Mining single nucleotide polymorphism (Snp) markers for accurate genotype identification and diversity analysis of chinese jujube (ziziphus jujuba mill.) germplasm

10Citations
Citations of this article
9Readers
Mendeley users who have this article in their library.

Abstract

Chinese jujube (Ziziphus jujuba Mill.) is an economically important fruit tree with out-standing adaptability to marginal lands 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 a large panel of single nucleotide polymorphism (SNP) markers and validated 288 SNPs by genotyping 114 accessions of Chinese jujube germplasm. The validation resulted in the designation of a set of 192 polymorphic SNP markers that revealed a high rate of synonymous mislabeling in the 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, and the core members of the two groups showed a significant genetic differentiation (Fst = 0.16). The results supported the hypothesis that the cultivated Chinese jujube had multiple origins and multiple regions of domestication. The Neighbor-Joining dendrogram further revealed that this collection is comprised of multiple sub-groups, each including 1-13 closely related cultivars. Parentage analysis of cultivars with known pedigree information proved the efficacy of using these SNP markers for parentage verification. A subset of 96 SNPs with high information index was selected for future downstream application including gene bank management, verification of pedigrees in breeding programs, quality control for propagation of planting materials and support of the traceability and authentication of jujube products.

References Powered by Scopus

Fast and accurate short read alignment with Burrows-Wheeler transform

35156Citations
N/AReaders
Get full text

Inference of population structure using multilocus genotype data

28625Citations
N/AReaders
Get full text

The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

19348Citations
N/AReaders
Get full text

Cited by Powered by Scopus

Implementation of relevant fourth industrial revolution innovations across the supply chain of fruits and vegetables: A short update on Traceability 4.0

53Citations
N/AReaders
Get full text

Haplotype Analysis of Chloroplast Genomes for Jujube Breeding

18Citations
N/AReaders
Get full text

Non-destructive Identification of the geographical origin of red jujube by near-infrared spectroscopy and fuzzy clustering methods

5Citations
N/AReaders
Get full text

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Cite

CITATION STYLE

APA

Song, L., Cao, B., Zhang, Y., Meinhardt, L. W., & Zhang, D. (2021). Mining single nucleotide polymorphism (Snp) markers for accurate genotype identification and diversity analysis of chinese jujube (ziziphus jujuba mill.) germplasm. Agronomy, 11(11). https://doi.org/10.3390/agronomy11112303

Readers' Seniority

Tooltip

Professor / Associate Prof. 1

33%

PhD / Post grad / Masters / Doc 1

33%

Researcher 1

33%

Readers' Discipline

Tooltip

Agricultural and Biological Sciences 3

75%

Economics, Econometrics and Finance 1

25%

Article Metrics

Tooltip
Mentions
Blog Mentions: 1

Save time finding and organizing research with Mendeley

Sign up for free