Characterization and comparison of EST-SSR and TRAP markers for genetic analysis of the Japanese persimmon Diospyros kaki

Luo, Chun; F, Zhang; Zhang, Q L; Guo, Dayong; Luo, Zhitian

doi:10.4238/2013.january.9.3

Cited by 10 publications

(9 citation statements)

References 35 publications

(35 reference statements)

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“…Comparing the similarity coefficient matrices obtained by the integration of SCoT+ISSR, SCoT and ISSR using the Mantel test, a high correlation coefficient was observed between the integrated data with SCoT (r = 0.9237) and ISSR (r = 0.8480), demonstrating that the information revealed by the SCoT+ISSR markers was more accurate; therefore, the integration of the SCoT and ISSR markers, in theory, was expected to decrease the effect of their independent inaccuracies and be more effective in detecting genomic variation and in realizing a better or more complete analysis of genetic diversity by covering different regions of the entire genome. This conclusion was similar to that of previous reports (Li et al, 2011;Luo et al, 2013;Rachayya et al, 2012). This is the first report to integrate SCoT and ISSR data to elaborate on the genetic relationships and diversity among sugarcane parental clones, which can help reveal the genetic diversity of sugarcane parental clones from different aspects, and provide a more scientific basis for the establishment of an effective system for the evaluation of genetic diversity in sugarcane.…”

Section: Discussionsupporting

confidence: 82%

Assessment of Genetic Relationship and Diversity among Chinese Sugarcane Parental Clones using SCoT and ISSR Markers

Chen¹,

Shen²,

Xu³

et al. 2017

IJAB

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Sugarcane is an allopolyploid crop with ≥120 or more chromosomes, of which~5.0-10% are Saccharum spontaneum and 90-95% are S. officinarum. The genetic characteristics of sugarcane provides a complex genetic background. The objective of this study was to use two molecular marker systems, start codon targeted (SCoT) and inter-simple sequence repeat (ISSR), to assess the genetic relationship and diversity of 75 sugarcane parental clones from Chinese sugarcane breeding program. Twenty-four SCoT primers produced 227 loci, of which 200 (88.11%) were polymorphic, whereas 15 ISSR primers resulted in a total of 146 loci, with 123 (84.25%) being polymorphic. Mean polymorphism information content values of 0.8152 and 0.8361 were detected using SCoT and ISSR primers, respectively. The genetic similarity coefficients ranged from 0.542 between ROC22 and HoCP95-988 to 0.831 between ROC25 and ROC20, with a mean value of 0.687 based on SCoT+ISSR data set. The unweighted pair group method of arithmetic averages (UPGMA) clusters and principal coordinate analysis (PCA) gave similar results. The 75 Chinese sugarcane parental clones were clustered into two main groups (A and B). Group A was primarily comprised of 42 clones from all Q-series, all CP-, HoCP-, or LCP-series, all YT-series and three Erianthus arundinaceus F4 innovative parental clones, etc., while 33 parental clones of Group B contained all TT-series, all GT-series, three Saccharum officinarum species, etc. The genetic similarity was high among the Q-series, CP-series, HoCP-series and YT-series. The genetic relationship was close among TT-series, GT-series and three S. officinarum species, while the genetic similarity between YT-series and TT-series or GT-series was low. There was an abundant genetic diversity among these sugarcane parental clones however the parental clones bred by the same breeding organization have a narrow genetic basis. This information was useful for selecting crossing parents and combinations. Correlation detection between SCoT and ISSR was not significant, but highly complementary, indicating that the combination of the two marker systems could avoid biases based on a single marker.

