Transcriptome Analysis of Ten Days Post Anthesis Elongating Fiber in the Upland Cotton (<i>Gossypium hirsutum</i>) Chromosome Substitution Line CS-B25 — Oak Academic Publishing
Research ArticleOpen AccessGoogle Scholar indexed
Transcriptome Analysis of Ten Days Post Anthesis Elongating Fiber in the Upland Cotton (<i>Gossypium hirsutum</i>) Chromosome Substitution Line CS-B25
Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, USA
,
Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, USA
,
Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
,
USDA-ARS, Crop Science Research Laboratory, Mississippi State, MS, USA
,
USDA-ARS, Crop Science Research Laboratory, Mississippi State, MS, USA
,
Center of Genomics and Bioinformatics, Academy Sciences of Uzbekistan, Tashkent, Uzbekistan
,
Center of Genomics and Bioinformatics, Academy Sciences of Uzbekistan, Tashkent, Uzbekistan
,
Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, USA
,
Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
1 Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, USA
2 Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, USA
3 Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
4 USDA-ARS, Crop Science Research Laboratory, Mississippi State, MS, USA
5 USDA-ARS, Crop Science Research Laboratory, Mississippi State, MS, USA
6 Center of Genomics and Bioinformatics, Academy Sciences of Uzbekistan, Tashkent, Uzbekistan
7 Center of Genomics and Bioinformatics, Academy Sciences of Uzbekistan, Tashkent, Uzbekistan
8 Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, USA
9 Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
A chromosome substitution line, CS-B25, was developed by the substitution of chromosome pair 25 of Gossypium hirsutum TM-1 with the homologous pair of chromosome 25 from G. barbadense , a double haploid Pima 3-79 line. CS-B25 has improved fiber traits compared to its parent TM-1. To explore the molecule mechanisms underlying improved fiber traits, deep sequencing of total RNA was used to compare gene expression in fibers of CS-B25 and TM-1 at 10 days post anthesis (10-DPA). A total of 1872 differentially expressed genes (DEGs) were detected between the two lines, with 1175 up-regulated and 697 down-regulated in CS-B25. Gene Ontology (GO) enrichment analysis of the expression data by Generally Applicable Gene-set Enrichment (GAGE) and ReviGO indicated that the most prevalent Biological Process GO terms associated with DEGs included DNA-templated transcription, response to oxidative stress, and cellulose biosynthesis. Enriched Molecular Function GO terms included structural constituents of cytoskeleton, peroxidase activity, cellulose synthase (UDP-forming) activity, and transcription regulatory region sequence-specific DNA binding factors. GAGE was also used to find enriched KEGG pathways, and the highly represented pathways were Biosynthesis of Amino Acids, Starch and Sucrose Metabolism, Phenylpropanoid Biosynthesis, Protein Processing in Endoplasmic Reticulum, and Plant Hormone Signal Transduction. Many of the identified DEGs are involved in cytoskeleton and cell wall metabolism. The results of gene expression data have provided new insight into the molecular mechanisms of fiber development during the fiber elongation stage and would offer novel candidate genes that may be utilized in cotton fiber quality improvement.
Basra, A.S. and Malik, C. (1984) Development of the Cotton Fiber. International Review of Cytology, 89, 65-113. https://doi.org/10.1016/S0074-7696(08)61300-5
DeLanghe, E.A.L. (1986) Lint Development. In: Mauney, J.R. and Stewart, J.M., Ed., Cotton Physiology, The Cotton Foundation, Memphis, 325-349.
Tyagi, P., Gore, M.A., Bowman, D.T., Campbell, B.T., Udall, J.A. and Kuraparthy, V. (2014) Genetic Diversity and Population Structure in the US Upland Cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics, 127, 283-295. https://doi.org/10.1007/s00122-013-2217-3
Stelly, D.M., Saha, S., Raska, D.A., Jenkins, J.N., McCarty, J.C. and Gutierres, O.A. (2005) Registration of 17 Upland (Gossypium hirsutum) Cotton Germplasm Lines Disomic for Different G. barbadense Chromosome or Arm Substitutions. Crop Science, 45, 2663-2665. https://doi.org/10.2135/cropsci2004.0642
Saha, S., Wu, J., Jenkins, J.N., McCarty, J.C., Stelly, D.M., Percy, R.G., Raska, D.A. and Gutierrez, O.A. (2004) Effect of Chromosome Substitutions from Gossypium barbadense L. 3-79 into G. hirsutum L. TM-1 on Agronomic and Fiber Traits. The Journal of Cotton Science, 8, 162-169.
