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Etienne Bucher and colleagues use a combination of short- and long-read sequencing, along with optical mapping technologies, to produce the high-quality de novo assembly of the apple genome. They identify a new repetitive retrotransposon sequence and analyze DNA methylation data in relation to important agronomic traits. Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple ( Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.

Scab, caused by the ascomycete fungus Venturia pirina, leads to severe damage on European pear varieties resulting in a loss of commercial value and requiring frequent use of fungicides. Identifying scab resistance genes, developing molecular markers linked to these genes and establishing marker-assisted selection would be an effective way to improve European pear breeding for scab resistance. Most of the European pear cultivars (Pyrus communis) are currently reported to be sensitive. The pear cultivar ‘Navara’ was shown to carry a major scab resistance gene whose phenotypic expression in seedling progenies was a typical stellate necrosis symptom. The resistance gene was called Rvp1, for resistance to V. pirina, and was mapped on linkage group 2 of the pear genome close to microsatellite marker CH02b10. This genomic region is known to carry a cluster of scab resistance genes in apple indicating a first functional synteny for scab resistance between apple and pear.

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 (R ² = 17.2–39.1 %). In addition, QTLs were detected on LG5 (R ² = 10.8 %) of PEAR3 and on LG15 of ‘Moonglow’ (R ² = 13.7 %).

Deleterious epistatic interactions in plant inter- and intraspecific hybrids can cause a phenomenon known as hybrid necrosis, characterized by a typical seedling phenotype whose main distinguishing features are dwarfism, tissue necrosis and in some cases lethality. Identification of the chromosome regions associated with this type of incompatibility is important not only to increase our understanding of the evolutionary diversification that led to speciation but also for breeding purposes. Development of molecular markers linked to the lethal genes will allow breeders to avoid incompatible inbred combinations that could affect the expression of important agronomic tratis co-segregating with these genes. Although hybrid necrosis has been reported in several plant taxa, including Rosaceae species, this phenomenon has not been described previously in pear. In the interspecific pear population resulting from a cross between PEAR3 ( Pyrus bretschneideri × Pyrus communis ) and ‘Moonglow’ ( P. communis ), we observed two types of hybrid necrosis, expressed at different stages of plant development. Using a combination of previously mapped and newly developed genetic markers, we identified three chromosome regions associated with these two types of lethality, which were genetically independent. One type resulted from a negative epistatic interaction between a locus on linkage group 5 (LG5) of PEAR3 and a locus on LG1 of ‘Moonglow’, while the second type was due to a gene that maps to LG2 of PEAR3 and which either acts alone or more probably interacts with another gene of unknown location inherited from ‘Moonglow’. Fruit trees: preventing lethal crosses in pear A newly identified deleterious effect in cross-bred pears could be prevented by identifying the genetic regions involved. Adverse interactions between genes from the two parents of a hybrid—akin to an autoimmune response—can cause dwarfing, tissue damage and death, a phenomenon known as hybrid necrosis. Although recognized in several plant species, it has not before been seen in pears. An international team led by David Chagné of the New Zealand Institute for Plant and Food Research identified two types of hybrid necrosis in pears. Using modern genetic screening techniques, they then located two interacting gene regions causing ‘Type 1’ necrosis, and one implicated in ‘Type 2’; a second region remains to be identified. Their discoveries may shed light on the evolutionary history of pears, and will help breeders select compatible parents when breeding new varieties.

The improvement of perennial fruit trees through traditional breedingmethods is a long-term effort because of their long generation time. Theproduction of haploid and doubled haploid plants should offer newpossibilities for genetic studies and breeding work. In this study, haploidclones of pear were treated in vitro by oryzalin for chromosomedoubling; the level of ploidy was assessed by flow cytometry. Oryzalinappeared to be an efficient agent for chromosome doubling, the optimalconcentrations range from 200 to 300 μM. For homozygosityassessment, analyses of isozyme markers were carried out, together withmicrosatellite markers PCR-amplified with primers initially developed forapple. The use of isozyme markers confirmed homozygosity of all thedoubled haploid clones except for one. The microsatellite markers can beused earlier than isozymes for checking homozygosity during theprogramme of haploid and doubled haploid clones production. Truedoubled haploid clones of pear were obtained in less than one year andtheir acclimatisation in greenhouse has already started.[PUBLICATION ABSTRACT]

Scab is one of the major fungal diseases infecting pear trees, causing the greatest economic losses. Identifying and pyramiding scab resistance factors should help in breeding new resistant pear cultivars. We have identified and mapped two new pear resistance loci against the fungal pathogen Venturia pirina. The first locus, mapped both as a major gene and as a QTL, is located on linkage group (LG) 01 of the hybrid P3480, deriving from the European pear cultivar ‘Wilder.’ It colocalizes with the Vnk resistance gene found in the Asian pear cultivar ‘Kinchaku’ against Venturia nashicola. A second locus, mapped as a QTL, is located on LG04 of the interspecific cultivar ‘Euras.’ In a small ‘Euras’ × P3480 progeny, seven seedlings carrying the resistant alleles at both loci have been selected using SSR markers.

