Genetic Dissection Of Agronomic Traits Using An Interspecific Chromosome Segments Substitution Lines Between Gossypium Hirsutum And G.barbadense

The narrow genetic basis of upland cotton limits its potential for genetic improvement.The excavation of excellent foreign genes from sea-island cotton is of great significance for improving the agronomic traits of upland cotton cultivars.To learn the genetic effect of Gossypium barbadense?Gb?in the background of G.hirsutum?Gh?,a set of interspecific chromosome segments substitution lines?CSSLs?were constructed.This study evaluated the efficacy of traditional molecular marker technology and high-throughput sequencing technology in identifying introgression segments,analyzed the genetics effects of agronomic traits such as yield,fiber quality traits and cottonseed oil content,carried the quantitative trait loci?QTL?mapping of the leaf size mutant materials,compared the gene expression network of the cottonessd oil accumulation between the Gh and Gb.The main results are as follows:1. Identification of introgression segments in the CSSLsIn this study,the genetic effects of interspecific chromosome substitution lines between Gh and Gb were analyzed.Firstly,traditional PCR-based molecular markers and whole-genome resequencing technology were used to identify introgression segments in the CSSLs.A total of 480 chromosome substitution fragments were detected in 325 materials using 515 molecular markers.The total length of the chromosome substitution segments was 2695.19 c M,covering 78.42%of the entire cotton genome,of which the A-subgenome was 73.73%and the D-subgenome was83.33%.Using whole genome resequencing technology,only 313 materials were detected to carry introgression segments.A total of 1,211 chromosome fragments from Gb were detected,ranging in length from 97 kb to 104.23 Mb,with an average length of 4.43 Mb,covering 86.11%of the entire cotton genome.In this study,we also analyzed the genetic loci of mutation phenotypes in the CSSLs,such as leaf type,open-bud and fuzz-less mutation.A total of 14 agronomic traits of the CSSLs were investigated.Most of these traits showed continuous distribution characteristic expect the seed index,and there was significant correlation between traits.Combined with field test phenotypic data and genotypic data from whole-genome resequencing,QTL detection was performed and a total of 64 QTL loci distributed on 20 chromosomes were detected.Among these QTL,38 and 26 were located on A-subgenome and D-subgenome,respectively.The phenotypic variance explained of these QTL were region from 0.73%?14.67%.The additive effect of fiber quality in the CSSLs was evaluated,and we found that both of the genetic background from Gh and Gb contributed to the improvement of fiber quality.The additive effects of fiber traits mainly come from the Gh?35.73%?,and the Gb only contributed 22.83%for fiber quality.The chromosome A11 showed a high additive effect on fiber traits in the Gh background,and no effects was detected form Gb on chromosome D07.The evaluation of the additive effect of fiber quality traits provides guidance for making full use of the dominant resources of genetic background between land and sea.2. Fine mapping QTL of the leaf size mutantsThe leaf size of the line N35 showed transgressive segregation in the CSSLs,and was significantly larger than the Gh parent Emian22.The line carried an introgression segment from the Gb on chromosome A11.We used the genetic linkage mapping to analyze the related QTL for controlling leaf size.A major QTL was detected by different softwares in the primary F₂ population containing 272 individuals.And in the fine-mapping F₂ population containing 2,292 individuals,both of the software Win QTLcart2.5 and Icimapping 4.0 can detected QTL at 16 Mb?17 Mb.Utilizing two lines?N12and N125?carring the same introgression segments on A11 in the CSSLs,the candidate interval for controlling the leaf size was finally defined in 10.75 Mb?13.75 Mb and16.57 Mb?16.66 Mb.According to the annotation information and tissues espression pattern information,25 candidate genes were identified in the QTL interval,most of which were related to hormone signal metabolism pathways.3. Differential expression analysis of cottonseed oil-related genes between Gh and GbSignificant differences were found in the cottonseed oil content?SOC?between Gb“3-79”and Gh“Emian22”.We sequenced transcriptome of embryos at different developmental stages from Gh and Gb,and found that there was a significant difference in the gene expression between Gh and Gb during the 20 DPA period of cottonseed development.The number of down-regulated genes in Gh was significantly greater than that of Gb in the"30 DPA vs 20 DPA".The expression of lipid metabolism-related genes during cottonseed development was analyzed.The difference in oil content between Gh and Gb was caused by the differences of expression abundance and duration of a series of genes,including PDHC,SAD and FATA.We also found the transcription factors WRI1,NF-YB6 and b ZIP?DPBF?play important roles in cottonseed oil synthesis.Based on the associated regions of QTL and high SOC introgression lines,19 candidate genes potentially controlling SOC were identified,which provided a basis for further analysis of the genetic mechanism of lipid metabolism in cotton.This study is the first to introduce whole-genome resequencing technology into the genetic research of interspecific CSSLs in cotton.The results of this study provide guidance for the construction of CSSLs in the future.The mining of QTL loci for agronomic traits and analysis of the sources of fiber quality additive effect in the CSSLs provide new insights guidance and germplasm resources for interspecific breeding in cotton.