Saha, S., Jenkins, J.N., Wu, J., McCarty, J.C., Gutierrez, O.A., Percy, R.G., Cantrell, R.G. and Stelly, D.M. (2006) Effects of Chromosome-Specific Introgression in Upland Cotton on Fiber and Agronomic Traits. Genetics, 172, 1927-1938. https://doi.org/10.1534/genetics.105.053371
Wu, J., Jenkins, J.N., McCarty, J.C., Saha, S. and Stelly, D.M. (2006) An Additive Dominance Model to Determine Chromosomal Effects in Chromosome Substitution Lines and Other Germplasms. Theoretical and Applied Genetics, 112, 391-399. https://doi.org/10.1007/s00122-005-0042-z
Jenkins, J.N., McCarty, J.C., Wu, J., Saha, S., Gutierrez, O.A., Hayes, R. and Stelly, D.M. (2007) Genetic Effects of Thirteen Gossypium barbadense L. Chromosome Substitution Lines in Top Crosses with Upland Cotton Cultivars: II. Fiber Quality Traits. Crop Science, 47, 561-570. https://doi.org/10.2135/cropsci2006.06.0396
Wu, J., Jenkins, J.N., McCarty, J.C. and Saha, S. (2010) Genetic Effects of Individual Chromosomes in Cotton Cultivars Detected by Using Chromosome Substitution Lines as Genetic Probes. Genetica, 138, 1171-1179. https://doi.org/10.1007/s10709-010-9507-3
Saha, S., Wu, J., Jenkins, J.N., McCarty, J., Hayes, R. and Stelly, D.M. (2010) Genetic Dissection of Chromosome Substitution Lines Discovered Novel Alleles in Gossypium barbadense L. with Potential for Improving Agronomic Traits Including Yield. Theoretical and Applied Genetics, 120, 1193-1205. https://doi.org/10.1007/s00122-009-1247-3
Wu, Z., Soliman, K.M., Bolton, J.J., Saha, S. and Jenkins, J.N. (2008) Identification of Differentially Expressed Genes Associated with Cotton Fiber Development in a Chromosomal Substitution Line (CS-B22sh). Functional & Integrative Genomics, 8, 165-174. https://doi.org/10.1007/s10142-007-0064-5
Wan, C.Y. and Wilkins, T.A. (1994) A Modified Hot Borate Method Significantly Enhances the Yield of High-Quality RNA from Cotton (Gossypium hirsutum L.). Analytical Biochemistry, 223, 7-12. https://doi.org/10.1006/abio.1994.1538
Zhang, T., Hu, Y., Jiang, W., Fang, L., Guan, X., Chen, J., Zhang, J., Saski, C.A., Scheffler, B.E., Stelly, D.M., et al. (2015) Sequencing of Allotetraploid Cotton (Gossypium hirsutum L. acc. TM-1) Provides a Resource for Fiber Improvement. Nature Biotechnology, 33, 531-537. https://doi.org/10.1038/nbt.3207
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R. and Salzberg, S.L. (2013) TopHat2: Accurate Alignment of Transcriptomes in the Presence of Insertions, Deletions and Gene Fusions. Genome Biology, 14, R36. https://doi.org/10.1186/gb-2013-14-4-r36
Anders, S., Pyl, P.T. and Huber, W. (2015) HTSeq—A Python Framework to Work with High-Throughput Sequencing Data. Bioinformatics, 31, 166-169. https://doi.org/10.1093/bioinformatics/btu638
Robinson, M.D., McCarthy, D.J. and Smyth, G.K. (2010) EdgeR: A Bioconductor Package for Differential Expression Analysis of Digital Gene Expression Data. Bioinformatics, 26, 139-140. https://doi.org/10.1093/bioinformatics/btp616
Luo, W., Friedman, M.S., Shedden, K., Hankenson, K.D. and Woolf, J.P. (2009) GAGE: Generally Applicable Gene Set Enrichment for Pathway Analysis. BMC Bioinformatics, 10, 161. https://doi.org/10.1186/1471-2105-10-161
Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M. and Sherlock, G. (2000) Gene Ontology: Tool for the Unification of Biology. Nature Genetics, 25, 25-29. https://doi.org/10.1038/75556
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H. and Kanehisa, M. (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research, 27, 29-34. https://doi.org/10.1093/nar/27.1.29
