SSR-based population structure, molecular diversity and identity cards of Ziziphus species from Pakistan and China

Abstract

Research work on the genetic diversity within Pakistani and Chinese Ziziphus species is limited, and to date, no single report on the application of DNA barcoding attempt for identification of Ziziphus species is available in literature. Therefore, the current study was designed to assess diversity and relationships among Ziziphus species genotypes and to develop a unique identity card and for their conservation. The study has used 99 simple sequence repeats (SSR) markers for gaining insights into the genetic diversity within 200 genotypes of four Ziziphus species. Successful amplification was achieved with 59 SSRs; and was applied for understanding the population structure and relationships among the Ziziphus species/genotypes. Unique SSR fingerprints of three highly polymorphic loci were used for developing molecular identity cards for each genotype. A total of 158, 165, 168, 157 and 168 alleles were amplified from Z. jujuba Mill., Z. nummularia (Burm.f.) Wight & Arn., Z. oxyphylla Edgew. (Pakistani origin), Z. mauritiana Lam. and Z. jujuba Mill., (Chinese origin) respectively. Alleles per locus ranged from 2 to 6, averaging 2.83, 2.82, 3.366, 2.80 and 3.09. Analysis of molecular variance (AMOVA) revealed high genetic variability (83%) whereas; fixation index (0.014) and gene flow estimates (1.32) indicated frequent gene flow within Ziziphus species. STRUCTURE and PCA analysis resolved all genotypes into five populations. Further, molecular identity cards were developed for all genotypes. The overall results indicated prevalence of genetic variability and relationships among Ziziphus species; yet the same Z. jujuba species across geographical boundaries has retained unique alleles and this may facilitate development of agronomically desirable and genetically improved Ziziphus cultivars.