ArticleBMC genomics2013
Heterogeneity in the entire genome for three genotypes of peach [Prunus persica (L.) Batsch] as distinguished from sequence analysis of genomic variants.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Genome-wide association analysis ofFrontiers in plant science · 2023Article
- MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation.Scientific reports · 2017Article
- Genome-Wide Single-Nucleotide Polymorphisms in CMS and Restorer Lines Discovered by Genotyping Using Sequencing and Association with Marker-Combining Ability for 12 Yield-Related Traits inFrontiers in plant science · 2017Article
- The First Molecular Identification of an Olive Collection Applying Standard Simple Sequence Repeats and Novel Expressed Sequence Tag Markers.Frontiers in plant science · 2017Article
- Evolutionary Genomics of Peach and Almond Domestication.G3 (Bethesda, Md.) · 2016Article
- Mutation rate analysis via parent-progeny sequencing of the perennial peach. I. A low rate in woody perennials and a higher mutagenicity in hybrids.Proceedings. Biological sciences · 2016Article
- Evolutionary origin of Rosaceae-specific active non-autonomous hAT elements and their contribution to gene regulation and genomic structural variation.Plant molecular biology · 2016Article
- Article
- Genomic variants of genes associated with three horticultural traits in apple revealed by genome re-sequencing.Horticulture research · 2014Article
- Genome-Wide Discovery of DNA Polymorphisms in Mei (Plant molecular biology reporterArticle
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5 authors.
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Abstract
backgroundPeach [Prunus persica (L.) Batsch] is an economically important fruit crop that has become a genetic-genomic model for all Prunus species in the family Rosaceae. A doubled haploid reference genome sequence length of 227.3 Mb, a narrow genetic base contrasted by a wide phenotypic variability, the generation of cultivars through hybridization with subsequent clonal propagation, and the current accessibility of many founder genotypes, as well as the pedigree of modern commercial cultivars make peach a model for the study of inter-cultivar genomic heterogeneity and its shaping by artificial selection.
resultsThe quantitative genomic differences among the three genotypes studied as genomic variants, included small variants (SNPs and InDels) and structural variants (SV) (duplications, inversions and translocations). The heirloom cultivar 'Georgia Belle' and an almond by peach introgression breeding line 'F8,1-42' are more heterogeneous than is the modern cultivar 'Dr. Davis' when compared to the peach reference genome ('Lovell'). A pair-wise comparison of consensus genome sequences with 'Lovell' showed that 'F8,1-42' and 'Georgia Belle' were more divergent than were 'Dr. Davis' and 'Lovell'.
conclusionsA novel application of emerging bioinformatics tools to the analysis of ongoing genome sequencing project outputs has led to the identification of a range of genomic variants. Results can be used to delineate the genomic and phenotypic differences among peach genotypes. For crops such as fruit trees, the availability of old cultivars, breeding selections and their pedigrees, make them suitable models for the study of genome shaping by artificial selection. The findings from the study of such genomic variants can then elucidate the control of pomological traits and the characterization of metabolic pathways, thus facilitating the development of protocols for the improvement of Prunus crops.
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