed in fibers and participates in fiber elongation[J]. Plant Cell,2005,17(3):859-875.
[46]Li X, Fan X, Wang X, et al. The cotton ACTIN1 gene is functionally expressed in fibers and participates in fiber elongation[J]. The Plant cell,2005,17(3):859-875.
[47]Liu K, Han M, Zhang C, et al.. Comparative proteomic analysis reveals the mechanisms governing cotton fiber differentiation and initiation [J]. Journal of proteomics,2012,75(3):845-856.
[48]Loguercio L L, Zhang J, Wilkins T A. Differential regulation of six novel MYB-domain genes defines two distinct expression patterns in allotetraploid cotton (Gossypium hirsutum L.)[J]. Molecular and General Genetics MGG,1999,261(4-5):660-671.
[49]Ludwig S R, Oppenheimer D G, Silflow C D, et al. Characterization of the alpha-tubulin gene family of Arabidopsis thaliana[J]. Proceedings of the National Academy of Sciences,1987, 84(16):5833-5837.
[50]Luo M, Pei Y, Xiao Y, et al. GhDET2, a steroid 5a-reductase, plays an important role in cotton fiber cell initiation and elongation[J]. The Plant Journal,2007,51(3):419-430.
[51]Ni Z, Hu Z, Jiang Q, et al. GmNFYA3, a target gene of miR169, is a positive regulator of plant tolerance to drought stress[J]. Plant molecular biology,2013,82(1-2):113-129.
[52]Nomura T, Takeuchi K, Yoneyama K, et al. Brassinosteroid Deficiency Due to Truncated Steroid 5α-Reductase Causes Dwarfism in the lk Mutant of Pea[J]. Plant Physiology,2004, 135(4):2220-2229.
[53]Padmalatha K V, Rawat B, Leelavathi S, et al. Genome-wide transcriptomic analysis of cotton under drought stress reveal significant down-regulation of genes and pathways involved in fibre elongation and up-regulation of defense responsive genes[J]. Plant Molecular Biology,2012, 78(3):223-246.
[54]Paterson A H, Wendel J F, Gundlach H, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres[J]. Nature,2012,492(7429):423-427.
[55]Pear J R, Kawagoe Y, Schreckengost W E, et al. Higher plants contain homologs of the bacterial celA genes encoding the catalytic subunit of cellulose synthase[J]. Proceedings of the National Academy of Sciences,1996,93(22):12637-12642.
[56]Press M C, Graves J D, Stewart G R. Transpiration and Carbon Acquisition in Root Hemiparasitic Angiosperms[J]. Journal of Experimental Botany,1988,39(8):1009-1014.
[57]Qin Y M, Zhu Y X. How cotton fibers elongate:a tale of linear cell-growth mode[J]. Curr Opin Plant Biol,2011,14(1):106-111.
[58]Qin Y和Z Y. How cotton fibers elongate:a tale of linear cell-growth mode[J]. Current opinion in plant biology,2011,14(1):106-111.
[59]Ruan Y L, Llewellyn D J, Furbank R T. The control of single-celled cotton fiber elongation by developmentally reversible gating of plasmodesmata and coordinated expression of sucrose and K+transporters and expansin[J]. Plant Cell,2001,13(1):47-60.
[60]Ruan Y, Llewellyn D J, Furbank R T. Suppression of sucrose synthase gene expression represses cotton fiber cell initiation, elongation, and seed development J]. The Plant Cell Online,2003, 15(4):952-964.
[61]Russell D W和W. Steroid 5 alpha-reductase:two genes/two enzymes[J]. Annual review of biochemistry,1994,63(1):25-61.
[62]Saha S, Kinzler K W, Vogelstein B, et al. A phosphatase associated with metastasis of colorectal cancer[J]. Science (New York, N.Y.),2001,294(5545):1343-1346.
[63]Samuel Yang S, Town C D, Jeffrey Chen Z, et al. Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton[J]. The Plant Journal,2006,47(5):761-775.
[64]Shi Y, Zhu S, Mao X, et al. Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation[J]. The Plant Cell Online, 2006a,18(3):651-664.
[65]Shi Y, Zhu S, Mao X, et al. Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation[J]. The Plant Cell Online, 2006b,18(3):651-664.
[66]Shi Y, Zhu Y, Zhu S, et al. Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation[J]. The Plant cell,2006, 18(3):651-664.
[67]Smart L B, Vojdani F, Maeshima M, et al. Genes involved in osmoregulation during turgor-driven cell expansion of developing cotton fibers are differentially regulated[J]. Plant Physiology,1998, 116(4):1539-1549.
[68]Stewart J M. Fiber Initiation on the Cotton Ovule (Gossypium Hirsutum)[J]. American Journal of Botany,1975,62(7):723-730.
[69]Sun Y, Veerabomma S, Abdel-Mageed H A, et al. Brassinosteroid regulates fiber development on cultured cotton ovules[J]. Plant and cell physiology,2005,46(8):1384-1391.
