As a result of the genetic selection for prolificacy and the improvements in the environment and farms management, litter size has increased in the last few years so that energy requirements of the lactating sow are greater. In addition, selection for feed efficiency of growing pigs is also conducted in maternal lines, and this has led to a decrease in appetite and feed intake that is extended to the lactation period, so the females are not able to obtain the necessary energy and nutrients for milk production and they mobilize their energetic reserves. When this mobilization is excessive, reproductive and health problems occur which ends up in an early sow culling. In this context, it has been suggested to improve feed efficiency at lactation through genetic selection. The aim of this study is to know, in a Duroc population, the genetic determinism of sow feed efficiency during lactation and traits involved in its definition, as well as genetic and environmental associations between them. The studied traits are daily lactation feed intake (dLFI), daily sow weight balance (dSWB), backfat thickness balance (BFTB), daily litter weight gain (dLWG), sow residual feed intake (RFI) and sow restricted residual feed intake (RRFI) during lactation. Data corresponded to 851 parities from 581 Duroc sows. A Bayesian analysis was performed using Gibbs sampling. A four-trait repeatability animal model was implemented including the systematic factors of batch and parity order, the standardized covariates of sow weight (SWf) and litter weight (LWs) at farrowing for all traits and lactation length for BFTB. The posterior mean (posterior SD) of heritabilities were: 0.09 (0.03) for dLFI, 0.37 (0.07) for dSWB, 0.09 (0.03) for BFTB, 0.22 (0.05) for dLWG, 0.04 (0.02) for RFI and null for RRFI. The genetic correlation between dLFI and dSWB was high and positive (0.74 (0.11)) and null between dLFI and BFTB. Genetic correlation was favourable between RFI and dLFI and BFTB (0.71 (0.16) and −0.69 (0.18)), respectively. The other genetic correlations were not statistically different from zero. The phenotypic correlations were low and positive between dLFI and dSWB (0.27 (0.03), dSWB and BFTB (0.25 (0.04)), and between dLFI and dLWG (0.16 (0.03)). Therefore, in the population under study, the improvement of the lactation feed efficiency would be possible either using RFI, which would not have unfavourable correlated effects, or through an index including its component traits.

Breeding entire males is an alternative to surgical castration to improve their welfare. However, entire males may have a major quality defect called boar taint. Boar taint is partly due to the presence of androstenone in fat. In this study, we estimated the genetic parameters between androstenone and production traits to evaluate the consequences of selection against boar taint for traits of interest. We focused on growth traits, meat quality, lesions, hormone levels and computerised tomography measurements in purebred Piétrain (P) or Piétrain cross Large White (X) entire males. The number of measured animals varied from 670 P and 734 X for hormones concentrations to 553 P and 645 X for computerised tomography measurements. Skin lesions were measured on live pigs shortly after mixing, at the end of the fattening period, and on carcasses. Heritabilities of traits measured by tomography ranged from low to high: femur density (P: 0.34, X: 0.69), loin eye area (P: 0.53, X: 0.88) and loin eye density (P: 0.12, X: 0.18). The mean number of lesions at each stage was lower in purebred pigs than in crossbreds (entering the fattening stage 4.01 in P and 4.68 in X; before slaughter 3.72 in P and 4.22 in X; on carcass 4.50 in P and 4.96 in X). We also observed a decrease in the average number of lesions between the two stages in live pigs. We found high genetic correlations between stages in purebred pigs (0.74 to 0.76) but low correlations (−0.30 to 0.29) in crossbred pigs. Selection aiming to decrease fat androstenone is feasible (h2 = 0.57 in P and h2 = 0.71 in X). It would have overall positive effects on meat production and quality traits. Selection aiming to reduce plasma oestradiol would strongly reduce the level of fat androstenone (rg = 0.89 in P and rg = 0.84 in X). Selection against oestradiol is easier and less invasive since it would only require a blood sample rather than a fat biopsy in live animals.

