title: Comparative transcriptome analysis of short fiber mutants Ligon-lintless 1 and 2 reveals common mechanisms pertinent to fiber elongation in cotton (Gossypium hirsutum L.).
abstract: Understanding the molecular processes affecting cotton (Gossypium hirsutum) fiber development is important for developing tools aimed at improving fiber quality. Short fiber cotton mutants Ligon-lintless 1 (Li1) and Ligon-lintless 2 (Li2) are naturally occurring, monogenic mutations residing on different chromosomes. Both mutations cause early cessation in fiber elongation. These two mutants serve as excellent model systems to elucidate molecular mechanisms relevant to fiber length development. Previous studies of these mutants using transcriptome analysis by our laboratory and others had been limited by the fact that very large numbers of genes showed altered expression patterns in the mutants, making a targeted analysis difficult or impossible. In this research, a comparative microarray analysis was conducted using these two short fiber mutants and their near isogenic wild type (WT) grown under both field and greenhouse environments in order to identify key genes or metabolic pathways common to fiber elongation. Analyses of three transcriptome profiles obtained from different growth conditions and mutant types showed that most differentially expressed genes (DEGs) were affected by growth conditions. Under field conditions, short fiber mutants commanded higher expression of genes related to energy production, manifested by the increasing of mitochondrial electron transport activity or responding to reactive oxygen species when compared to the WT. Eighty-eight DEGs were identified to have altered expression patterns common to both short fiber mutants regardless of growth conditions. Enrichment, pathway and expression analyses suggested that these 88 genes were likely involved in fiber elongation without being affected by growth conditions.
authors.affiliation: Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America.
authors.forename: Matthew K
authors.initials: MK
authors.lastname: Gilbert
authors.affiliation: Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America.
authors.forename: Hee Jin
authors.initials: HJ
authors.lastname: Kim
authors.affiliation: The Samuel Roberts Noble Foundation, Genomics Core Facility, Ardmore, Oklahoma, United States of America.
authors.forename: Yuhong
authors.initials: Y
authors.lastname: Tang
authors.affiliation: Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America.
authors.forename: Marina
authors.initials: M
authors.lastname: Naoumkina
authors.affiliation: Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America.
authors.forename: David D
authors.initials: DD
authors.lastname: Fang
mesh_terms: D019295:Computational Biology; D032561:Cotton Fiber; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D056726:Genetic Association Studies; D003368:Gossypium / Q000235:genetics* / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D009154:Mutation; D010641:Phenotype; D015203:Reproducibility of Results; D013312:Stress, Physiological / Q000235:genetics; D059467:Transcriptome
references.citation: Nucleic Acids Res. 2003 May 15;31(10):2534-43
references.pmid: 12736302
references.citation: Plant Cell Physiol. 2005 Feb;46(2):339-55
references.pmid: 15695462
references.citation: J Mol Biol. 1997 Jun 20;269(4):459-67
references.pmid: 9217250
references.citation: Plant J. 2004 Mar;37(6):914-39
references.pmid: 14996223
references.citation: Genomics. 2012 Jul;100(1):42-50
references.pmid: 22576057
references.citation: Plant J. 2008 Aug;55(3):504-13
references.pmid: 18410479
references.citation: Plant Physiol. 2008 Feb;146(2):554-65
references.pmid: 18065553
references.citation: Theor Appl Genet. 2005 Oct;111(6):1137-46