[70]Suzuki Y, Saso K, Fujioka S, et al. A dwarf mutant strain of Pharbitis nil, Uzukobito (kobito), has defective brassinosteroid biosynthesis[J]. The Plant Journal,2003,36(3):401-410.
[71]Tan J, Tu L, Deng F, et al. Exogenous Jasmonic Acid Inhibits Cotton Fiber Elongation[J]. Journal of Plant Growth Regulation,2012,31(4):599-605.
[72]Udall J A, Swanson J M, Haller K, et al. A global assembly of cotton ESTs[J], Genome research, 2006,16(3):441-450.
[73]Van Deynze A, Stoffel K, Lee M, et al. Sampling nucleotide diversity in cotton[J]. BMC plant biology,2009,9(1):125.
[74]Wang J, Wang L, Wang S, et al. Control of Plant Trichome Development by a Cotton Fiber MYB Gene[J]. The Plant Cell,2004,16(9):2323-2334.
[75]Wang K, Wang Z, Li F, et al. The draft genome of a diploid cotton Gossypium raimondii[J]. Nature genetics,2012,44(10):1098-1103.
[76]Wang Q Q, Liu F, Chen X S, et al. Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant[J]. Genomics,2010,96(6):369-376.
[77]Wang S, Wang J, Yu N, et al.. Control of plant trichome development by a cotton fiber MYB gene[J]. The Plant Cell Online,2004,16(9):2323-2334.
[78]Whittaker D J 和 T. Gene-specific changes in alpha-tubulin transcript accumulation in developing cotton fibers[J]. Plant physiology,1999,121(1):181-188.
[79]Wilkins T A, Arpat A, Sickler B. Cotton fiber genomics:Developmental mechanisms[J]. Pflanzenschutz-Nachrichten Bayer,2005,58(1):119-139.
[80]Wu Y, Llewellyn D J, White R, et al. Laser capture microdissection and cDNA microarrays used to generate gene expression profiles of the rapidly expanding fibre initial cells on the surface of cotton ovules[J]. Planta,2007,226(6):1475-1490.
[81]Wu Y, Machado A C, White R G, et at. Expression profiling identifies genes expressed early during lint fibre initiation in cotton[J]. Plant & cell physiology,2006,47(1):107-127.
[82]Xie F, Sun G, Stiller J W, et al. Genome-wide functional analysis of the cotton transcriptome by creating an integrated EST database[J]. PloS one,2011a,6(11):e26980.
[83]Xie F, Sun G, Stiller J W, et al.. Genome-wide functional analysis of the cotton transcriptome by creating an integrated EST database[J]. PLoS One,2011b,6(11):e26980.
[84]Xu S M, Brill E, Llewellyn D J, et al.. Overexpression of a potato sucrose synthase gene in cotton accelerates leaf expansion, reduces seed abortion, and enhances fiber production[J]. Mol Plant, 2012,5(2):430-441.
[85]陈敏,江明锋,蔡应繁,等.陆地棉突变体腺体形成时期的基因表达谱[J].江苏农业学报,2010,26(3)：476-481.
[86]陈蔷,崔百明,黎娟华,等.棉花纤维品质分子改良研究进展[J].中国生物工程杂志,2009,29(5)：111-115.
[87]杜雄明,刘国强,陈光.论我国棉花育种的基础种质[J].植物遗传资源学报,2004,5(1)：69-74.
[88]房栋,吕俊宏,郭旺珍,等.一个新的棉花MYB类基因(GhTF1)的克隆及染色体定位分析[J].作物学报,2008,34(2)：207-211.
[89]缑金营.棉花纤维发育研究：表达谱和代谢谱分析[D]：中国科学院研究生院(上海生命科学研究院),2006.
[90]郭惠明.陆地棉纤维发育相关基因Ghkob的克隆及功能分析[D]：中国农业科学院,2005.
[91]郭佳茹,胡雪虹,杨郁文,等.海岛棉MYB转录因子GbMYB5基因启动子的克隆及其在拟南芥中的表达特性分析[J].江苏农业学报,2012,(05)：957-962.
[92]郭旺珍,孙敬,张天真.棉花纤维品质基因的克隆与分子育种[J].科学通报,2003,48(5)：410-417.
[93]胡根海,喻树迅.棉花基因克隆研究进展[J].棉花学报,2005,17(4)：240-244.
[94]胡根海,喻树迅.利用改良的CTAB法提取棉花叶片总RNA[J].棉花学报,2007,19(1)：69-70.
[95]胡雪虹,陈天子,杨郁文,等.棉花MYB转录因子基因GbMYB5的克隆及表达分析[J].江苏农业学报,2012,(01)：12-17.
[96]蒋建雄,张天真.一个陆地棉半胱氨酸蛋白酶全长cDNA的克隆及其序列特征分析[J].作物学报,2004,30(5)：512-515.
[97]赖晓娟,陈海敏,杨锐,等.藻类基因组研究进展[J].遗传,2013,35(6)：735-744.
[98]李龙云,于霁雯,翟红红,等.利用基因芯片技术筛选棉纤维伸长相关基因[J].作物学报,2011,37(1)：95-104.
