@article{usala_macciotta_bergamaschi_maltecca_fix_schwab_shull_tiezzi_2021, title={Genetic Parameters for Tolerance to Heat Stress in Crossbred Swine Carcass Traits}, volume={11}, ISSN={["1664-8021"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85101217596&partnerID=MN8TOARS}, DOI={10.3389/fgene.2020.612815}, abstractNote={Data for loin and backfat depth, as well as carcass growth of 126,051 three-way crossbred pigs raised between 2015 and 2019, were combined with climate records of air temperature, relative humidity, and temperature–humidity index. Environmental covariates with the largest impact on the studied traits were incorporated in a random regression model that also included genomic information. Genetic control of tolerance to heat stress and the presence of genotype by environment interaction were detected. Its magnitude was more substantial for loin depth and carcass growth, but all the traits studied showed a different impact of heat stress and different magnitude of genotype by environment interaction. For backfat depth, heritability was larger under comfortable conditions (no heat stress), as compared to heat stress conditions. Genetic correlations between extreme values of environmental conditions were lower (∼0.5 to negative) for growth and loin depth. Based on the solutions obtained from the model, sires were ranked on their breeding value for general performance and tolerance to heat stress. Antagonism between overall performance and tolerance to heat stress was moderate. Still, the models tested can provide valuable information to identify genetic material that is resilient and can perform equally when environmental conditions change. Overall, the results obtained from this study suggest the existence of genotype by environment interaction for carcass traits, as a possible genetic contributor to heat tolerance in swine.}, journal={FRONTIERS IN GENETICS}, author={Usala, Maria and Macciotta, Nicolo Pietro Paolo and Bergamaschi, Matteo and Maltecca, Christian and Fix, Justin and Schwab, Clint and Shull, Caleb and Tiezzi, Francesco}, year={2021}, month={Feb} }
 @article{tiezzi_bergamaschi_howard_maltecca_2020, title={43 Feed efficiency and behavior are associated with gut microbiome in three breeds of pigs}, volume={98}, ISSN={0021-8812 1525-3163}, url={http://dx.doi.org/10.1093/jas/skaa278.044}, DOI={10.1093/jas/skaa278.044}, abstractNote={Abstract
               Feed efficiency and behavior are important traits in the pork industry for economic, welfare, and environmental aspects. The gut microbiota plays an important role in nutrient digestibility and it is likely to influence these traits. The aim of this study was to characterize the feed efficiency, feeding behavior and gut microbiome relationships of pigs belonging to three different breeds. Individual body weight, feed intake and rate of Duroc (n = 222), Landrace (n = 244), and Large White (n = 221) pigs were recorded. Rectal fecal samples were collected from each animal at three time points (T1, start of trial; T2, mid-trial; T3, end of trial) and used for microbiome 16S rRNA gene sequencing. Individual feed intake and body weight were edited to obtain average daily gain (ADG), average daily feed intake (ADFI), feed conversion ratio (FCR), average daily feeding rate (ADFR), average feed intake per visit (AFIV), average daily number of visits to feeder (ANVD), average daily occupation time (AOTD), average occupation time per visit (AOTV). The impact of gut microbiome on the traits studied was present and seemed to depend on the breed and the time point of recording. At T1, Oscillibacter and Phascolarctobacterium had negative impact on ANVD and ADFI in Duroc, Ruminococcus had negative impact on ADFI in Landrace and Parvimonas, Escherichia and Anaerovibrio had negative impact on ADFI and ANVD in Large White. At T2, Lactobacillus showed a positive impact on ADFR in Landrace and on ADFI in Large White. At T3, Ruminococcus, Faecalibacterium and Dorea had a positive impact on ADFI in Duroc, Staphylococcous had positive impact on ADFR in Landrace and Peptoniphilus had negative impact on ADFI in Large White. Gut microbiome may have an heterogenous impact on the regulation of feeding behavior and feed efficiency depending on the host genotype.}, number={Supplement_4}, journal={Journal of Animal Science}, publisher={Oxford University Press (OUP)}, author={Tiezzi, Francesco and Bergamaschi, Matteo and Howard, Jeremy and Maltecca, Christian}, year={2020}, month={Nov}, pages={24–24} }
