Genome-wide SSR marker analysis to understand the genetic diversity and population sub-structure in Akebia trifoliata

Abstract

Genetic diversity is usually regarded as an important role for understanding the origin, evolution and environmental adaptation of species. A total of 174 living collections of Akebia trifoliata and 72 highpolymorphism-potential (HPP) simple sequence repeat (SSR) markers were employed to systematically explore the diversity and structure of this species. The average number of alleles (Na), Shannon's information index (I), number of effective alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He) and polymorphism information content (PIC) values were 9.01, 1.64, 4.98, 0.56, 0.72 and 0.69, respectively, and the linkage disequilibrium (LD) locus pairs percentage was on 1.17%. The PIC value of AK78 was the highest (0.92), while that of AK53 was the lowest (0.21). Sixty of 72 loci exhibited high polymorphism, while only one exhibited low polymorphism. In addition, the average PIC of chromosomes varied from 0.56 to 0.79. The genetic diversity of the SCB population was the highest, while that of NQH was the lowest. Further analysis of SCB suggested that JSJ-MJ, in the main part of the Heng Duan Mountain zone, had the highest genetic diversity and could be the origin centre of A. trifoliata. The main migration route of A. trifoliata could have been latitudinally from western to eastern China along the Yangtze River. Structure, cluster and principal coordinate analyses yielded similar results, revealing that the 6 populations could be divided into 2 groups or clusters. The geographic origin of several unknown accessions, such as Alc-166, Alc-171, Alc-172 and Alc-174, was revealed by cluster analysis. Overall, the results suggested that the living collections of A. trifoliata had high genetic diversity, good representativeness, and low duplication, which will bene t A. trifoliata germplasm collection, preservation, and breeding applications.