[99]李荣华,郭培国,Guihua,等.用基因芯片技术分析铝胁迫下小麦的基因表达谱[J].生物 技术通讯,2007,18(4)：581-586.
[100]李武,倪薇,林忠旭,等.海岛棉遗传多样性的SRAP标记分析[J].作物学报,2008,(05)：893-898.
[101]李锡花,吴嫚,于霁雯,等.棉花纤维发育早期RNA-Seq转录组分析[J].棉花学报,2013,(03)：189-196.
[102]刘迪秋.陆地棉纤维特异表达基因的克隆与表达研究[D]：华中农业大学,2007.
[103]刘进元,赵广荣.棉花纤维品质改良的分子工程[J].植物学报：英文版,2000,42(10)：991-995.
[104]罗明.GhDET2和GhKTNl在棉花纤维细胞发育中的功能[D]：西南大学,2007.
[105]骆蒙.基于抑制差减杂交方法的小麦抗白粉病相关基因表达谱研究[D]：中国农业科学院,2001.
[106]骆蒙,贾继增.植物基因组表达序列标签(EST)计划研究进展[J].生物化学与生物物理进展,2001,(04)：494-497.
[107]孟红岩,杜雄明,张春义,等.棉花转录因子基因GhMS3的克隆及其启动子功能的鉴定[J].中国农业科学,2010,43(17)：3489-3498.
[108]潘玉欣,马骏,张桂寅,等.棉纤维次生壁加厚期cDNA-AFLP表达谱剖析和转录组图谱构建[J].科学通报,2007,(12)：1425-1429.
[109]祁云霞,刘永斌,荣威恒.转录组研究新技术:RNA-Seq及其应用[J].遗传,2011,(11)：1191-1202.
[110]沈法富.短季棉衰老的激素变化及衰老相关基因的克隆[D]：中国农业科学院,2004.
[111]孙继勇.基因表达谱的数据分析[J].国际病理科学与临床杂志,2005,(05)：14-17.
[112]孙亮先,袁建军.EST技术在植物基因克隆和基因表达谱研究中的应用[J].泉州师范学院学报,2003,21(4)：63-67.
[113]索金凤,普莉,梁小娥,等.棉花胚珠内种皮特异基因GhIAA16的分离鉴定[J].植物学报：英文版,2004,46(4)：472-479.
[114]滕晓坤,肖华胜.基因芯片与高通量DNA测序技术前景分析[J].中国科学：C辑,2008,38(10)：891-899.
[115]涂礼莉.海岛棉纤维发育相关基因表达谱分析及功能基因的发掘[D]：华中农业大学,2007.
[116]王诚.棉花不成熟纤维突变基因(im)的定位及突变体纤维次生壁加厚期表达谱分析[D]：南京农业大学,2012.
[117]王春晖,赵云雷,王红梅,等.适用于转录组测序的棉花幼根总RNA提取方法筛选[J].棉花学报,2013,25(4)：372-376.
[118]王建民,张春兰,秦孜娟,等.转录组与RNA-Seq技术[J].生物技术通报,2012,(12)：51-56.
[119]王力娜,范术丽,宋美珍,等.植物MADS-bo基因的研究进展[J].生物技术通报,2010,(08)：12-19.
[120]王雅琴,石淼,张新宇,等.棉花GhMYB113基因的克隆与表达分析[J].西北植物学报,2013,33(5)：878-884.
[121]韦朝领,高香凤,江昌俊,等.基因表达谱差异显示技术及其在植物对害虫取食诱导反应 研究中的应用(综述)[J].安徽农业大学学报,2006,33(1)：94-99.
[122]吴东,喻树迅,范术丽,等.棉花MADS-box蛋白基因(GhMADS-13)的克隆和表达分析[J].基因组学与应用生物学,2009,28(2)：223-228.
[123]吴琼,孙超,陈士林,等.转录组学在药用植物研究中的应用[J].世界科学技术：中医药现代化,2010,(3)：457-462.
[124]肖月华,罗明,韦宇拓,等.棉花纤维起始期基因表达的cDNA-AFLP分析[J].农业生物技术学报,2003,(01)：20-24.
[125]辛婧.海岛棉纤维发育相关转录因子GbSBP8的克隆及表达研究[D]：上海交通大学,2007.
[126]邢朝柱,喻树迅.棉花杂种优势表达机理研究进展[J].棉花学报,2004,16(6)：379-382.
[127]徐楚年,张仪,余炳生,等.棉花四个栽培种纤维发育早期扫描电镜的比较研究[J].北京农业大学学报,1987,(03)：255-262.
[128]杨郁文,何冰,张保龙,等.一个棉花类受体蛋白激酶基因的克隆与表达分析[J].棉花学报,2011,23(1)：15-21.
[129]杨召恩,杨作仁,刘坤,等.一个亚洲棉MYB家族新基因的克隆及特征分析[J].中国农业科学,2013,(01)：195-204.
[130]喻树迅,范术丽.我国棉花遗传育种进展与展望[J].棉花学报,2003,15(2)：120-124.
