Genetic variation for the duration of pre-anthesis development in durum wheat and its interaction with vernalization treatment and photoperiod

A recombinant inbred durum wheat population was grown under three contrasting regimes: long days following vernalization (LDV), long days without vernalization (LD), and short days following vernalization (SDV). The length of several pre-anthesis stages and the number of leaves and the phyllochron were measured. Different groups of genes were involved in determining the phenology in the three treatments, as demonstrated by a quantitative trait locus (QTL) analysis. The length of the period required to reach the terminal spikelet stage was correlated with the time to anthesis only in the case of LDV- and LD-grown plants where the timing of anthesis depended on the final leaf number. However, for SDV-grown plants, anthesis date was more dependent on the length of the period between the terminal spikelet stage and anthesis and was independent of leaf number. The involvement of the phyllochron in determining the duration of pre-anthesis development was also treatment-dependent. QTL mapping of the various flowering time associated traits uncovered some novel loci (such as those associated with the phyllochron), in addition to confirming the presence of several well-established loci

Determination of milk production losses and variations of fat and protein percentages according to different levels of somatic cell count in Valle del Belice dairy sheep

The somatic cell count (SCC) of milk is widely used to monitor udder health and the milk quality and because of its positive genetic correlation with mastitis this trait was included in breeding schemes of dairy sheep. The aim of this study was to estimate the loss in milk yield (MY) and related composition resulting from different levels of somatic cell count in Valle del Belice dairy sheep. Data were collected between 2006 and 2016 in 15 flocks following an A4 recording scheme. Somatic cell count (SCC), fat and protein percentage (F% and P%) were determined using mid-infrared spectroscopy. To evaluate loss in test day MY, F% and P%, five different classes of SCC were arbitrarily defined: SCC1 ⤠500 à 103, 500 à 103 2000 à 103. To estimate the loss of milk production and quality a linear model, with test day milk production traits as dependent variable, was used. Furthermore, the effect of order of parity and season of lambing were investigated to study the effects on milk production traits. Least squares means were computed for milk production traits and the differences between means were determined by Fischer's least significant difference. The estimated losses in MY according to the level of used SCC were approximately 16% whereas there was an increase of 0.06% and 0.29% for fat and protein percentage, respectively. Apart from environmental factors and management, this study confirms that high levels of somatic cell count in sheep milk are associated with milk yield losses and changes in milk composition. Results suggest that it is necessary to implement a program aimed to reduce the milk somatic cell count in ewes' milk, with the aim of improving the quality of ewes' milk and dairy products

Early post-cooling brain magnetic resonance for the prediction of neurodevelopmental outcome in newborns with hypoxic-ischemic encephalopathy

Aim and objectives: This study aimed to evaluate the predictive role of early post-cooling brain magnetic resonance for developmental outcome in newborns with hypoxic-ischemic encephalopathy. Materials and methods: A retrospective cohort study was performed on 29 consecutive patients through magnetic resonance evaluation (visual analysis of the images and scoring of the detected lesions; mean diffusivity of semioval centre and lenticular nuclei; and area under the curve of basal ganglia N-acetylaspartate at proton magnetic resonance spectroscopic imaging) and Griffiths Mental Development Scales-third edition at 12 and 24 months. Results: Brain magnetic resonance was performed at a mean age of 5.7 ± 3.7 days. Newborns with no/minor magnetic resonance abnormalities had a better developmental outcome than patients with moderate or severe lesions. Structural and spectroscopic abnormalities in basal ganglia resulted in the most significant predictors for an unfavorable outcome. Conclusion: Normal magnetic resonance in early post-cooling phases is strongly associated with a favorable developmental outcome

Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep

Copy number variation (CNV) is a major source of genomic structural variation. The aim of this study was to detect genomic CNV regions (CNVR) in Valle del Belice dairy sheep population and to identify those affecting milk production traits. The GO analysis identified possible candidate genes and pathways related to the selected traits. We identified CNVs in 416 individuals genotyped using the Illumina OvineSNP50 BeadChip array. The CNV association using a correlation-trend test model was examined with the Golden Helix SVS 8.7.0 tool. Significant CNVs were detected when their adjusted p-value was <0.01 after false discovery rate (FDR) correction. We identified 7,208 CNVs, which gave 365 CNVRs after aggregating overlapping CNVs. Thirty-one CNVRs were significantly associated with one or more traits included in the analysis. All CNVRs, except those on OAR19, overlapped with quantitative trait loci (QTL), even if they were not directly related to the traits of interest. A total of 222 genes were annotated within the significantly associated CNVRs, most of which played important roles in biological processes related to milk production and health-related traits. Identification of the genes in the CNVRs associated with the studied traits will provide the basis for further investigation of their role in the metabolic pathways related to milk production and health traits

Detection of genomic regions underlying milk production traits in Valle del Belice dairy sheep using regional heritability mapping

