Development Of InDel Markers And Association Analysis Of Fiber Quality Related Traits In Jute (Corchorus Spp.)

Jute,including white jute and dark jute,is one of the important fibre crops second to cotton.The improvement of fiber quality is a major goal of jute breeding.Using natural populations as experimental materials,important gene loci that controlling phenotypic traits by the method of association analysis could be dissected.In this study,300 different original accessions were used as research materials to measure 6 bast fiber quality related traits in 2016 and 2017.And the population structure and association analysis were conducted using SSR and InDel markers covering the whole genome.The main results are as follows:1.To identify the candidate genes involved in GA3 stress response in bast fiber and develop InDel markers,the transcriptomes of bast fiber of Huangma 179,the national super fine germplasm,under two different conditions at the vegetable stages were compared using RNA-Seq.The results showed that 22995903 clean reads were generated using Illumina paired-end sequencing.De novo assembly yielded 48,914 unigenes with an average length of 903 bp.By sequence similarity searching for known proteins,27962(57.16%)genes were annotated for their function at least one data library.172 genes were assigned to starch and sucrose metabolic pathway which was related with cellulose biosynthesis.The electron expression profiles showed that 14 genes were sensitive to GA3.Among them,5 genes were down regulated,and 9 genes were up regulated.In addition,216 GO accessions contained differentially expressed genes(DEGs)after GA3 stress.Among them,156 GO accessions contained up regulated genes,and 97 GO accessions contained down regulated genes.In KEGG,2 DEGs were assigned to 4 KEGG pathways after GA3 stress.In order to enrich the molecular markers,4815 InDel markers were developed by using 48914 unigene sequences.From the results of different fragment lengths,<5 bp has the highest InDels frequency and the most abundant content,the 5 InDels bp is the middle,and the>10 bp is the lowest.According to different frequency results,the types contained AG showed the highest frequency.2.747 pairs of polymorphic primers were screened by using 24 varieties of jute varieties(lines),and 213 alleles were totally detected.The polymorphic information content(PIC)value was between 0.0370 and 0.9281,and the average PIC was 0.7289.The polymorphism detection of InDel showed that 136(78.6%)pairs of primers could successfully amplify polymorphic,and 119(68.8%)pairs had at least two bands.It was found that the polymorphism of SSR markers was more abundant by comparison with InDel markers.Using the polymorphic primers,300 jute natural accessions that come from 11 countries and regions could be divided into two categories:white jute(Corchorus capsularis)and dark jute(Corchorus olitorius).Among them,Cc can be divided into two subgroups,and Co can be divided into three.The results of the phylogenetic tree further show that the result of the analysis of the structure analysis is credible.According to the genetic similarity coefficient,we could infer that the Corchorus olitorius probably was originated from Africa,and then spread to China.The Corchorus capsularis might originate in China,and the Corchorus olitorius might happen earlier than Corchorus capsularis.Based on the analysis of relative kinship(Q)and linkage disequilibrium(LD)of the natural population,it is determined that it can be used for subsequent association analysis.3.Six bast fiber quality related traits of 300 tested materials were identified.The variation of phenotypes showed there are abundant variation among these traits and the coefficient of variation varied from 12.57%to 19.31%.Six bast fiber quality related traits includes cellulose content(vegetable growth),cellulose content(technical mature),lignin content(vegetable growth),lignin content(technical mature),fiber fineness(technical mature)and fiber strength(technical mature).Variance analysis indicated that variation of these traits among varieties were significant(p<0.01)while the variation between the years was not significant(p>0.05),suggesting that these traits are less affected by the external environment,and mainly depends on the genotypes of these accesions.Correlation analysis showed that the content of cellulose was negatively correlated to the content of lignin,and positively correlated to the fiber strength and the fiber fineness.Association analysis was conducted on the detected the six bast fiber quality related traits using the compressed mixed linear model(cMLM).In total,97 associated loci were significant(p<0.05).Out of them,23 loci were significant at the level of p<0.01.The phenotypic variations explained(PVE)ranged from 6.68%to 35.91%.Some of the same markers are also associated in the two subgroups.Combined with single marker analysis and real-time PCR,5 candidate genes were identified,including bZIP family proteins related to fiber quality.The genetic loci of six bast fiber quality related traits dissecting by Association analysis in the present study will lay a foundation for the screening of improved varieties and functional analysis of subsequent key genes,which has theoretical and practical value for improving fiber quality of jute.