Genetic diversity of Ziziphus mauritiana germplasm based on SSR markers and ploidy level estimation

A set of reliable SSR markers were developed for Ziziphus mauritiana. The genetic relationship of Z. mauritiana germplasms was generally consistent with their geographical origin, and low diversity in the maternal lineage was revealed. Ziziphus mauritiana, known as Indian jujube, is an important fruit crop that is native to southern Asia and eastern Africa. There is a variety of germplasm resources, and particularly many new cultivars were selected and introduced into wide tropical regions in recent years. However, there are few practical molecular markers for cultivar authentication and genetic analysis. In this study, we developed 55 polymorphic nuclear SSR markers based on restriction-site associated DNA sequences and transcriptome sequencing. We selected 14 robust nSSR markers for further analysis of 117 Z. mauritiana accessions from four countries (45 from China, 39 from Vietnam, 25 from Pakistan and 8 from Myanmar). In total, 137 alleles were detected and DNA fingerprints for each accession were constructed. Cluster analysis based on the unweighted pair group method with arithmetic mean displayed that most accessions clustered consistently with their geographic origin. In addition, there was common and high degree polyploidization based on nSSR and flow cytometry analyses. Only two of the 50 SSR loci in noncoding regions from the chloroplast genome had polymorphisms, and 5 haplotypes in total were identified among the 117 accessions. Haplotype C with 89 accessions was the most dominant haplotype and presented in four countries. This indicates low diversity in the maternal lineage of tested Z. mauritiana germplasm. Our research provides reliable marker resources for cultivar authentication and new insights into the genetic diversity, polyploidization and domestication of Z. mauritiana.