Yu, J., Jung, S., Cheng, C.-H., Ficklin, S.P., Lee, T., Zheng, P., Jones, D., Percy, R.G. and Main, D. (2013) CottonGen: A Genomics, Genetics and Breeding Database for Cotton Research. Nucleic Acids Research, 42, D1229-D1236. https://doi.org/10.1093/nar/gkt1064
Supek, F., Bosnjak, M., Skunca, N. and Smuc, T. (2011) REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms. PLoS ONE, 6, e21800. https://doi.org/10.1371/journal.pone.0021800
Sun, Q., Jiang, H., Zhu, X., Wang, W., He, X., Shi, Y., Yuan, Y., Du, X. and Cai, Y. (2013) Analysis of Sea-Island and Upland Cotton in Response to Verticillium dahlia Infection by RNA Sequencing. BMC Genomics, 14, 852. https://doi.org/10.1186/1471-2164-14-852
Livak, K.J. and Schmittgen, T.D. (2001) Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2 -ΔΔCT Method. Methods, 25, 402-408. https://doi.org/10.1006/meth.2001.1262
Egamberdiev, S., Saha, S., Salakhutdinov, I., Jenkins, J.N., Deng, D., Khurshut, E. and Abdurakhmonov, I. (2016) Comparative Assessment of Genetic Diversity in Cytoplasmic and Nuclear Genome of Upland Cotton. Genetica, 144, 289-306. https://doi.org/10.1007/s10709-016-9898-x
Liao, W., Zhang, J., Xu, N. and Peng, M. (2010) The Role of Phytohormones in Cotton Fiber Development. Russian Journal of Plant Physiology, 57, 462-468. https://doi.org/10.1134/S1021443710040023
Rudus, I., Sasiak, M. and kepczyński, J. (2013) Regulation of Ethylene Biosynthesis at the Level of 1-Aminocyclopropane-1-Carboxylate Oxidase (ACO) Gene. Acta Physiologiae Plantarum, 35, 295-307. https://doi.org/10.1007/s11738-012-1096-6
Kim, H.-S., Kim, S.J., Abbasi, N., Bressan, R.A., Yun, D.-J., Yoo, S.-D., Kwon, S.-Y. and Choi, S.-B. (2010) The DOF Transcription Factor Dof5.1 Influences Leaf Axial Patterning by Promoting Revoluta Transcription in Arabidopsis. The Plant Journal, 64, 524-535. https://doi.org/10.1111/j.1365-313X.2010.04346.x
Prasad, M.E., Schofield, A., Lyzenga, W., Liu, H. and Stone, S. (2010) Arabidopsis RING E3 Ligase XBAT32 Regulates Lateral Root Production through Its Role in Ethylene Biosynthesis. Plant Physiology, 153, 1587-1596. https://doi.org/10.1104/pp.110.156976
Pech, J.C., Latché, A. and Bouzayen, M. (2010) Ethylene Biosynthesis. In: Davies, P.J., Ed., Plant Hormones: Biosynthesis, Signal Transduction, Action, 3rd Edition, Springer, Dordrecht, 115-136. https://doi.org/10.1007/978-1-4020-2686-7_6
Gosti, F., Beaudoin, N., Serizet, C., Webb, A.A.R., Vartanian, N. and Giraudat, J. (1999) ABI1 Protein Phosphatase 2C Is a Negative Regulator of Abscisic Acid Signaling. Plant Cell, 11, 1897-1909. https://doi.org/10.1105/tpc.11.10.1897
Gilbert, M.K., Bland, J.M., Shockey, J.M., Cao, H., Hinchliffe, D.J., Fang, D.D. and Naoumkina, M. (2013) A Transcript Profiling Approach Reveals an Abscisic Acid-Specific Glycosyltransferase (UGT73C14) Induced in Developing Fiber of Ligon Lintless-2 Mutant of Cotton (Gossypium hirsutum L.). PLoS ONE, 8, e75268. https://doi.org/10.1371/journal.pone.0075268
Huang, G.-Q., Gong, S.-Y., Xu, W.-L., Li, W., Li, P., Zhang, C.-J., Li, D.-D., Zheng, Y., Li, F.-G. and Li, X.-B. (2013) A Fasciclin-Like Arabinogalactan Protein, GhFLA1, Is Involved in Fiber Initiation and Elongation of Cotton. Plant Physiology, 161, 1278-1290. https://doi.org/10.1104/pp.112.203760
Deng, T., Yao, H., Wang, J., Wang, J., Xue, H. and Zuo, K. (2016) GhLTPG1, a Cotton GPI-Anchored Lipid Transfer Protein, Regulates the Transport of Phosphatidylinositol Monophosphates and Cotton Fiber Elongation. Scientific Reports, 6, Article No. 26829.
