Gene expression profile analysis of Ligon lintless-1 (Li1) mutant reveals important genes and pathways in cotton leaf and fiber development

Gene

Volumn 535, Issue 2, 2014, Pages 273-285

  Ding, Mingquan ^a,b   Jiang, Yurong ^a,b   Cao, Yuefen ^a,b   Lin, Lifeng ^c   He, Shae ^a,b   Zhou, Wei ^a,b   Rong, Junkang ^a,b  

^a ZHEJIANG A F UNIVERSITY   (China)

^b The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province   (China)

^c Nanosphere Inc   (United States)

Author keywords

Fiber development; Ligon lintless 1; RNA seq; Transcriptome

Indexed keywords

TRANSCRIPTOME;

ARTICLE; CONTROLLED STUDY; COTTON; DOWN REGULATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE MAPPING; GENE SEQUENCE; GOSSYPIUM HIRSUTUM; HEAT SHOCK PROTEIN GENE; KANDI LIKE GENE; LEAF MORPHOLOGY; LIGON LINTLESS 1; NONHUMAN; NUCLEOTIDE SEQUENCE; OVULE; PHENOTYPE; PLANT GENE; PLANT GENOME; PLANT LEAF; PLANT TISSUE; PRIORITY JOURNAL; TRANSCRIPTION FACTOR AS2 GENE; WRKY TRANSCRIPTION FACTOR GENE; YABBY5 GENE;

GOSSYPIUM HIRSUTUM;

1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID OXIDASE; 6-PHOSPHOGLUCONATE DEHYDROGENASE; 6PGDH; ACO; ADENINE NUCLEOTIDE TRANSPORTER 1; ADNI1; ALDEHYDE DEHYDROGENASE; ALDH; AP2; AP2-EREBP TRANSCRIPTION FACTORS; ARABIDOPSIS BETA-FRUCTOFURANOSIDASE; ARABIDOPSIS STARCH SYNTHASE 3; AS1; AS2; ASYMMETRIC LEAVES1; ASYMMETRIC LEAVES2; ATBFRUCT1; ATSS3; CDNA; CHLOROPHYLL A/B-BINDING PROTEIN; COX; CYTOCHROME C OXIDASE; DAY POST ANTHESIS; DEG; DEOXYRIBONUCLEOSIDE TRIPHOSPHATES; DIFFERENTIALLY EXPRESSED GENES; DNA COMPLEMENTARY TO RNA; DNTPS; DPA; EST; EXPRESSED SEQUENCE TAG; FALSE DISCOVERY RATE; FDR; FIBER DEVELOPMENT; FL; FUZZLESS-LINTLESS MUTANT; G-6-PDH; GA; GAPC; GENE ONTOLOGY; GHACT1; GHAPX; GHKCH1; GHPOX; GIBBERELLIC ACID; GL1; GLABROUS1; GLUCOSE-6-PHOSPHATE DEHYDROGENASE; GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE; GO; GOSSYPIUM HIRSUTUM ACTIN1; GOSSYPIUM HIRSUTUM ASCORBATE PEROXIDASE; GOSSYPIUM HIRSUTUM KINESIN1; GOSSYPIUM HIRSUTUM PEROXIDASE; HEAT SHOCK PROTEIN; HOMEOBOX PROTEIN KNOTTED-1-LIKE 1; HOMEOBOX PROTEIN KNOTTED-1-LIKE 2; HOMEOBOX PROTEIN KNOTTED-1-LIKE 6; HSP; IAA-BIOSYNTHETIC GENE IAAM; IAAM; KNAT1; KNAT2; KNAT6; LHCA; LHCB; LI1; LI2; LIGHT HARVESTING COMPLEX PROTEIN; LIGON LINTLESS-1; LIGON LINTLESS-2; MALATE DEHYDROGENASE; MDH; NAD; NAD(P)H DEHYDROGENASE; NDF4; NDH-DEPENDENT CYCLIC ELECTRON FLOW 4; PCR; PFK; PGK; PHOSPHOFRUCTOKINASE; PHOSPHOGLYCERATE KINASE; PHOTOSYSTEM I REACTION CENTER SUBUNIT III; PHOTOSYSTEM I REACTION CENTER SUBUNIT VI; PIP2; PIP2 AQUAPORINS; POLYMERASE CHAIN REACTION; PPDK; PSAF; PSAH; PSBQ; PYRUVATE ORTHOPHOSPHATE DIKINASE; REACTIVE OXYGEN SPECIES; REAL TIME PCR; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RFLP; RIBONUCLEASE; RNA-SEQ; RNASE; ROS; RT-PCR; SERINE HYDROXYMETHYLTRANSFERASE 4; SHM4; SIMPLE SEQUENCE REPEATS; SINGLE-STRAND CONFORMATION POLYMORPHISM; SSCP; SSR; SUBUNIT OF OXYGEN EVOLVING SYSTEM OF PHOTOSYSTEM II; TCA CYCLE; TRANSCRIPTOME; TRICARBOXYLIC ACID CYCLE; UBIQUITIN 7; UBQ7; UCP5; UDP-GLUCOSE 4-EPIMERASE GENE; UGE; UNCOUPLING PROTEIN 5; WIDE TYPE; WT; XTH; XYLOGLUCAN ENDOTRANSGLYCOSYLASES/HYDROLASES;

