Genetic characterization of worldwide Prunus domestica (plum) germplasm using sequence-based genotyping

Zhebentyayeva, Tetyana; Shankar, Vijay; Scorza, R.; Callahan, Ann M.; Ravelonandro, Michel; Castro, Sarah; DeJong, Theodore M.; Saski, Christopher; Dardick, Chris

doi:10.1038/s41438-018-0090-6

Cited by 67 publications

(75 citation statements)

References 44 publications

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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%

Molecular and Phenotypic Diversity of Traditional European Plum (Prunus domestica L.) Germplasm of Southern Italy

et al. 2019

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The European plum (Prunus domestica L.) is a worldwide distributed tree species. Italy has an ample number of traditional varieties, but many are neglected and at risk of extinction. This germplasm is still cultivated in rural areas in spite of the EU-28 crisis of the stone fruit sector. Traditional European plum varieties remain poorly characterized, strongly limiting their promotion in local markets, use for farm diversification, and exploitation for local gastronomic products. In this study, we carried out an investigation of the morphological and genetic diversity present in an ex-situ collection of 29 traditional varieties of P. domestica of the Campania region (Southern Italy). The combination of five continuous and five categorical fruit traits allowed us to phenotypically distinguish all the varieties. Similarly, the Simple Sequence Repeats (SSRs) employed (five genomic and five deriving from Expressed Sequence Tags) identified a unique molecular profile for each variety. Moreover, the data indicated that the phenotypic and molecular investigations provided different clustering, suggesting that the two analyses sampled different sources of diversity. The number and the distribution of the scored phenotypes as well as the indices of genetic diversity imply the presence of a wide-ranging variation, which may sustain the development of high-value, niche market products. Our work provided evidence that the implementation of measures for a combination of ex-situ and on-farm conservation of traditional European plum varieties should be preferred to avoid the loss of an ample diversity.

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Section: Discussionsupporting

confidence: 54%

Molecular and Phenotypic Diversity of Traditional European Plum (Prunus domestica L.) Germplasm of Southern Italy

et al. 2019

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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%

“…Data processing of Illumina reads was performed using Clemson University’s Palmetto Cluster high-performance computing resource as described by Zhebentyayeva et al (2019). Default settings of the Stacks 1.45 program ‘process_radtags’ (Catchen et al, 2011; Catchen et al, 2013; Rochette and Catchen, 2017) were used to demultiplex raw Illumina reads according to barcodes, discard reads with uncalled bases, discard reads with low quality scores, and filter reads for the presence of Pst I and Mse I restriction sites.…”

Section: Methodsmentioning

confidence: 99%

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Genome-wide sequence-based genotyping supports a nonhybrid origin ofCastanea alabamensis

Perkins

Zhebentyayeva

et al. 2019

Preprint

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The genus Castanea in North America contains multiple tree and shrub taxa of 10 conservation concern. The two species within the group, American chestnut (Castanea dentata) 11 and chinquapin (C. pumila sensu lato), display remarkable morphological diversity across their 12 distributions in the eastern United States and southern Ontario. Previous investigators have 13 hypothesized that hybridization between C. dentata and C. pumila has played an important role 14 in generating morphological variation in wild populations. A putative hybrid taxon, Castanea 15 alabamensis, was identified in northern Alabama in the early 20th century; however, the 16 question of its hybridity has been unresolved. We tested the hypothesized hybrid origin of C. 17 alabamensis using genome-wide sequence-based genotyping of C. alabamensis, all currently 18 recognized North American Castanea taxa, and two Asian Castanea species at >100,000 single-19 nucleotide polymorphism (SNP) loci. With these data, we generated a high-resolution 20 phylogeny, tested for admixture among taxa, and analyzed population genetic structure of the 21 study taxa. Bayesian clustering and principal components analysis provided no evidence of 22 admixture between C. dentata and C. pumila in C. alabamensis genomes. Phylogenetic analysis 23 of genome-wide SNP data indicated that C. alabamensis forms a distinct group within C. pumila 24 sensu lato. Our results are consistent with the model of a nonhybrid origin for C. alabamensis. 25 Our finding of C. alabamensis as a genetically and morphologically distinct group within the 26 North American chinquapin complex provides further impetus for the study and conservation of 27 the North American Castanea species. 28 29

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“…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%

Genetic diversity analysis of Chinese plum (Prunus salicinaL.) based on whole-genome resequencing

Xiao

Shen

Zhang

et al. 2020

Preprint

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Chinese plum (Prunus salicina L.), also known as Japanese plum, is gaining importance due to their extensive genetic diversity and nutritional attributes beneficial for human health. Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. Here, we construed high-density haplotype map by whole-genome resequencing of 67 Prunus accessions with a depth of ~20× to evaluate the genome-level diversity and population structure. The phylogenetic analysis, the principal component analysis, and the population structure profiling, indicated that the 67 plum accessions could be classified into four groups corresponding to their origin location, the southern cultivar group (SCG), the northern cultivar group (NCG), the foreign cultivar group (FG), and the mixed cultivar group (MG). Some cultivars from South China were clustered with the other three groups. The genetic diversity indices including the private allele number, the observed heterozygosity, the expected heterozygosity, and the nucleotide diversity of the SCG were higher than those of the NCG. The gene flow from the SCG to the FG was detected as well. We concluded that the origin center of Chinese plum was at the Yangtze River Basin in South China. This study provided genetic variation features and population structure of Chinese plum cultivars, laying a foundation for breeders to use diverse germplasm and allelic variants for improving Chinese plum varieties.

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Genetic characterization of worldwide Prunus domestica (plum) germplasm using sequence-based genotyping

Cited by 67 publications

References 44 publications

Molecular and Phenotypic Diversity of Traditional European Plum (Prunus domestica L.) Germplasm of Southern Italy

Molecular and Phenotypic Diversity of Traditional European Plum (Prunus domestica L.) Germplasm of Southern Italy

Genome-wide sequence-based genotyping supports a nonhybrid origin ofCastanea alabamensis

Genetic diversity analysis of Chinese plum (Prunus salicinaL.) based on whole-genome resequencing

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