Development of a high-resolution melting approach for reliable and cost-effective genotyping of PPVres locus in apricot (P. armeniaca)

Passaro, Marco; Geuna, F.; Bassi, D.; Cirilli, Marco

doi:10.1007/s11032-017-0666-0

Cited by 12 publications

(15 citation statements)

References 24 publications

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“…In this work, we present a new strategy to speed up while reducing costs of the current application of MAS for PPV resistance in apricot [18,24,28]. Here, we combine a high-throughput DNA extraction protocol that does not need sophisticated robotic systems and can be implemented in any regular laboratory, with PMC2 allele-specific PCR amplification using previously described primers [21] and agarose electrophoresis (Figure 1B).…”

Section: Resultsmentioning

confidence: 99%

“…WGSs of 73 cultivars were used in this study. Twenty-four of these WGSs and the 454 sequenced BAC clones belonging to the "Goldrich" PPVres locus R-haplotype were already screened in our previous works [20][21][22][23][24][25][26][27][28][29][30][31]. The other 49 WGSs were downloaded from the SRA repository (https://www.…”

Section: Wgs Mapping and Pmc2 Screeningmentioning

confidence: 99%

“…As a result of a genetic mapping approach, Soriano et al [18] reported the first successful MAS application for PPV resistance using 3 SSRs within the PPVres locus resolved by capillary electrophoresis. Afterwards, these SSRs were combined with a single sequence length polymorphism marker (ZP002) interrogating the ParPMC2-del resolved by capillary or acrylamide electrophoresis [24] and by high resolution melting [28]. However, specialized DNA testing services are needed to adopt these MAS approaches, and together with the economic costs, this could be a challenge [29].…”

Section: Introductionmentioning

confidence: 99%

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Cost-Effective and Time-Efficient Molecular Assisted Selection for PPV Resistance in Apricot Based on ParPMC2 Allele-Specific PCR

et al. 2020

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Plum pox virus (PPV) is the most important limiting factor for apricot (Prunus armeniaca L.) production worldwide, and development of resistant cultivars has been proven to be the best solution in the long-term. However, just like in other woody species, apricot breeding is highly time and space demanding, and this is particularly true for PPV resistance phenotyping. Therefore, marker-assisted selection (MAS) may be very helpful to speed up breeding programs. Tightly linked ParPMC1 and ParPMC2, meprin and TRAF-C homology (MATH)-domain-containing genes have been proposed as host susceptibility genes required for PPV infection. Contribution of additional genes to PPV resistance cannot be discarded, but all available studies undoubtedly show a strong correlation between ParPMC2-resistant alleles (ParPMC2res) and PPV resistance. The ParPMC2res allele was shown to carry a 5-bp deletion (ParPMC2-del) within the second exon that has been characterized as a molecular marker suitable for MAS (PMC2). Based on this finding, we propose here a method for PPV resistance selection in apricot by combining high-throughput DNA extraction of 384 samples in 2 working days and the allele-specific genotyping of PMC2 on agarose gel. Moreover, the PMC2 genotype has been determined by PCR or by using whole-genome sequences (WGS) in 175 apricot accessions. These results were complemented with phenotypic and/or genotypic data available in the literature to reach a total of 325 apricot accessions. As a whole, we conclude that this is a time-efficient, cost-effective and straightforward method for PPV resistance screening that can be highly useful for apricot breeding programs.

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Section: Resultsmentioning

confidence: 99%

Section: Wgs Mapping and Pmc2 Screeningmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Cost-Effective and Time-Efficient Molecular Assisted Selection for PPV Resistance in Apricot Based on ParPMC2 Allele-Specific PCR

et al. 2020

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“…The major QTL investigated is probably necessary but not sufficient for explaining resistance (Lambert et al, 2007; Soriano et al, 2008; Marandel et al, 2009; Dondini et al, 2011; Rubio et al, 2014; Mariette et al, 2016), and a second locus, named PPV1b in the literature to distinguish it from the first one ( PPV1a ) and not yet identified, should be required for the resistance being deployed (Mariette et al, 2016). The occurrence of two independent genes with epistatic effect could explain the genotype versus phenotype discrepancies found in our three recombinants (i.e., GPI in Figure 2 ) by testing markers, used for selection in apricot breeding, tightly linked to the PPV1a locus (Soriano et al, 2012; Zuriaga et al, 2013; Rubio et al, 2014; Passaro et al, 2017). Furthermore, the ambiguity in the detection of susceptibility and resistance symptoms still represents a bottleneck, hampering the precise scoring of the different phenotypic classes (Rubio et al, 2007; Rubio et al, 2014; Mariette et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Resistance to Sharka in Apricot: Comparison of Phase-Reconstructed Resistant and Susceptible Haplotypes of ‘Lito’ Chromosome 1 and Analysis of Candidate Genes