Although the tambaqui (Colossoma macropomum) is the most cultivated native fish species in Brazil, estimated breeding values for growth traits are rarely used for selection of superior individuals in commercial fingerling production. This study aimed to estimate the (co)variance components of growth traits. Body weight, length and width of 2500 tambaqui were determined at tagging and at 6 and 12 months after tagging in a commercial breeding programme in Brazil. Heritability estimates were low for traits measured at tagging (0.10 to 0.19) and moderate to high for traits measured at 6 and 12 months (0.23 to 0.81). Common full-sib effects were high at tagging (>73%), low at 6 months and negligible at 12 months. Positive genetic correlations were found among growth traits at 12 months (0.84 to 0.99) and between growth traits at 6 and 12 months (0.80 to 0.92). These results show that animal selection can be performed at 6 months after tagging. Expected genetic gains for growth traits ranged from 8% to 31%. A simulation of the sex ratio was performed, as individuals did not reach sexual maturity during the experimental period. Because of the sexual dimorphism, more accurate heritability estimates were obtained when considering the female proportion to be 90% in the high-weight group. The findings indicate that it is possible to obtain considerable genetic gains in growth by selecting for growth traits. The development of a tool to determine the sex of animals at early stages can improve the response to selection in tambaqui.

In the middle of the 20th century, increasing inbreeding rates were identified as a threat to livestock breeding. Consequences include reduced fertility, fitness and phenotypic expression of lethal alleles. An important step in mitigating this inbreeding was the introduction of optimum contribution selection (OCS). OCS facilitates the simultaneous management of genetic gain and inbreeding rates. However, using a standard OCS methodology for regional breeds with historical introgression for upgrading reasons could lead to reinforced selection on introgressed genetic material since those alleles improve the rate of genetic gain and reduce the average kinship in the population. Consequently, regional breeds may become genetically extinct if a standard OCS approach is used. Thus, the advanced OCS (aOCS) approach takes introgressed genetic material into account. The major goals of this study were to (i) gather key information on the feasibility of aOCS under practical conditions of the actual breeding scheme of Vorderwald cattle, (ii) identify superior strategies for implementing the actual scheme and (iii) examine whether historical breeding decisions to increase genetic gain by introgression from commercial breeds could have been avoided by using aOCS. Stochastic simulations were designed in this study to create populations from the historical gene pool by using aOCS. Simultaneously, all practical constraints of a breeding scheme were met. Thus, the simulated populations were comparable with real data. The annual genetic gain was higher in reality (1.56) than in the simulation scenarios (1.12–1.40). The introgressed genetic material increased to 61.3% in reality but was conserved at a final value of 15.3% (±0.78) across simulations. The classical rate of inbreeding and rate of native inbreeding were constrained to 0.092% on an annual basis. This value is equal to an effective population size of 100. The observed values for rates of inbreeding were 0.082–0.087% and 0.087–0.088% for classical and native kinship, respectively. The corresponding figures in reality were 0.067% and 0.184%, respectively. This study suggests that aOCS is feasible for Vorderwald cattle. Strategies for implementation are identified. Finally, we conclude that historical breeding decisions could have been avoided by using aOCS. The genetic gain would have been reduced by at least 12.2%, but the introgressed genetic material, genetic diversity and native genetic diversity would have been more desirable for a breed under conservation.

Leg weakness (LW) issues are a great concern for pig breeding industry. And it also has a serious impact on animal welfare. To dissect the genetic architecture of limb-and-hoof firmness in commercial pigs, a genome-wide association study was conducted on bone mineral density (BMD) in three sow populations, including Duroc, Landrace and Yorkshire. The BMD data were obtained by ultrasound technology from 812 pigs (including Duroc 115, Landrace 243 and Yorkshire 454). In addition, all pigs were genotyped using genome-by-sequencing and a total of 224 162 single-nucleotide polymorphisms (SNPs) were obtained. After quality control, 218 141 SNPs were used for subsequent genome-wide association analysis. Nine significant associations were identified on chromosomes 3, 5, 6, 7, 9, 10, 12 and 18 that passed Bonferroni correction threshold of 0.05/(total SNP numbers). The most significant locus that associated with BMD (P value = 1.92e−14) was detected at approximately 41.7 Mb on SSC6 (SSC stands for Sus scrofa chromosome). CUL7, PTK7, SRF, VEGFA, RHEB, PRKAR1A and TPO that are located near the lead SNP of significant loci were highlighted as functionally plausible candidate genes for sow limb-and-hoof firmness. Moreover, we also applied a new method to measure the BMD data of pigs by ultrasound technology. The results provide an insight into the genetic architecture of LW and can also help to improve animal welfare in pigs.