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.

We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII Long read sequencing (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (Mb) corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 chromosomes of the pear genome. About 50% (247 Mb) of the genome consists of repetitive sequences. Comparison with previous assemblies of Pyrus communis and Pyrus x bretschneideri confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted. Footnotes * The 'Data availability' section has been updated with the URL from the GDR database. In 'Genome sequencing and assembly' section added an analysis of telomeric sequence. Added haplotype map for BartlettDHv2. Added figures 8 and 9 and associated kmer analysis. Some minor formatting of species names.

The authors are withdrawing this paper owing to an accidental duplicate submission. Readers should instead see doi: https://doi.org/10.1101/651778. Footnotes * The authors are withdrawing this paper owing to an accidental duplicate submission. Readers should instead see doi: https://doi.org/10.1101/651778.

How best to treat rising prostate-specific antigen (PSA) concentration after radical prostatectomy is an urgent clinical question. Salvage radiotherapy delays the need for more aggressive treatment such as long-term androgen suppression, but fewer than half of patients benefit from it. We aimed to establish the effect of adding short-term androgen suppression at the time of salvage radiotherapy on biochemical outcome and overall survival in men with rising PSA following radical prostatectomy. This open-label, multicentre, phase 3, randomised controlled trial, was done in 43 French study centres. We enrolled men (aged ≥18 years) who had received previous treatment for a histologically confirmed adenocarcinoma of the prostate (but no previous androgen deprivation therapy or pelvic radiotherapy), and who had stage pT2, pT3, or pT4a (bladder neck involvement only) in patients who had rising PSA of 0·2 to less than 2·0 μg/L following radical prostatectomy, without evidence of clinical disease. Patients were randomly assigned (1:1) centrally via an interactive web response system to standard salvage radiotherapy (three-dimensional [3D] conformal radiotherapy or intensity modulated radiotherapy, of 66 Gy in 33 fractions 5 days a week for 7 weeks) or radiotherapy plus short-term androgen suppression using 10·8 mg goserelin by subcutaneous injection on the first day of irradiation and 3 months later. Randomisation was stratified using a permuted block method according to investigational site, radiotherapy modality, and prognosis. The primary endpoint was progression-free survival, analysed in the intention-to-treat population. This trial is registered with ClinicalTrials.gov, number NCT00423475. Between Oct 19, 2006, and March 30, 2010, 743 patients were randomly assigned, 374 to radiotherapy alone and 369 to radiotherapy plus goserelin. Patients assigned to radiotherapy plus goserelin were significantly more likely than patients in the radiotherapy alone group to be free of biochemical progression or clinical progression at 5 years (80% [95% CI 75–84] vs 62% [57–67]; hazard ratio [HR] 0·50, 95% CI 0·38–0·66; p<0·0001). No additional late adverse events occurred in patients receiving short-term androgen suppression compared with those who received radiotherapy alone. The most frequently occuring acute adverse events related to goserelin were hot flushes, sweating, or both (30 [8%] of 366 patients had a grade 2 or worse event; 30 patients [8%] had hot flushes and five patients [1%] had sweating in the radiotherapy plus goserelin group vs none of 372 patients in the radiotherapy alone group). Three (8%) of 366 patients had grade 3 or worse hot flushes and one patient had grade 3 or worse sweating in the radiotherapy plus goserelin group versus none of 372 patients in the radiotherapy alone group. The most common late adverse events of grade 3 or worse were genitourinary events (29 [8%] in the radiotherapy alone group vs 26 [7%] in the radiotherapy plus goserelin group) and sexual disorders (20 [5%] vs 30 [8%]). No treatment-related deaths occurred. Adding short-term androgen suppression to salvage radiotherapy benefits men who have had radical prostatectomy and whose PSA rises after a postsurgical period when it is undetectable. Radiotherapy combined with short-term androgen suppression could be considered as a reasonable option in this population. French Ministry of Health, AstraZeneca, and La Ligue Contre le Cancer.