Pub Date : 2026-01-20DOI: 10.1016/j.animal.2026.101765
I-T. Vourlaki, M. Piles, T. Jové-Juncà, Y. Ramayo-Caldas, R. Quintanilla, M. Ballester
Phenotypes in livestock are shaped by genetic variation as well as downstream regulatory mechanisms, making the prediction of complex traits a key challenge for animal breeding. Transcriptomic data represent an intermediate biological layer between genotypes and phenotypes and may capture regulatory signals not fully explained by genomic information alone. The objective of this study was to evaluate the contribution of blood transcriptomic data, alone or combined with genomic information, to predict six immune, stress, and production traits in 255 Duroc pigs. Four traits were closely related to the sampled tissue and timepoint, whereas two were less biologically relevant. Bayesian regression methods (BayesC and RKHS) and a neural network linear mixed model were compared using either all transcripts or subsets selected by Partial Least Squares (PLS). High prediction accuracy was obtained for immunity-related traits, such as gamma delta T cells and leukocyte counts, with correlations of 0.74 and 0.67, respectively, when transcriptomic data were used. Moderate improvements were observed for cortisol prediction (r = 0.39), whereas SNP-based models performed best for carcass weight (r = 0.45). PLS-based feature selection showed that a small subset of features can perform equally well or better than the whole transcriptomic dataset and identified biologically relevant candidate genes, including MAF, SOX13, DDIT4, and FOS. In conclusion, blood transcriptomic data substantially improved prediction performance for traits biologically related to the sampled tissue, whereas SNP-based models performed better for less relevant traits, and combining omics provided only modest and non-significant gains; feature selection was essential to enhance prediction performance, computational efficiency, and to facilitate the identification of immune-related candidate genes.
{"title":"Incorporating genomic and transcriptomic effects in joint linear and non-linear structural models for predicting complex traits in pigs","authors":"I-T. Vourlaki, M. Piles, T. Jové-Juncà, Y. Ramayo-Caldas, R. Quintanilla, M. Ballester","doi":"10.1016/j.animal.2026.101765","DOIUrl":"10.1016/j.animal.2026.101765","url":null,"abstract":"<div><div>Phenotypes in livestock are shaped by genetic variation as well as downstream regulatory mechanisms, making the prediction of complex traits a key challenge for animal breeding. Transcriptomic data represent an intermediate biological layer between genotypes and phenotypes and may capture regulatory signals not fully explained by genomic information alone. The objective of this study was to evaluate the contribution of blood transcriptomic data, alone or combined with genomic information, to predict six immune, stress, and production traits in 255 Duroc pigs. Four traits were closely related to the sampled tissue and timepoint, whereas two were less biologically relevant. Bayesian regression methods (BayesC and RKHS) and a neural network linear mixed model were compared using either all transcripts or subsets selected by Partial Least Squares (<strong>PLS</strong>). High prediction accuracy was obtained for immunity-related traits, such as gamma delta T cells and leukocyte counts, with correlations of 0.74 and 0.67, respectively, when transcriptomic data were used. Moderate improvements were observed for cortisol prediction (r = 0.39), whereas SNP-based models performed best for carcass weight (r = 0.45). PLS-based feature selection showed that a small subset of features can perform equally well or better than the whole transcriptomic dataset and identified biologically relevant candidate genes, including <em>MAF</em>, <em>SOX13</em>, <em>DDIT4</em>, and <em>FOS</em>. In conclusion, blood transcriptomic data substantially improved prediction performance for traits biologically related to the sampled tissue, whereas SNP-based models performed better for less relevant traits, and combining omics provided only modest and non-significant gains; feature selection was essential to enhance prediction performance, computational efficiency, and to facilitate the identification of immune-related candidate genes.</div></div>","PeriodicalId":50789,"journal":{"name":"Animal","volume":"20 3","pages":"Article 101765"},"PeriodicalIF":4.2,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146147523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-20DOI: 10.1016/j.animal.2026.101764
