Genome-wide Association Study of Bolting Related Traits in Carrot
[Objective]Carrot plants are prone to early bolting under the influence of low temperature and long sunshine.Exploring SNP loci and candidate genes associated with carrot bolting traits would be beneficial for the breeding of new carrot varieties that are resistant to bolting.[Method]This study used 240 carrot germplasm resources as materials to investigate the characteristics of carrot bolt(bolt time,bolt rate,bolt height,and bolt speed)in 2021 and 2022,respectively.Through DNA sequencing and SNP variation detection,high-quality SNP loci obtained from quality control were used for genome-wide association study(GWAS)of bolting related traits.[Result]The bolting traits of 240 carrot germplasm resources demonstrated rich genetic diversity.After analyzing the 2-year data,it was found that there was significant variation in the phenotypes of each trait,with the highest coefficient of variation for bolting rate being 144.32%and 187.89%,and the lowest coefficient of variation for bolting time being 94.89%and 74.63%,respectively.The BLUE value reduced the error caused by the environment,with the lowest coefficient of variation being 22.53%.The correlation analysis results showed that the bolting rate in 2021 was significantly positively correlated with the bolting traits in 2022,and was extremely significantly correlated with the BLUE value.The BLUE value was highly significantly correlated with other traits except for no significant correlation with the bolt time in 2021.Based on the group structure analysis and cluster analysis,the associated groups were divided into four subgroups.Through a 2-year GWAS of the correlation among bolting traits,a total of 344 SNP marker loci were detected that were significantly correlated with bolting traits.Among them,20 multi-effect loci were significantly correlated with 2 or more bolting traits,and the same loci can be considered as the same SNP.Based on the annotation information,29 candidate genes related to bolting were screened,of which 14 genes had inhibitory effects on bolting and flowering,and 13 genes that promoted bolting and flowering were mainly related to the photoperiod pathway,vernalization pathway,and flowering integron.The mechanism of action of the other two genes was not yet clear and thus further verification is needed.[Conclusion]Multiple SNP loci associated with bolting traits were obtained by GWAS analysis,and related candidate genes were identified.
carrotgermplasm resourcesboltinggenome-wide association tudysnp marker
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