 @article{bergamaschi_maltecca_schillebeeckx_mcnulty_schwab_shull_fix_tiezzi_2020, title={Heritability and genome-wide association of swine gut microbiome features with growth and fatness parameters}, volume={10}, ISSN={["2045-2322"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85086790625&partnerID=MN8TOARS}, DOI={10.1038/s41598-020-66791-3}, abstractNote={AbstractDespite recent efforts to characterize longitudinal variation in the swine gut microbiome, the extent to which a host’s genome impacts the composition of its gut microbiome is not yet well understood in pigs. The objectives of this study were: i) to identify pig gut microbiome features associated with growth and fatness, ii) to estimate the heritability of those features, and, iii) to conduct a genome-wide association study exploring the relationship between those features and single nucleotide polymorphisms (SNP) in the pig genome. A total of 1,028 pigs were characterized. Animals were genotyped with the Illumina PorcineSNP60 Beadchip. Microbiome samples from fecal swabs were obtained at weaning (Wean), at mid-test during the growth trial (MidTest), and at the end of the growth trial (OffTest). Average daily gain was calculated from birth to week 14 of the growth trial, from weaning to week 14, from week 14 to week 22, and from week 14 to harvest. Backfat and loin depth were also measured at weeks 14 and 22. Heritability estimates (±SE) of Operational Taxonomic Units ranged from 0.025 (±0.0002) to 0.139 (±0.003), from 0.029 (±0.003) to 0.289 (±0.004), and from 0.025 (±0.003) to 0.545 (±0.034) at Wean, MidTest, and OffTest, respectively. Several SNP were significantly associated with taxa at the three time points. These SNP were located in genomic regions containing a total of 68 genes. This study provides new evidence linking gut microbiome composition with growth and carcass traits in swine, while also identifying putative host genetic markers associated with significant differences in the abundance of several prevalent microbiome features.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Bergamaschi, Matteo and Maltecca, Christian and Schillebeeckx, Constantino and McNulty, Nathan P. and Schwab, Clint and Shull, Caleb and Fix, Justin and Tiezzi, Francesco}, year={2020}, month={Jun} }
 @article{khanal_maltecca_schwab_fix_bergamaschi_tiezzi_2020, title={Modeling host-microbiome interactions for the prediction of meat quality and carcass composition traits in swine}, volume={52}, ISBN={1297-9686}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85088852317&partnerID=MN8TOARS}, DOI={10.1186/s12711-020-00561-7}, abstractNote={Abstract
Background
The objectives of this study were to evaluate genomic and microbial predictions of phenotypes for meat quality and carcass traits in swine, and to evaluate the contribution of host-microbiome interactions to the prediction. Data were collected from Duroc-sired three-way crossbred individuals (n = 1123) that were genotyped with a 60 k SNP chip. Phenotypic information and fecal 16S rRNA microbial sequences at three stages of growth (Wean, Mid-test, and Off-test) were available for all these individuals. We used fourfold cross-validation with animals grouped based on sire relatedness. Five models with three sets of predictors (full, informatively reduced, and randomly reduced) were evaluated. ‘Full’ included information from all genetic markers and all operational taxonomic units (OTU), while ‘informatively reduced’ and ‘randomly reduced’ represented a reduced number of markers and OTU based on significance preselection and random sampling, respectively. The baseline model included the fixed effects of dam line, sex and contemporary group and the random effect of pen. The other four models were constructed by including only genomic information, only microbiome information, both genomic and microbiome information, and microbiome and genomic information and their interaction.

Results
Inclusion of microbiome information increased predictive ability of phenotype for most traits, in particular when microbiome information collected at a later growth stage was used. Inclusion of microbiome information resulted in higher accuracies and lower mean squared errors for fat-related traits (fat depth, belly weight, intramuscular fat and subjective marbling), objective color measures (Minolta a*, Minolta b* and Minolta L*) and carcass daily gain. Informative selection of markers increased predictive ability but decreasing the number of informatively reduced OTU did not improve model performance. The proportion of variation explained by the host-genome-by-microbiome interaction was highest for fat depth (~ 20% at Mid-test and Off-test) and shearing force (~ 20% consistently at Wean, Mid-test and Off-test), although the inclusion of the interaction term did not increase the accuracy of predictions significantly.

Conclusions
This study provides novel insight on the use of microbiome information for the phenotypic prediction of meat quality and carcass traits in swine. Inclusion of microbiome information in the model improved predictive ability of phenotypes for fat deposition and color traits whereas including a genome-by-microbiome term did not improve prediction accuracy significantly.
