The Peach v2.0 Release : An Improved Genome Sequence for Bridging the Gap Between Genomics and Breeding in Prunus

Since its release the high quality peach genome sequence (Peach v1.0) has fostered studies on comparative genomics as well as on genetic diversity, domestication and crop improvement in Prunus and related species. To improve the chromosome-scale assembly and genome annotation we performed further analyses. Extensive mapping data allowed the improvement of Peach v2.0 assembly in terms of fraction of mapped (99.2%) and orientated (97.9%) sequences and correction of misassembly issues (about 12.2 Mb of incorrectly positioned sequences). Assembled resequencing data (42x) improved base accuracy and contiguity: 859 SNPs and 1,347 Indels were corrected and 212 gaps were closed. As a result the contiguity of Peach v2.0 improved with a contig L50 of 255.4 kb (previously 214.2 kb) and a contig N50 of 250 (previously 294). Repeat annotation was enhanced including low copy repeats and the complete sequence and location of 1,157 non autonomous Helitrons. Gene prediction and annotation were improved using transcript assemblies obtained from 2.2 billion of RNA seq reads from different peach tissues and organs. In total, after masking with the improved repeat annotation, 26,873 protein-coding genes were predicted in Peach v2.1 annotation, 991 less than those predicted in Peach v1.0. Gene annotation was highly enhanced with the prediction of almost 20,000 new isoforms. The new peach release with improved assembly and annotation will be a pivotal resource for comparative genomics in the plant kingdom and will serve as a foundation for studies bridging the gap between genomics and breeding in Prunus and related species

QTL mapping for brown rot (Monilinia fructigena) resistance in an intraspecific peach (Prunus persica L. Batsch) F1 progeny

Brown rot (BR) caused by Monilinia spp. leads to significant post-harvest losses in stone fruit production, especially peach. Previous genetic analyses in peach progenies suggested that BR resistance segregates as a quantitative trait. In order to uncover genomic regions associated with this trait and identify molecular markers for assisted selection (MAS) in peach, an F1 progeny from the cross "Contender" (C, resistant) 7 "Elegant Lady" (EL, susceptible) was chosen for quantitative trait loci (QTL) analysis. Over two phenotyping seasons, skin (SK) and flesh (FL) artificial infections were performed on fruits using a Monilinia fructigena isolate. For each treatment, infection frequency (if) and average rot diameter (rd) were scored. Significant seasonal and intertrait correlations were found. Maturity date (MD) was significantly correlated with disease impact. Sixty-three simple sequence repeats (SSRs) plus 26 single-nucleotide polymorphism (SNP) markers were used to genotype the C 7 EL population and to construct a linkage map. C 7 EL map included the eight Prunus linkage groups (LG), spanning 572.92 cM, with an average interval distance of 6.9 cM, covering 78.73 % of the peach genome (V1.0). Multiple QTL mapping analysis including MD trait as covariate uncovered three genomic regions associated with BR resistance in the two phenotyping seasons: one containing QTLs for SK resistance traits near M1a (LG C 7 EL-2, R2 = 13.1-31.5 %) and EPPISF032 (LG C 7 EL-4, R2 = 11-14 %) and the others containing QTLs for FL resistance, near markers SNP_IGA_320761 and SNP_IGA_321601 (LG3, R2 = 3.0-11.0 %). These results suggest that in the C 7 EL F1 progeny, skin resistance to fungal penetration and flesh resistance to rot spread are distinguishable mechanisms constituting BR resistance trait, associated with different genomic regions. Discovered QTLs and their associated markers could assist selection of new cultivars with enhanced resistance to Monilinia spp. in fruit

An investigation of the subacute effects of ecstasy on neuropsychological performance, sleep and mood in regular ecstasy users

