Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species.

Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype-environment and genotype-phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.

Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine.

BACKGROUND: Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots pine (Pinus sylvestris L.), a genomic prediction study was conducted with 694 individuals representing 183 full-sib families that were genotyped with genotyping-by-sequencing (GBS) and phenotyped for growth and wood quality traits. 8719 SNPs were used to compare different genomic with pedigree prediction models. Additionally, four prediction efficiency methods were used to evaluate the impact of genomic breeding value estimations by assigning diverse ratios of training and validation sets, as well as several subsets of SNP markers. RESULTS: Genomic Best Linear Unbiased Prediction (GBLUP) and Bayesian Ridge Regression (BRR) combined with expectation maximization (EM) imputation algorithm showed slightly higher prediction efficiencies than Pedigree Best Linear Unbiased Prediction (PBLUP) and Bayesian LASSO, with some exceptions. A subset of approximately 6000 SNP markers, was enough to provide similar prediction efficiencies as the full set of 8719 markers. Additionally, prediction efficiencies of genomic models were enough to achieve a higher selection response, that varied between 50-143% higher than the traditional pedigree-based selection. CONCLUSIONS: Although prediction efficiencies were similar for genomic and pedigree models, the relative selection response was doubled for genomic models by assuming that earlier selections can be done at the seedling stage, reducing the progeny testing time, thus shortening the breeding cycle length roughly by 50%.

3 Hz postural tremor: A specific and sensitive sign of cerebellar dysfunction in patients with cerebellar ataxia.

OBJECTIVE: 3 Hz postural tremor was described in patients with anterior cerebellar lobe atrophy, however sensitivity and specificity of this sign in degenerative cerebellar diseases has not yet been evaluated. Our aim was to assess the 3 Hz tremor in patients with cerebellar ataxia, compare its sensitivity and specificity with other posturography parameters and to find out a correlation of intensity of 3 Hz tremor with ataxia severity. METHODS: 30 patients with degenerative cerebellar ataxia, a control group of 30 patients with compensated peripheral vestibulopathy and 40 healthy volunteers were examined by posturography. 3 Hz tremor was assessed both qualitatively and quantitatively, its sensitivity and specificity were compared with other standard posturography parameters. RESULTS: 3 Hz postural tremor was detected in 90% of patients with cerebellar ataxia, with 100% specificity and 90% sensitivity. The sensitivity and specificity of quantitative analysis of 3 Hz tremor was largely superior to standard posturography parameters when differentiating patients with cerebellar ataxia from vestibular impairment and healthy controls. CONCLUSION: 3 Hz postural tremor is highly sensitive and specific sign of cerebellar impairment in patients with cerebellar ataxia. SIGNIFICANCE: Evaluation of 3 Hz postural tremor should be a standard part of posturography examination when considering a cerebellar impairment.

Non-destructive wood density assessment of Scots pine (Pinus sylvestris L.) using Resistograph and Pilodyn.

We tested two methods for non-destructive assessment of wood density of Scots pine standing trees: one based on penetration depth of a steel pin (Pilodyn) and the other on micro-drilling resistance (Resistograph). As a benchmark we used wood density data from x-ray analysis (SilviScan). We assessed in total 622 trees of 175 full-sib families growing in a single progeny test. Pilodyn was applied with bark (PIL) and without bark (PILB). Raw Resistograph drilling profiles (RES) were adjusted (RESTB) in order to eliminate increasing trend caused by needle friction. Individual narrow-sense heritability of benchmark SilviScan density (DEN; 0.46) was most closely approached by that of adjusted RESTB (0.43). Heritabilities were lower for unadjusted RES (0.35) as well as for PIL and PILB (both 0.32). Additive genetic correlations of the benchmark DEN with RES, RESTB, PIL and PILB were 0.89, 0.96, 0.59 and 0.71, respectively. Our results suggest that Resistograph is a more reliable tool than Pilodyn for wood density assessment of Scots pine; however, we highly recommend adjusting Resistograph drilling profiles prior to further analyses.

Balance rehabilitation therapy by tongue electrotactile biofeedback in patients with degenerative cerebellar disease.

Few clinical studies have evaluated physiotherapeutic interventions in patients with degenerative cerebellar ataxia. Investigations on the effectiveness of biofeedback-based interventions for training postural control in these patients have not been conducted yet. The aim of the present study was to assess the effectiveness of a 2-week intensive tongue-placed electrotactile biofeedback program for patients with progressive cerebellar ataxia. Subjects were seven adult patients suffering from cerebellar degeneration. Postural control was assessed with static posturography in two sensory conditions eyes open/closed on firm surface. For quantification of postural behavior, we used area, sway path and mean velocity of the centre of foot pressure (CoP). Effects of treatment were determined by comparing Pre, Post and one month follow-up (Retention) experimental sessions. Analysis of measured CoP parameters for tests on firm surface showed a significant main effect of visual condition and no difference across test sessions under open eyes condition. Under eyes closed condition, there were significant differences between Pre versus Post and Pre versus Retention, while the difference Post versus Retention was not significant. Our results suggest that a balance rehabilitation program with postural exercise performed with a head position-based tongue-placed biofeedback system could significantly improve bipedal postural control in patients suffering from degenerative cerebellar ataxia.

Exercise with visual feedback improves postural stability after vestibular schwannoma surgery.

We analyzed the effect of 2-week individualized visual feedback-based balance training on the postural control of patients undergoing retrosigmoid microsurgical removal of vestibular schwannoma. We performed prospective evaluation of 17 patients allocated into two groups: feedback group (9 patients, mean age 37 years) and standard physiotherapy group (8 patients, mean age 44 years). Patients in both the groups were treated once per day by intensive rehabilitation from 5th to 14th postoperative day. Rehabilitation of patients in the feedback group was performed using the visual feedback and force platform. Results were evaluated on the beginning and at the end of rehabilitation program (e.g. 5th and 14th postoperative day). Outcome measures included posturography during quiet stance under four different conditions by the modified Clinical Test for Sensory Interaction of Balance. Body sway was evaluated from center of foot pressure. Compensation of Center of pressure (CoP) parameters in stance on firm surface was similar in the control and feedback groups. However, in stance on foam surface with eyes closed the patients from the feedback group were better compensated and CoP parameters differed significantly (p < 0.05). This prospective clinical study suggests that specific exercises with visual feedback improve vestibulospinal compensation in patients after vestibular schwannoma surgery and thus can improve their quality of life.

Female reproductive success variation in a Pseudotsuga menziesii seed orchard as revealed by pedigree reconstruction from a bulk seed collection.

The impact of female reproductive success on the mating system, gene flow, and genetic diversity of the filial generation was studied using a random sample of 801 bulk seed from a 49-clone Pseudotsuga menziesii seed orchard. We used microsatellite DNA fingerprinting and pedigree reconstruction to assign each seed's maternal and paternal parents and directly estimated clonal reproductive success, selfing rate, and the proportion of seed sired by outside pollen sources. Unlike most family array mating system and gene flow studies conducted on natural and experimental populations, which used an equal number of seeds per maternal genotype and thus generating unbiased inferences only on male reproductive success, the random sample we used was a representative of the entire seed crop; therefore, provided a unique opportunity to draw unbiased inferences on both female and male reproductive success variation. Selfing rate and the number of seed sired by outside pollen sources were found to be a function of female fertility variation. This variation also substantially and negatively affected female effective population size. Additionally, the results provided convincing evidence that the use of clone size as a proxy to fertility is questionable and requires further consideration.