Young stock survival is a trait of crucial importance in cattle breeding as calf mortality leads to economic losses and represents an animal welfare issue. The aim of this study was to estimate genetic parameters and sire breeding values for young stock survival in beef x dairy crossbred calves. Two traits were analysed with a univariate animal model: young stock survival between 1 to 30 days and 31 to 200 days after birth. Breed combinations with Belgian Blue sires outperformed all other sire breeds. The lowest survival rates were found for breed combinations with Jersey dams or Blonde d’Aquitaine sires. The results showed low but significant heritabilities (0.045 to 0.075) for both survival traits. Differences in breeding values between sires ranged from −2.5% to 3.5% and from −5.4% to 4.7% survival from 1 to 30 days and 31 to 200 days, respectively. Based on these findings, we concluded that it is feasible to breed for improved young stock survival in beef x dairy crossbred calves. This will hopefully contribute to increasing the survival rate of the calves and reduce economic losses for the farmers.

Combining different swine populations in genomic prediction can be an important tool, leading to an increased accuracy of genomic prediction using single nucleotide polymorphism (SNP) chip data compared with within-population genomic. However, the expected higher accuracy of multi-population genomic prediction has not been realized. This may be due to an inconsistent linkage disequilibrium (LD) between SNPs and quantitative trait loci (QTL) across populations, and the weak genetic relationships across populations. In this study, we determined the impact of different genomic relationship matrices, SNP density and pre-selected variants on prediction accuracy using a combined Yorkshire pig population. Our objective was to provide useful strategies for improving the accuracy of genomic prediction within a combined population. Results showed that the accuracy of genomic best linear unbiased prediction (GBLUP) using imputed whole-genome sequencing (WGS) data in the combined population was always higher than that within populations. Furthermore, the use of imputed WGS data always resulted in a higher accuracy of GBLUP than the use of 80K chip data for the combined population. Additionally, the accuracy of GBLUP with a non-linear genomic relationship matrix was markedly increased (0.87% to 15.17% for 80K chip data, and 0.43% to 4.01% for imputed WGS data) compared with that obtained with a linear genomic relationship matrix, except for the prediction of XD population in the combined population using imputed WGS data. More importantly, the application of pre-selected variants based on fixation index (Fst) scores improved the accuracy of multi-population genomic prediction, especially for 80K chip data. For BLUP|GA (BLUP approach given the genetic architecture), the use of a linear method with an appropriate weight to build a weight-relatedness matrix led to a higher prediction accuracy compared with the use of only pre-selected SNPs for genomic evaluations, especially for the total number of piglets born. However, for the non-linear method, BLUP|GA showed only a small increase or even a decrease in prediction accuracy compared with the use of only pre-selected SNPs. Overall, the best genomic evaluation strategy for reproduction-related traits for a combined population was found to be GBLUP performed with a non-linear genomic relationship matrix using variants pre-selected from the 80K chip data based on Fst scores.

Single nucleotide polymorphisms (SNPs) able to describe population differences can be used for important applications in livestock, including breed assignment of individual animals, authentication of mono-breed products and parentage verification among several other applications. To identify the most discriminating SNPs among thousands of markers in the available commercial SNP chip tools, several methods have been used. Random forest (RF) is a machine learning technique that has been proposed for this purpose. In this study, we used RF to analyse PorcineSNP60 BeadChip array genotyping data obtained from a total of 2737 pigs of 7 Italian pig breeds (3 cosmopolitan-derived breeds: Italian Large White, Italian Duroc and Italian Landrace, and 4 autochthonous breeds: Apulo-Calabrese, Casertana, Cinta Senese and Nero Siciliano) to identify breed informative and reduced SNP panels using the mean decrease in the Gini Index and the Mean Decrease in Accuracy parameters with stability evaluation. Other reduced informative SNP panels were obtained using Delta, Fixation index and principal component analysis statistics, and their performances were compared with those obtained using the RF-defined panels using the RF classification method and its derived Out Of Bag rates and correct prediction proportions. Therefore, the performances of a total of six reduced panels were evaluated. The correct assignment of the animals to its breed was close to 100% for all tested approaches. Porcine chromosome 8 harboured the largest number of selected SNPs across all panels. Many SNPs were included in genomic regions in which previous studies identified signatures of selection or genes (e.g. ESR1, KITL and LCORL) that could contribute to explain, at least in part, phenotypically or economically relevant traits that might differentiate cosmopolitan and autochthonous pig breeds. Random forest used as preselection statistics highlighted informative SNPs that were not the same as those identified by other methods. This might be due to specific features of this machine learning methodology. It will be interesting to explore if the adaptation of RF methods for the identification of selection signature regions could be able to describe population-specific features that are not captured by other approaches.