The aim of this study was to differentiate the subacute from the chronic effects of ecstasy. Regular ecstasy users who subsequently chose to take ecstasy (experimental group: E, N = 16) were compared with regular ecstasy users who opted not to (control group: C, N = 16). Groups were assessed with neuropsychological and psychometric measures at drug-free baseline before ecstasy use and 1 and 4 days after use. Ecstasy users who consumed ecstasy (E) did not differ from those who did not (C) in relation to age, estimated IQ, personality or past substance use, including ecstasy. At baseline, E reported being more energetic, lively and cheerful whereas the day after ecstasy use they reported being more muddled, afraid, sad and dejected than C. However, this was not significant after controlling for sleep deprivation. Mood returned to baseline within 3 days and there were no group differences in Beck depression inventory scores at any of the three testing sessions. There were no subacute effects of ecstasy on working memory, story recall, impulsivity, or decision-making. However, at baseline and the day after use ecstasy users made poorer decisions, and were less sensitive to punishment, in the Somatic marker sensitivity test. These findings suggest that previous reports of marked subacute effects of ecstasy use may have been confounded by chronic polydrug use before use, co-substance use and sleep disturbances after use

Elevated impulsivity and impaired decision-making in abstinent Ecstasy (MDMA) users compared to polydrug and drug-naive controls.

Ecstasy (MDMA; 3,4-methylenedioxymethamphetamine) has a well-recognized neurotoxic effect on central serotonergic (5-HT) systems in animals, and there is some evidence of persistent serotonergic dysregulation in human ecstasy users. Serotonin is believed to mediate impulsive behavior and effective decision-making. Thus, the aim of the present study was to investigate impulsive behavior and decision-making in abstinent regular ecstasy users. Three groups were compared: 'ecstasy users' (recreational ecstasy users who reported modest use of illicit drugs other than cannabis), 'polydrug controls' (ecstasy naïve illicit drug users), and 'drug-naïve controls'. All participants completed personal details and general drug history questionnaires, the National Adult Reading Test, Matching Familiar Figures Test (MFF20), a risky decision-making task (RDMT), and the Card Arranging Reward Responsivity Objective Test (CARROT). The groups did not differ on the CARROT measure of responsiveness to financial incentive; however, the ecstasy group displayed significantly elevated MFF20 impulsivity, and showed reduced discrimination between magnitudes of prospective gains and losses when making risky decisions, compared to the 'polydrug' and 'drug-naïve' control groups. These findings may reflect a vulnerability of 5-HT systems in the orbital prefrontal cortex and interconnected corticolimbic circuitry to the cumulative neurotoxic effects of ecstasy and have clinical significance for regular ecstasy users. The combination of elevated impulsivity and impaired use of reinforcement cues in uncertain decision-making may comprise risk factors for continued drug abuse and everyday functioning

Genetic dissection of peach fruit quality traits

Genetics and genomics approaches are integrated to dissect key quality and agronomic traits in peach, such as fruit weight, composition of Volatile Organic Compounds (VOCs), resistance to pathogens and maturity date (MD). 213 peach accessions and five biparental populations were genotyped with advanced SNP platforms such as the 9K Illumina peach SNP array providing an ideal basis for GWAS and QTL analyses. Here, we report results from QTL analyses of VOCs in an F1 cross between two peach cultivars differing in their aroma profiles, Bolero and OroA. Based on gas chromatography‐mass spectrometry (GC‐MS) analysis of fruit essential oil, 43 QTLs were uncovered for 23 different VOCs and candidate genes were identified for two major QTLs. In parallel, to gain insight into gene expression differences that might be associated with the aroma profiles of Bolero and OroA, a novel microarray (uPEACH2.0) was specifically designed: transcriptomic comparisons at three developmental stages allowed the identification of 12 genes putatively involved in VOC biosynthesis. Due to the strong impact of MD on a number of fruit quality traits, we also report progress on QTL analysis in three different populations segregating for MD: in addition to the Bolero x OroA cross, F2 populations derived from Contender x Ambra and NJ Weeping x Bounty were used to map QTLs providing a robust framework for genetic analysis of MD. Analysis of genetic variations in some CG will be discussed