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

Abstract Prunus salicina 'Shazikongxinli' is one of the most economically valuable and reputable Prunus salicina varieties in China. Understanding the genetic diversity and population structure of 'Shazikongxinli' is crucial for excellent germplasm breeding and conservation of genetic resources. In the present study, the genetic variation status of 50 'Shazikongxinli' was assessed using morphological traits, IRAP and ISSR markers, while 18 other plum varieties were selected as outgroups. The results show that the average Shannon-Weaver diversity index (H') of 32 qualitative traits in 50 test 'Shazikongxinli' is 0.557, the average coefficient of variation of 11 quantitative traits is 15.57%, and a total of 232 and 105 polymorphic loci are obtained from 22 IRAP and 15 ISSR primers, respectively. All three marker systems show relatively rich polymorphism, especially the IRAP markers. This may be related to the nature of the retrotransposons in the IRAP markers, which may be more suitable for intraspecific variability detection than ISSR. In addition, all three markers cluster the 68-test germplasm into two groups, with all of 'Shazikongxinli' clustered into one group and most of the other plum varieties as outgroups clustered into another group. This suggests a relatively narrow genetic base within the current 'Shazikongxinli'. These results will be useful in understanding the genetic diversity of the germplasm resources of 'Shazikongxinli' and provide comprehensive information for the breeding of superior germplasm.