Development and mapping of peach candidate genes involved in fruit quality and their transferability and potential use in other Rosaceae species

Dantec, Loı̈ck Le; Cardinet, G.; Bonet, Julio; Fouché, Mathieu; Boudehri, Karima; Monfort, Amparo; Poëssel, Jean‐Luc; Moing, Annick; Dirlewanger, Elisabeth

doi:10.1007/s11295-010-0308-8

Cited by 24 publications

(21 citation statements)

References 67 publications

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“…In agreement with a previous report [7], the peach/nectarine phenotype was regarded as a dominant trait ( G locus). A total of 12 SNPs, covering about 7 Mb of LG 5 around the G locus, were mapped on the whole progeny (Figure 1).…”

Section: Resultssupporting

confidence: 91%

A Unique Mutation in a MYB Gene Cosegregates with the Nectarine Phenotype in Peach

et al. 2014

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Nectarines play a key role in peach industry; the fuzzless skin has implications for consumer acceptance. The peach/nectarine (G/g) trait was described as monogenic and previously mapped on chromosome 5. Here, the position of the G locus was delimited within a 1.1 cM interval (635 kb) based on linkage analysis of an F2 progeny from the cross ‘Contender’ (C, peach) x ‘Ambra’ (A, nectarine). Careful inspection of the genes annotated in the corresponding genomic sequence (Peach v1.0), coupled with variant discovery, led to the identification of MYB gene PpeMYB25 as a candidate for trichome formation on fruit skin. Analysis of genomic re-sequencing data from five peach/nectarine accessions pointed to the insertion of a LTR retroelement in exon 3 of the PpeMYB25 gene as the cause of the recessive glabrous phenotype. A functional marker (indelG) developed on the LTR insertion cosegregated with the trait in the CxA F2 progeny and was validated on a broad panel of genotypes, including all known putative donors of the nectarine trait. This marker was shown to efficiently discriminate between peach and nectarine plants, indicating that a unique mutational event gave rise to the nectarine trait and providing a useful diagnostic tool for early seedling selection in peach breeding programs.

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Section: Resultssupporting

confidence: 91%

A Unique Mutation in a MYB Gene Cosegregates with the Nectarine Phenotype in Peach

et al. 2014

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“…These CG studies have been mainly continued in peach with the assay of different ESTs developed and the search for genes responsible for fruit traits including quality (Trainotti et al 2003;Horn et al 2005;Ogundiwin et al 2009;Vecchietti et al 2009;Vizoso et al 2009;Bonghi et al 2010;Falchi et al 2010;Le Dantec et al 2010); development, abscission and ripening physiology (Rasori et al 2002); and storage (González-Agüero et al 2008;Ogundiwin et al 2008a;Basset et al 2009;Tittarelli et al 2009;Falara et al, 2011). Part of these results have been biologically validated by real time quantitative PCR (qRT-PCR) (Ogundiwin et al 2008a;Tittarelli et al 2009).…”

Section: Early Transcriptome Analysis Inmentioning

confidence: 99%

New approaches to Prunus transcriptome analysis

et al. 2011

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The recent sequencing of the complete genome of the peach offers new opportunities for further transcriptomic studies in Prunus species in the called post-genomics era. First works on transcriptome analysis in Prunus species started in the early 2000s with the development of ESTs (expressed sequence tags) and the analysis of several candidate genes. Later, new strategies of massive analysis (high throughput) of transcriptomes have been applied, producing larger amounts of data in terms of expression of a large number of genes in a single experiment. One of these systems is massive transcriptome analysis using cDNA biochips (microarrays) to analyze thousands of genes by hybridization of mRNA labelled with fluorescence. However, the recent emergence of a massive sequencing methodology ("deep-sequencing") of the transcriptome (RNA-Seq), based on lowering the costs of DNA (in this cases complementary, cDNA) sequencing, could be more suitable than the application of microarrays. Recent papers have described the tremendous power of this technology, both in terms of profiling coverage and quantitative accuracy in transcriptomic studies. Now this technology is being applied to plant species, including Prunus. In this work, we analyze the potential in using this RNA-Seq technology in the study of Prunus transcriptomes and the development of genomic tools. In addition, the strengths and limitations of RNA-Seq relative to microarray profiling have been discussed.

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“…But recently, the Rosaceae family including almond (Wu et al, 2008), apple (Chágne et al, 2008), peach, and strawberry (Le Dantec et al, 2010), and Japanese apricot (Fang et al, 2006) joined the bandwagon following the completion of genome sequencing projects for apple, peach, and strawberry. In fact, SNPs from Rosaceae conserved orthologous sequences have been used for comparative analysis of peach ( Prunus persicsa ), apple ( Malus x domestica ), and strawberry ( Fragaria spp) and recently, for determination of genetic relationships in 30 sweet cherry cultivars and for construction of a SNP-based map (Cabrera et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Relatedness of Sweet Cherry (Prunus Avium L.) Cultivars Based on Single Nucleotide Polymorphic Markers

Martí¹,

Athanson²,

Koepke³

et al. 2012

Front. Plant Sci.

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Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD, and simple sequence repeat (SSR) markers. This study was carried out to assess the utility of single nucleotide polymorphism (SNP) markers generated from 3′ untranslated regions (UTR) for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars, and old cultivars imported from different parts of the world were screened with seven SSR markers developed from other Prunus species and with 40 SNPs obtained from 3′ UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity, and polymorphic information content values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, “Stella” was separated from “Compact Stella.” This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3′ UTR SNPs for genetic fingerprinting, parentage verification, gene mapping, and study of genetic diversity in sweet cherry.

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Development and mapping of peach candidate genes involved in fruit quality and their transferability and potential use in other Rosaceae species

Cited by 24 publications

References 67 publications

A Unique Mutation in a MYB Gene Cosegregates with the Nectarine Phenotype in Peach

A Unique Mutation in a MYB Gene Cosegregates with the Nectarine Phenotype in Peach

New approaches to Prunus transcriptome analysis

Genetic Diversity and Relatedness of Sweet Cherry (Prunus Avium L.) Cultivars Based on Single Nucleotide Polymorphic Markers

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