Z. Meng , Y. Liu , W. Yang , J. Wang , P.H. Li , R.H. Huang , W.J. Wu
Backfat thickness, a key selection trait in pig-breeding programmes, has traditionally been measured as a homogeneous layer. However, backfat is anatomically structured into three distinct layers, and each layer likely contributes differently to carcass quality. In addition, previous studies have shown that the deposition of the third layer of backfat is phenotypically correlated with intramuscular fat (IMF). Therefore, targeted selection for specific backfat layers, particularly the third layer, represents a potential strategy to increase IMF content while maintaining a high lean meat percentage. However, the genetic architecture of these distinct porcine backfat layers remains poorly understood. The aim of this study was to estimate the genetic parameters and identify key candidate genes underlying the three backfat layers. We collected B-mode ultrasound images from 561 Landrace pigs to measure individual layer thickness, followed by DNA extraction, genotyping, genetic parameter estimation, and a genome-wide association study (GWAS). Our measurements showed that the first layer of backfat (FBF) is the thickest, followed by the second (SBF) and the third (TBF) layers. Genetic parameter estimation yielded heritability estimates of 0.37, 0.42, 0.38, 0.34, 0.32, 0.24, and 0.21 for total backfat (BF), FBF, FBF/BF, SBF, SBF/BF, TBF, and TBF/BF, respectively. Through integrated analysis of GWAS, Bayesian fine-mapping, and gene annotation, we identified 15 non-redundant candidate genes associated with different backfat layers. These included two genes (SOAT1 and ACBD6) shared by BF and SBF, LPL for BF and FBF, and CAND1 for TBF and TBF/BF. Additionally, SERPINA12 and SERPINA6 were associated with BF; PRKAG1 and PRDM16 with FBF; EPRS1 and SLC39A10 with FBF/BF; PTGES and CRAT with SBF; and ACLY, CAVIN1, and PDZRN3 with SBF/BF. Our results indicate that each layer is governed by a distinct set of genes, which advances our understanding of the genetic basis of backfat layers in pigs.
{"title":"Genome-wide association study identified genomic regions and putative candidate genes affecting different backfat layers in Landrace pigs","authors":"Z. Meng , Y. Liu , W. Yang , J. Wang , P.H. Li , R.H. Huang , W.J. Wu","doi":"10.1016/j.animal.2026.101764","DOIUrl":"10.1016/j.animal.2026.101764","url":null,"abstract":"<div><div>Backfat thickness, a key selection trait in pig-breeding programmes, has traditionally been measured as a homogeneous layer. However, backfat is anatomically structured into three distinct layers, and each layer likely contributes differently to carcass quality. In addition, previous studies have shown that the deposition of the third layer of backfat is phenotypically correlated with intramuscular fat (<strong>IMF</strong>). Therefore, targeted selection for specific backfat layers, particularly the third layer, represents a potential strategy to increase IMF content while maintaining a high lean meat percentage. However, the genetic architecture of these distinct porcine backfat layers remains poorly understood. The aim of this study was to estimate the genetic parameters and identify key candidate genes underlying the three backfat layers. We collected B-mode ultrasound images from 561 Landrace pigs to measure individual layer thickness, followed by DNA extraction, genotyping, genetic parameter estimation, and a genome-wide association study (<strong>GWAS</strong>). Our measurements showed that the first layer of backfat (<strong>FBF)</strong> is the thickest, followed by the second (<strong>SBF</strong>) and the third (<strong>TBF</strong>) layers. Genetic parameter estimation yielded heritability estimates of 0.37, 0.42, 0.38, 0.34, 0.32, 0.24, and 0.21 for total backfat (<strong>BF</strong>), FBF, FBF/BF, SBF, SBF/BF, TBF, and TBF/BF, respectively. Through integrated analysis of GWAS, Bayesian fine-mapping, and gene annotation, we identified 15 non-redundant candidate genes associated with different backfat layers. These included two genes (<em>SOAT1</em> and <em>ACBD6</em>) shared by BF and SBF, <em>LPL</em> for BF and FBF, and <em>CAND1</em> for TBF and TBF/BF. Additionally, <em>SERPINA12</em> and <em>SERPINA6</em> were associated with BF; <em>PRKAG1</em> and <em>PRDM16</em> with FBF; <em>EPRS1</em> and <em>SLC39A10</em> with FBF/BF; <em>PTGES</em> and <em>CRAT</em> with SBF; and <em>ACLY</em>, <em>CAVIN1</em>, and <em>PDZRN3</em> with SBF/BF. Our results indicate that each layer is governed by a distinct set of genes, which advances our understanding of the genetic basis of backfat layers in pigs.