}, number={1}, journal={GENETICS SELECTION EVOLUTION}, author={Khanal, Piush and Maltecca, Christian and Schwab, Clint and Fix, Justin and Bergamaschi, Matteo and Tiezzi, Francesco}, year={2020} }
 @article{bittante_negrini_bergamaschi_cecchinato_toledo-alvarado_2020, title={Pure-breeding with sexed semen and crossbreeding with semen of double-muscled sires to improve beef production from dairy herds: Factors affecting heifer and cow fertility and the sex ratio}, volume={103}, ISSN={["1525-3198"]}, DOI={10.3168/jds.2019-17932}, abstractNote={Using sexed semen to produce purebred replacement heifers makes it possible to mate a large proportion of dairy cows to double-muscled sires and to quantitatively and qualitatively improve beef production and increase the income from dairy herds. Net profit first depends on changes in the farm's overall fertility rate. The objective of this study was to analyze the conception rate in herds using a combination of conventional dairy semen (for pure- and crossbreeding), X-sorted dairy semen (to produce purebred replacement heifers), and conventional beef semen (for terminal crossbreeding). Data were obtained from 50,785 inseminations of 15,580 dairy cows (78% Holstein-Friesian, 15% Brown Swiss, 2% Simmental, and 5% crossbreds) from 106 dairy farms (average milk yield 35.1 ± 9.4 kg/d, with 3.76 ± 0.83% fat and 3.32 ± 0.39% protein contents). To account for the main potential confounders, we used separate generalized linear mixed-effects models for cows and virgin heifers. The results showed that the odds ratio of conception improved (1.00 to 1.34) with an increase in the average milk yield of the herd but worsened (1.12 to 0.70) with an increase in the milk yield of individual cows within herd. The summer months showed a strong reduction in the odds ratio of conception in cows (0.56 in July and August) but not in virgin heifers. Multiparous cows had a lower odds ratio of conception (0.85) than primiparous cows (1.00). The order of insemination did not affect the fertility of the cows or heifers, whereas the odds ratio of conception improved with advancing lactation (1.00 to 2.12). The Simmental cows were more fertile than Holstein-Friesians (1.37 vs. 1.00), whereas the fertility of the heifers was not affected by breed. Taking all these possible confounders into account simultaneously, in pure-breeding the odds ratio of conception using sexed semen did not differ from that using conventional dairy semen in cows (0.90 vs. 1.00) or in virgin heifers (0.95 vs. 1.00). However, crossbreeding using conventional beef and dairy semen improved the odds ratio of conception (1.10 and 1.17, respectively) in cows (1.37 using beef semen) and heifers (1.25 using dairy semen). The proportion of newborn heifer calves was ≥90% using sexed dairy semen. The combined use of sexed semen, especially on heifers, to produce purebred replacement females and beef semen to produce terminal crossbred calves was shown to have the potential to increase overall herd fertility, which could be further improved using sexed dairy semen to produce dairy crossbreds instead of purebred replacement heifers.}, number={6}, journal={JOURNAL OF DAIRY SCIENCE}, author={Bittante, Giovanni and Negrini, Riccardo and Bergamaschi, Matteo and Cecchinato, Alessio and Toledo-Alvarado, Hugo}, year={2020}, month={Jun}, pages={5246–5257} }
 @article{bittante_negrini_bergamaschi_ni_patel_toledo-alvarado_cecchinato_2021, title={Purebreeding with sexed semen and crossbreeding with semen from double-muscled sires to improve beef production from dairy herds: Live and slaughter performances of crossbred calves}, volume={104}, ISSN={["1525-3198"]}, DOI={10.3168/jds.2020-18436}, abstractNote={The use of sexed semen to produce purebred replacement heifers allows a large proportion of dairy cows to be mated to beef sires, and quantitative and qualitative improvements to be made to beef production from dairy herds. The major dairy and beef breeds are undergoing rapid genetic improvement as a result of more efficient selection methods, prompting a need to evaluate the meat production of crossbred beef × dairy cattle produced using current genetics. As part of a large project involving 125 commercial dairy farms, we evaluated the combined use of purebreeding with sexed semen and crossbreeding with semen from beef sires, particularly double-muscled breeds. A survey of 1,530 crossbred calves revealed that, whereas purebred dairy calves are destined almost exclusively for veal production, beef × dairy crossbred calves are also destined for beef production after fattening on either the dairy farm of