The objectives of this study were to analyse the differences in the genetic determination of functional longevity in five Spanish lines of rabbits and to check how different systematic factors might affect this genetic determination. Four of the lines were maternal (lines A, V, H and LP), these lines were established selecting base generation animals according to different criteria, but in the subsequent generations all of them were selected for litter size at weaning. The other is the paternal line R, this line was constituted by selecting animals with an outstanding daily growth rate. The trait analysed, length of productive life, was the time in days between the date of the first positive pregnancy test and the date of culling or death of a doe. Four models extended from the Cox proportional hazard model were used to analyse data of each line separately and jointly. The complete model (Model 1) included the fixed effect of year-season (YS) combination, positive palpation order (OPP), that is, reproductive cycle, physiological status of the doe (PS) at service and number of kits born alive (NBA) in each kindling as time-dependent factors. The inbreeding coefficient was fitted as a continuous covariate and the animal’s additive genetic effect was also fitted to the model (Model 1). The other models were identical to Model 1 but excluding OPP (Model 2) or PS (Model 3) or NBA (Model 4), which were explored to assess the consequence on additive variance estimates of not correcting for these animal-dependent factors. Estimated effective heritabilities of longevity were 0.07 ± 0.03, 0.03 ± 0.02, 0.14 ± 0.09, 0.05 ± 0.04, 0.02 ± 0.01 and 0.04 ± 0.01 for lines A, V, H, LP, R and for the merged data set, respectively. Removing the PS from the model led to an increase in the estimated additive genetic variance in all lines (0.17 ± 0.05, 0.05 ± 0.03, 0.29 ± 0.19, 0.29 ± 0.20, 0.07 ± 0.04 and 0.05 ± 0.02 for lines A, V, H, LP, R and the merged data set, respectively). The highest hazard of death and/or culling was observed during the first two parities and decreased as the order of parity progressed. Does non-pregnant-non-lactating had the highest risk of death or culling. The does that had zero kits born alive incurred the highest risk, and this risk decreased as the NBA increased. In conclusion, the consideration of longevity as selection criterion for the studied rabbit lines is not recommended.

The widespread use of genome-wide association studies resulted in the discovery of genomic regions associated with fatty acid (FA) composition in different porcine tissues, but little information exists about the genes involved in FA composition of meat obtained from heavy pigs selected for the production of Italian dry-cured hams. To this objective, we genotyped with a single nucleotide polymorphism (SNP) panel 795 Italian Large White heavy pigs to identify the markers and genomic regions associated with Semimembranosus muscle FA profile. Heritability estimates for intramuscular fat FA profile were of low-to-moderate magnitude, suggesting that these traits may be improved with genomic selection. On the whole, 45 SNPs were significantly associated with 14 FAs, and 4 of them (ALGA008109, ALGA0081097, CASI0010164 and SIRI0000267) were associated with more than 1 FA. The palmitoleic : palmitic and oleic : stearic ratios displayed the highest number of significant markers and the most significant associations (Bonferroni adjusted P < 5.00E−07). Of particular interest, the palmitoleic : palmitic ratio was strongly associated with markers located at 111 to 114 Mb on chromosome 14, in the same chromosomal region where Stearoyl-CoA desaturase Δ9 (SCD) gene is located. Several significant chromosomal regions were found; some of them harbour key genes playing pivotal roles in FA desaturation and elongation, such as SCD and some members of the Elongation of Very Long-Chain FA (ELOVL) gene family. The results suggest that the identification of causal mutations in these regions may provide a set of markers useful for selection schemes aimed at improving FA composition in pork products.