</div></div>","PeriodicalId":50789,"journal":{"name":"Animal","volume":"20 3","pages":"Article 101764"},"PeriodicalIF":4.2,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146147524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-20DOI: 10.1016/j.animal.2026.101763
V.L. Sacanell , L.M. Plà-Aragonés , J. Pomar
Optimisation of slaughter weight is crucial for efficient farm management in all-in-all-out systems, but growth variability within pig batches complicates uniform marketing. This study aimed to reduce heterogeneity by developing a decision support system (DSS) for precision feeding, improving BW performance, thereby reducing batch variability. A 103-day commercial trial involving 365 pigs compared conventional 3-phase feeding with individual precision feeding (IPF). Two control groups, Control A and Control B (n = 81 each, six pens/group), received diets with stepwise standardised ileal digestible lysine (SID Lys) concentrations (8.80, 9.80, 10.60 g/kg and 9.00, 10.00, 10.80 g/kg, respectively) from traditional feeders, with feed intake recorded manually. In contrast, the IPF group (n = 203, nine pens) utilised robotic feeders to provide individually tailored diets. These were formulated in real-time by blending high (11.83 g/kg) and low (6.59 g/kg) SID Lys feeds. A DSS, integrating a nutritional model, stakeholder directives (minimum and limited daily decreases in the SID Lys concentration), and a qualitative model, calculated each pig’s requirements based on automatically collected real-time BW and feed intake data. Performance metrics were similar across all groups. However, the IPF group (18.55 g/kg) was more efficient in utilising SID Lys, requiring less per kg of live weight gain than Control A (19.67 g/kg) and Control B (19.71 g/kg). When pigs were classified by initial BW – heavy (HBW, IPF: 26; Control A: 23; Control B: 20 animals), moderate (MBW, IPF: 98; Control A: 39; Control B: 41 animals) and light-body-weight (LBW, IPF: 79; Control A: 19; Control B: 20 animals) – the IPF group showed an improvement of 4.2–6.8 kg in growth performance for HBW, and 2.6–4.3 kg in LBW, compared to controls, although not statistically significant. While overall batch variability remained similar (CV: 11.6% IPF, 11.9% Control A, 12.2% Control B), the IPF group was more homogeneous among LBW pigs (9.5%) compared to controls (11.5% and 13.8%). Greater HBW variation in IPF group balanced overall variability. Although direct feed cost savings and nitrogen excretion reductions were not achieved – attributed to technical feed distribution issues in the final phase and higher CP baselines in the experimental diets – an economic estimation revealed that the system’s profitability was driven by output maximisation. In conclusion, the DSS proved feasible for real-time commercial application, successfully enhancing nutrient utilisation efficiency and optimising the growth of animals at the extremes of the population distribution.
{"title":"Evaluating a precision feeding decision support system for improving growth performance of growing-finishing pigs on a commercial farm","authors":"V.L. Sacanell , L.M. Plà-Aragonés , J. Pomar","doi":"10.1016/j.animal.2026.101763","DOIUrl":"10.1016/j.animal.2026.101763","url":null,"abstract":"<div><div>Optimisation of slaughter weight is crucial for efficient farm management in all-in-all-out systems, but growth variability within pig batches complicates uniform marketing. This study aimed to reduce heterogeneity by developing a decision support system (<strong>DSS</strong>) for precision feeding, improving BW performance, thereby reducing batch variability. A 103-day commercial trial involving 365 pigs compared conventional 3-phase feeding with individual precision feeding (<strong>IPF</strong>). Two control groups, Control A and Control B (n = 81 each, six pens/group), received diets with stepwise standardised ileal digestible lysine (<strong>SID Lys</strong>) concentrations (8.80, 9.80, 10.60 g/kg and 9.00, 10.00, 10.80 