CLUSTER ANALYSIS; COTTON FIBER; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GOSSYPIUM; HEAT-SHOCK PROTEINS; METABOLIC NETWORKS AND PATHWAYS; MOLECULAR SEQUENCE ANNOTATION; MUTATION; PHENOTYPE; PLANT LEAVES; SIGNAL TRANSDUCTION;

EID: 84891164203     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2013.11.017     Document Type: Article

References (52)

1. An C., Saha S., Jenkins J.N., Scheffler B.E., Wilkins T.A., Stelly D.M. Transcriptome profiling, sequence characterization, and SNP-based chromosomal assignment of the EXPANSIN genes in cotton. Mol. Genet. Genomics 2007, 278:539-553.
2. Arpat A.B., Waugh M., Sullivan J.P., Gonzales M., Frisch D., et al. Functional genomics of cell elongation in developing cotton fibers. Plant Mol. Biol. 2004, 54:911-929.
3. Audic S., Claverie J.M. The significance of digital gene expression profiles. Genome Res. 1997, 7:986-995.
4. Blomster T., et al. Apoplastic reactive oxygen species transiently decrease auxin signaling and cause stress-induced morphogenic response in Arabidopsis. Plant Physiol. 2011, 157:1866-1883.
5. Bolton J.J., Soliman K.M., Wilkins T.A., Jenkins J.N. Aberrant Expression of Critical Genes during Secondary Cell Wall Biogenesis in a Cotton Mutant, Ligon Lintless-1 (Li-1). Comp. Funct. Genomics. 2009, 659301.
6. Chalfun-Junior A., Franken J., Mes J.J., Marsch-Martinez N., Pereira A., Angenent G.C. ASYMMETRIC LEAVES2-LIKE1 gene, a member of the AS2/LOB family, controls proximal-distal patterning in Arabidopsis petals. Plant Mol. Biol. 2005, 57:559-575.
7. Conesa A., Gotz S., Garcia-Gomez J.M., Terol J., Talon M., Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21:3674-3676.
8. Cosgrove D.J. Wall structure and wall loosening. A look backwards and forwards. Plant Physiol. 2001, 125:131-134.
9. Du Z., Zhou X., Ling Y., Zhang Z., Su Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2010, 38:W64-W70.
10. Gou J.Y., Wang L.J., Chen S.P., Hu W.L., Chen X.Y. Gene expression and metabolite profiles of cotton fiber during cell elongation and secondary cell wall synthesis. Cell Res. 2007, 17:422-434.
11. Griffee F., Ligon L.L. Occurrence of lintless cotton plants and the inheritance of the character 'lintless'. J. Am. Soc. Agron. 1929, 21:711-717.
12. Hauser M.T., Harr B., Schlotterer C. Trichome distribution in Arabidopsis thaliana and its close relative Arabidopsis lyrata: molecular analysis of the candidate gene GLABROUS1. Mol. Biol. Evol. 2001, 18:1754-1763.
13. Hinchliffe D.J., et al. A combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton. BMC Genomics 2011, 12:445.
14. Ho M.H., Saha S., Jenkins J.N., Ma D.P. Characterization and promoter analysis of a cotton RING-type ubiquitin ligase (E3) gene. Mol. Biotechnol. 2010, 46:140-148.
15. Hovav R., Udall J.A., Hovav E., Rapp R., Flagel L., Wendel J.F. A majority of cotton genes are expressed in single-celled fiber. Planta 2008, 227:319-329.
16. Jiang J., Zhang T. Extraction of total RNA in cotton tissues with CTAB-acidic phenolic method. Cotton Science 2003, 15:166-167.