Vorderwald cattle are a regional cattle breed from the Black Forest in south western Germany. In recent decades, commercial breeds have been introgressed to upgrade the breed in performance traits. On one hand, native genetic diversity of the breed should be conserved. On the other hand, moderate rates of genetic gain are needed to satisfy breeders to keep the breed. These goals are antagonistic, since the native proportion of the gene pool is negatively correlated to performance traits and the carriers of introgressed alleles are less related to the population. Thus, a standard Optimum Contribution Selection (OCS) approach would lead to reinforced selection on migrant contributions (MC). Our objective was the development of strategies for practical implementation of an OCS approach to manage the MC and native genetic diversity of regional breeds. Additionally, we examined the organisational efforts and the financial impacts on the breeding scheme of Vorderwald cattle. We chose the advanced Optimum Contribution Selection (aOCS) to manage the breed in stochastic simulations based on real pedigree data. In addition to standard OCS approaches, aOCS facilitates the management of the MC and the rate of inbreeding at native alleles. We examined two aOCS strategies. Both strategies maximised genetic gain, while strategy (I) conserved the MC in the breeding population and strategy (II) reduced the MC at a predefined annual rate. These two approaches were combined with one of three flows of replacement of sires (FoR strategies). Additionally, we compared breeding costs to clarify about the financial impact of implementing aOCS in a young sire breeding scheme. According to our results, conserving the MC in the population led to significantly (P < 0.01) higher genetic gain (1.16 ± 0.13 points/year) than reducing the MC (0.88 ± 0.10 points/year). In simulation scenarios that conserved the MC, the final value of MC was 57.6% ± 0.004, while being constraint to 58.2%. However, reducing the MC is only partially feasible based on pedigree data. Additionally, this study proves that the classical rate of inbreeding can be managed by constraining only the rate of inbreeding at native alleles within the aOCS approach. The financial comparison of the different breeding schemes proved the feasibility of implementing aOCS in Vorderwald cattle. Implementing the modelled breeding scheme would reduce costs by 1.1% compared with the actual scheme. Reduced costs were underpinned by additional genetic gain in superior simulation scenarios compared to expected genetic gain in reality (+4.85%).

The net benefit from investing in any technology is a function of the cost of implementation and the expected return in revenue. The objective of the present study was to quantify, using deterministic equations, the net monetary benefit from investing in genotyping of commercial females. Three case studies were presented reflecting dairy cows, beef cows and ewes based on Irish population parameters; sensitivity analyses were also performed. Parameters considered in the sensitivity analyses included the accuracy of genomic evaluations, replacement rate, proportion of female selection candidates retained as replacements, the cost of genotyping, the sire parentage error rate and the age of the female when it first gave birth. Results were presented as an annualised monetary net benefit over the lifetime of an individual, after discounting for the timing of expressions. In the base scenarios, the net benefit was greatest for dairy, followed by beef and then sheep. The net benefit improved as the reliability of the genomic evaluations improved and, in fact, a negative net benefit of genotyping was less frequent when the reliability of the genomic evaluations was high. The impact of a 10% point increase in genomic reliability was, however, greatest in sheep, followed by beef and then dairy. The net benefit of genotyping female selection candidates reduced as replacement rate increased. As genotyping costs increased, the net benefit reduced irrespective of the percentage of selection candidates kept, the replacement rate or even the population considered. Nonetheless, the association between the genotyping cost and the net benefit of genotyping differed by the percentage of selection candidates kept. Across all replacement rates evaluated, retaining 25% of the selection candidates resulted in the greatest net benefit when genotyping cost was low but the lowest net benefit when genotyping cost was high. Genotyping breakeven cost was non-linearly associated with the percentage of selection candidates retained, reaching a maximum when 50% of selection candidates were retained, irrespective of replacement rate, genomic reliability or the population. The genotyping breakeven cost was also non-linearly associated with replacement rate. The approaches outlined within provide the back-end framework for a decision support tool to quantify the net benefit of genotyping, once parameterised by the relevant population metrics.