g/kg, respectively) from traditional feeders, with feed intake recorded manually. In contrast, the IPF group (n = 203, nine pens) utilised robotic feeders to provide individually tailored diets. These were formulated in real-time by blending high (11.83 g/kg) and low (6.59 g/kg) SID Lys feeds. A DSS, integrating a nutritional model, stakeholder directives (minimum and limited daily decreases in the SID Lys concentration), and a qualitative model, calculated each pig’s requirements based on automatically collected real-time BW and feed intake data. Performance metrics were similar across all groups. However, the IPF group (18.55 g/kg) was more efficient in utilising SID Lys, requiring less per kg of live weight gain than Control A (19.67 g/kg) and Control B (19.71 g/kg). When pigs were classified by initial BW – heavy (<strong>HBW</strong>, IPF: 26; Control A: 23; Control B: 20 animals), moderate (MBW, IPF: 98; Control A: 39; Control B: 41 animals) and light-body-weight (<strong>LBW</strong>, IPF: 79; Control A: 19; Control B: 20 animals) – the IPF group showed an improvement of 4.2–6.8 kg in growth performance for HBW, and 2.6–4.3 kg in LBW, compared to controls, although not statistically significant. While overall batch variability remained similar (CV: 11.6% IPF, 11.9% Control A, 12.2% Control B), the IPF group was more homogeneous among LBW pigs (9.5%) compared to controls (11.5% and 13.8%). Greater HBW variation in IPF group balanced overall variability. Although direct feed cost savings and nitrogen excretion reductions were not achieved – attributed to technical feed distribution issues in the final phase and higher CP baselines in the experimental diets – an economic estimation revealed that the system’s profitability was driven by output maximisation. In conclusion, the DSS proved feasible for real-time commercial application, successfully enhancing nutrient utilisation efficiency and optimising the growth of animals at the extremes of the population distribution.</div></div>","PeriodicalId":50789,"journal":{"name":"Animal","volume":"20 3","pages":"Article 101763"},"PeriodicalIF":4.2,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146147526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-16DOI: 10.1016/j.animal.2026.101760
M. Spoelstra , G. Duguma , A. Ebro , J. van der Lee , J. ten Napel
Genetic variation in environmental sensitivity (ES) among breeds underscores the importance of accounting for genotype-by-environment (G × E) interactions in breeding programmes. This is especially true for countries where there is a large variation in location production systems and environmental conditions and where farms use crossbreeding. We present a systematic framework for assessing G × E by combining genomic reconstruction of an individual animal’s breed composition with characterisation of production environment diversity, using factor analysis of mixed data (FAMD) and linear mixed models. Data from 288 farms in Ethiopia were analysed as a case study, which included weekly performance records, household parameters, daily meteorological data, and genotypes from 780 crossbred cows. To test G × E, the following context parameters were considered: agroecological zone (AEZ), market proximity, and farm size. Results showed that the best performances for milk yield (MY), age at first calving (AFC), and calf BW were generally observed on large, urban farms. However, MY, number of services per conception (NSC), and AFC improved with increasing exotic ancestry up to about 60%, beyond which these traits levelled off or declined. Antagonistic relationships among performance traits and their interactions with breed composition were also observed. While MY, calf BW, and AFC generally improved with increasing exotic ancestry, NSC was negatively affected by some ancestral breeds. Specifically, Holsteins exhibited consistently high NSC (3.52–4.66 ± 1.12) across all AEZ and market proximities, highlighting a limitation of their use in crossbreeding strategies with respect to fertility. Our study demonstrates that breed−by−environment interactions can be assessed using field data and genotypes collected from crossbred animals in highly diverse production systems. However, the study design is inevitably unbalanced for breed composition, which limits the ability to assess the performance of breed combinations not well represented in the studied population.
