Identification Of Candidate Genes And Genome-wide Association Studies Of Traits Related To Early Maturity,Yield And Fiber Quality In Upland Cotton(Gossypium Hirsutum L.)

Cotton?Gossypium spp.?is the most important natural textile fiber source worldwide.Upland cotton?Gossypium hirsutum L.?is the most widely cultivated tetraploid cotton species and accounts for 95% of annual worldwide cotton production.The early maturity,yield and fiber quality are the most important breeding target traits in cotton.Over the last two decades,many QTLs related to the above-mentioned target traits have been identified using QTL-mapping methods and association mapping based on SSR markers.However,few QTLs for the most important breeding target traits have been identified genome-wide association studies?GWAS?based on single nucleotide polymorphism?SNP?loci in upland cotton.To better understand the genetic architecture of the most important breeding target traits in upland cotton,a population consisting of 355 upland cotton germplasm accessions was phenotypically characterized for 14 traits in four environments and was genotyped using the specific-locus amplified fragment sequencing?SLAF-seq?approach,A total of 81,675 SNPs covered all 26 chromosomes in 355 upland cotton accessions were discovered using SLAF-seq.GWASs and identification of candidate genes of 14 traits were subsequently performed.Forty-one significant associations with early maturity traits were successfully identified via GWAS;the SNP loci of 29 of the 41 associations were distributed on chromosome Dt3.Among these associated SNP loci,the SNP locus rsDt3:13562854 associated significantly with five traits related to early maturity?WGP,FT,FBP,NFFB and YPBF?were identified through GWAS and explained 9.34%¹4.13% of the phenotypic variance with 6.77¹0.10 of-log10?P?value.A total of 32 genes were annotated in the 1 Mb adjacent genomic regions of the SNP allele?rsDt3:13562854?.The high expression levels of CotAD₀1947 were detected in the leaves,and the expression of CotAD₀1947 in the early-maturing varieties was significantly higher than that in the late-maturing varieties from the two-leaf stage to the four-leaf stage.These data provide support for CotAD₀1947 as a candidate gene for early maturity in upland cotton.Twelve SNPs associated with lint percentage were detected via GWAS,in which five SNP loci distributed on chromosomes At3 and At4 and explained 9.42%¹2.88% of the phenotypic variance with-log10?P?> 6.21.Two SNP loci?rsAt4:15572813 and rsAt4:15573052?on chromosome At4 showed significant marker-trait associations with the highest-log10?P?values,which were detected in BLUP and each of the four environments simultaneously.Additionally,three SNP loci?rsAt3:43538238,rsAt3:43631774,and rsAt3:43631819?on chromosome At3 were associated with the target trait in BLUP and three of the four environments at the same time.These results indicated that there were two major-effect QTLs for lint percentage on chromosomes At3 and At4.Furthermore,the expression levels of 47 putative candidate genes in adjacent genomic regions of five significantly associated SNP loci were analyzed using RNA-seq data from ten upland cotton?TM-1?tissues.Gh_A02G1268 was predominantly expressed in fiber-5 DPA,and its expression levels in fiber-5 DPA were 300-fold higher than in the seeds in TM-1,suggesting its potential role in increasing the lint percentage and improving fiber quality in upland cotton.A total of 16,10 and 7 SNPs were associated with fiber length?FL?,fiber strength?FS?and fiber uniformity?FU?,respectively.Most importantly,two major genomic regions?MGR1 and MGR2?on chromosome Dt7 were identified.The MGR1 consisted of nine SNP loci associated significantly with FL;two SNPs in MGR2 had significant associations with both FL and FS.Four genes?CotAD₂2823,CotAD₂2824,CotAD₂2825 and CotAD₃5088?annotated within the MGR1 and MGR2 might be candidate genes potentially underlying FL and FS.The distinct distributions of the favorable haplotype among the five different-source groups were found in MGR1 and MGR2.The favorable haplotype frequencies?FHF?in the lines obtained from YR,YZR and USA were higher than those in the accessions from NW and LN.Furthermore,we also found that the FHF of varieties from South Xinjiang were higher than those of varieties from North Xinjiang.This result suggests that the two FHFs were higher in accessions from low-latitude regions than in those from high-latitude regions in China.However,the genetic diversity of lines from the low-latitude regions was lower than the diversity of lines from the high-latitude regions in China.Furthermore,the genetic diversity of MGR1 and MGR2 was higher than that of chromosome Dt7.The genetic diversity of the accessions that included FHs exhibited a higher value than the diversity of accessions that included UFHs.These results indicate that FHs have undergone artificial selection during upland cotton breeding in recent decades in China.