Development and applicability of GBS approach for genomic studies in Japanese plum (<i>Prunus salicina</i> Lindl.)

Salazar, J.; Pacheco, Igor; Zapata, Patricio; Shinya, Paulina; Ruiz, David; Martínez‐Gómez, Pedro; Infante, Rodrigo

doi:10.1080/14620316.2018.1543559

Cited by 9 publications

(11 citation statements)

References 39 publications

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“…SNPs identified from GBS have been previously used in Prunus for phylogenetic and population structure analysis in apricot 37 using 90 accessions of different origins and DNA digestion using ApeKI restriction enzyme. Single-digest GBS was also used for phylogenetic analysis using 11 Japanese plum cultivars to explore their natural allelic diversity in relation to the most important phenology events and fruit quality traits 38 . In this work, we used a double-digest strategy (PstI/MspI) and deep coverage paired-end sequencing for genome-wide representation of each Prunus sample.…”

Section: Discussionmentioning

confidence: 99%

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Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function

Guajardo

Solís

Almada

et al. 2020

Sci Rep

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Genotyping-by-Sequencing (GBS) was applied in a set of 53 diploid Prunus rootstocks and five scion cultivars from three subgenera (Amygdalus, Prunus and Cerasus) for genome-wide SNP identification and to assess genetic diversity of both Chilean and Spanish germplasm collections. A group of 45,382 high quality SNPs (MAF >0.05; missing data <5%) were selected for analysis of this group of 58 accessions. These SNPs were distributed in genic and intergenic regions in the eight pseudomolecules of the peach genome (Peach v2.0), with an average of 53% located in exonic regions. The genetic diversity detected among the studied accessions divided them in three groups, which are in agreement with their current taxonomic classification. SNPs were classified based on their putative effect on annotated genes and KOG analysis was carried out to provide a deeper understanding of the function of 119 genes affected by high-impact SNPs. Results demonstrate the high utility for Prunus rootstocks identification and studies of diversity in Prunus species. Also, given the high number of SNPs identified in exonic regions, this strategy represents an important tool for finding candidate genes underlying traits of interest and potential functional markers for use in marker-assisted selection.

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Section: Discussionmentioning

confidence: 99%

“…In Prunus species, single-digest GBS has been used for identification of a high number of SNPs for linkage maps construction [32][33][34][35] and analysis of population genetic structure [36][37][38] . The use of double-digest GBS in Prunus has not been reported as far as the authors know.…”

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confidence: 99%

Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function

Guajardo

Solís

Almada

et al. 2020

Sci Rep

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“…Pigment changes during Japanese dogwood fruit development can be associated with the shift of colour from green‐orange hues, known to be generated by chlorophyll and carotenoid compounds, 39 to red tones, defined by anthocyanin pigments. Chlorophyll breakdown is common in latter stages of fruit development and has previously been investigated in apple, persimmon and several other fruit species 39–41 …”

Section: Resultsmentioning

confidence: 99%

“…Chlorophyll breakdown is common in latter stages of fruit development and has previously been investigated in apple, persimmon and several other fruit species. [39][40][41] Data on lipophilic antioxidants in lesser-known fruit species are very scarce and no study has ever reported their composition in Cornus fruit. Lower contents of tocopherols and plastid pigments have been reported for Sorbus aria and Sorbus aucuparia fruits.…”

Section: Tocopherols and Plastid Pigmentsmentioning

confidence: 99%

Physico‐chemical characterization of Cornus kousa Burg. fruit: determining optimal maturity for fresh consumption

et al. 2020

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BACKGROUND: Japanese dogwood (Cornus kousa Burg.) is a popular ornamental plant which develops edible compound fruit utilized in traditional Asian medicine. Previous compositional studies have focused on a small fraction of secondary metabolites at a single maturity stage. In order to address the question of optimal ripeness of Japanese dogwood fruit for consumption the study provides a comprehensive insight into its primary and secondary metabolic profile. RESULTS: The aim of the study was to investigate biochemical composition and morphological traits of Japanese dogwood (Cornus kousa Burg.) fruit at four maturity stages: GF, green fruit; BF, fruit with a defined red blush; RF, ripe fruit; OF, over-ripe fruit. Fruit was characterized by a nearly spherical shape, decreased water content in later stages of ripeness and highest a* values at RF and OF stages. Total sugars increased significantly from GF to OF stage and total organic acids and vitamin C decreased with maturation. Japanese dogwood fruit was characterized by four major phenolic groups: anthocyanins (three), flavonols (eight) hydroxycinnamic acids (three) and flavonoids (one) as well as by four lipophilic antioxidants: tocopherols (two), xanthophylls (five), carotenes (two) and chlorophylls (two). The progression of fruit ripening caused faster accumulation of individual phenolic compounds and lipophilic antioxidants which resulted in significantly higher total phenolic content at the RF and OF stages. CONCLUSION: Japanese dogwood fruit is a rich alternative source of ascorbic acid, ⊍-tocopherol, flavonols and anthocyanins and should be consumed fresh at fully developed red colour of compound berries when their composition is optimal.

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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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Development and applicability of GBS approach for genomic studies in Japanese plum (Prunus salicina Lindl.)

Cited by 9 publications

References 39 publications

Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function

Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function

Physico‐chemical characterization of Cornus kousa Burg. fruit: determining optimal maturity for fresh consumption

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

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