[131]张德静.GhPRP5基因在棉纤维发育中的功能研究[D]：华中师范大学,2012.
[132]张辉,汤文开,谭新,等.棉纤维发育及其相关基因表达调控研究进展[J].植物学通报,2007,24(2)：127-133.
[133]张延明,曲敏,徐香玲,等.表达序列标签(EST)分析及其在小麦研究中的应用[J].黑龙江农业科学,2007,(01)：82-85.
[134]张智俊,罗淑萍,谭晓风.基因表达快速分析新技术-MPSS简介[J].生物技术,2003,(02)：40-41.
[135]赵浩勤,张国政,李佳梅,等.SAGE技术及其应用[J].江西农业学报,2008,20(6)：36-39.
[136]赵林华,肖诚,何颖辉,等.类风湿性关节炎基因表达谱研究进展[J].中国中医药信息杂志,2004,11(7)：652-654.
[137]朱华玉.利用棉纤维发育相关基因研究不同棉种的起源与进化[D]：南京农业大学,2010.
[2]Al-Ghazi Y, Bourot S, Arioli T, et al. Transcript profiling during fiber development identifies pathways in secondary metabolism and cell wall structure that may contribute to cotton fiber quality[J]. Plant Cell Physiol,2009,50(7):1364-1381.
[3]Ansorge W J. Next-generation DNA sequencing techniques[J]. New biotechnology,2009, 25(4):195-203.
[4]Arioli T, Birch R, Cork A, et al. Molecular Analysis of Cellulose Biosynthesis in Arabidopsis[J]. Science,1998,279(5351):717-720.
[5]Arpat A B, Wilkins T A, Waugh M, et al. Functional genomics of cell elongation in developing cotton fibers[J]. Plant molecular biology,2004,54(6):911-929.
[6]Arpat A, Waugh M, Sullivan J P, et al. Functional genomics of cell elongation in developing cotton fibers[J]. Plant molecular biology,2004,54(6):911-929.
[7]Bannigan A, Baskin T I. Directional cell expansion--turning toward actin[J]. Curr Opin Plant Biol, 2005,8(6):619-624.
[8]Basra A S, Malik C P. Development of the cotton fiber[J]. Int Rev Cytol,1984,89(1):65-113.
[9]Byers R L, Harker D B, Yourstone S M, et al. Development and mapping of SNP assays in allotetraploid cotton[J]. Theor Appl Genet,2012,124(7):1201-1214.
[10]Chee P W, Draye X, Jiang C, et al. Molecular dissection of phenotypic variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach:Ⅲ. Fiber length[J]. Theoretical and applied genetics,2005,111(4):772-781.
[11]Chen X, Guo W, Liu B, et al. Molecular mechanisms of fiber differential development between G. barbadense and G. hirsutum revealed by genetical genomics[J]. PloS one,2012,7(1):e30056.
[12]Chory, Li. Gibberellins, brassinosteroids and light-regulated development[J]. Plant, Cell and Environment,1997,20(6):801-806.
[13]Cosgrove D J. Wall structure and wall loosening. A look backwards and forwards[J]. Plant Physiology,2001,125(1):131-134.
[14]Cosgrove D J. Loosening of plant cell walls by expansins[J]. Nature,2000,407(6802):321-326.
[15]Delmer D P, Pear J R, Andrawis A, et al. Genes encoding small GTP-binding proteins analogous to mammalian rac are preferentially expressed in developing cotton fibers[J]. MGG Molecular & General Genetics,1995,248(1):43-51.
[16]Diatchenko L, Sverdlov E D, Siebert P D, et al. Suppression subtractive hybridization:a method for generating differentially regulated or tissue-specific cDNA probes and libraries[J]. Proceedings of the National Academy of Sciences of the United States of America,1996, 93(12):6025-6030.
[17]Fujioka S, Chory J, Sakurai A, et al. The Arabidopsis deetiolated2 mutant is blocked early in brassinosteroid biosynthesis [J]. The Plant cell,1997,9(11):1951-1962.
[18]Fujioka S, Yokota T. Biosynthesis and metabolism of brassinosteroids[J]. Annual Review of Plant Biology,2003,54(1):137-164.
[19]Gou J Y, Wang L J, Chen S P, et al.. Gene expression and metabolite profiles of cotton fiber during cell elongation and secondary cell wall synthesis[J]. Cell Res,2007,17(5):422-434.
[20]Gou J, Wang L, Chen S, et al. Gene expression and metabolite profiles of cotton fiber during cell elongation and secondary cell wall synthesis[J]. Cell research,2007,17(5):422-434.
[21]Grabherr M G, Zeng Q, Chen Z, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome[J]. Nature biotechnology,2011,29(7):644-652.
[22]Graves D A, Stewart J M. Chronology of the differentiation of cotton (Gossypium hirsutum L.) fiber cells[J]. Planta,1988,175(2):254-258.