et al. 2019

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Sharka, a common disease among most stone fruit crops, is caused by the Plum Pox Virus (PPV). Resistant genotypes have been found in apricot (Prunus armeniaca L.), one of which—the cultivar ‘Lito’ heterozygous for the resistance—has been used to map a major quantitative trait locus (QTL) on linkage group 1, following a pseudo-test-cross mating design with 231 individuals. In addition, 19 SNP markers were selected from among the hundreds previously developed, which allowed the region to be limited to 236 kb on chromosome 1. A ‘Lito’ bacterial artificial chromosome (BAC) library was produced, screened with markers of the region, and positive BAC clones were sequenced. Resistant (R) and susceptible (S) haplotypes were assembled independently. To refine the assembly, the whole genome of ‘Lito’ was sequenced to high coverage (98×) using PacBio technology, enabling the development of a detailed assembly of the region that was able to predict and annotate the genes in the QTL region. The selected cultivar ‘Lito’ allowed not only to discriminate structural variants between the two haplotypic regions but also to distinguish specific allele expression, contributing towards mining the PPVres locus. In light of these findings, genes previously indicated (i.e., MATHd genes) to have a possible role in PPV resistance were further analyzed, and new candidates were discussed. Although the results are not conclusive, the accurate and independent assembly of R and S haplotypes of ‘Lito’ is a valuable resource to predict and test alternative transcription and regulation mechanisms underpinning PPV resistance.

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“…In a previous study, researchers developed novel HRM markers to detect plum pox virus (PPV) resistance by targeting PPV resistance locus in Prunus armeniaca. According to the results, PPV resistance locus could be detected by using a reliable and user-friendly method HRM (Passaro et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Distinguishing the Protected Designation of Origin Apricot (Prunus armeniaca L. cv. Şalak) from Closely Related Cultivars by High Resolution Melting

Hürkan¹

2021

Commagene Journal of Biology

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The apricot cultivar Prunus armeniaca cv. Şalak (registered as "Iğdır Kayısısı") is a Protected Designation of Origin (PDO) apricot and produced in Aras Basin (Iğdır, Turkey) region. Authenticating the special products, which has adulteration potential, by DNA based methods is reliable and cost-effective. The aim of the current study is to distinguish the PDO apricot from closely related cultivars by High Resolution Melting. We tested 12 SSR markers previously validated for Prunus spp. by means of distinguishing the ability of five closely related apricot cultivars that are Şalak (AS), Hasanbey (HB), Hacıhaliloğlu (HH), Kabaaşı (KB), and Şekerpare (SK) produced in Turkey. Capillary electrophoresis validation showed 11 of 12 markers amplified unique fragments for the cultivars. HRM analysis combined with the Principal Component Analysis (PCA) successfully distinguished the PDO AS from closely related cultivars. HRM analysis combined with PCA can be a cost-effective and reliable authenticating method for PDO food products.

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Development of a high-resolution melting approach for reliable and cost-effective genotyping of PPVres locus in apricot (P. armeniaca)

Cited by 12 publications

References 24 publications

Cost-Effective and Time-Efficient Molecular Assisted Selection for PPV Resistance in Apricot Based on ParPMC2 Allele-Specific PCR

Cost-Effective and Time-Efficient Molecular Assisted Selection for PPV Resistance in Apricot Based on ParPMC2 Allele-Specific PCR

Resistance to Sharka in Apricot: Comparison of Phase-Reconstructed Resistant and Susceptible Haplotypes of ‘Lito’ Chromosome 1 and Analysis of Candidate Genes

Distinguishing the Protected Designation of Origin Apricot (Prunus armeniaca L. cv. Şalak) from Closely Related Cultivars by High Resolution Melting

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