birth or by specialized fatteners. In veal production, compared with Belgian Blue-sired calves (taken as the reference), double-muscled INRA 95-sired calves had a lighter slaughter weight (303 vs. 346 kg), but a greater dressing percent (62.3 vs. 58.4%). Limousin (also known as Limousine)-sired calves had a smaller average daily gain (1.26 vs. 1.34 kg/d), and lighter slaughter (314 vs. 346 kg) and carcass weights (182 vs. 201 kg). Lastly, Simmental-sired calves had a similar growth rate, but lighter carcass weight (177 vs. 201 kg), smaller dressing percentage (55.3 vs. 58.4%), and smaller muscularity scores (3.25 vs. 3.72). In the case of young bulls and heifers fattened on the dairy farm of birth, Belgian Blue-, Piemontese (also known as Piedmontese)-, and Limousin-sired calves performed similarly; the only exception was that Piemontese-sired calves had a greater dressing percentage. Belgian Blue- and Limousin-sired calves performed similarly when fattened by specialized beef producers. In both veal and beef production, the effects of dam breed were less important than sire breed. Considering the entire project, we can conclude that the combined use of sexed semen for purebreeding and conventional beef semen for terminal crossbreeding improves meat production from dairy herds, especially when the sires are double-muscled beef breeds.}, number={3}, journal={JOURNAL OF DAIRY SCIENCE}, author={Bittante, Giovanni and Negrini, Riccardo and Bergamaschi, Matteo and Ni, Qianlin and Patel, Nageshvar and Toledo-Alvarado, Hugo and Cecchinato, Alessio}, year={2021}, month={Mar}, pages={3210–3220} }
 @article{bittante_negrini_bergamaschi_cecchinato_toledo-alvarado_2020, title={Short communication: Pure-breeding with sexed semen and crossbreeding with semen from double-muscled sires to improve beef production from dairy herds: Weight and value of calves}, volume={103}, ISSN={["1525-3198"]}, DOI={10.3168/jds.2019-18011}, abstractNote={The use of sexed semen to produce purebred replacement heifers allows a large proportion of dairy cows to be mated to double-muscled sires and for quantitative and qualitative improvements to be made to beef production from dairy herds. A survey of 1,285 crossbred calves showed that they are destined not only for veal production (like purebred dairy calves) but also for beef production. Crossbred calves obtained from Belgian Blue sires (sold on average at 34 d of age and 64 kg of weight) had a higher market value (€363/calf) than those obtained from double-muscled INRA 95 sires (€297/calf, used for veal production) and from Limousin sires (€216/calf for veal and €271/calf for beef production). As a sire breed, Simmental did not differ significantly from Belgian Blue, but as a dam breed, the crossbred calves fetched a higher price (€5.11/kg) than when Holstein was the dam breed (€4.50/kg). Compared with heifer calves, crossbred bull calves at sale were younger (34.1 vs. 37.2 d) and heavier (64.0 vs. 62.6 kg of live weight), fetched a higher price (€5.13 vs. €4.99/kg), and had a greater value (€328 vs. €312/calf). As the value of purebred dairy calves was about €80 to €100/calf, we are able to confirm that the combined use of sexed semen for pure-breeding and conventional beef semen for terminal crossbreeding can increase the income from dairy farms, especially when the sires are double-muscled beef bulls.}, number={6}, journal={JOURNAL OF DAIRY SCIENCE}, author={Bittante, Giovanni and Negrini, Riccardo and Bergamaschi, Matteo and Cecchinato, Alessio and Toledo-Alvarado, Hugo}, year={2020}, month={Jun}, pages={5258–5262} }
 @article{patel_bergamaschi_cagnin_bittante_2020, title={Exploration of the effect of farm, breed, sex and animal on detailed mineral profile of beef and their latent explanatory factors}, volume={55}, ISSN={["1365-2621"]}, DOI={10.1111/ijfs.14455}, abstractNote={SummaryMinerals in meat vary with different extrinsic and intrinsic sources; therefore, we aimed to quantify different sources of variation in mineral profile of beef. Longissimus thoracis muscle (N.182) from young bulls and heifers was analysed using ICP‐OES for 6 macrominerals, 5 essential microminerals and 9 environmental microminerals. Results of mixed models show that breed and sex have little effect on mineral profile. Major sources of variation, such as farm, individual animal within farm and side/sample within animal, differed markedly from mineral to mineral, affecting reproducibility coefficients. Multivariate factor analysis revealed that five latent factors explained 69% of the co‐variance of 20 minerals. The first was a quantitative factor, followed by others based on Na‐Fe‐Cu, on K‐B‐Pb, on Fe‐Mn and on Zn content, respectively. In conclusion, minerals’ major source of variation depends on complex relationships between the animal’s genetics, physiology, farm environment, management and feeding, whose understanding is favoured by latent factor analyses.}, number={3}, journal={INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY}, author={Patel, Nageshvar and Bergamaschi, Matteo and Cagnin, Massimo and Bittante, Giovanni}, year={2020}, month={Mar}, pages={1046–1056} }