[23]Huang G Q, Gong S Y, Xu W L, et al. A fasciclin-like arabinogalactan protein, GhFLAl, is involved in fiber initiation and elongation of cotton[J]. Plant Physiol,2013,161(3):1278-1290.
[24]Iseli C, Jongeneel C V, Bucher P. ESTScan:a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences[J]. Proc Int Conf Intell Syst Mol Biol, 1999:138-148.
[25]Ji S, Lu Y, Feng J, et al. Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and cDNA array [J]. Nucleic acids research,2003, 31(10):2534-2543.
[26]Jin X, Li Q, Xiao G, et al.. Using Genome-Referenced Expressed Sequence Tag Assembly to Analyze the Origin and Expression Patterns of Gossypium hirsutum Transcripts[J]. Journal of integrative plant biology,2013,55(7):576-585.
[27]John M E. Tissue-Specific and Developmental Regulation of Cotton Gene FbL2A:Demonstration of Promoter Activity in Transgenic Plants[J]. Plant Physiology,1996,112(3):1331-1341.
[28]John, Keller. Characterization of mRNA for apraline-rich protein of cotton fiber[J]. Plant Physiol, 1995,108:669-676.
[29]John, L C. Gene Expression in Cotton (Gossypium hirsutum L.) Fiber:Cloning of the mRNAs[J], Proceedings of the National Academy of Sciences of the United States of America,1992, 89(13):5769-5773.
[30]Joshi P C, Wadhwani A M, Johri B M. Morphological and embryological studies of Gossypium L[C],1967.
[31]Kasukabe Y, Fujisawa K, Nishiguchi S, et al.. Production of cotton fiber with improved fiber characteristics[Z]. Google Patents,2003.
[32]Kim D, Pertea G, Trapnell C, et al. TopHat2:accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions[J]. Genome Biology (Online Edition),2013,14:R36.
[33]Kim H J, Triplett B A. Cotton fiber growth in planta and in vitro. Models for plant cell elongation and cell wall biogenesis[J]. Plant Physiology,2001,127(4):1361-1366.
[34]Kwak P B, Wang Q Q, Chen X S, et al. Enrichment of a set of microRNAs during the cotton fiber development[J]. BMC genomics,2009,10(1):457.
[35]Lacape J, Claverie M, Vidal R O, et al. Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton[J]. PloS one,2012,7(11):e48855.
[36]Langmead B, Trapnell C, Pop M, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome[J]. Genome Biol,2009,10(3):R25.
[37]Laosinchai W, Cui X, Brown R M. A full cDNA of cotton cellulose synthase has high homology with the Arabidopsis RSW1 gene and cotton CelA1 (Accession No. AF 200453)(PGR 00-002)[J]. Plant Physiol,2000,122:291.
[38]Lee J J, Chen Z J, Hassan O S S, et al. Developmental and gene expression analyses of a cotton naked seed mutant[J]. Planta,2006,223(3):418-432.
[39]Lee J J, Woodward A W, Chen Z J. Gene expression changes and early events in cotton fibre development[J]. Annals of botany,2007a,100(7):1391-1401.
[40]Lee J J, Woodward A W, Chen Z J. Gene Expression Changes and Early Events in Cotton Fibre Development[J]. Annals of Botany,2007b,100(7):1391-1401.
[41]Lee Y, Choi D, Kende H. Expansins:ever-expanding numbers and functions [J]. Current opinion in plant biology,2001,4(6):527-532.
[42]Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools[J]. Bioinformatics,2009,25(16):2078-2079.
[43]Li L, Wang X, Huang G, et al. Molecular characterization of cotton GhTUA9 gene specifically expressed in fibre and involved in cell elongation[J]. Journal of experimental botany,2007a, 58(12):3227-3238.
[44]Li L, Wang X, Huang G, et al. Molecular characterization of cotton GhTUA9 gene specifically expressed in fibre and involved in cell elongation[J]. Journal of experimental botany,2007b, 58(12):3227-3238.
[45]Li X B, Fan X P, Wang X L, et al. The cotton ACTIN1 gene is functionally expressed in fibers and participates in fiber elongation[J]. Plant Cell,2005,17(3):859-875.
[46]Li X, Fan X, Wang X, et al. The cotton ACTIN1 gene is functionally expressed in fibers and participates in fiber elongation[J]. The Plant cell,2005,17(3):859-875.
[47]Liu K, Han M, Zhang C, et al.. Comparative proteomic analysis reveals the mechanisms governing cotton fiber differentiation and initiation [J]. Journal of proteomics,2012,75(3):845-856.
[48]Loguercio L L, Zhang J, Wilkins T A. Differential regulation of six novel MYB-domain genes defines two distinct expression patterns in allotetraploid cotton (Gossypium hirsutum L.)[J]. Molecular and General Genetics MGG,1999,261(4-5):660-671.
[49]Ludwig S R, Oppenheimer D G, Silflow C D, et al. Characterization of the alpha-tubulin gene family of Arabidopsis thaliana[J]. Proceedings of the National Academy of Sciences,1987, 84(16):5833-5837.
