Identifying the genetic diversity, genetic structure and a core collection of Ziziphus jujuba Mill. var. jujuba accessions using microsatellite markers

Abstract

Ziziphus is a genus of spiny shrubs and small trees in the Rhamnaceae family. This group has a controversial taxonomy, with more than 200 species described, including Chinese jujube (Ziziphus jujuba Mill. var. jujuba) and Indian jujube (Z. mauritiana), as well as several other important cultivated fruit crops. Using 24 SSR markers distributed across the Chinese jujube genome, 962 jujube accessions from the two largest germplasm repositories were genotyped with the aim of analyzing the genetic diversity and structure and constructing a core collection that retain high genetic diversity. A molecular profile comparison revealed 622 unique genotypes, among which 123 genotypes were genetically identical to at least one other accessions. STRUCTURE analysis and multivariate analyses (Cluster and PCoA) roughly divided the accessions into three major groups, with some admixture among groups. A simulated annealing algorithm and a heuristic algorithm were chosen to construct the core collection. A final core of 150 accessions was selected, comprising 15.6% of the analyzed accessions and retaining more than 99.5% of the total alleles detected. We found no significant differences in allele frequency distributions or in genetic diversity parameters between the chosen core accessions and the 622 genetically unique accessions. This work contributes to the understanding of Chinese jujube diversification and the protection of important germplasm resources.

Comparison of Representative and Custom Methods of Generating Core Subsets of a Carrot Germplasm Collection

“…See, for example, Upadhyaya et al (2003), Malosetti and Abadie (2001), Diwan et al (1995), and Xu et al (2016). See, for example, Upadhyaya et al (2003), Malosetti and Abadie (2001), Diwan et al (1995), and Xu et al (2016).…”

“…Morphological descriptors, agronomic performance, and neutral genetic markers such as simple sequence repeats (SSRs) or microsatellites have also been used to construct core collections. See, for example, Upadhyaya et al (2003), Malosetti and Abadie (2001), Diwan et al (1995), and Xu et al (2016). However, morphological classification does not always provide a good measure of genetic relatedness (Tanksley and McCouch, 1997).…”

Genetic variability and relationship studies of Ber Ziziphus nummularia (Burm. F.) using morphological and molecular markers

“…6,7 Zadber pulp contains 12-23% TSS, 0.13-1.42% acidity, 3.1-14.5% total sugars, 1.4-9.7% reducing sugars, 5.6% sucrose, 1.5% glucose, 2.1% fructose and 1.0% starch. 8 Zadber pulp is a rich source of vitamin C. 9 reported that ascorbic acid content in different cultivars ranged from 39-166 mg/100 g of pulp. Significant differences in allele frequency distributions and in genetic diversity parameters between the core accessions and the 622 genetically unique accessions done by 10 .…”

Genetic Improvement of Chinese Jujube for Disease Resistances: Status, Knowledge Gaps and Research Needs

“…Therefore, homonyms and synonyms are common among the names of jujube cultivars, and this restricts the sharing of correct information and materials among jujube researchers and hampers the use of jujube germplasm in breeding. Xu et al demonstrated that there was a high level of synonymous mislabeling (duplicates) in Chinese jujube germplasm, accounting for about half of the collection (47.3% of the 947 accessions) [53]. Song [54] used SNP markers to assess the genetic identity of 114 jujube cultivars and detected 17 synonymous groups, including 49 cultivars.…”