Genetic Basis Of The Agronomic Traits Of Brown Fibre Cotton Revealed By Linkage And Association Mapping

Brown fibre cotton,as the main type of colored cotton and environmentally friendly resource,plays an important role in the textile industry.In comparison with white fibre cotton,brown fibre cotton shows a worse fibre yield and quality,and traditional breeding is difficult to overcome the bottleneck of brown fibre cotton breeding.Therefore,a systematic dissection of the genetic basis of brown fibre cotton assisted by modern molecular genetics is beneficial for molecular marker-assisted breeding of brown fibre cotton,map-based clone of brown fibre gene and laying the the molecular mechanism basis of brown fibre development.Linkage and association mapping are two effective methods to uncover the genetic basis of agronomic traits of crops.Based on linkage and association mapping,we build a linkage population and collect a panel of natural brown fibre accessions to systematically study the genetic basis of brown fibre cotton.Firstly,we developed a linkage population by a white fibre cotton（G.hirsutum cv.HD208）a dark brown fibre mutant（ys）,which mutated from the distant species hybridization between sea-island and upland cotton,then,we performed genotyping with the traditional SSR;secondly,we collected a panel including 100 brown fibre accessions and 109 white fibre accessions,after that,we performed high-througput resequencing and case-control association analyses with this panel;thirdly,we investigated the agronomic traits with a 121-accession panel including100 brown fibre accessions and 21 representative white fibre accessions in multiple environments,and carried out genome-wide association study（GWAS）between agronomic traits and genotypes;lastly,we performed an in-depth analyses of the genetic inversion in the Lc₁locus with a dark brown fibre mutant and the 121-accession panel.The main results are as follows.1. Genetic dissection of fibre color,quality and yield of brown fibre cottonIn this study,we fine-mapped the major brown fibre locus（Lc₁）with 1 Mb physical interval by linkage analysis.In this interval,we isolated a co-segregation block with～0.52 Mb,and found a recombination hotspot closed to Lc₁.We dissected the Lc₁locus into two QTL:q BF-A07-1 and q BF-A07-2,the q BF-A07-1 locus mediates the production of brown fibre,while the q BF-A07-2 locus affects the color intensity of brown fibre.A candidate gene,Gh＿A07G2341,was identified in the q BF-A07-1 locus,Gh＿A07G2341showed a significant differential expression and abundant genetic variations between brown and white fibre cotton,Gh＿A07G2341 is a TT2 gene and belongs to MYB transcription factor family.Haplotype analysis indicated that introgression signature of G.barbadense have been retained in natural brown fibre germplasm and dark brown fibre mutant.We have identified 10 QTL for fibre yield and 19 QTL for fibre quality by GWAS,simultaneously,GWAS results suggested that q BF-A07-2 significantly affects the fibre color and negatively related with fibre yield and quality.2. Genetic dissection of a micro-inversion in brown fibre cottonIn this study,the genetic effects of a micro-inversion,Inv（A07）p1.09p2.23,was examined in brown fibre cotton at the individual and population genetic levels.The results showed that Inv（A07）p1.09p2.23 can be detected by high-throughput resequencing;simultaneously,micro-deletion,gene disruption（Ghir＿A07G000980）and abnormal gene expression occurred near the breakpoint of the inversion;Inv（A07）p1.09p2.23 existed in only dark brown fibre cotton,had undergone negative selection in elite brown fibre cultivars,and was significantly associated with fibre color and nine fibre traits;population genetic studies indicated that recombination was absent,nucleotide diversity was lower,and linkage disequilibrium was higher in the Inv（A07）p1.09p2.23 interval.3. Genetic dissection of two plant architecture traits in brown and white fibre cottonTwo plant architecture traits（plant height and fruit spur branch number）of the121-accession panel were investigated by field experiments in multiple environments,2,620,639 SNPs were identified in the 121-accession population by aligning resequencing data to the new reference genome.We have identified 5 QTL for plant height and 6 QTL for fruit spur branch number by GWAS;negative-effect alleles were enriched in elite cultivars by the QTL allele analyses;based on the associated QTL,gene annotation information and reported QTL,we have analyzed respective candidate genes and natural genetic variations responsible for four QTL;Ghir＿D02G017510 and Ghir＿D02G017600were identified as candidate genes for the q D02-FSBN-1 locus,and a premature start codon existed in Ghir＿D02G017510;Ghir＿A12G026570,a member of the pectin lyase family,was identified as the candidate gene of the q A12-FSBN-2 locus,and a significantly associated SNP,A12＿105366045（T/C）,can cause amino acid variation in the Ghir＿A12G026570 protein.