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Section: Discussionsupporting

confidence: 82%

Assessment of Genetic Relationship and Diversity among Chinese Sugarcane Parental Clones using SCoT and ISSR Markers

Chen¹,

Shen²,

Xu³

et al. 2017

IJAB

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“…Figure 1 shows the DNA amplification of the elite lineages of castor bean using TRAP markers. Studies using TRAP markers have been conducted with other crops: guaraná (total number of polymorphic bands ranged from 12 to 33, with 79% polymorphism, and fragment size between 100 and 800 bp) (Da Silva et al, 2016); Dendrobium (genotyped with 13 TRAP markers, obtaining 510 fragments, including 500 polymorphic fragments, and 97.8% polymorphism) (Feng et al, 2015); Diospyros kaki (genotyped with 36 combinations of TRAP primers with an amplification of 2184 fragments, of which 2072 were polymorphic fragments and 94.87% polymorphism) (Luo et al, 2013); and sugarcane (21 TRAP combinations, for sucrose synthesis, with an amplification of 340 polymorphic fragments, with an average of 16.2 fragments, and 9 TRAP combinations for drought tolerance, resulting in 155 polymorphic fragments, with an average of 17.2 fragments per primer combination) (Creste et al, 2010). These studies corroborate the results obtained for castor bean, because they show that TRAP markers are highly polymorphic and appropriate for studying genetic divergence and other applications, for example, mapping associations and QTLs.…”

Section: Resultsmentioning

confidence: 99%

Research Article Genetic divergence in elite castor bean lineages based on TRAP markers.

et al. 2017

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ABSTRACT. Castor bean (Ricinus communis L.) is a tropical plant of great commercial interest and a potential source of biodiesel. The development of genetically improved cultivars with high amounts of oil in the seeds and low ricin toxicity is crucial to increase the productivity of this crop. The use of TRAP (target region amplification polymorphism) markers to develop elite lineages and study genetic divergence is fundamental to advance the genetic improvement of this species. The goal of this study was to evaluate the genetic divergence among 40 elite lineages of R. communis, which belong to the NBIO-UFRB Genetic Improvement Program, using TRAP markers involved in the biosynthesis of oil and ricin. Total DNA was extracted and quantified from the leaf tissue of the castor bean plants, and 70 TRAP combinations (fixed and arbitrary primers) were used to genotype the 40 lineages. Of the 580 fragments amplified, 335 were polymorphic (58%). The genetic dissimilarity among the lineages was calculated by the Jaccard dissimilarity index using the UPGMA grouping method. A dendrogram was generated, and four groups formed, showing divergence among the elite lineages that favors selection. The TRAP 2 K.S. Simões et al. Genetics and Molecular Research 16 (3): gmr16039776 molecular markers were efficient at characterizing the genetic variability among the lineages and, because TRAP markers are functional markers involved in the biosynthesis of oil and ricin, they are important when studying the association between a marker and a candidate gene.

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“…Among the different molecular markers, SSRs, which are also called microsatellites, are the best-suited markers for genotyping the Diospyros genus (Luo et al, 2013). Guo and Luo (2006a, 2008, 2011 reported several SSR markers by ISSRsuppression PCR.…”

Section: Discussionmentioning

confidence: 99%

Development of simple sequence repeat markers in persimmon (Diospyros L.) and their potential use in related species

Yang¹,

Jing²,

Ruan³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Persimmon (Diospyros L.) is an economically important fruit in the world, and it has been recognized as a healthy nutrient supply for human consumption. In this study, 14 microsatellite markers were developed from an AG/TC and AC/TG-enriched genomic library of Chinese persimmon Mopanshi. Twelve polymorphic markers were selected in 4 related species; these markers showed transferability to the 4 related persimmon species. In addition, 10 simple sequence repeat (SSR) markers were used to detect the genetic diversity among 51 persimmon accessions from China, Japan, and Korea. A total of 57 polymorphic bands with an average of 5.7 bands per primer pair were observed. According to cluster analysis and principal coordinate analysis, all persimmon accessions could be divided into 4 groups. species of persimmon. These new SSR markers provide tools for evaluating genetic relatedness among different persimmon species.

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Characterization and comparison of EST-SSR and TRAP markers for genetic analysis of the Japanese persimmon Diospyros kaki

Cited by 10 publications

References 35 publications

Assessment of Genetic Relationship and Diversity among Chinese Sugarcane Parental Clones using SCoT and ISSR Markers

Assessment of Genetic Relationship and Diversity among Chinese Sugarcane Parental Clones using SCoT and ISSR Markers

Research Article Genetic divergence in elite castor bean lineages based on TRAP markers.

Development of simple sequence repeat markers in persimmon (Diospyros L.) and their potential use in related species

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