The present study investigates the genetic determinism of flowering and maturity dates, two traits highly affected by global climate change. Flowering and maturity dates were evaluated on five ...progenies from three Prunus species, peach, apricot and sweet cherry, during 3-8 years. Quantitative trait locus (QTL) detection was performed separately for each year and also by integrating data from all years together. High heritability estimates were obtained for flowering and maturity dates. Several QTLs for flowering and maturity dates were highly stable, detected each year of evaluation, suggesting that they were not affected by climatic variations. For flowering date, major QTLs were detected on linkage groups (LG) 4 for apricot and sweet cherry and on LG6 for peach. QTLs were identified on LG2, LG3, LG4 and LG7 for the three species. For maturity date, a major QTL was detected on LG4 in the three species. Using the peach genome sequence data, candidate genes underlying the major QTLs on LG4 and LG6 were investigated and key genes were identified. Our results provide a basis for the identification of genes involved in flowering and maturity dates that could be used to develop cultivar ideotypes adapted to future climatic conditions.
Apple scab caused by
Venturia inaequalis
is the most important fungal disease of apples (
Malus
×
domestica
). Currently, the disease is controlled by up to 15 fungicide applications to the crop per ...year. Resistant apple cultivars will help promote the sustainable control of scab in commercial orchards. The breakdown of the
Rvi6 (Vf)
major-gene based resistance, the most used resistance gene in apple breeding, prompted the identification and characterization of new scab resistance genes. By using a large segregating population, the
Rvi12
scab resistance gene was previously mapped to a genetic location flanked by molecular markers SNP_23.599 and SNP_24.482. Starting from these markers, utilizing chromosome walking of a Hansen’s baccata #2 (HB2) BAC-library; a single BAC clone spanning the
Rvi12
interval was identified. Following Pacific Biosciences (PacBio) RS II sequencing and the use of the hierarchical genome assembly process (HGAP) assembly of the BAC clone sequence, the
Rvi12
resistance locus was localized to a 62.3-kb genomic region. Gene prediction and in silico characterization identified a single candidate resistance gene. The gene, named here as
Rvi12_Cd5
, belongs to the LRR receptor-like serine/threonine-protein kinase family. In silico comparison of the resistance allele from HB2 and the susceptible allele from Golden Delicious (GD) identified the presence of an additional intron in the HB2 allele. Conserved domain analysis identified the presence of four additional LRR motifs in the susceptible allele compared to the resistance allele. The constitutive expression of
Rvi12_Cd5
in HB2, together with its structural similarity to known resistance genes, makes it the most likely candidate for
Rvi
12 scab resistance in apple.
Venturia inaequalis Resistance in Apple Gessler, C.; Patocchi, A.; Sansavini, S. ...
Critical reviews in plant sciences,
12/2006, Volume:
25, Issue:
6
Journal Article
Peer reviewed
Apple scab caused by Venturia inaequalis has evoked the interest for quite different reasons of scientists, agronomists, producers and consumers since over a century. Consumers select spotless ...apples, producers want to avoid damage, agronomists are asked to develop and implement control measures mostly based on fungicides, scientists are challenged to find cheaper and less questioned control measures. Under these premises a high number of publications have appeared dealing with almost all aspects of the interaction V. inaequalis-Malus. This review considers the advances of the past 10 years due to new genetic tools. It tries to reevaluate and value earlier works. The complex genetic of scab resistance in Malus is viewed in the context of single resistance genes, QTLs and functional interactions at molecular level. Consequences for breeding and for the creation of genetically modified apples are discussed.