{"title":"Assessing genotype-by-environment interaction in dairy cattle in case of a wide range of production environments, unstructured crossbreeding and no pedigree information","authors":"M. Spoelstra , G. Duguma , A. Ebro , J. van der Lee , J. ten Napel","doi":"10.1016/j.animal.2026.101760","DOIUrl":"10.1016/j.animal.2026.101760","url":null,"abstract":"<div><div>Genetic variation in environmental sensitivity (<strong>ES</strong>) among breeds underscores the importance of accounting for genotype-by-environment (<strong>G × E</strong>) interactions in breeding programmes. This is especially true for countries where there is a large variation in location production systems and environmental conditions and where farms use crossbreeding. We present a systematic framework for assessing G × E by combining genomic reconstruction of an individual animal’s breed composition with characterisation of production environment diversity, using factor analysis of mixed data (<strong>FAMD</strong>) and linear mixed models. Data from 288 farms in Ethiopia were analysed as a case study, which included weekly performance records, household parameters, daily meteorological data, and genotypes from 780 crossbred cows. To test G × E, the following context parameters were considered: agroecological zone (<strong>AEZ</strong>), market proximity, and farm size. Results showed that the best performances for milk yield (<strong>MY</strong>), age at first calving (<strong>AFC</strong>), and calf BW were generally observed on large, urban farms. However, MY, number of services per conception (<strong>NSC</strong>), and AFC improved with increasing exotic ancestry up to about 60%, beyond which these traits levelled off or declined. Antagonistic relationships among performance traits and their interactions with breed composition were also observed. While MY, calf BW, and AFC generally improved with increasing exotic ancestry, NSC was negatively affected by some ancestral breeds. Specifically, Holsteins exhibited consistently high NSC (3.52–4.66 ± 1.12) across all AEZ and market proximities, highlighting a limitation of their use in crossbreeding strategies with respect to fertility. Our study demonstrates that breed−by−environment interactions can be assessed using field data and genotypes collected from crossbred animals in highly diverse production systems. However, the study design is inevitably unbalanced for breed composition, which limits the ability to assess the performance of breed combinations not well represented in the studied population.</div></div>","PeriodicalId":50789,"journal":{"name":"Animal","volume":"20 3","pages":"Article 101760"},"PeriodicalIF":4.2,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146147525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.animal.2025.101741
H. Li, J.J. Han, Y. Li, T. Yang, K.Z. Liu, L.Y. Zhang, T. Fu, C.Y. Su
Global attention to food safety and antimicrobial resistance issues continues to rise, and the need for green, efficient antibiotic alternatives in the livestock industry has become urgent. Prebiotics and probiotics, owing to their significant efficacy in regulating intestinal health and enhancing host immunity, are regarded as promising alternative approaches. Xylooligosaccharides (XOS), as a high-efficiency prebiotic, can specifically promote the metabolism and proliferation of beneficial bacteria such as Bifidobacterium. Based on this, this study uses Holstein calves as research subjects. It systematically investigates the effects of XOS and Bifidobacterium animalis (BA), used alone or in combination, on growth performance, immune-antioxidant function, rumen fermentation characteristics, and microbial composition. It aims to reveal the synergistic effects of the two and to provide a scientifically based, antibiotic-free nutritional strategy to promote healthy calf breeding. Thirty-two 2-month-old male calves were allocated to four dietary treatments (n = 8): (1) control diet (CON), (2) CON with 2 g/d XOS (XOS), (3) CON with 5 g/d BA (BA), and (4) CON with 2 g/d XOS with 5 g/d BA (XOS-BA). The 63-day trial consisted of a 7-day adaptation period followed by a 56-day sampling period. Daily feed intake was recorded. On day 63, jugular blood was collected for serum biochemistry, immune and antioxidant analyses, and rumen fluid was sampled for volatile fatty acids, 16S rRNA sequencing, and metabolomics analyses. The XOS-BA group increased final BW (P = 0.004) and average daily gain (P = 0.024), and decreased the feed−to−gain ratio (P = 0.002). Furthermore, XOS-BA supplementation positively affected the ruminal microbiota, increasing the abundances of beneficial taxa, including Acidobacteria, Lactobacillus, and Bifidobacterium. Further analyses revealed that XOS-BA effectively alleviated oxidative stress and inflammatory responses. This was evidenced by increased plasma immunoglobulin A and glutathione levels (P < 0.05) and decreased malondialdehyde concentrations. Meanwhile, compared with other treatments, the rumen fermentation function of calves supplemented with XOS-BA was significantly improved, as reflected by elevated rumen fluid acetic acid concentration (P = 0.036). In-depth analyses indicated that XOS-BA enhanced systemic antioxidant capacity by elevating endogenous antioxidant indices and reducing oxidative products, while modulating retinol metabolism, unsaturated fatty acid biosynthesis, and mTOR signalling. Synbiotic supplementation of XOS-BA synergistically improves growth performance, enhances immune–antioxidant capacity, and modulates rumen microbiota and metabolism in calves, thereby offering a practical antibiotic-free strategy for calf production.