Liu, Q., Talbot, M. and Llewellyn, D.J. (2013) Pectin Methylesterase and Pectin Remodeling Differ in the Fibre Walls of Two Gossypium Species with Different Fibre Properties. PLoS ONE, 8, e65131. https://doi.org/10.1371/journal.pone.0065131
Whittaker, D.J. and Triplett, B.A. (1999) Gene Specific Changes in α-Tubulin Transcript Accumulation in Developing Cotton Fibers. Plant Physiology, 121, 181-188. https://doi.org/10.1104/pp.121.1.181
Szymanski, D.B. (2005) Breaking the WAVE Complex: The Point of Arabidopsis Trichomes. Current Opinion in Plant Biology, 8, 103-112. https://doi.org/10.1016/j.pbi.2004.11.004
Afzal, A.J., Wood, A.J. and Lightfoot, D.A. (2008) Plant Receptor-Like Serine Threonine Kinases: Roles in Signaling and Plant Defense. Molecular Plant-Microbe Interactions, 21, 507-517. https://doi.org/10.1094/MPMI-21-5-0507
Xu, S.-L., Rahman, A., Baskin, T.I. and Kieber, J.J. (2008) Two Leucine-Rich Repeat Receptor Kinases Mediate Signaling, Linking Cell Wall Biosynthesis and ACC Synthase in Arabidopsis. Plant Cell, 20, 3065-3079. https://doi.org/10.1105/tpc.108.063354
Hamann, T. (2015) The Plant Cell Wall Integrity Maintenance Mechanism—A Case Study of a Cell Wall Plasma Membrane Signaling Network. Phytochemistry, 112, 100-109. https://doi.org/10.1016/j.phytochem.2014.09.019
Zhong, Z., Lee, C., Zhou, J., McCarthy, R.L. and Ye, Z.-H. (2008) A Battery of Transcription Factors Involved in the Regulation of Secondary Cell Wall Biosynthesis in Arabidopsis. Plant Cell, 20, 2763-2782. https://doi.org/10.1105/tpc.108.061325
Ko, J.-H., Kim, W.-C., Kim, J.-Y., Ahn, S.-J. and Han, K.-H. (2012) MYB46-Mediated Transcriptional Regulation of Secondary Wall Synthesis. Molecular Plant, 5, 961-963. https://doi.org/10.1093/mp/sss076
Zhong, R. and Ye, Z.H. (2012) MYB46 and MYB83 Bind to the SMRE Sites and Directly Activate a Suite of Transcription Factors and Secondary Wall Biosynthetic Genes. Plant and Cell Physiology, 53, 368-380. https://doi.org/10.1093/pcp/pcr185
Shang, H., Li, W., Zou, C. and Yuan, Y. (2013) Analyses of the NAC Transcription Factor Gene Family in Gossypium raimondii Ulbr: Chromosomal Location, Structure, Phylogeny, and Expression Patterns. Journal of Integrative Plant Biology, 55, 663-676. https://doi.org/10.1111/jipb.12085
Zhang, B. and Liu, J.Y. (2016) Cotton Cytosolic Pyruvate Kinase GhPK6 Participates in Fast Fiber Elongation in a ROS-Mediated Manner. Planta, 244, 915-926. https://doi.org/10.1007/s00425-016-2557-8
Guo, K., Du, X., Tu, L., Tang, W., Wang, P., Wang, M., Liu, Z. and Zhang, X. (2016) Fibre Elongation Requires Normal Redox Homeostasis Modulated by Cytosolic Ascorbate Peroxidase in Cotton (Gossypium hirsutum). Journal of Experimental Botany, 67, 3289-3301. https://doi.org/10.1093/jxb/erw146
Ji, S.-J., Lu, Y.-C., Feng, J.-X., Wei, G., Li, J., Shi, Y.-H., Fu, Q., Liu, D., Luo, J.-C. and Zhu, Y.-X. (2003) Isolation and Analysis of Genes Preferentially Expressed during Early Cotton Fiber Development by Subtractive PCR and cDNA Array. Nucleic Acids Research, 31, 2534-2543. https://doi.org/10.1093/nar/gkg358