17. John M.E., Crow L.J. Gene expression in cotton (Gossypium hirsutum L.) fiber: cloning of the mRNAs. Proc. Natl. Acad. Sci. U. S. A. 1992, 89:5769-5773.
18. John M.E., Keller G. Metabolic pathway engineering in cotton: biosynthesis of polyhydroxybutyrate in fiber cells. Proc. Natl. Acad. Sci. U. S. A. 1996, 93:12768-12773.
19. Karaca M., Saha S., Jenkins J.N., Zipf A., Kohel R., Stelly D.M. Simple sequence repeat (SSR) markers linked to the Ligon lintless (Li(1)) mutant in cotton. J. Hered. 2002, 93:221-224.
20. Kohel R.J., Stelly D.M., Yu J. Tests of six cotton (Gossypium hirsutum L.) mutants for association with aneuploids. J. Hered. 2002, 93:130-132.
21. Kojima S., et al. Asymmetric leaves2 and Elongator, a histone acetyltransferase complex, mediate the establishment of polarity in leaves of Arabidopsis thaliana. Plant Cell Physiol. 2011, 52:1259-1273.
22. Kwak P.B., Wang Q.Q., Chen X.S., Qiu C.X., Yang Z.M. Enrichment of a set of microRNAs during the cotton fiber development. BMC Genomics 2009, 10:457.
23. Lee J., et al. Xyloglucan endotransglycosylase/hydrolase genes in cotton and their role in fiber elongation. Planta 2010, 232:1191-1205.
24. Li H.B., Qin Y.M., Pang Y., Song W.Q., Mei W.Q., Zhu Y.X. A cotton ascorbate peroxidase is involved in hydrogen peroxide homeostasis during fibre cell development. New Phytol. 2007, 175:462-471.
25. Li X., et al. Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP. Genome 2012, 55:459-470.
26. Li X., Yuan D., Zhang J., Lin Z., Zhang X. Genetic Mapping and Characteristics of Genes Specifically or Preferentially Expressed during Fiber Development in Cotton. PLoS One 2013, 8:e54444.
27. Li X.B., Fan X.P., Wang X.L., Cai L., Yang W.C. The cotton ACTIN1 gene is functionally expressed in fibers and participates in fiber elongation. Plant Cell 2005, 17:859-875.
28. Liu K., Sun J., Yao L., Yuan Y. Transcriptome analysis reveals critical genes and key pathways for early cotton fiber elongation in Ligon lintless-1 mutant. Genomics 2012, 100:42-50.
29. Ma J., et al. Transcriptome profiling analysis reveals that flavonoid and ascorbate-glutathione cycle are important during anther development in Upland cotton. PLoS One 2012, 7:e49244.
30. Malone J.H., Oliver B. Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biol. 2011, 9:34.
31. Mei W., Qin Y., Song W., Li J., Zhu Y. Cotton GhPOX1 encoding plant class III peroxidase may be responsible for the high level of reactive oxygen species production that is related to cotton fiber elongation. J. Genet. Genomics. 2009, 36:141-150.
32. Mortazavi S.M., Heidari P., Esfandiari H., Motamedi M. Trapezoid supracondylar femoral extension osteotomy for knee flexion contractures in patients with haemophilia. Haemophilia 2008, 14:85-90.
33. Padmalatha K.V., et al. Functional genomics of fuzzless-lintless mutant of Gossypium hirsutum L. cv. MCU5 reveal key genes and pathways involved in cotton fibre initiation and elongation. BMC Genomics 2012, 13:624.
