Phenotypic and transcriptomic analyses reveal major differences between apple and pear scab nonhost resistance

Nonhost resistance is the outcome of most plant/pathogen interactions, but it has rarely been described in Rosaceous fruit species. Apple (Malus x domestica Borkh.) have a nonhost resistance to Venturia pyrina, the scab species attacking European pear (Pyrus communis L.). Reciprocally, P. communis have a nonhost resistance to Venturia inaequalis, the scab species attacking apple. The major objective of our study was to compare the scab nonhost resistance in apple and in European pear, at the phenotypic and transcriptomic levels.  Macro- and microscopic observations after reciprocal scab inoculations indicated that, after a similar germination step, nonhost apple/V. pyrina interaction remained nearly symptomless, whereas more hypersensitive reactions were observed during nonhost pear/V. inaequalis interaction. Comparative transcriptomic analyses of apple and pear nonhost interactions with V. pyrina and V. inaequalis, respectively, revealed differences. Very few differentially expressed genes were detected during apple/V. pyrina interaction, preventing the inferring of underlying molecular mechanisms. On the contrary, numerous genes were differentially expressed during pear/V. inaequalis interaction, allowing a deep deciphering. Pre-invasive defense, such as stomatal closure, could be inferred, as well as several post-invasive defense mechanisms (apoplastic reactive oxygen species accumulation, phytoalexin production and alterations of the epidermis composition). In addition, a comparative analysis between pear scab host and nonhost interactions indicated that, although specificities were observed, two major defense lines seems to be shared in these resistances: cell wall and cuticle potential modifications and phenylpropanoid pathway induction. This first deciphering of the molecular mechanisms underlying a nonhost scab resistance in pear offers new possibilities for the genetic engineering of sustainable scab resistance in this species. Concerning nonhost scab resistance in apple, further analyses must be considered with the aid of tools adapted to this resistance with very few cells engaged

Genetic diversity, Population structure, parentage analysis, and construction of core collections in the French apple germplasm based on SSR markers

In-depth characterization of apple genetic resources is a prerequisite for genetic improvement and for germplasm management. In this study, we fingerprinted a very large French collection of 2163 accessions with 24 SSR markers in order to evaluate its genetic diversity, population structure and genetic relationships, to link these features with cultivar selection date or usage (old or modern, dessert or cider cultivars), and to construct core collections. Most markers were highly discriminating and powerful for varietal identification, with a probability of identity P(ID) over the 21 retained SSR loci close to 10-28. Pairwise comparisons revealed 34% redundancy and 18.5% putative triploids. The results showed that the germplasm is highly diverse with an expected heterozygosity He of 0.82 and observed heterozygosity Ho of 0.83. A Bayesian model-based clustering approach revealed a weak but significant structure in three subgroups (FST = 0.014-0.048) corresponding, albeit approximately, to the three subpopulations defined beforehand (Old Dessert, Old Cider and Moderncultivars). Parentage analyses established already known and yet unknown relationships, notably between old cultivars, with the frequent occurrence of cultivars such as ‘King of Pippin’ and ‘Calville Rouge d’Hiver’ as founders. Finally, core collections based on allelic diversity were constructed. A large dessert core collection of 278 cultivars contained 90% of the total dessert allelic diversity, whereas a dessert sub-core collection of 48 cultivars contained 71% of diversity. For cider apples, a 48-cultivars core collection contained 83% of the total cider allelic diversity

Acibenzolar-S-methyl and resistance quantitative trait loci complement each other to control apple scab and fire blight

International audienceDiversifying disease control methods is a key strategy to sustainably reduce pesticides. Plant genetic resistance has long been used to create resistant varieties. Plant resistance inducers (PRI) are also considered to promote crop health, but their effectiveness is partial and can vary according to the environment and the plant genotype. We investigated the putative interaction between intrinsic (genetic) and PRI-induced resistance in apple when affected by scab and fire blight diseases. A large F1 mapping population was challenged by each disease after a pre-treatment with acibenzolar-S-methyl (ASM) and compared with the water control. Apple scab and fire blight resistance quantitative trait loci (QTLs) were detected in both conditions and compared. ASM exhibited a strong effectiveness in reducing both diseases. When combined, QTL-controlled and ASM-induced resistance acted complementarily to reduce the symptoms from 85% to 100% depending on the disease. In our conditions, resistance QTLs were only slightly or rarely affected by ASM treatment, despite their probable implication in various stages of the resistance build-up. Implications of these results are discussed considering already known results, the underlying mechanisms, cross-protection of both types of resistance against pathogen adaptation, and practical application in orchard conditions

