title: Gene expression profile analysis of Ligon lintless-1 (Li1) mutant reveals important genes and pathways in cotton leaf and fiber development.
abstract: Ligon lintless-1 (Li1) is a monogenic dominant mutant of Gossypium hirsutum (upland cotton) with a phenotype of impaired vegetative growth and short lint fibers. Despite years of research involving genetic mapping and gene expression profile analysis of Li1 mutant ovule tissues, the gene remains uncloned and the underlying pathway of cotton fiber elongation is still unclear. In this study, we report the whole genome-level deep-sequencing analysis of leaf tissues of the Li1 mutant. Differentially expressed genes in leaf tissues of mutant versus wild-type (WT) plants are identified, and the underlying pathways and potential genes that control leaf and fiber development are inferred. The results show that transcription factors AS2, YABBY5, and KANDI-like are significantly differentially expressed in mutant tissues compared with WT ones. Interestingly, several fiber development-related genes are found in the downregulated gene list of the mutant leaf transcriptome. These genes include heat shock protein family, cytoskeleton arrangement, cell wall synthesis, energy, H2O2 metabolism-related genes, and WRKY transcription factors. This finding suggests that the genes are involved in leaf morphology determination and fiber elongation. The expression data are also compared with the previously published microarray data of Li1 ovule tissues. Comparative analysis of the ovule transcriptomes of Li1 and WT reveals that a number of pathways important for fiber elongation are enriched in the downregulated gene list at different fiber development stages (0, 6, 9, 12, 15, 18dpa). Differentially expressed genes identified in both leaf and fiber samples are aligned with cotton whole genome sequences and combined with the genetic fine mapping results to identify a list of candidate genes for Li1.
authors.affiliation: School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China.
authors.forename: Mingquan
authors.initials: M
authors.lastname: Ding
authors.affiliation: School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China.
authors.forename: Yurong
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China.
authors.forename: Yuefen
authors.initials: Y
authors.lastname: Cao
authors.affiliation: Nanosphere Inc., 4088 Commercial Drive, Northbrook, IL 60062, USA.
authors.forename: Lifeng
authors.initials: L
authors.lastname: Lin
authors.affiliation: School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China.
authors.forename: Shae
authors.initials: S
authors.lastname: He
authors.affiliation: School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhou
authors.affiliation: School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China. Electronic address: jkrong@yahoo.com.
authors.forename: Junkang
authors.initials: J
authors.lastname: Rong
mesh_terms: D016000:Cluster Analysis; D032561:Cotton Fiber; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D003368:Gossypium / Q000235:genetics* / Q000378:metabolism*; D006360:Heat-Shock Proteins / Q000235:genetics / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D009154:Mutation; D010641:Phenotype; D018515:Plant Leaves / Q000235:genetics* / Q000378:metabolism; D015398:Signal Transduction
chemical_list: D006360:Heat-Shock Proteins
keywords: 1-aminocyclopropane-1-carboxylic acid oxidase; 6-phosphogluconate dehydrogenase; 6PGDH; ACO; ADNI1; ALDH; AP2; AP2-EREBP transcription factors; AS1; AS2; ASYMMETRIC LEAVES1; ASYMMETRIC LEAVES2; ATBFRUCT1; ATSS3; Arabidopsis beta-fructofuranosidase; Arabidopsis starch synthase 3; COX; DEG; DNA complementary to RNA; DPA; EST; FDR; Fiber development; Fl; G-6-PDH; GA; GAPC; GL1; GLABROUS1; GO; GhACT1; GhAPX; GhKCH1; GhPOX; Gossypium hirsutum actin1; Gossypium hirsutum ascorbate peroxidase; Gossypium hirsutum kinesin1; Gossypium hirsutum peroxidase; HSP; IAA-biosynthetic gene iaaM; KNAT1; KNAT2; KNAT6; LHCA; LHCB; Li1; Li2; Ligon lintless-1; Ligon lintless-2; MDH; NAD; NAD(P)H dehydrogenase; NDF4; NDH-dependent cyclic electron flow 4; PCR; PFK; PGK; PIP2; PIP2 aquaporins; PPDK; PSAF; PSAH; PSBQ; RFLP; RNA-seq; RNase; ROS; RT-PCR; SHM4; SSCP; SSR; TCA cycle; Transcriptome; UBQ7; UCP5; UDP-glucose 4-epimerase gene; UGE; WT; XTH; adenine nucleotide transporter 1; aldehyde dehydrogenase; cDNA; chlorophyll a/b-binding protein; cytochrome c oxidase; dNTPs; day post anthesis; deoxyribonucleoside triphosphates; differentially expressed genes; expressed sequence tag; false discovery rate; fuzzless–lintless mutant; gene ontology; gibberellic acid; glucose-6-phosphate dehydrogenase; glyceraldehyde-3-phosphate dehydrogenase; heat shock protein; homeobox protein knotted-1-like 1; homeobox protein knotted-1-like 2; homeobox protein knotted-1-like 6; iaaM; light harvesting complex protein; malate dehydrogenase; phosphofructokinase; phosphoglycerate kinase; photosystem I reaction center subunit III; photosystem I reaction center subunit VI; polymerase chain reaction; pyruvate orthophosphate dikinase; reactive oxygen species; real time PCR; restriction fragment length polymorphism; ribonuclease; serine hydroxymethyltransferase 4; simple sequence repeats; single-strand conformation polymorphism; subunit of oxygen evolving system of photosystem II; tricarboxylic acid cycle; ubiquitin 7; uncoupling protein 5; wide type; xyloglucan endotransglycosylases/hydrolases