Charles-Eric Durel

Inheritance studies of apple scab resistance and identification of Rvi14, a new major gene that acts together with other broad-spectrum QTL.

Scab, caused by the fungal pathogen Venturia inaequalis, is the most common disease of cultivated apple (Malus xdomestica). The fungal races 6 and 7 have now overcome the major resistance gene Vf, which is widely used in apple breeding programmes. New breeding strategies to achieve durable resistance are thus necessary. The aim of this study was to determine the genetic basis of quantitative resistance of the apple cultivar Dülmener Rosenapfel, known to be scab resistant under different environmental conditions. An F1 progeny derived from the cross between the susceptible cultivar Gala and Dülmener Rosenapfel was tested in a greenhouse with a multi-isolate inoculum of V. inaequalis. Rvi14, a new major gene that conditions a chlorotic-type reaction, was mapped on linkage group (LG) 6 in a genomic region not known to be involved in disease resistance. A further three quantitative trait loci (QTL) for resistance were identified. One co-localized with Rvi14 on LG6, whereas the remaining two were detected on LG11 and LG17, in genomic regions already reported to carry broad-spectrum QTL in other genetic backgrounds. Since a selective genotyping approach was used to detect QTL, an expectation-maximization (EM) computation was used to estimate the corrected QTL contributions to phenotypic variation and was validated by entire progeny genotyping.

Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids

We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear (‘Old Home’בLouise Bon Jersey’) and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality.

Identification of serine/threonine kinase and nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes in the fire blight resistance quantitative trait locus of apple cultivar ‘Evereste’

Fire blight is the most destructive bacterial disease affecting apple (Malus×domestica) worldwide. So far, no resistance gene against fire blight has been characterized in apple, despite several resistance regions having been identified. A highly efficacious resistance quantitative trait locus (QTL) was localized on linkage group 12 (LG12) of the ornamental cultivar Evereste. A marker previously reported to be closely linked to this resistance was used to perform a chromosome landing. A bacterial artificial chromosome (BAC) clone of 189u2003kb carrying the fire blight resistance QTL was isolated and sequenced. New microsatellite markers were developed, and the genomic region containing the resistance locus was limited to 78u2003kb. A cluster of eight genes with homologies to already known resistance gene structures to bacterial diseases was identified and the corresponding gene transcription was verified. From this cluster, two genes were recognized in silico as the two most probable fire blight resistance genes showing homology with the Pto/Prf complex in tomato.

Dissecting apple tree architecture into genetic, ontogenetic and environmental effects: QTL mapping

The present study aimed to dissect tree architectural plasticity into genetic, ontogenetic and environmental effects over the first 4xa0years of growth of an apple F1 progeny by means of quantitative traits loci (QTL) mapping. Both growth and branching processes were phenotyped on the consecutive annual shoots of different axes within a tree. For each studied trait, predicted values (best linear unbiased predictors, BLUPs) of the genotypic (G) effect or its interaction with tree age (G×A) and climatic year (G×Y) were extracted from mixed linear models of repeated data. These BLUPs, which are independent from autocorrelations between repeated measurements, were used for QTL mapping. QTL detection power was improved by this two-step approach. For each architectural process, numerous QTLs were detected and some particularly interesting co-localised in common genomic regions, for internode lengthening, top diameter, and number and percentage of axillary shoots. When several QTLs were detected for a given trait, global models were estimated, which explained a maximum of 40% of the total variance for both internode length and top diameter and 28% for branching. QTLs detected for BLUPs of G×Y effects were interpreted as resulting from the interaction between genetic maximal potential of growth and climatic factors, while those for G×A effects were interpreted in relation to tree ontogeny. Most of the latter ones were found to be concomitant with key development stages during which the trait average started to decrease, but with different magnitudes depending on genotype.

Erosion of quantitative host resistance in the apple × Venturia inaequalis pathosystem

Theoretical approaches predict that host quantitative resistance selects for pathogens with a high level of pathogenicity, leading to erosion of the resistance. This process of erosion has, however, rarely been experimentally demonstrated. To investigate the erosion of apple quantitative resistance to scab disease, we surveyed scab incidence over time in a network of three orchards planted with susceptible and quantitatively resistant apple genotypes. We sampled Venturiainaequalis isolates from two of these orchards at the beginning of the experiment and we tested their quantitative components of pathogenicity (i.e., global disease severity, lesion density, lesion size, latent period) under controlled conditions. The disease severity produced by the isolates on the quantitatively resistant apple genotypes differed between the sites. Our study showed that quantitative resistance may be subject to erosion and even complete breakdown, depending on the site. We observed this evolution over time for apple genotypes that combine two broad-spectrum scab resistance QTLs, F11 and F17, showing a significant synergic effect of this combination in favour of resistance (i.e., favourable epistatic effect). We showed that isolates sampled in the orchard where the resistance was inefficient presented a similar level of pathogenicity on both apple genotypes with quantitative resistance and susceptible genotypes. As a consequence, our results revealed a case where the use of quantitative resistance may result in the emergence of a generalist pathogen population that has extended its pathogenicity range by performing similarly on susceptible and resistant genotypes. This emphasizes the need to develop quantitative resistances conducive to trade-offs within the pathogen populations concerned.

