Genetic Mapping And Expression Analysis Of MiRNAs And Their Target Genes And Transcription Factors In Cotton

MicroRNAs (miRNAs) are small, endogenously expressed, non-coding RNA molecules that involved in gene transcription and expression; they play a role mainly through combining with specific target genes of mRNA sites to inhibit protein synthesis and cause mRNA to degrade. In2002, the first plant miRNA was reported, and since this time, more and more have been discovered. High-throughput sequencing and computational approaches are common techniques used to identify miRNAs and target genes. In this study, in order to map miRNAs and their target genes in cotton, we designed specific primers for miRNA precursors and target genes that had been published until April,2011. A total of83miRNAs primers and1,255target genes were obtained, and9miRNA polymorphic loci were mapped on7of the26cotton chromosomes. Also,156target gene polymorphic loci were mapped on each of the26cotton chromosomes. Interspecific linkage map showed even distribution of miRNAs markers and preferential distribution of target markers on the chromosomes. To map more miRNA loci, miRNA-based SRAP markers were used, and an additional54of the59polymorphic loci were mapped on each cotton chromosome except Chr01, Chr22, and Chr24. Finally, the network between miRNAs and their targets were constructed. All miRNAs and98target genes were selected for RT-PCR analysis, which revealed unique expression patterns across different fiber development stages between the parents. Our data offer an overview of miRNA, their targets, and their network in cotton; and the comparative expression analysis between G. hirsutum and G. barbadense provides a foundation for understanding miRNA regulation during cotton fiber development.Transcription factor is an important class of trans-acting factors, its play an important role in regulating growth and development process in cotton, and has an important relationship with fiber yield and fiber quality. This study explored the distribution of transcription factor markers on the chromosomes and expression at various fiber development stages in G. hirsutum and G. barbadense.1116transcription factor sequences belonged to50families were designed. Finally,976specific transcription factor primers were obtained, and31target gene polymorphic loci were mapped on the15cotton chromosomes,15transcription factor markers were mapped on Chr05, Chrll, Chrl9and Chr20, which accounted48.4%of all the markers. Interspecific linkage map showed preferential distribution of transcription factor markers on the chromosomes. Each family randomly selected two pairs of primers. Finally,85transcription factor primers were selected for RT-PCR analysis, which revealed expression differences in different fiber development stages between the parents. This indicates that transcription factors play a role in the process of growth and development of the fiber, which is of great significance for increasing fiber yield and improving fiber quality.