ArticleScientific reports2020
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.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
- A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.BMC genomics · 2025Article
- Genomic Variability Survey inInternational journal of molecular sciences · 2024Article
- Population structure and genetic diversity characterization of soybean for seed longevity.PloS one · 2022Article
- QTLs Identification for Iron Chlorosis in a Segregating Peach-Almond Progeny Through Double-Digest Sequence-Based Genotyping (SBG).Frontiers in plant science · 2022Article
- Genetic diversity of Norway spruce ecotypes assessed by GBS-derived SNPs.Scientific reports · 2021Article
- Tomato genomic prediction for good performance under high-temperature and identification of loci involved in thermotolerance response.Horticulture research · 2021Article
- Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants.Horticulture research · 2021Article
- The complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2021Article
- Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA.Scientific reports · 2021Article
- Fine-tuning the performance of ddRAD-seq in the peach genome.Scientific reports · 2021Article
- Biochemical Characterization and Differential Expression ofFrontiers in plant science · 2021Article
- Mapping Quantitative Trait Loci Associated With Graft (In)Compatibility in Apricot (Frontiers in plant science · 2021Article
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6 authors.
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Abstract
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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