Diversity across major and candidate genes in European local pig breeds

The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krskopolje (Krskopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwa-bisch-Hallisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population’s structure and relationships

Mood, Activity Participation, and Leisure Engagement Satisfaction (MAPLES): a randomised controlled pilot feasibility trial for low mood in acquired brain injury

Abstract: Background: Acquired brain injury (ABI) affects approximately 79.3 million individuals annually and is linked with elevated rates of depression and low mood. Existing methods for treating depression in ABI have shown mixed efficacy. Behavioural activation (BA) is a potentially promising intervention. Its premise is that individuals with low mood avoid planning and engaging in activities due to low expectations of a positive outcome. Consequently, their exposure to positive reinforcement is reduced, exacerbating low mood. BA aims to break this cycle by encouraging activity planning and engagement. It is unknown whether cognitive demands of traditional BA may undermine efficacy in ABI. Here, we assess the feasibility and acceptability of two groups designed to increase activity engagement. In the activity planning group (traditional BA), the importance of meaningful and positive activity will be discussed and participants encouraged to plan/engage in activities in everyday life. The activity engagement group (experiential BA) instead focuses on engagement in positive experiences (crafts, games, discussion) within the group. The primary aims are to evaluate the feasibility and acceptability of the two groups in ABI. A secondary aim is to explore relative efficacy of the groups compared to an equivalent period of waitlist controls. Method: This study outlines a parallel-arm pilot feasibility trial for individuals with low mood and ABI that compares a traditional vs experiential BA group vs waitlist controls. Adults (≥ 18 years) will be recruited from local ABI services and randomised to condition. Feasibility and acceptability will be assessed via recruitment, retention, attendance and participant feedback. Groups will be compared (pre- and post-intervention and 1 month follow-up) by assessing self-reported activity engagement. Secondary outcomes include self-report measures of depression, anxiety, post-traumatic distress related to the ABI, motivation, participation and sense of control over one’s life. Ethics and dissemination: The trial has been approved by the Health Research Authority of the NHS in the UK (East of England—Cambridge Central, REF 18/EE/0305). Results will inform future research on interventions for mood in ABI and be disseminated broadly via peer-reviewed journals, conference presentations and social media. Trial registration: ClinicalTrials.gov, NCT03874650 pre-results. Protocol version 2.1, March 5, 201

Mood, Activity Participation, and Leisure Engagement Satisfaction (MAPLES): Results From a Randomised Controlled Pilot Feasibility Trial for Low Mood in Acquired Brain Injury

Background: Acquired brain injury (ABI) is linked to increased depression risk. Existing therapies for depression in ABI (e.g., Cognitive Behavioural Therapy) have mixed efficacy. Behavioural Activation (BA), an intervention that encourages engaging in positively reinforcing activities, shows promise. The primary aims were to assess feasibility, acceptability, and potential efficacy of two 8-week BA groups. Methods: Adults (≥ 18 years) recruited from local ABI services, charities, and self-referral via social media were randomised to condition. The Activity Planning group (AP; “traditional” BA) trained participants to plan reinforcing activities over 8 weeks, the Activity Engagement group (AE; “experiential” BA) encouraged engagement in positive activities within session only. Both BA groups were compared to an 8-week Waitlist group (WL). The primary outcomes, feasibility and acceptability, were assessed via recruitment, retention, attendance, and qualitative feedback on groups. The secondary outcome, potential efficacy, was assessed via blinded assessments of self-reported activity levels, depression, and anxiety (at pre- and post-intervention and 1 month follow up) and were compared across trial arms. Data were collected in-person and remotely due to COVID-19. Results: N = 60 participants were randomised to AP (randomised n = 22; total n = 29), AE (randomised n = 22; total n = 28), or re-randomised following WL (total n = 16). Whether in-person or remote, AP and AE were rated as similarly enjoyable and. In exploring efficacy, 58.33% of AP members had clinically meaningful activity level improvements, relative to 50% AE and 38.5% WL. Both AP and AE groups had depression reductions relative to WL, but only AP participants demonstrated anxiety reductions relative to AE and WL. AP participants noted benefits of learning strategies to increase activities and learning from other group members. AE participants valued social discussion and choice in selecting in-session activities. Conclusions: Both in-person and remote group BA were feasible and acceptable in ABI. Though both traditional and experiential BA may be effective, these may have different mechanisms. Trial Registration: Clinicaltrials.gov, NCT03874650. Protocol version 2.3, May 26th 2020

Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via over-representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources

Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip

Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on FST outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions

Determination of fatty acid groups in intramuscular fat of various local pig breeds by FT-NIRS

The objective of the present study is to evaluate the potential use of FT-NIRS for predicting intramuscular fat (IMF) and fatty acid groups (MUFA; PUFA; PUFA n-3, PUFA n-6; SFA) on pig grounded muscles. The research considered 160 fresh samples of Longissimus collected from 12 European local pig breeds (TREASURE* project). For every sample, lipids were extracted from IMF and fatty acid profile was determinate by gas chromatography. Two aliquots of each sample were scanned using FT-NIRS Antaris II model. Mathematical pre-treatments (multiplicative scatter correction, 1st and 2nd derivate) were applied and outliers’ spectra were identified and removed when necessary. Partial least square regression was used on the average spectrum and the models validated using an external data set. Results are evaluated in terms of coefficient of regression and root mean square errors in calibration (R2-RMSE) and validation (Rp2-RMSEP). As expected, the best results were obtained for IMF with R2 higher than 0.99 and RMSE lower than 0.2. Unsaturated fatty acids, probably due to the absorption of the cis double bond in a specific region of near infrared spectra, obtain acceptable R2 (0.89 for MUFA and 0.75 for PUFA n-3 and PUFA n-6). SFA achieved a R2 of 0.81 that is lower than values reported in other studies probably because of the large variability of genotypes used. The validation models achieved both lower coefficients of determination and higher RMSEP than the calibration models; however, R2 differences between calibration and validation were smaller than 5%, except for SFA. Hence, the FT-NIRS seems promising to estimate the principal parameters of fatty acid groups on muscle samples from different European autochthonous pig breeds. Inclusion of other samples can improve the accuracy and the robustness of the models, especially considering the high variability of the samples. *Funded by European Union’s H2020 program (grant agreement No 634476)

Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds.

ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. PLINK software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via overrepresentation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n=32), Cinta Senese (n=26) and LithuanianWhite Old Type (n=22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources.FE1B-06B2-126F | José Pedro Pinto de AraújoN/