Shi, Y.H., Zhu, S.W., Mao, X.Z., Feng, J.X., Qin, Y.M., Zhang, L., et al. (2006) Transcriptome Profiling, Molecular Biological, and Physiological Studies Reveal a Major Role for Ethylene in Cotton Fiber Elongation. Plant Cell, 18, 651-664. https://doi.org/10.1105/tpc.105.040303
Wang, Q.Q., Liu, F., Chen, X.S., Ma, X.J., Zeng, H.Q. and Yang, Z.M. (2010) Transcriptome Profiling of Early Developing Cotton Fiber by Deep-Sequencing Reveals Significantly Differential Expression of Genes in a Fuzzless/Lintless Mutant. Genomics, 96, 369-376. https://doi.org/10.1016/j.ygeno.2010.08.009
Liang, W., Fang, L., Xiang, D., Hu, Y., Feng, H., Chang, L. and Zhang, T. (2015) Transcriptome Analysis of Short Fiber Mutant Ligon Lintless-1 (Li1) Reveals Critical Genes and Key Pathways in Cotton Fiber Elongation and Leaf Development. PLoS ONE, 10, e0143503. https://doi.org/10.1371/journal.pone.0143503
Micheli, F. (2001) Pectin Methylesterases: Cell Wall Enzymes with Important Roles in Plant Physiology. Trends in Plant Science, 6, 414-419. https://doi.org/10.1016/S1360-1385(01)02045-3
Bourquin, V., Nishikubo, N., Abe, H., Brumer, H., Denman, S., Eklund, M., Christiernin, M., Teeri, T.T., Sundberg, B. and Mellerowicz, E.J. (2002) Xyloglucan Endotransglycosylases Have a Function during the Formation of Secondary Cell Walls of Vascular Tissues. Plant Cell, 14, 3073-3088. https://doi.org/10.1105/tpc.007773
Lee, J., Burns, T.H., Light, G., Sun, Y., Fokar, M., Kasukabe, Y., et al. (2010) Xyloglucan Endotransglycosylase/Hydrolase Genes in Cotton and Their Role in Fiber Elongation. Planta, 232, 1191-1205. https://doi.org/10.1007/s00425-010-1246-2
Islam, M.S., Fang, D.D., Thyssen, G.N., Delhom, C.D., Liu, Y. and Kim, H.J. (2016) Comparative Fiber Property and Transcriptome Analyses Reveal Key Genes Potentially Related to High Fiber Strength in Cotton (Gossypium hirsutum L.) Line MD52ne. BMC Plant Biology, 16, 36. https://doi.org/10.1186/s12870-016-0727-2
Orford, S.J. and Timmis, J.N. (2000) Expression of a Lipid Transfer Protein Gene Family during Cotton Fibre Development. Biochimica et Biophysica Acta, 1483, 275-284. https://doi.org/10.1016/S1388-1981(99)00194-8
Hsu, C.Y., Creech, R.G., Jenkins, J.N. and Ma, D.P. (1999) Analysis of Promoter Activity of Cotton Lipid Transfer Protein Gene LTP6 in Transgenic Tobacco Plants. Plant Science, 143, 63-70. https://doi.org/10.1016/S0168-9452(99)00026-6
Liu, H.C., Creech, R.G., Jenkins, J.N. and Ma, D.P. (2000) Cloning and Promoter Analysis of the Cotton Lipid Transfer Protein Gene Ltp3. Biochimica et Biophysica Acta, 1487, 106-111. https://doi.org/10.1016/S1388-1981(00)00072-X
Ma, D.P., Liu, H.C., Tan, H., Creech, R.G., Jenkins, J.N. and Chang, Y.F. (1997) Cloning and Characterization of a Lipid Transfer Protein Gene Specifically Expressed in Fiber Cells. Biochimica et Biophysica Acta, 1344, 111-114. https://doi.org/10.1016/S0005-2760(96)00166-X
Li, Y.-L., Sun, J. and Xia, G.-X. (2005) Cloning and Characterization of a Gene for an LRR Receptor-Like Protein Kinase Associated with Cotton Fiber Development. Molecular Genetics and Genomics, 273, 217-224. https://doi.org/10.1007/s00438-005-1115-z