KEY MESSAGE : Proof of concept of Bayesian integrated QTL analyses across pedigree-related families from breeding programs of an outbreeding species. Results include QTL confidence intervals, ...individuals’ genotype probabilities and genomic breeding values. Bayesian QTL linkage mapping approaches offer the flexibility to study multiple full sib families with known pedigrees simultaneously. Such a joint analysis increases the probability of detecting these quantitative trait loci (QTL) and provide insight of the magnitude of QTL across different genetic backgrounds. Here, we present an improved Bayesian multi-QTL pedigree-based approach on an outcrossing species using progenies with different (complex) genetic relationships. Different modeling assumptions were studied in the QTL analyses, i.e., the a priori expected number of QTL varied and polygenic effects were considered. The inferences include number of QTL, additive QTL effect sizes and supporting credible intervals, posterior probabilities of QTL genotypes for all individuals in the dataset, and QTL-based as well as genome-wide breeding values. All these features have been implemented in the FlexQTL™ software. We analyzed fruit firmness in a large apple dataset that comprised 1,347 individuals forming 27 full sib families and their known ancestral pedigrees, with genotypes for 87 SSR markers on 17 chromosomes. We report strong or positive evidence for 14 QTL for fruit firmness on eight chromosomes, validating our approach as several of these QTL were reported previously, though dispersed over a series of studies based on single mapping populations. Interpretation of linked QTL was possible via individuals’ QTL genotypes. The correlation between the genomic breeding values and phenotypes was on average 90 %, but varied with the number of detected QTL in a family. The detailed posterior knowledge on QTL of potential parents is critical for the efficiency of marker-assisted breeding.
Apple scab is a disease caused by the fungus Venturia inaequalis, which leads to significant economic losses in apple production especially in temperate regions. Breeding programmes are attempting to ...introgress scab resistance genes from wild apple into commercial cultivars to control the disease. Most of the commercially available scab-resistant varieties to date rely on the Rvi6 (Vf) resistance gene from Malus floribunda 821. The evolution of new pathotypes of V. inaequalis, which have caused the breakdown of Rvi6-based resistance, at least in northern Europe, highlights the need for the characterisation and pyramiding of scab resistance genes from different sources for durable disease resistance. In this study, the scab resistance gene Rvi12 from Malus baccata ‘Hansen’s baccata #2’ was confirmed as mapping to apple linkage group 12 in the cross ‘Gala’ × ‘Hansen’s baccata #2’ in an interval between SSR markers Hi02d05 and CH02h11b. Using the ‘Golden Delicious’ genome sequence, novel SSR markers and SNPs were identified in the Rvi12 mapping interval and mapped in an extended mapping population of 1,285 plants. Rvi12 was fine-mapped to an interval spanning 958 kb of the ‘Golden Delicious’ genome sequence. The 18 SNPs fine-mapped to the Rvi12 interval were screened in eight apple breeding founders, and for 16 of the 18 SNPs, the alleles linked in coupling with the Rvi12 resistance locus were found only in ‘Hansen’s baccata #2’. The SNPs identified will thus be useful for the efficient identification of apple genotypes carrying the Rvi12 resistance locus.
Rosy apple aphid (
Dysaphis plantaginea
), is one of the major insect pests of apple, causing serious physical and economic damage to fruit production. A dominant resistance gene
Dp-fl
was previously ...mapped at the bottom of linkage group LG8 from the cultivar ‘Florina’, linked to the SSR CH01h10. The development of additional genetic markers mapping closer to
Dp-fl
was needed to position the gene accurately and to improve the effectiveness of marker-assisted breeding (MAB). The aims of this study were to identify single nucleotide polymorphisms (SNPs) in the region of
Dp-fl
and to position these SNPs relative to
Dp-fl
. To generate a fine map of the
Dp-fl
interval, a total of 191 plants segregating for resistance and derived from four different populations were tested with temperature-switch PCR (TSP) markers developed for SNPs located in the region of CH01h10. All the plants were phenotypically evaluated for aphid resistance and those data compared with the genetic data. These efforts resulted in positioning the
Dp-fl
resistance locus in a genetic interval corresponding to a physical distance of about 330 kb on the ‘Golden Delicious’ genome. The new markers were tested on several apple founder cultivars in order to test the specificity of the SNPs and, thus, the best markers for the MAB were identified. Finally, the 330-kb interval was analyzed for the identification of coding sequences and putative candidate genes for
D. plantaginea
resistance were identified.
