Genome-wide Association Studies Of Traits Related To Senescence In Upland Cotton (Gossypium Hirsutum L.)

Cotton is one of the most important cash crops and it is also an important natural fiber crop in the world.But premature senescence of cotton is difficult problem which directly affects the yield of cotton and economic interests of cotton farmers.It is the content of chlorophyll of leaves that is the most significant phenotype in plant senescence,which can reveal the levels of leaves senescence.In this research,a total of 92,842 SNPs were first detected by using the SLAF-seq technology.The content of chlorophyll in cotton leaves were measured at flowering and boll-setting period(FBP)and the boll opening period(BOP).The accessions were planted at Anyang,Henan and Huanggang,Hubei in two years(2016 and 2017).Then the GWAS analysis was taken to detect senescence associated with significant SNPs and candidate genes.The main results were shown as followed,According to the analysis of genetic diversity by SNP,The 355 accessions showed low diversity in China,because of limited in hereditary basis.And the 355 accessions can be divided into two subgroups by the analysises of population structure and PCA.Twenty-three significant associations with the content of chlorophyll(SPAD values and the absolute values)were identified via GWAS successfully.There were 17 significant SNPs in A group chromosomes and 6 in D group chromosomes.Then Twenty-five significant SNPs with the rate of chlorophyll were identified via GWAS.Twenty-four significant SNPs were found at A group chromosomes and only one at D group chromosomes.Therefore,the senescence related genes had a Disequilibrium of distribution at A and D chromosomes,and A group chromosomes had more senescence related genes than D.Furthermore,there were many same significant SNPs between the content of chlorophyll at BOP stage and the rate of chlorophyll,but not in FBP.The result suggested that the senescence related genes would be expressed at BOP stage.Two major QTL were detected via the analysis of haplotype and genotype.There were five significant SNPs(A10:25141633,A10:25141635,A10:25141645,A10:25141649 and A10:25141650)on A10 chromosome which only have two haplotypes and the other SNP A08:53831689 on A08 chromosome.Nine LD blocks were detected by LD blocks analysis,which included at least one significant SNP.Sixty-nine candidate genes were revealed and annotated from 9 LD blocks.These genes were included in CK,ABA,light signal and ROS,which were all related with senescence.