references.pmid: 16075204
references.citation: Bioinformatics. 2005 Sep 15;21(18):3674-6
references.pmid: 16081474
references.citation: Trends Plant Sci. 2009 Mar;14(3):125-32
references.pmid: 19230744
references.citation: Planta. 2008 Feb;227(3):539-58
references.pmid: 17929052
references.citation: Planta. 2006 Feb;223(3):418-32
references.pmid: 16254724
references.citation: Plant Cell Physiol. 2006 Jan;47(1):107-27
references.pmid: 16278222
references.citation: J Cell Biol. 1997 Aug 25;138(4):771-81
references.pmid: 9265645
references.citation: Clin Chem. 2009 Apr;55(4):611-22
references.pmid: 19246619
references.citation: Genome Biol. 2002 Jun 18;3(7):RESEARCH0034
references.pmid: 12184808
references.citation: Plant Physiol. 2013 Mar;161(3):1278-90
references.pmid: 23349362
references.citation: BMC Genomics. 2008 Oct 16;9:488
references.pmid: 18925949
references.citation: Proc Natl Acad Sci U S A. 1993 Aug 1;90(15):7411-3
references.pmid: 8346264
references.citation: Plant Cell. 1999 Jun;11(6):1129-40
references.pmid: 10368183
references.citation: BMC Genomics. 2013 Jun 17;14:403
references.pmid: 23767687
references.citation: Planta. 2000 Feb;210(3):391-9
references.pmid: 10750896
references.citation: Theor Appl Genet. 2013 Apr;126(4):963-70
references.pmid: 23397278
references.citation: PLoS One. 2009 May 29;4(5):e5744
references.pmid: 19478943
references.citation: Evol Dev. 2008 Sep-Oct;10(5):567-82
references.pmid: 18803775
references.citation: Proc Natl Acad Sci U S A. 1990 Apr;87(8):2936-40
references.pmid: 11607073
references.citation: Plant Physiol. 2009 Jan;149(1):370-83
references.pmid: 18971431
references.citation: Plant Physiol. 2001 Dec;127(4):1361-6
references.pmid: 11743074
references.citation: Acta Biochim Biophys Sin (Shanghai). 2012 Jul;44(7):555-64
references.pmid: 22595512
references.citation: Plant Physiol. 1977 Jun;59(6):1088-97
references.pmid: 16660000
references.citation: PLoS One. 2013 Sep 23;8(9):e75268
references.pmid: 24086489
references.citation: Comp Funct Genomics. 2009;:659301
references.pmid: 20148073
references.citation: Plant Cell Physiol. 2011 Feb;52(2):213-9
references.pmid: 21217125
references.citation: Plant Biotechnol J. 2009 Jan;7(1):13-23
references.pmid: 18761653
references.citation: Plant J. 2008 Jun;54(5):863-75
references.pmid: 18298672
references.citation: Protoplasma. 2011 Jul;248(3):579-90
references.pmid: 20878194
references.citation: J Hered. 2002 May-Jun;93(3):221-4
references.pmid: 12195042
references.citation: Nature. 2012 Dec 20;492(7429):423-7
references.pmid: 23257886
references.citation: PLoS One. 2013 Jun 05;8(6):e65131
references.pmid: 23755181
references.citation: Plant J. 2012 Jun;70(6):978-90
references.pmid: 22348445
references.citation: BMC Genomics. 2009 Aug 17;10:378
references.pmid: 19686594
references.citation: Gene. 2014 Feb 10;535(2):273-85
references.pmid: 24279997
references.citation: FEBS Lett. 2002 Oct 9;529(2-3):198-202
references.pmid: 12372600
references.citation: Curr Opin Plant Biol. 2011 Feb;14(1):106-11
references.pmid: 20943428
references.citation: J Biol Chem. 2011 Nov 18;286(46):39982-92
references.pmid: 21949134
references.citation: Plant Physiol. 2010 Oct;154(2):874-86
references.pmid: 20729393
references.citation: Plant Cell. 2005 Mar;17(3):859-75
references.pmid: 15722467
references.citation: Plant Cell. 2001 Jun;13(6):1333-46
references.pmid: 11402164
references.citation: BMC Genomics. 2011 Sep 09;12:445
references.pmid: 21902843
references.citation: BMC Genomics. 2013 Mar 07;14:155
references.pmid: 23497242
references.citation: Ann Bot. 2007 Dec;100(7):1391-401
references.pmid: 17905721
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W64-70
references.pmid: 20435677
references.citation: Plant Cell. 1995 Jul;7(7):1071-1083
references.pmid: 12242398