Association mapping of major economic traits and exploration of elite alleles in Prunus sibirica

Exploring elite alleles based on association analysis of economic traits will promote the breeding, development, and utilization of Prunus sibirica resources. This study used 113 P. sibirica clones with diverse provenances to perform association mapping of 20 economic traits based on 149 pairs of highly polymorphic simple sequence repeat (SSR) markers. Population structure analysis split the clones into three subgroups. General linear model (GLM) and mixed linear model (MLM) identified 117 SSR loci associated with 20 P. sibirica economic traits, specifically fruit (62 loci), nuclear (69), and kernel (46) traits. Phenotypic variation in these three sets of traits ranged 8.93–82.12% (GLM) or 0.23–84.82% (MLM), 10.96–56.65% (GLM) or 0.17–52.54% (MLM), and 5.17–59.41% (GLM) or 4.86–59.89% (MLM), respectively. Of the 117 marker SSR loci, 35 were simultaneously associated with two or more economic traits. In addition, phenotypic effects analysis identified 1842 elite alleles and seven typical materials related to key economic traits. We then designed elite parental combinations through crossing the typical materials. In conclusion, our study detected alleles and plant materials that allowed the identification of clones expressing desired traits of interest. These findings can be used for improved, targeted breeding of P. sibirica through marker-assisted selection.