Transcript Regulation Involved In Cotton Fiber Development In Ligon-lintless-1 Mutant(Gossypium Hirsutum L.)

Cotton fiber length is main factor to determine fiber quality in the textile industry throughout the world.The nature of single cell fiber elongation,acts as an excellent model for understanding gene expression related to fiber development.Ligon-linless-1 mutant has been the most important genotype used to study cotton fiber elongation.This cotton mutant provides an excellent model to study the molecular mechanisms of cotton fiber elongation.MYB and C2H2 zinc finger family proteins are play diverse roles in cotton growth and evolution.1)Characterization of the early fiber development gene,Ligon-lintiess-1?Li1?,using microarrayCotton fiber length is a key factor in determining fiber quality in the textile industry throughout the world.Understanding the molecular basis of fiber elongation would allow for improvement of fiber length.Ligon-lintless-1?Zil?is a monogenic dominant mutation that results in short fibers.This mutant provides an excellent model system to study the molecular mechanisms of cotton fiber elongation.Microarray technology and quantitative real time PCR?qRT-PCR?were used to evaluate differentially expressed genes?DEGs?in the Ligon-lintless-1?Lil?mutant compared to the wild type.Although the results showed only a few differentially expressed genes at-1,3 and 7 days post anthesis?DPA?;at 5 DPA,there were 1915 DEGs,including 984 up-regulated genes and 931 down-regulated genes.The critical stage for early termination of Lil fiber elongation vWas 5 DPA,as there were the most differentially expressed genes in this sample.The transcription factors and other proteins identified might contribute to umderstanding the molecular basis of early fiber elongation.Gene ontology analysis identified some key GO terms tihat impact the regulation of fiber development during early elongation.These results provide some fundamental information about the TFs that might provide new insight into umderstanding the molecular mechanisms controlling cotton fiber development.2)Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutumMYB family proteins are one of the most abundant transcription factors in the cotton plant and play diverse roles in cotton growth and evolution.Previously,few studies have been conducted in upland cotton,Gossypium hirsutum.The recent release of the G.hirsutum genome sequence provides a great opportunity to identify and characterize the entire upland cotton MYB protein family.In this study,we undertook a comprehensive genome-wide characterization and expression analysis of the MYB transcription factor family during cotton fiber development.A total of 524 non-redundant cotton MYB genes,among 1986 MYB and MYB-related putative proteins,were identified and classified into four subfamilies including 1R-MYB,2R-MYB,3R-MYB,and 4R-MYB.Based on phylogenetic tree analysis,MYB transcription factors were divided into 16 subgroups.The results showed that the majority?69.1%?of GhMYBs genes belong to the 2R-MYB subfamily in upland cotton.Our comparative genomics analysis has provided novel insights into the roles of MYB transcriptlon factors in cotton fiber development.These results provide the basis for a greater understanding of MYB regulatory networks and to develop new approaches to improve cotton fiber development.3)Comprehensive analysis of cotton C21H2-zinc finger transcription factors family and their expression analysis during fiber developmentC2H2 zinc finger proteins family are commonly found in plant and are known as key actors in regulating transcription and structure of chromatin.Many C2H2-zinc finger genes member have not been well characterized based on function and structure in cotton.Only a few of plant C2H2-zdnc finger genes have been studied while majority of C2H2-zinc finger proteins functions are still unknown.In this study,we conducted a broad comprehensive analysis and identified 386,196 and 296 C2H2-zinc finger genes in Gossypium hirsutum?upland cotton?,using Gossypium arboreum and Gossypium raimondii respectively.Based on the phylogenetic tree analysis the C2H2-zinc finger proteins were divided into 7 groups,which was supported by intron/exon analysis and conserved motifs.C2H2-zinc finger genes were distributed unequally across all cotton chromosomes with 278 duplicated gene events.Synonymous nucleotide substitution rates?Ka/Ks?analysis suggested that the cotton C2H2-zinc finger genes are under strong positive selection.In addition,the investigation of the Ka/Ks ratios showed that the duplication genes of C2H2-zinc finger family have restrictive functional divergence after the duplication events.Transcriptomic analysis?RNA-seq data?revealed that C2H2-zinc finger genes showed differential expression patterns in various developmental stages.This study provides a strong evidence for future practical genome study of C2H2-zinc finger proteins family in upland cotton.The results indicate that C2H2-zinc finger family might be involved in regulating cotton fiber development during initiation and elongation stages.This finding on C2H2-zinc finger proteins family will provide fundamental information for characterizing potentially important candidate genes involved in regulating fiber development.4)Long non-coding RNAs analysis and their functions in Ligon-lintless-1 mutant cotton during fiber developmentLong non-coding RNAs?LncRNAs?are part of the gene,which are not translated into proteins and play vital roles in plants growth and development.However,the presence of LncRNAs and how they function in Ligon-lintless-1 mutant during the early cessation of cotton fiber development are still not well understood.In order to investigate the function of LncRNAs in cotton fiber development,it is necessary and important to identify LncRNAs and their function in fiber cell development.In this study,we identified 18,333 LncRNAs,with the proportion of LincRNAs and anti-sense LncRNAs of?91.5%?and?8.5%?respectively,all transcribed from Ligon-lintless-1 and wild-type.Expression difference was detected in Ligon-lintless-1 and wild-type at 0 and 8 DPA.Gene Ontology and pathway analysis based on differentially expressed LncRNAs on target genes,identified fatty acid biosynthesis which give an indication of being negatively involved in cotton fiber development.The result of RNA-seq and RT-qPCR,clearly singles out two potential genes,LNC₀01237 and LNC₀17085,to be highly down regulated in mutant cotton,and these two LncRNAs are destabilized or repressed by ghr-miR2950.The results of this study provide fundamental evidence of involvement of LncRNAs in the molecular pathways governing cotton fiber development.