全球对食品安全和抗菌素耐药性问题的关注不断增加，畜牧业迫切需要绿色、高效的抗生素替代品。益生元和益生菌因其在调节肠道健康和增强宿主免疫方面的显着功效而被认为是有前途的替代方法。低聚木糖（Xylooligosaccharides， XOS）是一种高效益生元，能特异性促进双歧杆菌等有益菌的代谢和增殖。基于此，本研究以荷斯坦小牛为研究对象。系统研究了XOS和动物双歧杆菌（BA）单独或联合使用对生长性能、免疫抗氧化功能、瘤胃发酵特性和微生物组成的影响。它的目的是揭示两者的协同效应，并提供一个科学的，无抗生素的营养策略，以促进健康的小牛育种。选取32头2月龄雄性犊牛，分为4个饲粮处理（n = 8）：(1)对照组饲粮（CON），(2)对照组饲粮加2 g/d XOS (XOS),(3)对照组饲粮加5 g/d BA (BA),(4)对照组饲粮加2 g/d XOS加5 g/d BA （XOS-BA）。试验期63 d，预试期7 d，抽样期56 d。记录日采食量。第63天，采集颈静脉血进行血清生化、免疫和抗氧化分析，采集瘤胃液进行挥发性脂肪酸、16S rRNA测序和代谢组学分析。XOS-BA组提高了末重（P = 0.004）和平均日增重（P = 0.024），降低了料重比（P = 0.002）。此外，添加XOS-BA对瘤胃微生物群有积极影响，增加了有益类群的丰度，包括酸杆菌、乳杆菌和双歧杆菌。进一步分析发现，XOS-BA能有效缓解氧化应激和炎症反应。血浆免疫球蛋白A和谷胱甘肽水平升高证明了这一点
{"title":"Co-supplementation of xylooligosaccharides and Bifidobacterium animalis can regulate the blood parameters and rumen microbiota of calves, improving growth performance","authors":"H. Li, J.J. Han, Y. Li, T. Yang, K.Z. Liu, L.Y. Zhang, T. Fu, C.Y. Su","doi":"10.1016/j.animal.2025.101741","DOIUrl":"10.1016/j.animal.2025.101741","url":null,"abstract":"<div><div>Global attention to food safety and antimicrobial resistance issues continues to rise, and the need for green, efficient antibiotic alternatives in the livestock industry has become urgent. Prebiotics and probiotics, owing to their significant efficacy in regulating intestinal health and enhancing host immunity, are regarded as promising alternative approaches. Xylooligosaccharides (<strong>XOS</strong>), as a high-efficiency prebiotic, can specifically promote the metabolism and proliferation of beneficial bacteria such as <em>Bifidobacterium</em>. Based on this, this study uses Holstein calves as research subjects. It systematically investigates the effects of XOS and <em>Bifidobacterium animalis</em> (<strong>BA</strong>), used alone or in combination, on growth performance, immune-antioxidant function, rumen fermentation characteristics, and microbial composition. It aims to reveal the synergistic effects of the two and to provide a scientifically based, antibiotic-free nutritional strategy to promote healthy calf breeding. Thirty-two 2-month-old male calves were allocated to four dietary treatments (n = 8): (1) control diet (<strong>CON</strong>), (2) CON with 2 g/d XOS (XOS), (3) CON with 5 g/d BA (BA), and (4) CON with 2 g/d XOS with 5 g/d BA (XOS-BA). The 63-day trial consisted of a 7-day adaptation period followed by a 56-day sampling period. Daily feed intake was recorded. On day 63, jugular blood was collected for serum biochemistry, immune and antioxidant analyses, and rumen fluid was sampled for volatile fatty acids, 16S rRNA sequencing, and metabolomics analyses. The XOS-BA group increased final BW (<em>P</em> = 0.004) and average daily gain (<em>P</em> = 0.024), and decreased the feed−to−gain ratio (<em>P</em> = 0.002). Furthermore, XOS-BA supplementation positively affected the ruminal microbiota, increasing the abundances of beneficial taxa, including <em>Acidobacteria, Lactobacillus, and Bifidobacterium</em>. Further analyses revealed that XOS-BA effectively alleviated oxidative stress and inflammatory responses. This was evidenced by increased plasma immunoglobulin A and glutathione levels (<em>P</em> < 0.05) and decreased malondialdehyde concentrations. Meanwhile, compared with other treatments, the rumen fermentation function of calves supplemented with XOS-BA was significantly improved, as reflected by elevated rumen fluid acetic acid concentration (<em>P</em> = 0.036). In-depth analyses indicated that XOS-BA enhanced systemic antioxidant capacity by elevating endogenous antioxidant indices and reducing oxidative products, while modulating retinol metabolism, unsaturated fatty acid biosynthesis, and mTOR signalling. Synbiotic supplementation of XOS-BA synergistically improves growth performance, enhances immune–antioxidant capacity, and modulates rumen microbiota and metabolism in calves, thereby offering a practical antibiotic-free strategy for calf production.</div></div>","PeriodicalId":50789,"journal":{"name":"Animal","volume":"20 1","pages":"Article 101741"},"PeriodicalIF":4.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145919091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.animal.2025.101737
