| Cotton,as one of the most important natural fiber crops in the world,plays an important role in in our national economy.In recent years,development of textile technology and the growth of human living standards,the requirements for fiber quality are ever-increasing.The genetic basis of the existing Upland cotton varieties is relatively narrow,which limits the further improvement of the Upland cotton's fiber quality.The abundant variety resources of Gossypium provide a genetic material basis for Upland cotton breeding and genetic improvement.Interspecific hybridization strategy has been widely used in cotton breeding.Most of the agronomic traits in cotton,such as yield,fiber quality and so on,are quantitative traits,which are affected by the combined effects of the environment and multiple genes.At present,the information of cotton genome is constantly improved,and the combination of traits and QTLs at the whole genome level is helpful to analyze the genetic basis of related traits and supplement for cotton quality breeding.In this study,two G.hirsutum accessions with significant difference in fiber quality,J02-508 and ZRI015,were used as parental lines.Through genotyping-by-sequencing(GBS)technique,a high-density genetic linkage map was constructed and employed to identify QTLs related to fiber-related traits at the whole genome level.In addition,J02-508 was used as the research material to predict and analyze the candidate genes related to fiber length and verify their functions.At the same time,the phenomenon of segregation distortion in the F5 population was considered to analyze the genetic basis of excellent fiber quality,combining the complex genetic background information of the parent J02-508.The main results were as follows:1.In this study,six fiber yield and quality traits were estimated and analyzed,including boll weight,lint percentage,fiber length,fiber strength,fiber elongation,and fiber micronaire.There were significant(P < 0.005)or highly significant(P < 0.001)differences among all traits between the two parents,except for lint percentage and fiber elongation.The six traits showed continuous and approximate normal distribution in the four generations of F3,F4,F5 and F6.The fiber strength and fiber length showed significant and positive correlation among the four generations.There was no significant correlation between fiber strength and boll weight,lint percentage.To some extent,the offspring of J02-508 and ZRI015 weakened the negative correlation between fiber yield and quality,especially between fiber yield and fiber strength.2.Ten individual plants from each parent and 237 lines from F5 population were sequenced through GBS technique.Among the discovered polymorphic SNP markers between the parents,a total of 115,544 markers were obtained.Markers with a missing rate of more than 25% and the P value of the Chi-square test less than 0.001 were further filtered out,and finally,a total of 7,071 markers on 26 chromosomes were retained for constructing the genetic linkage map by software.The final genetic linkage map contained 4,060 markers and spanned a total of 2,388.07 c M,with an average interval between adjacent markers of 0.588 c M.Combining the phenotypic data of F5 and F6 generations,a total of 122 QTLs for six fiber yield and quality traits were identified.Among them,twenty-eight QTLs were simultaneously detected in two generations.The QTLs related with fiber length were concentrated on chromosome D11.For fiber strength,the QTL with the highest LOD value was detected on chromosome D08(6.42).3.There were many fiber length related QTLs clustered on chromosome D11.According to the analysis of gene structure and expression pattern,a candidate gene for fiber length,GH_D11G2586,was found near q FL-D11-4,which belonged to the SOT gene family.A comprehensive analysis of the SOT gene family in Gossypium was performed.A total of 245 SOT genes were identified from four cotton species,G.arboreum,G.raimondii,G.barbadense and G.hirsutum.And a total of 170 in 245 SOTs were further classified into four groups based on the orthologous relationships comparing with Arabidopsis.The expression pattern of GH_D11G2586 in different tissues and fiber developmental stages indicated that it might be involved in fiber development.GH_D11G2586-silenced plants treated by VIGS showed a shorter length of stem and leaf hairs than that of the blank and negative control plants.The stem and leaf hairs,as well as cotton fiber,were belonged to the epidermal cells,which might have similar fiber differentiation and development mechanisms.Accordingly,the results suggested that GH_D11G2586 might be involved in the fiber development process,and play a positive role in regulating fiber elongation.4.The Chi-square test of 25,018 polymorphic markers on the 26 chromosomes was performed.Unexpectedly,an abnormally segregation distortion ratio was found in this population.The average ratio of segregation distortion markers on all 26 chromosomes reached 83.13%.The highest ratio of segregation distortion markers was on the chromosome D08,reaching 99.39%.Considering all the segregation distortion markers on chromosome D08,a bin map was constructed by using all the polymorphic markers through R software.A simple Students' t test was performed to estimate the degree of correlation between fiber strength and bins.A linked low recombination region in the 7-60 Mb of genome region on chromosome D08 was identified,and the SNP markers in the interval were significantly correlated with fiber strength(-log10(P)> 16).Then we used Distorted Map software to correct the genetic distance between markers and redetected the QTL related with fiber strength.A fiber-related QTL(named as q FS_D08)was identified in the same interval with the LOD value of 11.42,explaining a phenotypic variation of 20.12%.5.According to the pedigree records of the two parents,J02-508 might contain a variety of exogenous genomic fragments from other cotton species.We tracked and identified the source of q FS-D08 in J02-508 using the resequencing data of 3,227 cotton materials that were sequenced or collected by our research group.Through clustering,comparison,PCR amplification and other methods,the alien fragment in J02-508 was determined in the region ranged from 7.073 to 60.027 Mb,which coincided with the physical interval of q FS_D08.Moreover,this region was introgressed from the chromosome CM013381.1 of wild diploid cotton,G.thurberi(D1),ranged from 5.299-36.270 Mb.In this study,a high-density genetic map was constructed to detect QTLs related to fiber yield and quality,laying a foundation for candidate gene mining of related traits and providing useful information for the research of cotton yield and quality improvement.This study also clarified the genetic background of excellent materials containing exogenous fragments,which was helpful to understand the relationship between exogenous introgression fragments and segregation distortion,and the importance of interspecific hybridization to increase fiber strength in cotton breeding. |
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