A Chinese jujube (Ziziphus jujuba Mill.) fruit-expressed sequence tag (EST) library: Annotation and EST-SSR characterization

Li, Jun; Liu, Huabo; Ma, Liying; Wang, Siqi; Gao, Junying; Li, Yingyue; Wu, Rongling; Pang, Xiaoming

doi:10.1016/j.scienta.2013.10.033

Cited by 26 publications

(21 citation statements)

References 48 publications

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“…Molecular markers are widely used to assess genetic diversity and to study the relationships among genotypes and populations of many species. To study the genetic diversity of the genus Ziziphus, the ISSR, RADP, SSR, SRAP markers have been widely used on Ziziphus spina-christi (Alansi et al, 2016;Moustafa et al 2016), Ziziphus mauritiana (Singh et al 2007;Singh et al 2014), Ziziphus jujuba (Li et al 2010;Ma et al 2011;Liu et al 2014;Zhang et al 2015;) and Ziziphus lotus (González-Robles et al 2016). Our work is the first to study the molecular diversity between natural populations of Ziziphus lotus L. Desf through several environments in Algeria and the second in the world.…”

Section: Discussionmentioning

confidence: 95%

GENETIC DIVERSITY OF FRUITS IN WILD JUJUBE (Ziziphus lotus L. DESF.) NATURAL POPULATIONS FROM ALGERIA

Dahlia¹,

Benito²,

Boussaid³

2019

AgricultForest

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Fruits from natural populations of wild jujube (Ziziphus lotus L. Desf.) collected from Algeria were evaluated through morphological and molecular markers. The analysis of variance revealed very highly significant differences for all the morphological characters studied (P <0.001) with coefficients of variation ranging from 7.57% to 31.84% indicating a strong variation between populations. The analysis of genetic diversity between Ziziphus lotus populations using 35 ISSR primers showed a moderate polymorphism (61.31%), a polymorphism information content of 0.35, a resolving power of 2.51 and a marker index of 0.79. Cluster analysis using SM model, classify the nine populations in two main clusters. This classification seems independent to climate change.

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Section: Discussionmentioning

confidence: 95%

GENETIC DIVERSITY OF FRUITS IN WILD JUJUBE (Ziziphus lotus L. DESF.) NATURAL POPULATIONS FROM ALGERIA

Dahlia¹,

Benito²,

Boussaid³

2019

AgricultForest

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“…The final assembly of Chinese jujube genome spans 437.65Mb (98.6% of the estimated size) with 321.45Mb anchored to the 12 pseudo-chromosomes (Liu et al, 2014). The 12 pseudochromosomes sequences were downloaded from GenBank (accession number: CM003114-CM003125) and scanned using MSDB v2.4 software (http://msdb.biosv.com) to identify all perfect microsatellites (Weber, 1990).…”

Section: Ssr Identification and Primer Designmentioning

confidence: 99%

“…Several studies have reported the development of SSR markers for jujube. For example, 66 expressed sequence tag-SSRs were developed from a Chinese jujube fruit cDNA library and amplified in six cultivars, but without evaluation of polymorphism (Liu et al, 2014). Using selectively amplified microsatellites, Ma, Wang & Liang (2011) constructed a set of 25 primer pairs, and an additional 31 primer pairs were developed from SSR-enriched genomic libraries (Wang et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

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Peer Review #1 of "Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.) (v0.1)"

Smulders¹

2016

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Chinese jujube (Ziziphus jujuba Mill. [Rhamnaceae]), native to China, is a major dried fruit crop in Asia. Although many simple sequence repeat (SSR) markers are available for phylogenetic analysis of jujube cultivars, few of these are validated on the level of jujube populations. In this study, we first examined the abundance of jujube SSRs with repeated unit lengths of 1-6 base pairs, and compared their distribution with those in Arabidopsis thaliana. We identified 280,596 SSRs in the assembled genome of jujube. The density of SSRs in jujube was 872.60 loci/Mb, which was much higher than in A. thaliana (221.78 loci/Mb). (A+T)-rich repeats were dominant in the jujube genome. We then randomly selected 100 SSRs in the jujube genome with long repeats and used them to successfully design 70 primer pairs. After screening using a series of criteria, a set of 20 fluorescently labeled primer pairs was further selected and screened for polymorphisms among three jujube populations. The average number of alleles per locus was 12.8. Among the three populations, mean observed and expected heterozygosities ranged from 0.858 to 0.967 and 0.578 to 0.844, respectively. After testing in three populations, all SSRs loci were in Hardy-Weinberg equilibrium (HWE) in at least one population. Finally, removing high null allele frequency loci and linked loci, a set of 17 unlinked loci was in HWE. These markers will facilitate the study of jujube genetic structure and help elucidate the evolutionary history of this important fruit crop.

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“…potassium, iron), etc. (Gao et al, 2011;Liu et al, 2014;Sun et al, 2008;Wang et al, 2011). Its extracts are used as food additives, such as analeptic, palliative, and antibacterial materials (Li, Ai, Yang, Liu, & Shan, 2013).…”

Section: Introductionmentioning

confidence: 99%

Winter jujube (Zizyphus jujuba Mill.) quality forecasting method based on electronic nose

et al. 2015

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A Chinese jujube (Ziziphus jujuba Mill.) fruit-expressed sequence tag (EST) library: Annotation and EST-SSR characterization

Cited by 26 publications

References 48 publications

GENETIC DIVERSITY OF FRUITS IN WILD JUJUBE (Ziziphus lotus L. DESF.) NATURAL POPULATIONS FROM ALGERIA

GENETIC DIVERSITY OF FRUITS IN WILD JUJUBE (Ziziphus lotus L. DESF.) NATURAL POPULATIONS FROM ALGERIA

Peer Review #1 of "Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.) (v0.1)"

Winter jujube (Zizyphus jujuba Mill.) quality forecasting method based on electronic nose

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