The aim of this study was to identify genomic regions underlying milk production traits in the Valle del Belice dairy sheep using regional heritability mapping (RHM). Repeated measurements for milk yield (MY), fat percentage and yield (F% and FY) and protein percentage and yield (P% and PY), collected over a period of 6 years (2006-2012) on 481 Valle del Belice ewes, were used for the analysis. Animals were genotyped with the Illumina 50k SNP chip. Variance components, heritabilities and repeatabilities within and across lactations were estimated, fitting parity, litter size, season of lambing and fortnights in milk, as fixed; and additive genetic, permanent environment within and across lactations, flock by test-day interaction and residual as random effects. For the RHM analysis, the model included the same fixed and random effects as before, plus an additional regional genomic additive effect (specific for the region being tested) as random. While the whole genomic additive effect was estimated using the genomic relationship matrix (GRM) constructed from all SNPs, the regional genomic additive effect was estimated from a GRM matrix constructed from the SNPs within each region. Heritability estimates ranged between 0.06 and 0.15, with repeatabilities being between 0.14 and 0.24 across lactations and between 0.23 and 0.39 within lactation for all milk production traits. A substantial effect of flock-test-day on milk production traits was also estimated. Significant genomic regions at either genome-wide (p < .05) or suggestive (i.e., one false positive per genome scan) level were identified on chromosome (OAR) 2, 3 and 20 for F% and on OAR3 for P%, with the regions on OAR3 in common between the two traits. Our results confirmed the role of LALBA and AQP genes, on OAR3, as candidate genes for milk production traits in sheep

Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations

The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study,we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) andMessinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as formilk yield, reproduction, and immune response, and are consistentwith the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource

Association between Grain Size and Shape and Quality Traits, and Path Analysis of Thousand Grain Weight in Iranian Bread Wheat Landraces from Different Geographic Regions

Grain characteristics, particularly grain weight, grain morphology, and grain protein content (GPC), are important components of grain yield and quality in wheat. A set of 98 bread wheat landraces from different geographic regions of Iran were used across 2013-2014 and 2014-2015 to determine the phenotypic diversity and relations between thousand grain weight (TGW), grain morphology and grain quality. A high-throughput method was used to capture grain size and shape. The genotypes were significantly different (P < 0.001) for all traits which reflects the high levels of diversity. A moderate to high broad sense heritability was found for all traits and ranged between 0.68 and 0.95 for grain yield and factor from density (FFD), respectively. Significant positive correlations were observed between TGW and grain size (or shape) exception of aspect ratio (AR) and roundness. However, grain quality traits, especially GPC had significant negative correlation with TGW. Based on stepwise regression analysis by taking TGW as dependent variable, grain volume, FFD, width, perimeter and Hardness Index (HI) were recognized as the most important traits and explained more than 99.3% of total variation of TGW. The path analysis revealed that FFD has maximum direct effect on TGW followed by volume, whereas perimeter and width had relatively less direct effect on TGW. According to cluster analysis, landraces separated into 5 clusters, and cluster III and IV had the maximum and minimum average for the most traits, respectively. Our study provides new knowledge on the relations between TGW, grain morphology and grain quality in bread wheat, which may aid the improvement of wheat grain weight trait in further research

A high-density consensus map of A and B wheat genomes

A durum wheat consensus linkage map was developed by combining segregation data from six mapping populations. All of the crosses were derived from durum wheat cultivars, except for one accession of T. ssp. dicoccoides. The consensus map was composed of 1,898 loci arranged into 27 linkage groups covering all 14 chromosomes. The length of the integrated map and the average marker distance were 3,058.6 and 1.6 cM, respectively. The order of the loci was generally in agreement with respect to the individual maps and with previously published maps. When the consensus map was aligned to the deletion bin map, 493 markers were assigned to specific bins. Segregation distortion was found across many durum wheat chromosomes, with a higher frequency for the B genome. This high-density consensus map allowed the scanning of the genome for chromosomal rearrangements occurring during the wheat evolution. Translocations and inversions that were already known in literature were confirmed, and new putative rearrangements are proposed. The consensus map herein described provides a more complete coverage of the durum wheat genome compared with previously developed maps. It also represents a step forward in durum wheat genomics and an essential tool for further research and studies on evolution of the wheat genome. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00122-012-1939-y) contains supplementary material, which is available to authorized users

Efficacy of ketamine in refractory convulsive status epilepticus in children: A protocol for a sequential design, multicentre, randomised, controlled, open-label, non-profit trial (KETASER01)

Introduction: Status epilepticus (SE) is a lifethreatening neurological emergency. SE lasting longer than 120 min and not responding to first-line and second-line antiepileptic drugs is defined as 'refractory' (RCSE) and requires intensive care unit treatment. There is currently neither evidence nor consensus to guide either the optimal choice of therapy or treatment goals for RCSE, which is generally treated with coma induction using conventional anaesthetics (high dose midazolam, thiopental and/or propofol). Increasing evidence indicates that ketamine (KE), a strong N-methyl-D-aspartate glutamate receptor antagonist, may be effective in treating RCSE. We hypothesised that intravenous KE is more efficacious and safer than conventional anaesthetics in treating RCSE. Methods and analysis: A multicentre, randomised, controlled, open-label, non-profit, sequentially designed study will be conducted to assess the efficacy of KE compared with conventional anaesthetics in the treatment of RCSE in children. 10 Italian centres/ hospitals are involved in enrolling 57 patients aged 1 month to 18 years with RCSE. Primary outcome is the resolution of SE up to 24 hours after withdrawal of therapy and is updated for each patient treated according to the sequential method. Ethics and dissemination: The study received ethical approval from the Tuscan Paediatric Ethics Committee (12/2015). The results of this study will be published in peer-reviewed journals and presented at international conferences