Construction of an integrated consensus map of the Apple genome based on four mapping populations

An integrated consensus genetic map for apple was constructed on the basis of segregation data from four genetically connected crosses (C1¿=¿Discovery × TN10-8, C2¿=¿Fiesta × Discovery, C3¿=¿Discovery × Prima, C4¿=¿Durello di Forli × Fiesta) with a total of 676 individuals using CarthaGene® software. First, integrated female¿male maps were built for each population using common female¿male simple sequence repeat markers (SSRs). Then, common SSRs over populations were used for the consensus map integration. The integrated consensus map consists of 1,046 markers, of which 159 are SSR markers, distributed over 17 linkage groups reflecting the basic chromosome number of apple. The total length of the integrated consensus map was 1,032 cM with a mean distance between adjacent loci of 1.1 cM. Markers were proportionally distributed over the 17 linkage groups (¿ 2¿=¿16.53, df¿=¿16, p¿=¿0.41). A non-uniform marker distribution was observed within all of the linkage groups (LGs). Clustering of markers at the same position (within a 1-cM window) was observed throughout LGs and consisted predominantly of only two to three linked markers. The four integrated female¿male maps showed a very good colinearity in marker order for their common markers, except for only two (CH01h01, CH05g03) and three (CH05a02z, NZ02b01, Lap-1) markers on LG17 and LG15, respectively. This integrated consensus map provides a framework for performing quantitative trait locus (QTL) detection in a multi-population design and evaluating the genetic background effect on QTL expression

Optimal Dithering Configuration Mitigating Rayleigh-Backscattering-Induced Distortion in Radioastronomic Optical Fiber Systems

In the context of Radioastronomic applications where the Analog Radio-over-Fiber technology is used for the antenna downlink, detrimental nonlinearity effects arise because of the interference between the forward signal generated by the laser and the Rayleigh backscattered one which is re-forwarded by the laser itself toward the photodetector. The adoption of the so called dithering technique, which involves the direct modulation of the laser with a sinusoidal tone and takes advantage of the laser chirping phenomenon, has been proved to reduce such Rayleigh Back Scattering - induced nonlinearities. The frequency and the amplitude of the dithering tone should both be as low as possible, in order to avoid undesired collateral effects on the received spectrum as well as keep at low levels the global energy consumption. Through a comprehensive analysis of dithered Radio over Fiber systems, it is demonstrated that a progressive reduction of the dithering tone frequency affects in a peculiar fashion both the chirping characteristics of the field emitted by the laser and the spectrum pattern of the received signal at the fiber end. Accounting for the concurrent effects caused by such phenomena, optimal operating conditions are identified for the implementation of the dithering tone technique in radioastronomic systems

Combining genetic resources and elite material populations to improve the accuracy of genomic prediction in apple

Genomic selection is an attractive strategy for apple breeding that could reduce the length of breeding cycles. A possible limitation to the practical implementation of this approach lies in the creation of a training set large and diverse enough to ensure accurate predictions. In this study, we investigated the potential of combining two available populations, i.e., genetic resources and elite material, in order to obtain a large training set with a high genetic diversity. We compared the predictive ability of genomic predictions within-population, across-population or when combining both populations, and tested a model accounting for population-specific marker effects in this last case. The obtained predictive abilities were moderate to high according to the studied trait and small increases in predictive ability could be obtained for some traits when the two populations were combined into a unique training set. We also investigated the potential of such a training set to predict hybrids resulting from crosses between the two populations, with a focus on the method to design the training set and the best proportion of each population to optimize predictions. The measured predictive abilities were very similar for all the proportions, except for the extreme cases where only one of the two populations was used in the training set, in which case predictive abilities could be lower than when using both populations. Using an optimization algorithm to choose the genotypes in the training set also led to higher predictive abilities than when the genotypes were chosen at random. Our results provide guidelines to initiate breeding programs that use genomic selection when the implementation of the training set is a limitation

Fruit quality characterization of new sweet cherry cultivars as a good source of bioactive phenolic compounds with antioxidant and neuroprotective potential

Sweet cherries (Prunus avium L.) are highly appreciated fruits for their taste, color, nutritional value, and beneficial health effects. In this work, seven new cultivars of sweet cherry were investigated for their main quality traits and nutraceutical value. The phytochemical profile of three classes of phenolic compounds and the antioxidant activity of the new cultivars were investigated through high-performance liquid chromatography with diode array detection (HPLC-DAD) and spectrophotometric assays, respectively, and compared with those of commonly commercialized cultivars. Cyanidine-3-O-rutinoside was the main anthocyanin in all genotypes, and its levels in some new cultivars were about three-fold higher than in commercial ones. The ORAC-assayed antioxidant capacity was positively correlated with the total anthocyanin index. The nutraceutical value of the new cultivars was investigated in terms of antioxidant/neuroprotective capacity in neuron-like SH-SY5Y cells. Results demonstrated that the new cultivars were more effective in counteracting oxidative stress and were also able to upregulate brain-derived neurotrophic factor (BDNF), a pro-survival neurotrophin, suggesting their potential pleiotropic role in counteracting neurodegenerations

