SSR analysis on genetic diversity of peach cultivars and comparison of different genetic similarity coefficients

Objective  To develop SSR primers based on peach ESTs in NCBI database, analyze genetic diversity of the major peach cultivars in Chengdu plain, investigate the applicability of different genetic similarity coefficients in SSR analysis of peach, and provide references for research on peach germplasm resources.

Method  In total 100 pairs of SSR primers selected from NCBI-EST database were used in PCR amplification for 12 peach cultivars with various morphology. Twenty primers which had high polymorphism and stability, and evenly distributed in eight linkage groups were selected for PCR amplification of 40 peach cultivars. Five genetic similarity coefficients were used to analyze the amplification results.

Result  Using 20 SSR primers, 68 polymorphic alleles were detected. The number of alleles per locus ranged from 2 to 5, with an average of 3.4. The polymorphism information content ranged from 0.36 to 0.73, and with an average of 0.54. The Jaccard genetic similarity coefficient ranged from 0.106 to 1.000. The Cophenetic correlation coefficient (r_c) of Jaccard coefficient was the highest being 0.772, followed by Dice coefficient being 0.719. The consistency of consensus trees between Dice and Jaccard coefficients were the highest with CI_c being 1.000. Nei's gene diversity index was 0.603 and 0.374 respectively at the species level and the level of different classified groups, the corresponding Shannon's information index was 1.041 and 0.591 respectively. The 40 peach cultivars were firstly divided into two major categories which were ornamental peach and edible peach, and then subdivided into different types of groups. The clustering result basically coincided with the traditional pedigree.

Conclusion  The SSR primers developed based on peach ESTs in NCBI database have high polymorphism and can be used for SSR analysis of peach. Jaccard and Dice coefficients are the most appropriate for SSR analysis of peach. In general, the genetic diversity of peach is abundant, but variation of the honey peach group is relatively low, and germplasm innovation of this group needs to be improved.