Differential selection pressures exerted by host resistance quantitative trait loci on a pathogen population: a case study in an apple × Venturia inaequalis pathosystem

Understanding how pathogens evolve according to pressures exerted by their plant hosts is essential for the derivation of strategies aimed at the durable management of resistant cultivars. The spectrum of action of the resistance factors in the partially resistant cultivars is thought to be an important determinant of resistance durability. However, it has not yet been demonstrated whether the pressures exerted by quantitative resistance are different according to their spectrum of action. To investigate selection pressures exerted by apple genotypes harbouring various resistance quantitative trait loci (QTLs) on a mixed inoculum of the scab disease agent, Venturia inaequalis, we monitored V.xa0inaequalis isolate proportions on diseased apple leaves of an F1 progeny using quantitative pyrosequencing technology and QTL mapping. Broad-spectrum resistances did not exert any differential selection pressures on the mixed inoculum, whereas narrow-spectrum resistances decreased the frequencies of some isolates in the mixture relative to the susceptible host genotypes. Our results suggest that the management of resistant cultivars should be different according to the spectrum of action of their resistance factors. The pyramiding of broad-spectrum factors or the use of a mixture of apple genotypes that carry narrow-spectrum resistance factors are two possible strategies for the minimization of resistance erosion.

When virulence originates from nonagricultural hosts: evolutionary and epidemiological consequences of introgressions following secondary contacts in Venturia inaequalis.

In pathogens, introgressions through secondary contacts between divergent populations from agricultural and nonagricultural disease reservoirs are expected to have crucial evolutionary and epidemiological implications. Despite the importance of this question for disease management, experimental demonstrations of these implications remain scarce. Recently, we identified a virulent population of the apple scab pathogen Venturia inaequalis that migrated from nonagricultural hosts to European domestic apple orchards. Here, we investigated the occurrence of gene flow between agricultural and nonagricultural populations sampled in two orchards, and thereafter its consequences on the pathogenicity of hybrids. Population genetic structure and demographic inferences based on the genotypes of 104 strains revealed a high amount of gene flow between the two populations in one orchard. In this site, mating between populations was made possible by the presence of a common host. Our results revealed an invasion of the virulent trait in the agricultural population; a main direction of introgression in hybrids from the agricultural to nonagricultural genetic backgrounds; and a population of hybrids with transgressive traits. We demonstrate a secondary contact with gene flow between divergent populations of pathogens. Our findings highlight evolutionary and epidemiological changes in pathogens and have concrete implications for sustainable disease management.

Genetic mapping of Cacopsylla pyri resistance in an interspecific pear (Pyrus spp.) population

Cacopsylla pyri (pear psylla) is one of the most serious pests of pear (Pyrus spp.) in Europe. It can cause high yield losses, and its control has become difficult since it has developed resistance to a wide range of pesticides. Pear breeders are developing new cultivars resistant to pear psyllids, and Asian species, such as Pyrus ussuriensis and Pyrus × bretschneideri, are good sources of resistance. Antixenosis and antibiosis resistance to psylla were both identified in pear; they may differ in the biological mechanism and probably have different genetic backgrounds. We crossed interspecific P. × bretschneideri × Pyrus communis hybrid PEAR3, resistant to pear psylla, with the susceptible European pear cultivar ‘Moonglow’ to obtain an F1 population for the genetic mapping of the resistance. Quantitative trait locus (QTL) analysis was carried out for antibiosis by measuring the number of surviving nymphs and the nymphal development, using a novel phenotyping protocol and a saturated genetic map made of single-nucleotide polymorphism (SNP) and microsatellite (simple sequence repeats (SSR)) markers. A stable QTL was detected on linkage group (LG) 8 of PEAR3 (R2u2009=u200917.2–39.1xa0%). In addition, QTLs were detected on LG5 (R2u2009=u200910.8xa0%) of PEAR3 and on LG15 of ‘Moonglow’ (R2u2009=u200913.7xa0%).

Sustainable deployment of QTLs conferring quantitative resistance to crops: first lessons from a stochastic model.

Quantitative plant disease resistance is believed to be more durable than qualitative resistance, since it exerts less selective pressure on the pathogens. However, the process of progressive pathogen adaptation to quantitative resistance is poorly understood, which makes it difficult to predict its durability or to derive principles for its sustainable deployment. Here, we study the dynamics of pathogen adaptation in response to quantitative plant resistance affecting pathogen reproduction rate and its colonizing capacity. We developed a stochastic model for the continuous evolution of a pathogen population within a quantitatively resistant host. We assumed that pathogen can adapt to a host by the progressive restoration of reproduction rate or of colonizing capacity, or of both. Our model suggests that a combination of quantitative trait loci (QTLs) affecting distinct pathogen traits was more durable if the evolution of repressed traits was antagonistic. Otherwise, quantitative resistance that depressed only pathogen reproduction was more durable. In order to decelerate the progressive pathogen adaptation, QTLs that decrease the pathogens maximum capacity to colonize must be combined with QTLs that decrease the spore production per lesion or the infection efficiency or that increase the latent period. Our theoretical framework can help breeders to develop principles for sustainable deployment of QTLs.

Polygenic inheritance of resistance to Cacopsylla pyri in a Pyrus communis × P. ussuriensis progeny is explained by three QTLs involving an epistatic interaction

Pear psylla (Cacopsylla pyri) causes severe damage on European pear cultivars, resulting in high yield losses. Its control has become difficult since it developed resistance to a wide range of pesticides, while the number of authorized molecules for pest control has decreased. Identifying pear psylla resistance factors should help breeding new resistant pear cultivars. We analyzed the quantitative resistance to psylla inherited from the genotype NY 10355 derived from Pyrus ussuriensis. Quantitative trait locus (QTL) analysis was carried out after counting the number of nymphs and estimating the nymphal development rate using a free-choice test performed on a large segregating progeny. We mapped two new loci for pear psylla resistance on linkage groups LG01 and LG04 of NY 10355 and confirmed the QTL previously detected on LG17. A strong epistatic interaction between the two QTLs detected on LG01 and LG17 appeared to be a major factor controlling the psylla infestation in the genotype NY 10355.