Niu, E., Cai, C., Zheng, Y., Shang, X. and Fang, L. (2016) Genome-Wide Analysis of CrRLK1L Gene Family in Gossypium and Identification of Candidate CrRLK1L Genes Related to Fiber Development. Molecular Genetics and Genomics, 291, 1137-1154. https://doi.org/10.1007/s00438-016-1169-0
Salih, H., Gong, W., He, S., Sun, G., Sun, J. and Du, X. (2016) Genome-Wide Characterization and Expression Analysis of MYB Transcription Factors in Gossypium hirsutum. BMC Genetics, 17, 129. https://doi.org/10.1186/s12863-016-0436-8
Pu, L., Li, Q., Fan, X., Yang, W. and Xue, Y. (2008) The R2R3 MYB Transcription Factor GhMYB109 Is Required for Cotton Fiber Development. Genetics, 180, 811-820. https://doi.org/10.1534/genetics.108.093070
Walford, S.A., Wu, Y., Ilewellyn, D.J. and Dennis, E.S. (2011) GhMYB25-Like: A Key Factor in Early Cotton Fibre Development. The Plant Journal, 65, 785-797. https://doi.org/10.1111/j.1365-313X.2010.04464.x
Hsu, C.Y., Jenkins, J.N., Saha, S. and Ma, D.P. (2005) Transcriptional Regulation of the Lipid Transfer Protein Gene LTP3 in Cotton Fibers by a Novel MYB Protein. Plant Science, 168, 167-181. https://doi.org/10.1016/j.plantsci.2004.07.033
Huang, J., Chen, F., Wu, S., Li, J. and Xu, W. (2016) Cotton GhMYB7 Is Predominantly Expressed in Developing Fibers and Regulates Secondary Cell Wall Biosynthesis in Transgenic Arabidopsis. Science China Life Sciences, 59, 194-205. https://doi.org/10.1007/s11427-015-4991-4
Walford, S.A., Wu, Y., Ilewellyn, D.J. and Dennis, E.S. (2012) Epidermal Cell Differentiation in Cotton Mediated by the Homeodomain Leucine Zipper Gene, GhHD-1. The Plant Journal, 71, 464-478.
Zahur, M., Asif, M.A., Zeeshan, N., Mehmood, S., Malik, M.F. and Asif, A.R. (2013) Homeobox Leucine Zipper Proteins and Cotton Improvement. Advances in Bioscience and Biotechnology, 4, 15-20. https://doi.org/10.4236/abb.2013.410A3003
Shang, H., Wang, Z., Zou, C., Zhang, Z., Li, W., Li, J., Shi, Y., Gong, W., Chen, T., Liu, A., Gong, J., Ge, Q. and Yuan, Y. (2016) Comprehensive Analysis of NAC Transcription Factors in Diploid Gossypium: Sequence Conservation and Expression Analysis Uncover Their Roles during Fiber Development. Science China Life Sciences, 59, 142-153. https://doi.org/10.1007/s11427-016-5001-1
Al-Ghazi, Y., Bourot, S., Arioli, T., Dennis, E.S. and Llewellyn, D.J. (2009) Transcript Profiling during Fiber Development Identifies Pathways in Secondary Metabolism and Cell Wall Structure That May Contribute to Cotton Fiber Quality. Plant and Cell Physiology, 50, 1364-1381. https://doi.org/10.1093/pcp/pcp084
Fang, L., Tian, R., Chen, J., Wang, S., Li, X., Wang, P. and Zhang, T. (2014) Transcriptomic Analysis of Fiber Strength in Upland Cotton Chromosome Introgression Lines Carrying Different Gossypium barbadense Chromosomal Segments. PLoS ONE, 9, e94642. https://doi.org/10.1371/journal.pone.0094642
Fang, L., Tian, R., Li, X., Chen, J., Wang, S., Wang, P. and Zhang, T. (2014) Cotton Fiber Elongation Network Revealed by Expression Profiling of Longer Fiber Lines Introgressed with Different Gossypium barbadense Chromosome Segments. BMC Genomics, 15, 838. https://doi.org/10.1186/1471-2164-15-838
