Construction of a Genome-Wide Copy Number Variation Map and Association Analysis of Black Spot in Jujube

Copy number variation (CNV) is a common source of genomic structural variation by altering the number of DNA fragments, which in turn affects phenotypic variation and gene expression levels. However, there have been no reports of CNV in Chinese jujube (<i>Ziziphus jujuba</i> Mill.). In this study, we identified 16,570 CNVs from "Yuhong" × "Jiaocheng 5" and 140 hybrid progeny materials, of which 3607 CNVs were deletion type and 12,963 CNVs were duplication type. The distribution of CNVs in the Chinese jujube genome was systematically described, and the CNV genetic map of the whole genome level of the Chinese jujube hybrid offspring was constructed. Based on the field investigations, 13 individuals with severe black spot disease and no disease were analyzed for trait association. A total of 1837 CNVs were detected at the significant level of association, of which 1371 were duplication type and 466 were deletion type. And the GO (Gene Ontology) annotation item identified a systemic acquired resistance (SAR), and eight genes related to disease resistance were screened by the annotation. After validation by qPCR, these results further support the potential role in regulating black spot disease resistance. The constructed genome-wide CNV map of the hybrid progeny of Chinese jujube provides a new way of thinking for understanding the genetic basis of phenotypic variation of complex traits in Chinese jujube.