The cultivated apple is susceptible to several pests including the rosy apple aphid (RAA;
Dysaphis plantaginea
Passerini), control of which is mainly based on chemical treatments. A few cases of ...resistance to aphids have been described in apple germplasm resources, laying the basis for the development of new resistant cultivars by breeding. The cultivar ‘Florina’ is resistant to RAA, and recently, the
Dp-fl
locus responsible for its resistance was mapped on linkage group 8 of the apple genome. In this paper, a chromosome walking approach was performed by using a ‘Florina’ bacterial artificial chromosome (BAC) library. The walking started from the available tightly linked molecular markers flanking the resistance region. Various walking steps were performed in order to identify the minimum tiling path of BAC clones covering the
Dp-fl
region from both the “resistant” and “susceptible” chromosomes of ‘Florina’. A genomic region of about 279 Kb encompassing the
Dp-fl
resistance locus was fully sequenced by the PacBio technology. Through the development of new polymorphic markers, the mapping interval around the resistance locus was narrowed down to a physical region of 95 Kb. The annotation of this sequence resulted in the identification of four candidate genes putatively involved in the RAA resistance response.
Sharka is one of the most serious viral diseases affecting stone fruit species and, in apricot, resistance to its viral agent, the Plum Pox Virus (PPV), is conferred by one major quantitative trait ...locus (QTL), named PPVres for PPV resistance. Previous studies indicated that PPV-resistant cultivars and breeding progenies can be selected by using a set of SSR markers (named PGS) targeting the PPVres locus. However, before these markers can be employed for marker-assisted selection, they were validated in a wide range of genetic backgrounds and environments. We used a total of 11 mapping populations issued from three distinct environments to confirm that this marker set located within the QTL adequately predicted PPV resistance. In this study, we show that selection of PPV-resistant material based only on markers co-localizing with the PPVres major locus is not fully reliable. Indeed, genotype-phenotype discrepancies were observed depending on the progeny and the PPV-resistant/susceptible parents. While most of the PPV-resistant individuals displayed the resistant alleles, a significant number of PPV-susceptible individuals showed the same resistant haplotype. An effect of the PPV strain used for phenotyping was also demonstrated. We thus hypothesize that the presence of other factors or genes involved in the mechanism of resistance to sharka in apricot could explain these unexpected results. Our work indicates that the current PGS marker set is not broadly applicable for MAS and that marker-assisted breeding based on the sole PPVres locus is not sufficient to unambiguously select PPV-resistant apricot cultivars.
The existence of different levels of susceptibility to fire blight (Erwinia amylovora) in European pear (Pyrus communis L.) cultivars suggests that it is possible to identify QTLs related to ...resistance in pear germplasm. Given the polygenic nature of this trait, we designed two genetic maps of the parental lines ‘Passe Crassane’ (susceptible) and ‘Harrow Sweet’ (resistant) using SSRs, MFLPs, AFLPs, RGAs and AFLP-RGAs markers. RGA-related markers should theoretically map in chromosome regions coding for resistance genes. The ‘Passe Crassane’ map includes 155 loci, for a total length of 912 cM organised in 18 linkage groups, and the ‘Harrow Sweet’ map 156 loci, for a total length of 930 cM divided in 19 linkage groups; both maps have a good genome coverage when compared to the more detailed apple maps. Four putative QTLs related to fire blight resistance were identified in the map. A suite of molecular markers, including two AFLP-RGAs, capable of defining resistant and susceptible haplotypes in the analysed population was developed.
A polymerase chain reaction (PCR)-based method was developed to isolate microsatellite markers from large-insert genomic DNA clones of bacterial artificial chromosome (BAC) libraries. The method is ...fast and economic since it does not require subcloning. It was applied to isolate a microsatellite marker from a BAC clone of the chromosomal region containing the apple scab resistance gene Vf. The Vf gene of Malus floribunda 821 is the most widely used source of scab resistance in apple breeding. A second microsatellite was found on the extremity of a BAC clone flanking the Vf locus. The two microsatellites allowed the identification of the presence of the Vf gene in the scab-resistant accessions M. micromalus SA573-3, 'Golden Gem', M. prunifolia 19651 and MA 16 not previously known to carry this gene. They were also used to verify the correctness of the published genealogical tree of the Vf cultivar 'Florina', in which a probable mistake was identified. This analysis shows the importance of genotyping the Vf locus when choosing scab-resistant germplasm as parents in breeding programmes.
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