[50]Luo M, Pei Y, Xiao Y, et al. GhDET2, a steroid 5a-reductase, plays an important role in cotton fiber cell initiation and elongation[J]. The Plant Journal,2007,51(3):419-430.
[51]Ni Z, Hu Z, Jiang Q, et al. GmNFYA3, a target gene of miR169, is a positive regulator of plant tolerance to drought stress[J]. Plant molecular biology,2013,82(1-2):113-129.
[52]Nomura T, Takeuchi K, Yoneyama K, et al. Brassinosteroid Deficiency Due to Truncated Steroid 5α-Reductase Causes Dwarfism in the lk Mutant of Pea[J]. Plant Physiology,2004, 135(4):2220-2229.
[53]Padmalatha K V, Rawat B, Leelavathi S, et al. Genome-wide transcriptomic analysis of cotton under drought stress reveal significant down-regulation of genes and pathways involved in fibre elongation and up-regulation of defense responsive genes[J]. Plant Molecular Biology,2012, 78(3):223-246.
[54]Paterson A H, Wendel J F, Gundlach H, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres[J]. Nature,2012,492(7429):423-427.
[55]Pear J R, Kawagoe Y, Schreckengost W E, et al. Higher plants contain homologs of the bacterial celA genes encoding the catalytic subunit of cellulose synthase[J]. Proceedings of the National Academy of Sciences,1996,93(22):12637-12642.
[56]Press M C, Graves J D, Stewart G R. Transpiration and Carbon Acquisition in Root Hemiparasitic Angiosperms[J]. Journal of Experimental Botany,1988,39(8):1009-1014.
[57]Qin Y M, Zhu Y X. How cotton fibers elongate:a tale of linear cell-growth mode[J]. Curr Opin Plant Biol,2011,14(1):106-111.
[58]Qin Y和Z Y. How cotton fibers elongate:a tale of linear cell-growth mode[J]. Current opinion in plant biology,2011,14(1):106-111.
[59]Ruan Y L, Llewellyn D J, Furbank R T. The control of single-celled cotton fiber elongation by developmentally reversible gating of plasmodesmata and coordinated expression of sucrose and K+transporters and expansin[J]. Plant Cell,2001,13(1):47-60.
[60]Ruan Y, Llewellyn D J, Furbank R T. Suppression of sucrose synthase gene expression represses cotton fiber cell initiation, elongation, and seed development J]. The Plant Cell Online,2003, 15(4):952-964.
[61]Russell D W和W. Steroid 5 alpha-reductase:two genes/two enzymes[J]. Annual review of biochemistry,1994,63(1):25-61.
[62]Saha S, Kinzler K W, Vogelstein B, et al. A phosphatase associated with metastasis of colorectal cancer[J]. Science (New York, N.Y.),2001,294(5545):1343-1346.
[63]Samuel Yang S, Town C D, Jeffrey Chen Z, et al. Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton[J]. The Plant Journal,2006,47(5):761-775.
[64]Shi Y, Zhu S, Mao X, et al. Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation[J]. The Plant Cell Online, 2006a,18(3):651-664.
[65]Shi Y, Zhu S, Mao X, et al. Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation[J]. The Plant Cell Online, 2006b,18(3):651-664.
[66]Shi Y, Zhu Y, Zhu S, et al. Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation[J]. The Plant cell,2006, 18(3):651-664.
[67]Smart L B, Vojdani F, Maeshima M, et al. Genes involved in osmoregulation during turgor-driven cell expansion of developing cotton fibers are differentially regulated[J]. Plant Physiology,1998, 116(4):1539-1549.
[68]Stewart J M. Fiber Initiation on the Cotton Ovule (Gossypium Hirsutum)[J]. American Journal of Botany,1975,62(7):723-730.
[69]Sun Y, Veerabomma S, Abdel-Mageed H A, et al. Brassinosteroid regulates fiber development on cultured cotton ovules[J]. Plant and cell physiology,2005,46(8):1384-1391.
[70]Suzuki Y, Saso K, Fujioka S, et al. A dwarf mutant strain of Pharbitis nil, Uzukobito (kobito), has defective brassinosteroid biosynthesis[J]. The Plant Journal,2003,36(3):401-410.
[71]Tan J, Tu L, Deng F, et al. Exogenous Jasmonic Acid Inhibits Cotton Fiber Elongation[J]. Journal of Plant Growth Regulation,2012,31(4):599-605.
[72]Udall J A, Swanson J M, Haller K, et al. A global assembly of cotton ESTs[J], Genome research, 2006,16(3):441-450.
[73]Van Deynze A, Stoffel K, Lee M, et al. Sampling nucleotide diversity in cotton[J]. BMC plant biology,2009,9(1):125.
[74]Wang J, Wang L, Wang S, et al. Control of Plant Trichome Development by a Cotton Fiber MYB Gene[J]. The Plant Cell,2004,16(9):2323-2334.
[75]Wang K, Wang Z, Li F, et al. The draft genome of a diploid cotton Gossypium raimondii[J]. Nature genetics,2012,44(10):1098-1103.