34. Preuss M.L., Kovar D.R., Lee Y.R., Staiger C.J., Delmer D.P., Liu B. A plant-specific kinesin binds to actin microfilaments and interacts with cortical microtubules in cotton fibers. Plant Physiol. 2004, 136:3945-3955.
35. Qin Y.-M., Hu C.-Y., Zhu Y.-X. The ascorbate peroxidase regulated by H2O2 and ethylene is involved in cotton fiber cell elongation by modulating ROS homeostasis. Plant Signal. Behav. 2008, 3:194-196.
36. Qin Y.M., Zhu Y.X. How cotton fibers elongate: a tale of linear cell-growth mode. Curr. Opin. Plant Biol. 2011, 14:106-111.
37. Rong J., et al. A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 2004, 166:389-417.
38. Rong J., et al. Genetic mapping and comparative analysis of seven mutants related to seed fiber development in cotton. Theor. Appl. Genet. 2005, 111:1137-1146.
39. Ruan Y.L., Chourey P.S. A fiberless seed mutation in cotton is associated with lack of fiber cell initiation in ovule epidermis and alterations in sucrose synthase expression and carbon partitioning in developing seeds. Plant Physiol. 1998, 118:399-406.
40. Shao M.Y., et al. Regulation of cotton fiber elongation by xyloglucan endotransglycosylase/hydrolase genes. Genet. Mol. Res. 2011, 10:3771-3782.
41. Shi Y.H., et al. Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. Plant Cell 2006, 18:651-664.
42. Udall J.A., et al. Spotted cotton oligonucleotide microarrays for gene expression analysis. BMC Genomics 2007, 8:81.
43. Usadel B., et al. Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiol. 2005, 138:1195-1204.
44. Thaker V.S., V.S.R, Singh Y.D. Physiological and biochemical changes associated with cotton fibre development.VII. Carbohydrate metabolism. Acta Physiol Plant 1999, 21:57-61.
45. Wang H., Mei W., Qin Y., Zhu Y. 1-Aminocyclopropane-1-carboxylic acid synthase 2 is phosphorylated by calcium-dependent protein kinase 1 during cotton fiber elongation. Acta Biochim Biophys Sin (Shanghai) 2011, 43:654-661.
46. Wang K., et al. The draft genome of a diploid cotton Gossypium raimondii. Nat. Genet. 2012, 44:1098-1103.
47. Wang Q.Q., Liu F., Chen X.S., Ma X.J., Zeng H.Q., Yang Z.M. Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant. Genomics 2010, 96:369-376.
48. Xie F., Sun G., Stiller J.W., Zhang B. Genome-wide functional analysis of the cotton transcriptome by creating an integrated EST database. PLoS One 2011, 6:e26980.
49. Xu L., Xu Y., Dong A., Sun Y., Pi L., Huang H. Novel as1 and as2 defects in leaf adaxial-abaxial polarity reveal the requirement for ASYMMETRIC LEAVES1 and 2 and ERECTA functions in specifying leaf adaxial identity. Development 2003, 130:4097-4107.
50. Zhang B., Yang Y.W., Zhang Y., Liu J.Y. A high-confidence reference dataset of differentially expressed proteins in elongating cotton fiber cells. Proteomics 2013, 13:1159-1163.
51. Zhang M., et al. Spatiotemporal manipulation of auxin biosynthesis in cotton ovule epidermal cells enhances fiber yield and quality. Nat. Biotechnol. 2011, 29:453-458.
52. Zhao P.M., et al. Proteomic identification of differentially expressed proteins in the Ligon lintless mutant of upland cotton (Gossypium hirsutum L.). J. Proteome Res. 2010, 9:1076-1087.