Detection And Identification Of Candidate Genes For Bark Thickness In Ramie

Bark thickness（BT）is an important index for evaluating the yield of raw ramie or fiber,and a complex quantitative trait controlled by multiple genes.It is still poorly understood for the genetic basis of bark traits like BT in ramie.The detection and identification of quantitative trait loci and candidate genes that control bark thickness can help the breeding of high-yield and high-quality varieties for fiber use,as well as the researches on yield-related traits.In order to detect quantitative trait locus and candidate genes related to bark thickness in this study,the F₁separation population from the‘hejiangqinma’בZhongzhu No.1’and association population consisted of 319 core germplasms were used to conduct linkage analysis and genome-wide association study after phenotyping of bark thickness in one or two location with several years,respectively.Subsequently,these candidate genes were screened and identified using RNA-seq analysis and q RT-PCR.The main analysis results listed as follows:1.Parents genetic map and integrated genetic map were constructed using the F₁hybrid progeny of ‘hejiangqinma’בZhongzhu No.1’.The integrated map contains a total of 5,796 Bin markers distributed in 14 linkage groups.Each linkage group contains 271-572 Bin markers and covers a genetic distance of 130.888-346.035 c M.2.Bark thickness of 253 lines from F₁separation population and 319 germplasms of natural population was phenotyped in the field across 7 environments and 11 environments,respectively.The results of statistical analysis and calculation of broad-sense heritability suggested that bark thickness was abundantly various in two populations and mainly controlled by genotype.3.Through linkage analysis using Multiple-QTL Model（MQM）mapping method for phenotype data of separation population collected in multiple environments,41 QTLs were detected in more than two environments,among which two QTL were found across three environments.4.The natural population composed of 319 ramie core collection after genome resequencing underwent phenotype identification and genome-wide association analysis across a total of 11 growth environments in two experimental location.After GWAS for bark thickness through GLM+PCA model,there were 2,424,1037,341,2138,122,2,9,and 31 significant SNP detected in 9 environments,respectively.In addition,best linear unbiased prediction（BLUP）of the two test plots were analyzed by the MLM model,and 8 common SNPs were detected at the same time.74 stable SNPs were detected by the two association analysis methods.5.Through haplotype analysis and candidate gene detection of stable trait-related SNPs detected across multiple environments,a gene Bn WAK2（Maker00062604）related to cell wall synthesis and a gene Bn DCD（Maker00062509）that may be involved in regulating plant ethylene levels were found.5QTLs interval and 45 candidate genes were detected by integrating linkage mapping and association mapping for bark thickness.6.In the four growth stages of two varieties with different bark thickness,Rongjiangbaima 2 and tianbaoma were found to have significant differences in morphological structures like their fiber cell number and cell size.12 candidate genes related to bark thickness were identified by q RT-PCR.7.Differentially expressed genes（DEGs）related to fiber development were identified by RNA-seq analysis,and found some DEGs involved in the biological process of cell division,cell differentiation and cell wall organization and pathway of starch and sucrose metabolism and phenylpropanoid biosynthesis.The further verification using q RT-PCR identified 10 candidate genes,and among five genes were considered to be the key genes related to fiber development and bark thickness trait.