Genetic Diversity,Genome-wide Association Study And Transcriptome Analysis On Fiber Traits Of Sea Island Cotton

Sea island cotton,which is famous for high quality fiber and natural materials of high count yarn,is one of the four cultivated cotton.At present,sea island cotton mainly grow only in the United States,Egypt,Central Asia and Xinjiang of China,and China's total production accounts for about 35%of the world.Compared with upland cotton,there are few studies on sea island cotton resources at home and abroad,and most of them focus on limited number of standard strains,which is not conducive to the exploitation and utilization of their excellent genes and related research work.Compared with the past,new cotton varieties bred in recent years in Xinjiang have significantly improved in the main economic traits.Understanding their genetic basis is very necessary for guiding future breeding.Based on the Xinjiang island cotton varieties and the resources of the island cotton in the main producing countries of the world,this paper aims to analyze the population structure characteristics of the island cotton through panoramic analysis of diversity,and locate the fiber related QTL by correlation analysis.The transcriptome sequencing of different fiber development stages with excellent allelic variation further carried out for genes excavation,which will lay a foundation for molecular marker assisted breeding and fiber genetic improvement in the future.The main results are as follows:1.Study on the pedigree of Xinjiang island cotton varietiesAnalysis on Xinjiang island cotton breeding pedigree,found that the Xinjiang sea island cotton backbone parent is relatively single,and early intervention into a narrow genetic basis.But the late 2010s pedigree is complex,which belong to the Egyptian Central Asia type,and clustering results showed pedigree was consistent.With the continuous evolution of breeding,late bred varieties in the plant height,boll weight,seed index,fiber length,fiber strength,resistance to Fusarium wilt traits are better than previous cultivars,especially in rapidly increased boll period longer,boll number and the quality of fiber in the main cultivars.2.Genetic diversity and affinity of island cotton.By diversity analysis for 218 the world island cotton resources and a comprehensive assessment of the degree of variability of individual traits,it was found that the incidence of Fusarium wilt,plant height,first branch node,boll number and fiber strength was higher than the coefficient of variation.Materials of Xinjiang Tarim area had higher diversity in plant height,branch number,seed index,fiber strength;Uzbekistan materials in the number of fruit branches and boll number and Africa materials had a significant advantage in the single boll weight and lint percentage.To explore the genetic diversity of sea island cotton using molecular markers,genetic materiasl also showed that these island cotton had higher diversity.Nei's gene diversity index(H)variation was 0.2442?0.4998,and the average was 0.4145,of which material diversity of Xinjiang Tarim Region was the most abundant.Combined with phenotypic and molecular markers,the 218 accessions were divided into two categories.The first category of plant showed low plant and seed index and short fiber length;the second distribution was complex,and on the basis of the plant type it can be divided into 2 sub categories,5 sub class,and the same source of resources were in a cluster.3.Characteristics of island cotton population structure and chain imbalance.By analyzing the population structure of island cotton,the hierarchical relationship of different materials can be clearer understood.By using SSR molecular markers,it was showed that when the number of population was k=3,the island cotton resources can be separated,but there were subgroup structures.218 samples were studied by Hardy-Weinberg test,and island cotton genomic LD structure was estimated.6654 loci in linkage disequilibrium were detected in 160 SSR markers,accounting for all possible combinations of the 38.8%loci,of which 237 pairs of combinations with the existence of a higher level of chain imbalance(D>0.5).4.Correlation analysis between fiber characters of island cotton and SSR markers.Based on the analysis of sea island cotton population structure,through genome-wide association analysis in identification of island cotton SSR markers,each individual and the corresponding Q value as a covariate,and fiber traits variation of SSR locus mutation and regression analysis,it was detected that the mutations of 15 sites and fiber traits in sea island cotton was significantly correlated respectively in the P<0.05 level.5.Transcriptome analysis of fiber characters of the sea island cotton.Based on the transcriptional analysis of the fiber traits of the island cotton,the differentially expressed genes were enriched in the association of GTP related enzymes and so on in the molecular functional group.In biological process grouping,differentially expressed genes were enriched in biological processes such as nucleic acid-templated transcription and RNA synthesis(RNA biosynthetic process).3 genes which were related with fiber development and verified in the differential expression of screening,was preliminarily analyzed in their expression in ovule.It was found that these 3 genes played a role in the development of island cotton fiber,and further functional verification was needed later.