Fine Mapping And Candidate Gene Analysis Of Lint Percentage QTL (qLP-A01.1) In Cotton

Cotton is one of the most important fiber crops in the world.China is not only the world’s largest cotton producer but also the largest cotton consumer and importer.Fiber yield improvement remains a primary goal of cotton breedin Arabidopsis Fiber yield is a quantitative trait which is controlled by multiples genes and easily influenced by the environment.Compared with traditional breeding methods,molecular marker-assisted selection can significantly improve breeding efficiency.Identifying genes or QTLs controlling fiber yield is essential for molecular marker-assisted selection breeding.In this study,we developed InDel primers based on the sequences of Gossypium hirsutum and G.tomentosum genomes,constructed a high density genetic map within QTL-regionand identified QTL for lint percentage.Transcriptome data,q RT-PCR,and protein sequence comparison were carried out to detect candidate genes associated with lint percentage QTL.The main research findings are as follows:1.Genetic map of QTLregionA total of 39 InDel primer pairs were developed to update the genetic map in QTL-region.The update map contains 47 loci and covers 56.981 c M with an average distance of 1.21 c M between adjacent markers.Collinearity analysis showed a high synteny between genetic map and two physical maps corresponding to G.hirsutum and G.tomentosum.The accurate genetic map will preferably service for subsequently QTL fine-mapping.2.Fine-mapping of qLP-A01.1Based on the update genetic map and the phenotypic data of F₂,F_2:3 and F_2:4populations,qLP-A01.1 was finally anchored on a 0.704 c M interval flanked with A01＿110.074 and A01＿110.234.In F₂population,qLP_A01.1 was mapped into an interval of 25.47 c M flanked by A01＿56.32 and A01＿110.699.The additive effect of qLP_A01.1was 1.28%,and the phenotypic variation explained by qLP_A01.1 was 11.90%.The additive effect of q LI_A01.1 was 0.26 g,and the phenotypic variation explained by q LI_A01.1 was 6.40%.The favorable allele of qLP_A01.1 and q LI_A01.1 were contributed by HT＿390,a chromosome segment substitution line of G.tomentosum.In F_2:3 population,qLP_A01.1 and q LI_A01.1 were mapped into a 1.51 c M interval flanked by A01＿110.074 and A01＿110.252.The additive effect of qLP_A01.1 and q LI_A01.1were 1.00%and 0.20 g,respectively.And the phenotypic variation explained by qLP_A01.1 and q LI_A01.1were 4.60%and 1.90%,respectively.Moreover,qLP_A01.1 and q LI_A01.1 were furtherly mapped into a 0.70 c M interval flanked by A01＿110.074 and A01＿110.234 in F_2:4population.The additive effect of qLP_A01.1 was 0.45%,and the phenotypic variation explained by qLP_A01.1 was 4.90%.The additive effect of q LI_A01.1was 0.15 g,and the phenotypic variation explained by q LI_A01.1 was 3.90%.3.Candidate genes identification for lint percentage QTLThe QTL region（from A01＿110.074 to A01＿110.234）corresponded to 159 kb（106598572 bp-106758338 bp）and 163 kb（104964342 bp-105127523 bp）on chromosome A01 in G.hirsutum and G.tomentosum,respectively.There are fourteen annotated genes in this region,transcriptome analysis and RT-PCR analysis showed that only Gh＿A01G200600,Gh＿A01G200700,Gh＿A01G201000 and Gh＿A01G201500were expressed in fiber initiation stage.Gh＿A01G200700（GhTBL12）encodes trichosomal birefringent proteins.TBL family genes are involved in cell wall polysaccharide O-acetylation.Gh＿A01G201000（GhPAT23）encodes a protein S-acyltransferase（PATs）,a PAT family member that influences root hair growth and auxin transport.It had been reported that cell wall polysaccharide and auxin transport play a important role in fiber initiation.These results suggested that Gh＿A01G200700（GhTBL12）and Gh＿A01G201000（GhPAT23）may be the candidate gene controlling qLP_A01.1 on chromosome A01.