Effects of Sleep Deprivation on Brain Bioenergetics, Sleep, and Cognitive Performance in Cocaine-Dependent Individuals

In cocaine-dependent individuals, sleep is disturbed during cocaine use and abstinence, highlighting the importance of examining the behavioral and homeostatic response to acute sleep loss in these individuals. The current study was designed to identify a differential effect of sleep deprivation on brain bioenergetics, cognitive performance, and sleep between cocaine-dependent and healthy control participants. 14 healthy control and 8 cocaine-dependent participants experienced consecutive nights of baseline, total sleep deprivation, and recovery sleep in the research laboratory. Participants underwent [31]P magnetic resonance spectroscopy (MRS) brain imaging, polysomnography, Continuous Performance Task, and Digit Symbol Substitution Task. Following recovery sleep, [31]P MRS scans revealed that cocaine-dependent participants exhibited elevated global brain β-NTP (direct measure of adenosine triphosphate), α-NTP, and total NTP levels compared to those of healthy controls. Cocaine-dependent participants performed worse on the Continuous Performance Task and Digit Symbol Substitution Task at baseline compared to healthy control participants, but sleep deprivation did not worsen cognitive performance in either group. Enhancements of brain ATP levels in cocaine dependent participants following recovery sleep may reflect a greater impact of sleep deprivation on sleep homeostasis, which may highlight the importance of monitoring sleep during abstinence and the potential influence of sleep loss in drug relapse

Reconstruction of multi-generation pedigrees involving numerous old apple cultivars thanks to whole-genome SNP data

A number of European apple cultivars are old, some of them dating back to the Renaissance, Middle Ages or even earlier. Many other cultivars have been developed during subsequent times. In order to decipher the relationships that link some of these old cultivars, whole-genome SNP data (~ 250K) for over 1400 genotypes were analyzed to infer first-degree relationships and reconstruct pedigrees. We used simple exclusion tests based on a count of Mendelian error to identify up to a thousand potential parent-offspring duos, including 295 complete parent-offspring trios and a hundred duos that could be oriented. grand-parents for some missing parents could also be inferred. Combining all this information allowed us to reconstruct pedigrees (up to 6 generations) highlighting the central role of major founders such as ‘Reinette Franche’, ‘Margil’, and ‘Alexander’. Haplotypes were deduced from genotypic data and pedigrees, and used to measure haplotype sharing between supposedly unrelated cultivars, allowing investigating further links between them.To our knowledge, such a large analysis to reconstruct multigeneration pedigrees involving (very) old cultivars selected over such time has never before been performed in perennial fruit species

An overview of the position and robustness of scab resistance QTLs and major genes by aligning of genetic maps in five apple progenies

In the frame of the D.A.R.E. project, five mapping populations have been studied for partial scab resistance against several races of Venturia inaequalis. A main objective was to identify QTLs (quantitative traits loci) with broad spectrum of resistance towards a wide range of strains of the fungus. Genetic markers (mainly SSR and AFLP) were tested on each population and genetic maps were constructed for both parents of each population. Meanwhile, pathological tests with several isolates of different races of V. inaequalis were performed. Four major genomic regions appear to be involved in scab resistance: they are located on linkage groups (LG) LG-1, LG-2, LG-11, and LG-17. Some other linkage groups carry either QTLs or major resistance genes that are isolate specific: a QTL on LG-5, Vd on LG-10, and Vg on LG-12. The QTL region located on LG-17 clearly exhibited the widest spectrum of resistanc

Local European cultivars as sources of durable scab resistance in apple

The Vf resistance gene has been widely used in apple breeding programmes to control Venturia inaequalis, the causal agent of scab, the major apple disease. Since the appearance of new strains that are able to overcome this major gene, research in Europe has been focused on durable resistance. The objective of one task of the European DARE project was to find cultivars which show a broad spectrum of resistance to the different scab races. This collaborative work involved 6 partners who tested 36 cultivars with various local scab inocula collected in the participating countries and with 8 monoconidial strains belonging to known races or isolated and characterized in the frame of the DARE project. Tests were performed each year from 1998 to 2001. Symptoms were assessed using macroscopic scoring scales. Some microscopic observations were performed; these resulted in a better knowledge of the host/pathogen interaction. Very diverse and complex resistance behaviours were found: the cultivars which showed the widest range of resistance were mostly local cultivars and some newly selected hybrids combining major genes and partial resistance. It would be worthwhile to include these individuals as parents in apple breeding programmes to improve the durability of scab resistance. Some methodologies and strategies to reach this goal will be proposed