MiRNA Expression Profile Analysis And Their Target Genes Identification During Fiber Initiation In Transgenic IaaM Cotton Germplasm

Cotton?Gossypium hirsutum?is one of the most important fiber crops.Cotton fiber comes from the ovule epidermal cells,and its initiation period plays a critical roles in yield and quality.Exogenous auxin could induce the production of in vitro ovule fiber,indicating that auxin is effective in cotton fiber development.iaaM?tryptophan monooxy genase?,which is the key gene of IAA synthesis pathway,were transferred into ji-14 and successfully expressed in cotton under the control of seed-specific promoter FBP7 and simultaneously the endogenous IAA was significantly up-regulated to increase the number of cotton fiber.This study was designed to investigate the expression of miRNAs in the initiation and differentiation stage of cotton fiber by using transgenic cotton germplasm IF11,further to explore the mechanism of the initiation and differentiation of fiber,which may lay a fundation for the improvement of cotton yeid and quality.1.Totally 18 small RNA libraries were constructed by using two cotton meterials IF11 and IF11?none?,and sampled at three stages,1d before blooming?-1DPA?,1d after blooming??1DPA?and 3d after blooming?+3DPA?.These libraries were separated and named into 6 groups,CK1?-1?+3DPA?,CK2?-1?+3DPA?,CK3?-1?+3DPA?,IAA1?-1?+3DPA?,IAA2?-1?+3DPA?and IAA3?-1?+3DPA?.Each library was identified by high throughput deep sequencing to distinguish miRNAs related to cotton fiber development.Main results shown as follows:A total of 226 miRNAs,include 57 known miRNAs?belonging to 51 families?and 169 new miRAs,were predicted by taking the published genome sequence of the upland cotton of Nanjing Agricultural University as reference.2.The differentially expressed miRNAs between the two samples are all new,there are 3 miRNAs?GhmiR-novel₃2,GhmiR-novel₁55,GhmiR-novel₂06?up-regulated and 3 miRNA?GhmiR-novel₅2,GhmiR_novel₂94,GhmiR-novel₂09?down-regulated in the-1DPA;5miRNAs?GhmiR_novel₁32,GhmiR-novel₁80,GhmiR-novel₂04,GhmiR-novel₂29,GhmiR-novel₃08?up-regulated and 2miRNAs?GhmiR-novel₁19,GhmiR-novel₂56?down-regulated in the +1DPA of both samples;one miRNAs?GhmiR-novel₂65?down-regulated in the +3DPA of both samples.The large numbers of new miRNAs found in this study,on one hand enrich the cotton database,on the other hand supply more evidence for the future study of cotton fiber development and molecular breeding.3.Through the bioinformatics analysis,the target genes of GhmiR-novel₂94 is Gh_A10G0203,which functional annotations is related to ubiquitin-mediated proteolysis,GhmiR-novel₅2 targets Gh_A05G3434 gene and GhmiR-novel₅2 targets Gh_A05G3434,Gh_A05G3434 and Gh_D04G0157,their functional annotation are MYB33,these five target genes confirmed that involved in fiber development,so it suggesting that novel₅2,novel₂56 and novel₅2 may play a potential role in fiber development by regulating target genes respectively.