Escape from p21-mediated Oncogene-induced Senescence Leads to Cell Dedifferentiation and Dependence on Anti-apoptotic Bcl-xL and MCL1 Proteins

International audienceOncogene-induced senescence (OIS) is a tumor suppressor response that induces permanent cell cycle arrest in response to oncogenic signaling. Through the combined activation of the p53-p21 and p16-Rb suppressor pathways, OIS leads to the transcriptional repression of proliferative genes. Although this protective mechanism has been essentially described in primary cells, we surprisingly observed in this study that the OIS program is conserved in established colorectal cell lines. In response to the RAS oncogene and despite the inactivation of p53 and p16INK4, HT29 cells enter senescence, up-regulate p21WAF1, and induce senescence-associated heterochromatin foci formation. The same effect was observed in response to B-RAFv600E in LS174T cells. We also observed that p21WAF1 prevents the expression of the CDC25A and PLK1 genes to induce cell cycle arrest. Using ChIP and luciferase experiments, we have observed that p21WAF1 binds to the PLK1 promoter to induce its down-regulation during OIS induction. Following 4–5 weeks, several clones were able to resume proliferation and escape this tumor suppressor pathway. Tumor progression was associated with p21WAF1 down-regulation and CDC25A and PLK1 reexpression. In addition, OIS and p21WAF1 escape was associated with an increase in DNA damage, an induction of the epithelial-mesenchymal transition program, and an increase in the proportion of cells expressing the CD24low/CD44high phenotype. Results also indicate that malignant cells having escaped OIS rely on survival pathways induced by Bcl-xL/MCL1 signaling. In light of these observations, it appears that the transcriptional functions of p21WAF1 are active during OIS and that the inactivation of this protein is associated with cell dedifferentiation and enhanced survival.</p

A population genomics approach for unraveling the genetic bases of differentiation between dessert and cider apples

Understanding the processes that occurred during domestication remains one of the central questions in genetics. In addition to fundamental importance, it can indeed provide knowledge on the genetic bases for further crop improvement. As an example, apple is one of the most important fruit crops in temperate regions, having both an economic and a cultural value. Dessert apples are used for consumption as fruits while cider apples are used to produce cider. Yet few traits are known to be different, despite overlapping between dessert and cider apples, namely fruit size and bitterness. A population genomics approach was used for detecting loci involved in the differentiation between cider and dessert apples, on two core collections of old cultivars, one for dessert apples and one for cider apples. A set of 96 gene fragments, localized in 6 areas of the apple genome bearing QTLs for traits of agronomic interest, was re-sequenced and the Illumina 8K SNP chip was used to genotype these two collections. The low estimates of per locus differentiation (ie Fst) between dessert and cider apples indicated that these two pools recently derive from common ancestors, except for 2 genomic regions exhibiting higher Fst values and potentially involved in selective processes. Departure from neutrality was also tested for each “population” using Tajima’s D and Fu and Li’s D and several areas of the genome were found to have significant decrease of both. Such knowledge could be helpful in new selection programs, bringing their efficiency to a higher level

Slow erosion of a quantitative apple resistance to Venturia inaequalis based on an isolate-specific Quantitative Trait Locus

Quantitative plant resistance affects the aggressiveness of pathogens and is usually considered more durable than qualitative resistance. However, the efficiency of a quantitative resistance based on an isolate-specific Quantitative Trait Locus (QTL) is expected to decrease over time due to the selection of isolates with a high level of aggressiveness on resistant plants. To test this hypothesis, we surveyed scab incidence over an eight-year period in an orchard planted with susceptible and quantitatively resistant apple genotypes. We sampled 79 Venturia inaequalis isolates from this orchard at three dates and we tested their level of aggressiveness under controlled conditions. Isolates sampled on resistant genotypes triggered higher lesion density and exhibited a higher sporulation rate on apple carrying the resistance allele of the QTL T1 compared to isolates sampled on susceptible genotypes. Due to this ability to select aggressive isolates, we expected the QTL T1 to be non-durable. However, our results showed that the quantitative resistance based on the QTL T1 remained efficient in orchard over an eight-year period, with only a slow decrease in efficiency and no detectable increase of the aggressiveness of fungal isolates over time. We conclude that knowledge on the specificity of a QTL is not sufficient to evaluate its durability. Deciphering molecular mechanisms associated with resistance QTLs, genetic determinants of aggressiveness and putative trade-offs within pathogen populations is needed to help in understanding the erosion processe