2019
DOI: 10.1038/s41438-018-0090-6
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Genetic characterization of worldwide Prunus domestica (plum) germplasm using sequence-based genotyping

Abstract: Prunus domestica commonly known as European plum is a hexaploid fruit tree species cultivated around the world. Locally it is used for fresh consumption, in jams or jellies, and the production of spirits while commercially the fruit is primarily sold dried (prunes). Despite its agricultural importance and long history of cultivation, many questions remain about the origin of this species, the relationships among its many pomological types, and its underlying genetics. Here, we used a sequence-based genotyping … Show more

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Cited by 69 publications
(75 citation statements)
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“…We observed very few high pair-wise similarities (i.e., >0.9), which is consistent with the lack of sports and/or Essentially Derived Varieties (EDV) originating from formal breeding [49]. A reduced number of nuclear SSRs offers obvious advantages for screening large populations however, we cannot exclude that a higher number of SSRs or the implementation of DNA sequence-based approaches [50], may be necessary to discriminate very similar varieties or to solve cases of putative homonymy.…”
Section: Discussionsupporting
confidence: 54%
“…We observed very few high pair-wise similarities (i.e., >0.9), which is consistent with the lack of sports and/or Essentially Derived Varieties (EDV) originating from formal breeding [49]. A reduced number of nuclear SSRs offers obvious advantages for screening large populations however, we cannot exclude that a higher number of SSRs or the implementation of DNA sequence-based approaches [50], may be necessary to discriminate very similar varieties or to solve cases of putative homonymy.…”
Section: Discussionsupporting
confidence: 54%
“…Genotyping-by-sequencing (GBS) libraries were prepared using a modified version of the methods of Elshire et al (2011), as described by Zhebentyayeva et al (2019). We followed all aspects of the GBS library preparation protocol of Zhebentyayeva et al (2019), with one exception—we double-digested DNA samples with Pst I and Mse I.…”
Section: Methodsmentioning
confidence: 99%
“…Genotyping-by-sequencing (GBS) libraries were prepared using a modified version of the methods of Elshire et al (2011), as described by Zhebentyayeva et al (2019). We followed all aspects of the GBS library preparation protocol of Zhebentyayeva et al (2019), with one exception—we double-digested DNA samples with Pst I and Mse I. Briefly, we performed double digestion of DNA samples, ligated fragments to Illumina sequencing adapters and custom barcoded adapters (see Appendix S4 for barcode sequences), pooled samples, then purified the pooled samples using a QIAquick PCR purification kit (Qiagen, Valencia, California, USA).…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…Overcoming the above-mentioned problems, DNA-based markers became widely applied in plum genetic diversity analysis, including random amplified polymorphic DNAs (RAPDs) [5,10], simple sequence repeats (SSRs) [11][12][13], inter-simple sequence repeats (ISSRs) [2,14]. In addition, benefiting from the advances in next-generation sequencing (NGS) technologies, genotyping by sequencing (GBS), provides a great wealth of information that makes it possible to identify thousands of single nucleotide polymorphisms (SNPs), which, after adequate filtering, allow us to carry out detailed genetic diversity studies [7,[15][16][17].…”
Section: Introductionmentioning
confidence: 99%