Genetic Diversity And Genome-wide Association Study On Fiber Quality And Yield Traits Of Derived Sea Island Cotton Cultivars In Xinjiang

Because of its excellent fiber quality and stress resistance,sea island cotton occupies an important economic position in Chinese national economy.In this study,220 native derived sea island cotton varieties in Xinjiang were selected and tested in Xinjiang and Hainan province from 2017 to 2018.Through genetic diversity and genome-wide association study,the genetic relationship between Xinjiang native derived sea island cotton varieties was revealed,and fiber quality and yield traits genes were excavated to provide theoretical basis for the utilization of genetic resources and more efficient cultivation of new varieties.The chapter’s main findings are as follows.(1)Genetic diversity.By calculating the coefficient of variation and genetic diversity index of fiber quality and agronomic traits of 220 Xinjiang native derived sea island cotton varieties,the average variation coefficient and genetic diversity index of five fiber quality traits were 7.71%and 2.162,respectively.The average variation coefficient and genetic variation of the eight agronomic traits were 13.57%and 2.016,respectively.Cluster analysis showed that germplasms were classified into four groups based on fiber quality traits,of which there were signifiicant differences and the groupⅢ was the best.Based on agronomic traits,germplasms were divided into three groups,of which the group I not only produced the highest yield but also had good plant characteristics.The results of principal component analysis showed that the cumulative rate of four principal components was 66.69%.All of these above showed that the genetic variation of native derived sea island cotton varieties in Xinjiang was relatively large,and there were significant differences about materials between different breeding companies,but the overall genetic diversity index was poor,and the exchange of materials among different companies was not obvious.Therefore,attention should also be paid to the introduction of exogenous germplasm resources and the strengthening of material exchange among breeding units in their genetic improvement.(2)Population structure and linkage disequilibrium analysis.Through genome-wide re-sequencing of 220 native derived sea island cotton varieties in Xinjiang,5.78 Tb data and 336507 high-quality SNPs were produced.There were 9055 SNPs in the coding region,including 5792(1.72%)non-synonymous mutations.The neighbour-joining tree,population structure analysis and principal component analysis were constructed with high quality SNPs.220 germplasms were divided into four subgroups.Linkage disequilibrium analysis showed that LD in all populations decreased sharply in 100 Kb,but eventually reached a high equilibrium.The results of nucleotide diversity and population differentiation showed that the π values of all populations ranged from 1.12×10-4 to 1.37×10-4,and the Fst values ranged from 0.258 to 0.324.The sea island cotton has been domesticated to a higher degree,the genetic diversity was poor,and the differentiation among populations was low.However,due to the genetic improvement in different breeding directions,the genetic diversity of was increased.(3)Genome-wide Association analysis.A total of 680 related SNPs was identified by genome-wide association analysis on fiber quality and yield traits of 220 native derived sea island cotton varieties in Xinjiang,of which 495 were related to fiber quality and 185 were related to yield.Manhattan plots showed that 43,55,39 and 67 significant SNPs were detected for fiber uniformity,lint percentage,fiber length and fiber elongation,respectively.These results laid a foundation for further improvement of fiber quality and yield traits of sea island cotton.