Assessment of genetic diversity of Prunus salicina 'Shazikongxinli' by morphological traits and molecular markers

Abstract

Prunus salicina 'Shazikongxinli' is one of China’s most economically valuable and reputable Prunus salicina cultivars. Understanding the genetic diversity and population structure of 'Shazikongxinli' is imperative for excellent germplasm breeding and the preservation of genetic resources. This work used morphological markers, inter-retrotransposon amplified polymorphism (IRAP), and inter simple sequence repeat (ISSR) to assess the genetic variation status of 50 'Shazikongxinli', with 18 plum cultivars selected as the control outgroup. The results showed that the average Shannon–Weaver diversity index (H') of 32 qualitative traits in 50 tests 'Shazikongxinli' was 0.557, the average coefficient of variation of 11 quantitative traits was 15.57%, and a total of 232 and 105 polymorphic loci were obtained from 22 IRAP and 15 ISSR primers, respectively. All three marker systems showed relatively rich polymorphism, especially the IRAP markers. This might be related to the nature of the retrotransposons in the IRAP markers, which might be more suitable for intraspecific variability detection than ISSR. In addition, all three markers clustered the 68 tested germplasms into two groups. All of 'Shazikongxinli' clustered into one group, and most outgroup plum cultivars clustered into another group. This suggested a relatively narrow genetic base within the 'Shazikongxinli' population. These results would be useful in understanding the genetic diversity of the germplasm resources of 'Shazikongxinli' and provide a basic theoretical reference for breeding superior germplasm.