An experiment of divergent selection for intramuscular fat was carried out at Universitat Politècnica de València. The high response of selection in intramuscular fat content, after nine generations of selection, and a multidimensional scaling analysis showed a high degree of genomic differentiation between the two divergent populations. Therefore, local genomic differences could link genomic regions, encompassing selective sweeps, to the trait used as selection criterion. In this sense, the aim of this study was to identify genomic regions related to intramuscular fat through three methods for detection of selection signatures and to generate a list of candidate genes. The methods implemented in this study were Wright’s fixation index, cross population composite likelihood ratio and cross population – extended haplotype homozygosity. Genomic data came from the 9th generation of the two populations divergently selected, 237 from Low line and 240 from High line. A high single nucleotide polymorphism (SNP) density array, Affymetrix Axiom OrcunSNP Array (around 200k SNPs), was used for genotyping samples. Several genomic regions distributed along rabbit chromosomes (OCU) were identified as signatures of selection (SNPs having a value above cut-off of 1%) within each method. In contrast, 8 genomic regions, harbouring 80 SNPs (OCU1, OCU3, OCU6, OCU7, OCU16 and OCU17), were identified by at least 2 methods and none by the 3 methods. In general, our results suggest that intramuscular fat selection influenced multiple genomic regions which can be a consequence of either only selection effect or the combined effect of selection and genetic drift. In addition, 73 genes were retrieved from the 8 selection signatures. After functional and enrichment analyses, the main genes into the selection signatures linked to energy, fatty acids, carbohydrates and lipid metabolic processes were ACER2, PLIN2, DENND4C, RPS6, RRAGA (OCU1), ST8SIA6, VIM (OCU16), RORA, GANC and PLA2G4B (OCU17). This genomic scan is the first study using rabbits from a divergent selection experiment. Our results pointed out a large polygenic component of the intramuscular fat content. Besides, promising positional candidate genes would be analysed in further studies in order to bear out their contributions to this trait and their feasible implications for rabbit breeding programmes.

The production of beef cattle in the Atlantic Forest biome mostly takes place in pastoral production systems. There are millions of hectares covered with pastures in this biome, including degraded pasture (DP), and only small area of the original Atlantic Forest has been preserved in tropics, implying that actions must be taken by the livestock sector to improve sustainability. Intensification makes it possible to produce the same amount, or more beef, in a smaller area; however, the environmental impacts must be assessed. Regarding climate change, the C dynamics is essential to define which beef cattle systems are sustainable. The objectives of this study were to investigate the C balance (t CO2e./ha per year), the intensity of C emission (kg CO2e./kg BW or carcass) and the C footprint (t CO2e./ha per year) of pasture-based beef cattle production systems, inside the farm gate and considering the inputs. The results were used to calculate the number of trees to be planted in beef cattle production systems to mitigate greenhouse gas (GHG) emissions. The GHG emission and C balance, for 2 years, were calculated based on the global warming potential (GWP) of AR4 and GWP of AR5. Forty-eight steers were allotted to four grazing systems: DP, irrigated high stocking rate pasture (IHS), rainfed high stocking rate pasture (RHS) and rainfed medium stocking rate pasture (RMS). The rainfed systems (RHS and RMS) presented the lowest C footprints (−1.22 and 0.45 t CO2e./ha per year, respectively), with C credits to RMS when using the GWP of AR4. The IHS system showed less favorable results for C footprint (−15.71 t CO2e./ha per year), but results were better when emissions were expressed in relation to the annual BW gain (−10.21 kg CO2e./kg BW) because of its higher yield. Although the DP system had an intermediate result for C footprint (−6.23 t CO2e./ha per year), the result was the worst (−30.21 CO2e./kg BW) when the index was expressed in relation to the annual BW gain, because in addition to GHG emissions from the animals in the system there were also losses in the annual rate of C sequestration. Notably, the intensification in pasture management had a land-saving effect (3.63 ha for IHS, 1.90 for RHS and 1.19 for RMS), contributing to the preservation of the tropical forest.