| Cotton is one of the important economic crops related to the national economy and people’s livelihood,and cotton fiber is indispensable to the development of the textile industry.At present,the main cotton varieties used in production are Gossypium hirsutum(G.hirsutum)and Gossypium barbadense(G.barbadense).G.barbadense has excellent fibre quality and is mainly supplied to the premium textile industry,but which is poorly adapted to the environment and has a narrow cultivation range.G.hirsutum has the characteristics of strong environmental adaptability and high yield,which is currently the most widely planted variety,but its fiber quality is poor compared G.barbadense.Chromosome segment substitution line(CSSL)expands the genetic diversity of G.hirsutum and promotes the excavation of excellent foreign genes from G.barbadense,which can accelerate the breeding process for improving the fibre quality of G.hirsutum.In this study,using G.barbadense 3-79,G.hirsutum Emian22 and chromosome segment substitution line N182 which fibre quality improved,we investigated the molecular mechanism of fibre length improvement in N182 by combining Nanopore c DNA and NGS sequencing techniques to resolve the differences between the three cotton cultivars at the level of transcriptional expression and alternative splicing in fibre development stage.The main results are as follows:(1)We constructed full-length transcript profiles of 3-79,Emian22 and N182 during fibre development.Using Nanopore c DNA and NGS sequencing techniques,241,631,268,622 and 250,950 full-length transcripts were identified in 3-79,Emian22 and N182,which covered 43,243,45,806 and 43,869 annotated coding genes.In different cotton varieties,the amount of expression gene gradually decreases as the fibre develops.The analyses of alternative splicing events during fibre development showed that 125,199,140,802 and 130,432 alternative splicing events were identified in 3-79,Emian22 and N182,which the highest frequently event was intron retention.(2)Different patterns of alternative splicing and expression occurred in homoeologous genes between subgenomes of allotetraploid cotton.The bias of alternative splicing and expression of homoeologous genes was opposite,with more homoeologous genes showed the expression bias towards Dt subgenome and more homoeologous genes showed the alternative splicing bias towards At subgenome.During fibre development in 3-79,Emian22 and N182,0 DPA had the highest number of expression biased gene and 15 DPA had the lowest number of expression biased gene.After comparing the expression bias of three cotton varieties,there were 396,443,470,325 and 429 genes showing completely different expression bias patterns between Emian22 and 3-79 respectively,5,8,1,2 and8 genes showing completely different expression bias patterns between Emian22 and N182.(3)Differences in transcriptional regulation during fiber development in three cotton cultivars.At the level of alternative splicing,there were 533,484,559 and 672 differentially alternative splice between Emian22 and N182,which corresponding to419,402,450,538 and 648 differentially alternative splicing genes(DASGs).GO enrichment analysis showed that the DASGs was mainly enriched in cytoskeleton and microtubule binding.At the level of transcriptional expression,there were 12,587,11,249,11,852,12,131 and 11,619 differentially expressed genes(DEGs)between Emian22 and 3-79,and there were 1,495,611,327,1,178 and 1,376 differentially expressed genes between Emian22 and N182.Genes with consistent trends between the two groups were considered as functional DEGs,which mainly enriched in hydrolase activity,cellular polysaccharide metabolic process,cellular carbohydrate metabolic process,cell wall organization or biogenesis,peroxidase activity and ion transport.Combining the analysis of functional genes,transcription factors related to fibre cell wall and plant hormone signal transduction pathways,a regulatory network for differential fibre development of N182 was postulated.In the signal transduction pathway of BRs,the differentially expressed Gh14-3-3 interacted with BRI1 to influence the expression of XTH which involved in cell wall polysaccharide hydrolysis;and in the signal transduction pathway of JAs,the differentially expressed MYC induced the expression of TBL which involved in acetylation modification of cell wall polysaccharides.Those DEGs co-regulated the development of the cell wall,promoted fibre cell elongation and ultimately improved mature fibre length. |
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