Fine-mapping Of Short Fiber Mutant Gene Li₁ And Transcriptome Analysis Of Ligon Lintless-1（li1） Mutant In Upland Cotton

Cotton fiber is an important natural fiber for the textile industry in the world.Fiber length is an important trait,which directly affect the quality of textiles.Ligon lintless-1(Li1)is a monogenic dominant mutant and with short fibers(-6mm)at maturity in upland cotton(Gossypium hirsutum).This presents a model to study molecular and cellular processes involved with fiber elongation.Because of homozygous dominant lethal effect,we can only acquisition heterozygous Li1 mutant(Li1 li1)and homozygote wild type(li1 li1)plants(li1)after introduction to China.Illuminating the forming mechanisms of short fiber mutantions will help us improve cotton yield and fiber quality through molecular design.In this paper,we have studied the genetic and transcriptome analysis of fiber elongation by using Li1 mutant.The main results are as follows:SEM results showed that there no significant difference of ovules and fibers from Li1 mutant and li1 from-3 DP A to 1 DP A.Both of them fibers showed no exception initiation phenomenon on 0 DP A,and fibers morphology and length appeared nearly the same during the early elongation stage of fiber development on 1 DP A.However,significant differences in fiber appearance were adverted on 3 DPA.Li1 fiber seemed more distorted than the wild type li1 on this stage,moreover minor a difference occurs in the length of the fibers on 5 DPA.It is considered that the fiber phenotype of the mutant becomes evident by approximately 3 DPA.These phenomena indicate that the retarded fiber elongation in Li1 is largely dictated by early structural and molecular events.In this study,we firstly developed three backcross populations:(Li1×Hai7124)(Ligon lintless)×Hai7124,(Li-R×Hai7124)(Ligon lintless)×Hai7124 and li1×(Li1×Hai7124)(Ligon lintless).We using three BC1 populations with 3,879 individuals analysis SSR markers associated with Li1 gene to construction of linkage map.In the(Li1×Hai7124)(Ligon lintless)×Hai7124 BC1 population,we found that SSR marker W4551 is completely linked with the Li1 gene.In the(Li-R×Hai7124)(Ligon lintless)×Hai7124 BC1 population Li1 gene was mapped between W3627 and W4571,and they had a genetic distance of 0.006cM and 0.044cM from Li1 gene,respectively.In the li1×(Li1×Hai7124)(Ligon lintless)BC1 population,Li1 was mapped between W4806 and W1960,and they had a genetic distance of 0.309cM and 0.198cM from Li1 gene,respectively.Final integration results of the three populations of linkage,Li1 gene was final mapped between W3627 and W4571,and they had a genetic distance of 0.017cM and 0.009cM from Li1 gene,respectively.Our results illustrate that the genetic interval contains only eight candidate genes(ORF1-ORF8)in TM-1 genomic sequence,and of which ORF1 was annotation as actin gene.qPCR analysis showed that the gene is predominant expression in wild-type leaf and early development fiber.VIGS transient expression suggested that the gene was silenced in cotton result in leaf curl deformity and plant growth is slow.Transcriptome sequencing of Li1 and its wild type(li1)during the early elongation stage of fiber development period and leaf tissue were investigated using Illumina HiSeqTM 2000 System.A variety of methods were used to analyze common different expression genes(DEGs)between wild type and Li1 mutant,including,Mapman functional enrichment analysis,and KEGG pathway enrichment analysis.Functional enrichment analysis with mapman display common differentially expressed genes is mainly related to protein metabolism,RNA metabolism,cell,hormone,signal transduction,transport,development etc.It is very important that functional integrity of plant cell walls for maintaining plant cell morphology and cell life activities.Glucose is the important precursor of cell wall polysaccharides synthesis.MapMan pathway enrichment analysis found that most of related genes were suppressed in the mutant in ovules and leaves in the the process of synthesis UDP-D-glucose by glucose-1-phosphate.In this pathway at 3 DPA one of three related genes down-regulated and two up-regulated;four genes at 5 DPA down-regulated;eight down-regulated of 10 related genes at 8 DPA and the other two up-regulated;in leaf tissue one of five down-regulated in the mutant.These results suggest that the synthesis process of polysaccharides in Li1 mutant was suppressed.