Dou, L., Zhang, X., Pang, C., Song, M., Wei, H., Fan, S. and Yu, S. (2014) Genome-Wide Analysis of the WRKY Gene Family in Cotton. Molecular Genetics and Genomics, 289, 1103-1121. https://doi.org/10.1007/s00438-014-0872-y
Yu, J.Z., Ulloa, M., Hoffman, S.M., Kohel, R.J., Pepper, A.E., Fang, D.D., Percy, R.G. and Burke, J.J. (2014) Mapping Genomic Loci for Cotton Plant Architecture, Yield Components, and Fiber Properties in an Interspecific (Gossypium hirsutum L. x G. barbadense L.) RIL Population. Molecular Genetics and Genomics, 289, 1347-1367. https://doi.org/10.1007/s00438-014-0930-5
Bartkuhn, M. and Renkawitz, R. (2008) Long Range Chromatin Interactions Involved in Gene Regulation. Biochimica et Biophysica Acta, 1783, 2161-2166. https://doi.org/10.1016/j.bbamcr.2008.07.011
Miele, A. and Dekker, J. (2008) Long-Range Chromosomal Interactions and Gene Regulation. Molecular BioSystems, 4, 1046-1057. https://doi.org/10.1039/b803580f
Dekker, J., Rippe, K., Dekker, M. and Kleckner, N. (2002) Capturing Chromosome Conformation. Science, 295, 1306-1311. https://doi.org/10.1126/science.1067799
Haigler, C.H., Betancur, L., Stiff, M.R. and Tuttle, J.R. (2012) Cotton Fiber: A Powerful Single-Cell Model for Cell Wall and Cellulose Research. Front Plant Science, 3, 104. https://doi.org/10.3389/fpls.2012.00104
Mei, H., Zhu, X., Guo, W., Cai, C. and Zhang, T. (2014) Exploitation of Chinese Upland Cotton Cultivar Germplasm Resources to Mine Favorable QTL Alleles Using Association Mapping. In: Abdurakhmonov, I.Y., Ed., World Cotton Germplasm Resources, Intech, Rijeka, 55-85.
Zhang, Z., Li, J.W., Muhammad, J., Cai, J., Jia, F., Shi, Y.Z., et al. (2015) High Resolution Consensus Mapping of Quantitative Trait Loci for Fiber Strength, Length and Micronaire on Chromosome 25 of the Upland Cotton (Gossypium hirsutum L.). PLoS ONE, 10, e0135430. https://doi.org/10.1371/journal.pone.0135430
Abdurakhmonov, I.Y., Saha, S., Jenkins, J.N., Buriev, Z.T., Shermatov, S.E., Scheffler, B.E., et al. (2009) Linkage Disequilibrium Based Association Mapping of Fiber Quality Traits in G. hirsutum L. Variety Germplasm. Genetica, 136, 401-417. https://doi.org/10.1007/s10709-008-9337-8
Sun, F.D., Zhang, J.H., Wang, S.F., Gong, W.K., Shi, Y.Z., Liu, A.Y., Li, J.W., Gong, J.W., Shang, H.H. and Yuan, Y.L. (2012) QTL Mapping for Fiber Quality Traits across Multiple Generations and Environments in Upland Cotton. Molecular Breeding, 30, 569-582. https://doi.org/10.1007/s11032-011-9645-z
Liang, Q., Hu, C., Hua, H., Li, Z. and Hua, J. (2013) Construction of a Linkage Map and QTL Mapping for Fiber Quality Traits in Upland Cotton (Gossypium hirsutum L.). Chinese Science Bulletin, 58, 3233-3243. https://doi.org/10.1007/s11434-013-5807-1
Qin, H., Chen, M., Yi, X., Bie, S., Zhang, C., Zhang, Y., et al. (2015) Identification of Associated SSR Markers for Yield Component and Fiber Quality Traits Based on Frame Map and Upland Cotton Collections. PLoS ONE, 10, e0118073. https://doi.org/10.1371/journal.pone.0118073