Development and characterization of microsatellite markers for sour jujube (<i>Ziziphus jujuba</i>var.<i>spinosa</i>)

Zhang, Chunmei; Yin, Xiao; Li, Xingang; Huang, Jian; Wang, Changzhu; Lian, Chunlan

doi:10.5958/j.0975-6906.73.3.052

Cited by 6 publications

(3 citation statements)

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“…Compared with the genomic SSRs, EST-SSRs have several special advantages due to either a relatively higher transferability or a potential gene function [23] , which have been evaluated in many studies [24] – [27] . Currently, only a few SSR and EST-SSR primers have been developed in Chinese jujube [28] , [29] and sour jujube [30] . The lack of suitable mapping populations and larger high-throughput marker collection limits gene isolation and breeding in Chinese jujube.…”

Section: Introductionmentioning

confidence: 99%

De Novo Assembly and Characterization of the Fruit Transcriptome of Chinese Jujube (Ziziphus jujuba Mill.) Using 454 Pyrosequencing and the Development of Novel Tri-Nucleotide SSR Markers

Lin

et al. 2014

PLoS ONE

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Chinese jujube (Ziziphus jujuba Mill.) is an economically important deciduous tree that has high therapeutic value and health benefits. However, a lack of sequence data and molecular markers have constrained genetic and breeding studies for better fruit quality and other traits in Chinese jujube. In this study, two combined cDNA libraries of ‘Dongzao’ fruit representing the early and late stages of fruit development were constructed and sequenced on the 454 GS FLX Titanium platform. In total, 1,124,197 reads were generated and then de novo assembled into 97,479 unigenes. A total of 52,938 unigenes were homologous to genes in the NCBI non-redundant sequence database. A total of 33,123 unigenes were assigned to one or more Gene Ontology terms, and 16,693 unigenes were classified into 319 Kyoto Encyclopedia of Genes and Genomes pathways. The results showed that the Smirnoff-Wheeler pathway was the main pathway for the biosynthesis of ascorbic acid in Chinese jujube. The number of differentially expressed genes between the two stages of fruit development was 1,764, among which 974 and 790 genes were up-regulated and down-regulated, respectively. Furthermore, 9,893 sequences were identified containing SSRs. 93 primer pairs designed from the sequences with a tri-nucleotide repeat showed successful PCR amplification and could be validated in Chinese jujube accessions and Z. mauritiana Lam and Z. acidojujuba as well, of which 71 primer pairs were polymorphic. The obtained transcriptome provides a most comprehensive resource currently available for gene discovery and the development of functional markers in Z. jujuba. The newly developed microsatellite markers could be used in applications such as genetic linkage analysis and association studies, diversity analysis, and marker-assisted selection in Chinese jujube and related species.

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Section: Introductionmentioning

confidence: 99%

De Novo Assembly and Characterization of the Fruit Transcriptome of Chinese Jujube (Ziziphus jujuba Mill.) Using 454 Pyrosequencing and the Development of Novel Tri-Nucleotide SSR Markers

Lin

et al. 2014

PLoS ONE

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“…Among these markers, SSRs have become the genetic marker of choice due to a high reproducibility and ability to identify high levels of genetic polymorphism, co-dominance, broad genome distributions, and genetic diversity. A great amount of SSR markers have been developed for Z. jujuba 8 9 10 and sour jujube 11 ( Ziziphus jujuba var. spinosa), which have been used for linkage map construction (unpublished data) and genetic diversity estimations 4 5 .…”

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confidence: 99%

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

Gao

Du³

et al. 2016

Sci Rep

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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.

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“…jujuba var. spinosa 24 . The absence of high-throughput marker collection is a major bottleneck in conducting studies on population genetics and high density mapping in Z .…”

Section: Introductionmentioning

confidence: 99%

Transcriptome sequence analysis and mining of SSRs in Jhar Ber (Ziziphus nummularia (Burm.f.) Wight & Arn) under drought stress

Yadav

Lone

Gaikwad

et al. 2018

Sci Rep

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Ziziphus nummularia (Burm.f.) Wight & Arn., a perennial shrub that thrives in the arid regions, is naturally tolerant to drought. However, there are limited studies on the genomics of drought tolerance in Ziziphus sp. In this study, RNA-sequencing of one month old seedlings treated with PEG 6000 was performed using Roche GS-FLX454 Titanium pyrosequencing. A total of 367,176 raw sequence reads were generated, and upon adapter trimming and quality filtration 351,872 reads were assembled de novo into 32,739 unigenes. Further characterization of the unigenes indicated that 73.25% had significant hits in the protein database. Kyoto encyclopedia of genes and genomes database (KEGG) identified 113 metabolic pathways from the obtained unigenes. A large number of drought-responsive genes were obtained and among them differential gene expression of 16 highly induced genes was validated by qRT-PCR analysis. To develop genic-markers, 3,425 simple sequence repeats (SSRs) were identified in 2,813 unigene sequences. The data generated shall serve as an important reservoir for the identification and characterization of drought stress responsive genes for development of drought tolerant crops.

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Development and characterization of microsatellite markers for sour jujube (Ziziphus jujubavar.spinosa)

Cited by 6 publications

References 0 publications

De Novo Assembly and Characterization of the Fruit Transcriptome of Chinese Jujube (Ziziphus jujuba Mill.) Using 454 Pyrosequencing and the Development of Novel Tri-Nucleotide SSR Markers

De Novo Assembly and Characterization of the Fruit Transcriptome of Chinese Jujube (Ziziphus jujuba Mill.) Using 454 Pyrosequencing and the Development of Novel Tri-Nucleotide SSR Markers

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

Transcriptome sequence analysis and mining of SSRs in Jhar Ber (Ziziphus nummularia (Burm.f.) Wight & Arn) under drought stress

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