Assessing genetic integrity of Chinese jujube cultivars using Single Nucleotide Polymorphism (SNP) markers

Authors: SONG, LIHUA - Ningxia University; ZHANG, HAO - Ningxia University; LI, ZHANWEI - Ningxia University; Meinhardt, Lyndel; Zhang, Dapeng

Submitted to: Agronomy
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/10/2021
Publication Date: 11/15/2021
Citation: Song, L., Zhang, H., Li, Z., Meinhardt, L.W., Zhang, D. 2021. Assessing genetic integrity of Chinese jujube cultivars using Single Nucleotide Polymorphism (SNP) markers. Agronomy. 11:2303. https://doi.org/10.3390/agronomy11112303.
DOI: https://doi.org/10.3390/agronomy11112303

Interpretive Summary: Chinese jujube (Ziziphus jujuba Mill.) is an economically important fruit tree in Asia with outstanding adaptability to marginal land and fringe climate conditions. As a potential new crop for the Southwest region of the United States, jujube’s late-spring flushing makes it a good alternative crop to fruits that suffer late-spring frosts. However, a lack of germplasm information and high levels of mislabeling in the collection severely limit the use of the germplasm for breeding improvement in jujube. In the present study, 384 single nucleotide polymorphism (SNP) markers were developed and validated by genotyping 114 accessions of jujube germplasm accessions from China. A subset of 96 SNP markers was selected for further use such as jujube genebank management, verification of parental lines and pedigrees in breeding program, quality control for propagation of planting materials and support traceability and authentication of jujube products. This information will be used by plant breeders, germplasm curators, extension specialist and ultimately jujube producers to improve the utilization and productivity of this potential new tree crop.

Technical Abstract: Chinese jujube (Ziziphus jujuba Mill.) is an economically important fruit tree with outstanding adaptability to marginal land and a broad range of climate conditions. There are over 800 cultivars, mostly landraces from China. However, a high rate of mislabeling in Chinese jujube germplasm restricts the sharing of information and materials among jujube researchers and hampers the use of jujube germplasm in breeding. In the present study, we developed 384 single nucleotide polymorphism (SNP) markers and validated 384 SNPs by genotyping 114 accessions of Chinese jujube germplasm from China. The validation resulted in designation of a set of 192 polymorphic SNP markers that revealed a high rate of synonymous mislabeling in this jujube germplasm collection in Ningxia, China. A total of 17 groups of duplicates were detected, encompassing 49 of the 114 Chinese jujube cultivars. Model-based population stratification revealed two germplasm groups, which differ significantly between their core members (Fst = 0.16; P<0.01). The results supported the hypothesis that the cultivated Chinese jujube had a multiple origin and multiple domestication. The Neighbor-Joining dendrogram further revealed that this collection is constituted by numerous sub-groups, each including 1-13 closely related cultivars. Parentage analysis on cultivars with pedigree information proved efficacy of using these SNP markers for parentage verification. A subset of 96 SNP markers was selected for future downstream application including jujube genebank management, verification of parental lines and pedigrees in breeding program, quality control for propagation of planting materials and support traceability and authentication of jujube products.