Identification and characterization of 74 novel polymorphic EST-SSR markers in the tea plant, <i>Camellia sinensis</i>
 (Theaceae)

Jin, Qiang; Zhou, Yan; Lei, Chun; Yao, Ming-Zhe; Jin, Ji Qiang; Wang, Xin Chao; Chen, Liang

doi:10.3732/ajb.1000376

Cited by 50 publications

(27 citation statements)

References 8 publications

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“…The N A per locus at each SSR locus ranged from 3 to 6, with an average of 4.6, which is comparable to the polymorphisms at SSR loci reported in maize (2 to 13, with an average of 6.5; Labate et al, 2003), tea (2 to 7, with an average of 4.39; Ma et al, 2010), or cucumber (2 to 8, with an average of 3.44; Mu et al, 2008), respectively. In addition, the average PIC in this study was 0.45 compared to 0.31 and 0.51 reported in similar studies in other tomato populations (Tam et al, 2005;Benor et al, 2008).…”

Section: Discussionsupporting

confidence: 54%

Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers

Korir¹,

Diao²,

Tao³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. The genetic diversity and relationship of 42 tomato varieties sourced from different geographic regions was examined with EST-SSR markers. The genetic diversity was between 0.18 and 0.77, with a mean of 0.49; the polymorphic information content ranged from 0.17 to 0.74, with a mean of 0.45. This indicates a fairly high degree of diversity among these tomato varieties. Based on the cluster analysis using unweighted pair-group method with arithmetic average (UPGMA), all the tomato varieties fell into 5 groups, with no obvious geographical distribution characteristics despite their diverse sources. The principal component analysis (PCA) supported the clustering result; however, relationships among varieties were more complex in the PCA scatterplot than in the UPGMA dendrogram. This information about the genetic relationships between these tomato lines helps distinguish these 42 varieties and will be useful for tomato variety breeding and selection. We confirm that the EST-SSR marker system is useful for studying genetic diversity among tomato varieties. The high degree of polymorphism and the large number of bands obtained per assay shows that SSR is the most informative marker system for tomato genotyping for purposes of rights/protection and for the tomato industry in general. It is recommended that these varieties be subjected to identification using an SSR-based manual cultivar identification diagram strategy or other easy-to-use and referable methods so as to provide a complete set of information concerning genetic relationships and a readily usable means of identifying these varieties.

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Section: Discussionsupporting

confidence: 54%

Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers

Korir¹,

Diao²,

Tao³

et al. 2014

Genet. Mol. Res.

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“…DNA polymorphisms within and/or between the grape F 1 population from the cross between "Early Rose" and "Red Globe" varieties were investigated on the basis of EST-derived and non-EST SSR markers, and polymorphisms were observed based on allele frequencies at each locus examined. The number of alleles per locus at EST-derived and non-EST-SSR ranged from 2 to 6 and 2 to 5, respectively, with an average of 3.12 for EST-derived and 2.12 for non-EST SSRs, which is comparable to the polymorphisms at SSR loci that were reported in maize (2 to 13, with an average of 6.5; Labate et al, 2003), tea (2 to 7, with an average of 4.39; Ma et al, 2010), and cucumber (2 to 8, with an average of 3.44; Mu et al, 2008). The EST-derived SSR markers showed a maximum PIC value of 1 and a minimum PIC value of 0.33.…”

Section: Comparison Of Est-derived and Non-est Ssrssupporting

confidence: 56%

Characterization of EST-derived and non-EST simple sequence repeats in an F1 hybrid population of Vitis vinifera L.

Kayesh¹,

Bilkish²,

Liu³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. Among different classes of molecular markers, expressed sequence tags (ESTs) are a new resource for developing simple sequence repeat (SSR) functional markers for genotyping and genetic mapping in F 1 hybrid populations of Vitis vinifera L. Recently, because of the availability of an enormous amount of data for ESTs in the public domain, the emphasis has shifted from genomic SSRs to EST-SSRs, which belong to transcribed regions of the genome and may have a role in gene expression or function. The objective of this study was to assess the polymorphisms among 94 F 1 hybrids from "Early Rose" and "Red Globe" using 25 EST-derived and 25 non-EST SSR markers. A total collection of 362,375 grape ESTs that were retrieved from the National Center for Biotechnology Information (NCBI) and 2522 EST-SSR sequences were identified. From them, 205 primer pairs were randomly selected, including 176 pairs that were EST-derived and 29 non-EST SSR primer pairs, for polymerase chain reaction amplification. A total Characterization of EST and non-EST SSRs in grapevine of 131 alleles were amplified using 50 pairs of primers; 78 alleles were amplified using EST-derived SSR primers and 53 were from non-EST SSR primers. At most, 6 and 5 alleles were amplified by EST-derived and non-EST SSR primers, respectively. The EST-derived SSR markers showed a maximum polymorphic information content (PIC) value of 1 and a minimum of 0.33 while non-EST SSR markers had maximum and minimum PIC values of 1 and 0.25, respectively. The average PIC value was 0.56 for EST-derived SSR markers and 0.45 for non-EST SSR markers.

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“…Compared to dominant markers, SSR markers are co-dominant, highly reproducible, multi-allelic, and widely used in plant sciences (Hajmansoor et al, 2013) for germplasm characterization (Varshney et al, 2005;Peng et al, 2015;Queiroz et al, 2015), identification of genetic diversity (Gurcan et al, 2015;Jo et al, 2015;Mahjbi et al, 2016;Mornkham et al, 2016;Neiva et al, 2016), germplasm fingerprinting (Zhang et al, 2015), and integration of genetic linkage maps (Lai et al, 2013). For C. sinensis, SSR markers have been widely used to identify germplasm genetic diversity (Taniguchi et al, 2014), construction of linkage maps (Tan et al, 2013) and DNA-fingerprinting (Ujihara et al, 2009;Ma et al, 2010). Based on the C. sinensis sequences in the NCBI (National Center for Biotechnology Information), three SSR markers for C. japonica were developed (Ueno and Tsumura, 2009).…”

Section: Introductionmentioning

confidence: 99%

Genetic relationships in a germplasm collection of Camellia japonica and Camellia oleifera using SSR analysis

Zhao¹,

Ruan²,

Ding³

et al. 2017

Genet. Mol. Res.

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Identification and characterization of 74 novel polymorphic EST-SSR markers in the tea plant, Camellia sinensis (Theaceae)

Abstract: These new polymorphic and transferable EST-SSR markers will have potential for applications in genetic diversity evaluation, molecular fingerprinting identification, comparative genomics analysis, and genetic mapping in the tea plant.

Cited by 50 publications

References 8 publications

Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers

Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers

Characterization of EST-derived and non-EST simple sequence repeats in an F1 hybrid population of Vitis vinifera L.

Genetic relationships in a germplasm collection of Camellia japonica and Camellia oleifera using SSR analysis

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