[76]Wang Q Q, Liu F, Chen X S, et al. Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant[J]. Genomics,2010,96(6):369-376.
[77]Wang S, Wang J, Yu N, et al.. Control of plant trichome development by a cotton fiber MYB gene[J]. The Plant Cell Online,2004,16(9):2323-2334.
[78]Whittaker D J 和 T. Gene-specific changes in alpha-tubulin transcript accumulation in developing cotton fibers[J]. Plant physiology,1999,121(1):181-188.
[79]Wilkins T A, Arpat A, Sickler B. Cotton fiber genomics:Developmental mechanisms[J]. Pflanzenschutz-Nachrichten Bayer,2005,58(1):119-139.
[80]Wu Y, Llewellyn D J, White R, et al. Laser capture microdissection and cDNA microarrays used to generate gene expression profiles of the rapidly expanding fibre initial cells on the surface of cotton ovules[J]. Planta,2007,226(6):1475-1490.
[81]Wu Y, Machado A C, White R G, et at. Expression profiling identifies genes expressed early during lint fibre initiation in cotton[J]. Plant & cell physiology,2006,47(1):107-127.
[82]Xie F, Sun G, Stiller J W, et al. Genome-wide functional analysis of the cotton transcriptome by creating an integrated EST database[J]. PloS one,2011a,6(11):e26980.
[83]Xie F, Sun G, Stiller J W, et al.. Genome-wide functional analysis of the cotton transcriptome by creating an integrated EST database[J]. PLoS One,2011b,6(11):e26980.
[84]Xu S M, Brill E, Llewellyn D J, et al.. Overexpression of a potato sucrose synthase gene in cotton accelerates leaf expansion, reduces seed abortion, and enhances fiber production[J]. Mol Plant, 2012,5(2):430-441.
[85]陈敏,江明锋,蔡应繁,等.陆地棉突变体腺体形成时期的基因表达谱[J].江苏农业学报,2010,26(3)：476-481.
[86]陈蔷,崔百明,黎娟华,等.棉花纤维品质分子改良研究进展[J].中国生物工程杂志,2009,29(5)：111-115.
[87]杜雄明,刘国强,陈光.论我国棉花育种的基础种质[J].植物遗传资源学报,2004,5(1)：69-74.
[88]房栋,吕俊宏,郭旺珍,等.一个新的棉花MYB类基因(GhTF1)的克隆及染色体定位分析[J].作物学报,2008,34(2)：207-211.
[89]缑金营.棉花纤维发育研究：表达谱和代谢谱分析[D]：中国科学院研究生院(上海生命科学研究院),2006.
[90]郭惠明.陆地棉纤维发育相关基因Ghkob的克隆及功能分析[D]：中国农业科学院,2005.
[91]郭佳茹,胡雪虹,杨郁文,等.海岛棉MYB转录因子GbMYB5基因启动子的克隆及其在拟南芥中的表达特性分析[J].江苏农业学报,2012,(05)：957-962.
[92]郭旺珍,孙敬,张天真.棉花纤维品质基因的克隆与分子育种[J].科学通报,2003,48(5)：410-417.
[93]胡根海,喻树迅.棉花基因克隆研究进展[J].棉花学报,2005,17(4)：240-244.
[94]胡根海,喻树迅.利用改良的CTAB法提取棉花叶片总RNA[J].棉花学报,2007,19(1)：69-70.
[95]胡雪虹,陈天子,杨郁文,等.棉花MYB转录因子基因GbMYB5的克隆及表达分析[J].江苏农业学报,2012,(01)：12-17.
[96]蒋建雄,张天真.一个陆地棉半胱氨酸蛋白酶全长cDNA的克隆及其序列特征分析[J].作物学报,2004,30(5)：512-515.
[97]赖晓娟,陈海敏,杨锐,等.藻类基因组研究进展[J].遗传,2013,35(6)：735-744.
[98]李龙云,于霁雯,翟红红,等.利用基因芯片技术筛选棉纤维伸长相关基因[J].作物学报,2011,37(1)：95-104.
[99]李荣华,郭培国,Guihua,等.用基因芯片技术分析铝胁迫下小麦的基因表达谱[J].生物 技术通讯,2007,18(4)：581-586.
[100]李武,倪薇,林忠旭,等.海岛棉遗传多样性的SRAP标记分析[J].作物学报,2008,(05)：893-898.
[101]李锡花,吴嫚,于霁雯,等.棉花纤维发育早期RNA-Seq转录组分析[J].棉花学报,2013,(03)：189-196.
[102]刘迪秋.陆地棉纤维特异表达基因的克隆与表达研究[D]：华中农业大学,2007.
[103]刘进元,赵广荣.棉花纤维品质改良的分子工程[J].植物学报：英文版,2000,42(10)：991-995.
[104]罗明.GhDET2和GhKTNl在棉花纤维细胞发育中的功能[D]：西南大学,2007.
[105]骆蒙.基于抑制差减杂交方法的小麦抗白粉病相关基因表达谱研究[D]：中国农业科学院,2001.
