A Genome-Scale Mining Of Single-Copy Nuclear Gene Markers For Ziziphus Jujuba Var. Spinosa And Implications For Genetic Study

Nowadays, the breeding of Ziziphus jujuba encounters substantial difficulties in cultivation process. The wild relative of jujube, Z. jujuba var. spinosa (also called sour jujube), has long been treated as the important gene pool for the genetic breeding of cultivated jujube. However, the mining of important functional genes in this significant lineage has been seldom manipulated due to the lack of information about genetic diversity and evolutionary history. In the present study, a novel set of single-copy nuclear gene markers were developed and characterized. Thirteen single-copy nuclear gene markers were developed following a genome-wide scanning of jujube genome. The single-copy nuclear gene markers showed relatively high level of nucleotide variation (pi= 0.00513, theta w= 0.00531). None of the results of neutrally tests showed significant difference, indicating that all the markers conformed to the neutral evolution model. STRUCTURE and phylogenetic analysis showed admixture of these two lineages, supporting the domestication of cultivated jujube from sour jujube. The single-copy nuclear gene markers are powerful for genetic study of Z. jujuba var. spinosa and provide useful genetic information for future protection and conservation management of this important lineage. Furthermore, these markers could be useful for future population genetics, phylogeney and phylogeographic research in Ziziphus, even in Rhamnaceae.