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Additional file 1: Figure S1. Decline in genetic correlation between the two breeding goal traits over generations of selection. The figure shows the genetic correlation between breeding goals in a scenario without balancing selection and avoiding carrier���carrier matings. Points show the average over replicates, with the error bars being the 5 and 95 percentiles. Figure S2. Distribution of offspring per sire used in the simulation. The figure shows the number of offspring per sire proportioned to sires in that decile. Figure S3. Balancing selection on the lethal allele has little effect on genetic gain in the simulation. The figure shows the average genetic values for simulated populations at generations 1, 5, 10, 15 and 20 for the two breeding goals, with error bars showing the 5 and 95 percentiles.

With the advent of genomics, nowadays there is a possibility to further understand the genetic background of economically relevant traits in horses. However, in the case of highly polygenic and complex traits, such as movement traits, this achievement might be more challenging. Application of Genome-Wide Association Studies (GWAS) was successful, especially for highly heritable traits, such as conformation and disease-related traits. Another important aspect to consider is the availability of data collected in a large cohort of animals ; indeed the GWAS approach has been mainly applied in studies with great population size. Nevertheless, combining novel motion technology, which allows more objective measurements, with genotype data might help to further unravel the genetic background of movement traits also in breeds with unavailability of large number of genotyped horses. Thus, in this study, we aimed to perform a GWAS analysis in the Bardigiano horse breed, an Italian breed traditionally used in agriculture. We used the Equisense motion® sensor, which consists of a gyroscope and an accelerometer to objectively record several gaits-related traits linked with the horse’s health, performance, and physical condition. A total of 185 horses were genotyped with the GGP Equine 70k ® SNP chip. The quality control of the genotype data was performed in Plink v 1.9 and the GWAS analysis in R Software. To assess the association with genotype information, a linear mixed model was used, corrected for sex, the sampling date, and for biometrical measurements. We mostly found significant results on the trot gait, for example, for the symmetry we found 9 significantly associated SNPs. In the proximity of those SNPs (windows size±250 kb) 22 protein-coding genes, 3 miRNA, and 7 lncRNA were identified. Some of those genes have known function in collagen structure and the control of the synapsis response. Further analysis of those genes might permit to enhance the use of genomics in the Bardigiano horse breed which is facing the conversion from agricultural to riding purposes.

The management of reproduction of local breeds of pigs is the key factor influencing their reproductive efficiency, genetic and biodiversity. The production of offspring and their further raising make the basis of production organization, as well as management strategies in conservation procedure for local pig breeds. The aim of this study was to analyse and evaluate Litter Size (LS) traits in two autochthonous pig breeds accord-ing to their similarity in breeding procedure, as Management of Farrowing (MF) and Number of Sows per Herd (NSH), to improve their reproductive performance and self-sustainability.Data analysis included 2026 parities of Black Slavonian (BS)and 906 of Nero di Parma (NP), from the 1st to 10th parity(PAR). The LS traits referred to Total Number of Born (TNB), Number of Born Alive (NBA) and Number of Weaned (NW)piglets. Data analysis was performed using GLM (SAS). Five effects with two double interactions were included in the model of calculation to analyse the possible factors influencing between-breed differences in reproductive efficiency. The following effects were tested: breed (BR), PAR, four season of farrowing (SF) according to calendar year, NSH (three levels: 1-3, 4-10 and ˃10 reproductive sows per herd) and MF (two levels: controlled farrowing in roofed premises and farrowing at uncontrolled and non-roofed sites) with interaction in the scalar equation as BR*MF and BR*NSH. The results were expressed as Least Squares Means±SE. Pooled farrowing analysis showed TNB to be lower in BS (6.93 ± 0.08) compared with NP sows (8.31 ± 0.13), with significant effects (p

Local pig populations such as Black Slavonian (BS) and Nero di Parma (NP) contribute to genetic diversity and represent a unique genetic material of the Mediterranean region. The objective of this study was to evaluate differences between the two genotypes in reproductive efficiency, as one of the most important factors for biological and economic sustainability of breeding. Data were collected from 1835 parities of 685 sows (264 BS and 421 NP). The following parameters were included in the analysis: total number of born (TNB), number of born alive (NBA), number of stillborn (NSB), number of weaned (NW) piglets. The effects included in the model were analyzed (GLM procedure in SAS), separately for each parity (from 1st to ≥4th) and for all parities taken together. The following fixed effects were tested: breed (BR), herd (HD), interactions breed*herd (BR*HD), year-month of farrowing (YMF) and parity order (PO) ; boar (BO) was added as a random effect. Primiparous BS vs. NP sows showed 5.9±1.9 vs.7.3±2.1 TNB and 5.6±2.1 vs. 6.9±2.3 NBA, with 0.25±0.96 vs. 0.38±1.20 NSB and 5.0±2.4 vs. 5.5±2.7 NW, respectively. BR, BO and YMF had a significant effect (P0.05) were found in 3rd parity sows, with 7.1±2.1 vs. 8.1±2.1 TNB and 6.6±2.4 vs. 7.8±2.4 NBA, 0.40±1.13 vs. 0.29±1.10 NSB and 6.4±2.4 vs. 6.3±2.6 NW, for BS and NP, respectively. Fourth and >4th parity sows showed 7.4±2.4 vs. 8.3±2.4 TNB, 6.9±2.6 vs. 8.1±2.5 NBA, 0.53±1.31 vs. 0.31±0.91 NSB and 6.2±2.9 vs. 6.8±2.7 NW, for BS and NP, respectively, with a significant effect (P

The aim of this study was to analyse the litter size traits in two genotypes of pig population with black coat: Black Slavonian (BS) and “Nero di Parma” (NP). Data analysis included records from the 1st to 4th parity separately, and all parities (from 1st to 11th) for the following traits: Total Number of Born (TNB), Number of Born Alive (NBA), and Number of Weaned (NW) piglets, collected from 296 BS and 421 NP sows. Litter size traits from 1st to 4th parity was analysed separately for each breed and ANOVA Repetead Measure test was used to calculate the difference between parities. The analysis of seasonality in all parities was performed using the General Linear Model.Significant differences (P

Black Slavonian (BS) and Nero di Parma (NP) pig breeds are an essential part of biological diversity of southern Europe as distinctive rustic exterior and black genotypes reared in semi-extensive systems. Environmental factors such as changes in ambient temperature and photoperiod have a significant role in the variability of reproductive performance of sows. Genetic characterization is a fundamental prerequisite in the strategies and management for the resources that local breeds possess to maintain genetic diversity as a primary key to reduce the risk of extinction. The aim of the present study was to investigate the variation of litter size traits between hot (spring to summer) and cold (autumn to winter) season. Data analysis included 2349 records of parities within all parities analysed for litter size traits as follows: Total Number of Born (TNB), Number of Born Alive (NBA), Number of Still Born (NSB), and Number of Weaned (NW) piglets collected from 717 sows (296 BS and 421 NP) from 2007 to 2014. Analysis of variance was applied using the General Linear Model (GLM) procedure in SAS. The fixed effects included in the model were breed (BR), herd (HD), season (SE), parity (PR), interaction between breed and herd (BR*HD), and interaction between breed and season (BR*SE). For each trait, the least square means with standard errors were calculated. Statistically significant effects (P