[106]骆蒙,贾继增.植物基因组表达序列标签(EST)计划研究进展[J].生物化学与生物物理进展,2001,(04)：494-497.
[107]孟红岩,杜雄明,张春义,等.棉花转录因子基因GhMS3的克隆及其启动子功能的鉴定[J].中国农业科学,2010,43(17)：3489-3498.
[108]潘玉欣,马骏,张桂寅,等.棉纤维次生壁加厚期cDNA-AFLP表达谱剖析和转录组图谱构建[J].科学通报,2007,(12)：1425-1429.
[109]祁云霞,刘永斌,荣威恒.转录组研究新技术:RNA-Seq及其应用[J].遗传,2011,(11)：1191-1202.
[110]沈法富.短季棉衰老的激素变化及衰老相关基因的克隆[D]：中国农业科学院,2004.
[111]孙继勇.基因表达谱的数据分析[J].国际病理科学与临床杂志,2005,(05)：14-17.
[112]孙亮先,袁建军.EST技术在植物基因克隆和基因表达谱研究中的应用[J].泉州师范学院学报,2003,21(4)：63-67.
[113]索金凤,普莉,梁小娥,等.棉花胚珠内种皮特异基因GhIAA16的分离鉴定[J].植物学报：英文版,2004,46(4)：472-479.
[114]滕晓坤,肖华胜.基因芯片与高通量DNA测序技术前景分析[J].中国科学：C辑,2008,38(10)：891-899.
[115]涂礼莉.海岛棉纤维发育相关基因表达谱分析及功能基因的发掘[D]：华中农业大学,2007.
[116]王诚.棉花不成熟纤维突变基因(im)的定位及突变体纤维次生壁加厚期表达谱分析[D]：南京农业大学,2012.
[117]王春晖,赵云雷,王红梅,等.适用于转录组测序的棉花幼根总RNA提取方法筛选[J].棉花学报,2013,25(4)：372-376.
[118]王建民,张春兰,秦孜娟,等.转录组与RNA-Seq技术[J].生物技术通报,2012,(12)：51-56.
[119]王力娜,范术丽,宋美珍,等.植物MADS-bo基因的研究进展[J].生物技术通报,2010,(08)：12-19.
[120]王雅琴,石淼,张新宇,等.棉花GhMYB113基因的克隆与表达分析[J].西北植物学报,2013,33(5)：878-884.
[121]韦朝领,高香凤,江昌俊,等.基因表达谱差异显示技术及其在植物对害虫取食诱导反应 研究中的应用(综述)[J].安徽农业大学学报,2006,33(1)：94-99.
[122]吴东,喻树迅,范术丽,等.棉花MADS-box蛋白基因(GhMADS-13)的克隆和表达分析[J].基因组学与应用生物学,2009,28(2)：223-228.
[123]吴琼,孙超,陈士林,等.转录组学在药用植物研究中的应用[J].世界科学技术：中医药现代化,2010,(3)：457-462.
[124]肖月华,罗明,韦宇拓,等.棉花纤维起始期基因表达的cDNA-AFLP分析[J].农业生物技术学报,2003,(01)：20-24.
[125]辛婧.海岛棉纤维发育相关转录因子GbSBP8的克隆及表达研究[D]：上海交通大学,2007.
[126]邢朝柱,喻树迅.棉花杂种优势表达机理研究进展[J].棉花学报,2004,16(6)：379-382.
[127]徐楚年,张仪,余炳生,等.棉花四个栽培种纤维发育早期扫描电镜的比较研究[J].北京农业大学学报,1987,(03)：255-262.
[128]杨郁文,何冰,张保龙,等.一个棉花类受体蛋白激酶基因的克隆与表达分析[J].棉花学报,2011,23(1)：15-21.
[129]杨召恩,杨作仁,刘坤,等.一个亚洲棉MYB家族新基因的克隆及特征分析[J].中国农业科学,2013,(01)：195-204.
[130]喻树迅,范术丽.我国棉花遗传育种进展与展望[J].棉花学报,2003,15(2)：120-124.
[131]张德静.GhPRP5基因在棉纤维发育中的功能研究[D]：华中师范大学,2012.
[132]张辉,汤文开,谭新,等.棉纤维发育及其相关基因表达调控研究进展[J].植物学通报,2007,24(2)：127-133.
[133]张延明,曲敏,徐香玲,等.表达序列标签(EST)分析及其在小麦研究中的应用[J].黑龙江农业科学,2007,(01)：82-85.
[134]张智俊,罗淑萍,谭晓风.基因表达快速分析新技术-MPSS简介[J].生物技术,2003,(02)：40-41.
[135]赵浩勤,张国政,李佳梅,等.SAGE技术及其应用[J].江西农业学报,2008,20(6)：36-39.
[136]赵林华,肖诚,何颖辉,等.类风湿性关节炎基因表达谱研究进展[J].中国中医药信息杂志,2004,11(7)：652-654.
[137]朱华玉.利用棉纤维发育相关基因研究不同棉种的起源与进化[D]：南京农业大学,2010.