High density SNP mapping and QTL analysis for fruit quality characteristics in peach (Prunus persica L.)

Martínez-García, Pedro J.; Parfitt, Dan E.; Ogundiwin, Ebenezer A.; Fass, Joseph; Chan, Helen M.; Ahmad, Riaz; Lurie, Susan; Dandekar, Abhaya M.; Gradziel, Thomas M.; Crisosto, Carlos H.

doi:10.1007/s11295-012-0522-7

Cited by 93 publications

(83 citation statements)

References 55 publications

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“…These results could be explained by a misassembly in this region of peach genome (Verde et al 2013). Similar results have been obtained in other works of peach linkage mapping using SNP markers (Eduardo et al 2012;Martinez-Garcia et al 2013b). …”

Section: Ssr Marker Genotyping and Linkage Mapsupporting

confidence: 91%

QTL mapping for brown rot (Monilinia fructigena) resistance in an intraspecific peach (Prunus persica L. Batsch) F1 progeny

Pacheco

Bassi

Eduardo

et al. 2014

Tree Genetics & Genomes

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Brown rot (BR) caused by Monilinia spp. leads to significant post-harvest losses in stone fruit production, especially peach. Previous genetic analyses in peach progenies suggested that BR resistance segregates as a quantitative trait. In order to uncover genomic regions associated with this trait and identify molecular markers for assisted selection (MAS) in peach, an F1 progeny from the cross "Contender" (C, resistant)×"Elegant Lady" (EL, susceptible) was chosen for quantitative trait loci (QTL) analysis. Over two phenotyping seasons, skin (SK) and flesh (FL) artificial infections were performed on fruits using a Monilinia fructigena isolate. For each treatment, infection frequency (if) and average rot diameter (rd) were scored. Significant seasonal and intertrait correlations were found. Maturity date (MD) was significantly correlated with disease impact. Sixty-three simple sequence repeats (SSRs) plus 26 single-nucleotide polymorphism (SNP) markers were used to genotype the C×EL population and to construct a linkage map. C×EL map included the eight Prunus linkage groups (LG), spanning 572.92 cM, with an average interval distance of 6.9 cM, covering 78.73 % of the peach genome (V1.0). Multiple QTL mapping analysis including MD trait as covariate uncovered three genomic regions associated with BR resistance in the two phenotyping seasons: one containing QTLs for SK resistance traits near M1a (LG C× EL-2, R 2 =13.1-31.5 %) and EPPISF032 (LG C×EL-4, R 2 = 11-14 %) and the others containing QTLs for FL resistance, near markers SNP_IGA_320761 and SNP_IGA_321601 (LG3, R 2 =3.0-11.0 %). These results suggest that in the C× EL F1 progeny, skin resistance to fungal penetration and flesh resistance to rot spread are distinguishable mechanisms constituting BR resistance trait, associated with different genomic regions. Discovered QTLs and their associated markers could assist selection of new cultivars with enhanced resistance to Monilinia spp. in fruit.

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Section: Ssr Marker Genotyping and Linkage Mapsupporting

confidence: 91%

QTL mapping for brown rot (Monilinia fructigena) resistance in an intraspecific peach (Prunus persica L. Batsch) F1 progeny

Pacheco

Bassi

Eduardo

et al. 2014

Tree Genetics & Genomes

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“…An example is the study by Martínez-García et al (2013) in which maps were constructed for two peach populations. There was a previous map for one population (intraspecific population Pop-DG from a cross between the non-melting flesh 'Dr.…”

Section: Construction Of Genetic Mapsmentioning

confidence: 99%

Breeding rootstocks for Prunus species: Advances in genetic and genomics of peach and cherry as a model

Guajardo¹,

Hinrichsen

Muñoz

2015

Chilean J. Agric. Res.

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Prunus rootstock is an important choice in optimizing productivity of grafted cultivars. Nevertheless, many Prunus rootstocks are notoriously intolerant to hypoxia which is caused by waterlogging and/or heavy soils. There is no available information to help select Prunus rootstocks that are tolerant to stress conditions such as root hypoxia caused by excess moisture. Information from genetic maps has demonstrated a high level of synteny among Prunus species, and this suggests that they all share a similar genomic structure. It should be possible to identify the genetic determinants involved in tolerance to hypoxia and other traits in Prunus rootstocks by applying methods to identify regions of the genome involved in the expression of important traits; these have been developed mainly in peach which is the model species for the genus. Molecular markers that are tightly linked to major genes would be useful in marker-assisted selection (MAS) to optimize new rootstock selection. This article provides insight on the advances in the development of molecular markers, genetic maps, and gene identification in Prunus, mainly in peach; the aim is to provide a general approach for identifying the genetic determinants of hypoxia stress in rootstocks.

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“…Single nucleotide polymorphisms (SNPs) are widely used as molecular genetic markers in genetic linkage mapping (Martinez-Garcia et al, 2013), diversity analysis (Emanuelli et al, 2013), cultivar identification (Eduardo et al, 2013), and marker-assisted selection (MAS) (Verde et al, 2012). Recent studies of the peach have shown that SNPs are distributed at a frequency of one SNP for every 598 bp, one indel for every 4189 bp; moreover, variability is ~6-fold higher in noncoding regions when compared to coding regions (one SNP for every 390 bp in noncoding DNA vs one for every 1850 bp in coding DNA) (Aranzana et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Single nucleotide polymorphism analysis of the endopolygalacturonase gene in peach and its potential use in crossbreeding programs

Jiao

2015

Genet. Mol. Res.

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ABSTRACT. Single nucleotide polymorphisms (SNPs) are the most abundant sequence variations found in plant genomes and are widely used as molecular genetic markers in genetic diversity studies and crossbreeding programs. In this study, we examined 113 DNA sequences of the endopolygalacturonase (endo-PG) gene from 67 peach accessions and found a total of 56 SNPs and 6 insertion/ deletions (indels), with a frequency of 3, 1, and 3% for the transitions, transversions, and indels, respectively. Meanwhile, the majority of the observed SNPs were found in the intron regions, while only 2 variable sites and a single indel were detected in the exon regions. A dendrogram was obtained using neighbor-joining cluster analysis and divided into 2 main groups, providing evidence that most of the accessions of the clingstone nonmelting flesh phenotypes generally clustered together and were comparatively nonrelated to the "stony hard" peach cultivars, which were in a different branch altogether. Furthermore, 4 major haplotypes were formed and 3 cleaved amplified polymorphic sequence primer sets were mined according to fruit texture and stone adhesion, displaying their potential as candidate molecular markers SNP analysis of endopolygalacturonase in the peach for discriminating genotypes. This research will assist peach genetic enhancement by introducing a novel crossbreeding strategy.

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High density SNP mapping and QTL analysis for fruit quality characteristics in peach (Prunus persica L.)

Cited by 93 publications

References 55 publications

QTL mapping for brown rot (Monilinia fructigena) resistance in an intraspecific peach (Prunus persica L. Batsch) F1 progeny

QTL mapping for brown rot (Monilinia fructigena) resistance in an intraspecific peach (Prunus persica L. Batsch) F1 progeny

Breeding rootstocks for Prunus species: Advances in genetic and genomics of peach and cherry as a model

Single nucleotide polymorphism analysis of the endopolygalacturonase gene in peach and its potential use in crossbreeding programs

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