 @article{bergamaschi_maltecca_fix_schwab_tiezzi_2020, title={Genome-wide association study for carcass quality traits and growth in purebred and crossbred pigs}, volume={98}, ISSN={["1525-3163"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85078371039&partnerID=MN8TOARS}, DOI={10.1093/jas/skz360}, abstractNote={AbstractCarcass quality traits such as back fat (BF), loin depth (LD), and ADG are of extreme economic importance for the swine industry. This study aimed to (i) estimate the genetic parameters for such traits and (ii) conduct a single-step genome-wide association study (ssGWAS) to identify genomic regions that affect carcass quality and growth traits in purebred (PB) and three-way crossbred (CB) pigs. A total of 28,497 PBs and 135,768 CBs pigs were phenotyped for BF, LD, and ADG. Of these, 4,857 and 3,532 were genotyped using the Illumina PorcineSNP60K Beadchip. After quality control, 36,328 SNPs were available and were used to perform an ssGWAS. A bootstrap analysis (n = 1,000) and a signal enrichment analysis were performed to declare SNP significance. Genome regions were based on the variance explained by significant 10-SNP sliding windows. Estimates of PB heritability (SE) were 0.42 (0.019) for BF, 0.39 (0.020) for LD, and 0.35 (0.021) for ADG. Estimates of CB heritability were 0.49 (0.042) for BF, 0.27 (0.029) for LD, and 0.12 (0.021) for ADG. Genetic correlations (SE) across the two populations were 0.81 (0.02), 0.79 (0.04), and 0.56 (0.05), for BF, LD, and ADG, respectively. The variance explained by significant regions for each trait in PBs ranged from 1.51% to 1.35% for BF, from 4.02% to 3.18% for LD, and from 2.26% to 1.45% for ADG. In CBs, the variance explained by significant regions ranged from 1.88% to 1.37% for BF, from 1.29% to 1.23% for LD, and from 1.54% to 1.32% for ADG. In this study, we have described regions of the genome that determine carcass quality and growth traits of PB and CB pigs. These results provide evidence that there are overlapping and nonoverlapping regions in the genome influencing carcass quality and growth traits in PBs and three-way CB pigs.}, number={1}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Bergamaschi, Matteo and Maltecca, Christian and Fix, Justin and Schwab, Clint and Tiezzi, Francesco}, year={2020}, month={Jan} }
 @article{patel_bergamaschi_magro_petrini_bittante_2019, title={Relationships of a Detailed Mineral Profile of Meat with Animal Performance and Beef Quality}, volume={9}, ISSN={["2076-2615"]}, DOI={10.3390/ani9121073}, abstractNote={The mineral profile of beef is a subject of human health interest, but also animal performance and meat quality. This study analyzes the relationships of 20 minerals in beef inductively coupled plasma-optical emission spectrometry (ICP-OES) with three animal performance and 13 beef quality traits analyzed on 182 samples of Longissimus thoracis. Animals’ breed and sex showed limited effects. The major sources of variation (farm/date of slaughter, individual animal within group and side/sample within animal) differed greatly from trait to trait. Mineral contents were correlated to animal performance and beef quality being significant 52 out of the 320 correlations at the farm/date level, and 101 out of the 320 at the individual animal level. Five latent factors explained 69% of mineral co-variation. The most important, “Mineral quantity” factor correlated with age at slaughter and with the beef color traits. Two latent factors (“Na + Fe + Cu” and “Fe + Mn”) correlated with performance and beef color traits. Two other (“K-B-Pb” and “Zn”) correlated with beef chemical composition and the latter also with carcass weight and daily gain, and beef color traits. Beef cooking losses correlated with “K-B-Pb”. Latent factor analysis appears be a useful means of disentangling the very complex relationships that the minerals in beef have with animal performance and beef quality traits.}, number={12}, journal={ANIMALS}, author={Patel, Nageshvar and Bergamaschi, Matteo and Magro, Luciano and Petrini, Andrea and Bittante, Giovanni}, year={2019}, month={Dec} }