Determination of Chromosome Number and Genetic Diversity using SSR and RAPD Markers in Ziziphus jujuba Mill.

Abstract

Abstract The jujube is very important in Iran's horticultural sector and its value-added is very high for per cubic meter of water consumed. The chromosome number and genetic diversity of 25 jujube trees from different regions of South Khorasan province were assessed using 24 simple sequence repeat (SSR) and 16 random amplified polymorphic DNA (RAPD) markers. The polymorphism percentage was 100% and 67.59% with SSR and RAPD, respectively. The Shannon's information index (I), Nei's gene diversity (H), and effective allele (Ae) were higher for SSR (1.44, 0.72 and 4.21, respectively) than for RAPD (0.46, 0.30 and 1.49, respectively). A high level of genetic differentiation and low level of gene flow were detected by SSR (Fst= 0.29, Nm= 0.61) and RAPD (Gst= 0.47, Nm= 0.85). SSR identified 26 genotype-specific alleles while RAPD identified 3 unique bands. In SSR markers, the mean observed heterozygosity (0.67) was higher than mean expected heterozygosity (0.51), and the mean inbreeding coefficient was negative (-0.33), which indicated heterozygosity excess in the investigated samples. The cluster analysis classified the samples into 6, 7 and 6 groups based on SSR, RAPD, and SSR+RAPD, respectively. Although some of the examined samples were suckers from the same genotypes, they were distinguished by both markers, revealing a somatic mutation occurrence among them. In general, SSR had a better ability than RAPD to accommodate the suckers belonging to the same genotypes in the same groups. The chromosome number in all samples was diploid.