S. Icely, S.C. Mansbridge, A.M. Mackenzie, A.H. Stewart
Rearing piglets in large litters where there are supernumerary piglets compared to functional teats presents a challenge in maintaining piglet health by avoiding successive fostering, whilst minimising mortality caused by starvation. Supplementary milk (SM) provision to litters during the suckling period has been shown to reduce preweaning mortality, but there has been no characterisation of which piglets consume SM and the subsequent performance effects. Using electronic identification (RFID) tags and an antenna at the SM bowl, it was possible to record the duration of each visit for each individual piglet. Multiplying individual piglet weight and duration of SM visits for each day, and summing for the litter showed a positive relationship with daily weighed litter SM consumption during lactation, yielding a regression equation with r2 = 0.84. Therefore, the daily duration of visits to the SM bowl was considered a proxy measure of daily individual piglet SM consumption. Litter SM consumption during lactation, measured both by weighing SM and by calculation using the regression equation, was greater in litters where there were supernumerary piglets compared to functional teats (IS), than in litters where there were no supernumerary piglets (S). Litter weight at each timepoint was greater for IS litters than for S litters, but average piglet weight was lower. Piglets with very high duration of SM visits/d during the final week of lactation were lightest at weaning, and at d 54 postweaning, with the lowest postweaning average daily gain (ADG). Piglets suckling posterior teats had a higher duration of SM visits/d than piglets suckling anterior teats, throughout lactation. Piglets observed as non-sucklers on d 14 had the highest du/d throughout the suckling period and were lightest at weaning. The SM DM feed conversion ratio for non-suckling pigs predicted using the regression equation was 0.88. This was higher than the predicted 0.70 for piglets suckling sow milk, indicating lower efficiency of piglet growth from SM. This may be due to reduced fat and protein content of SM compared to sow’s milk; therefore, further investigation of the composition of SM and refinement of the formulation is warranted. Validation of the methodology employed to estimate SM consumption from the duration of SM visits/d is also necessary.
{"title":"The importance of sow functional teat assessment and provision of supplementary milk to enhance performance of piglets reared in large litters","authors":"S. Icely, S.C. Mansbridge, A.M. Mackenzie, A.H. Stewart","doi":"10.1016/j.animal.2025.101737","DOIUrl":"10.1016/j.animal.2025.101737","url":null,"abstract":"<div><div>Rearing piglets in large litters where there are supernumerary piglets compared to functional teats presents a challenge in maintaining piglet health by avoiding successive fostering, whilst minimising mortality caused by starvation. Supplementary milk (<strong>SM</strong>) provision to litters during the suckling period has been shown to reduce preweaning mortality, but there has been no characterisation of which piglets consume SM and the subsequent performance effects. Using electronic identification (<strong>RFID</strong>) tags and an antenna at the SM bowl, it was possible to record the duration of each visit for each individual piglet. Multiplying individual piglet weight and duration of SM visits for each day, and summing for the litter showed a positive relationship with daily weighed litter SM consumption during lactation, yielding a regression equation with r<sup>2</sup> = 0.84. Therefore, the daily duration of visits to the SM bowl was considered a proxy measure of daily individual piglet SM consumption. Litter SM consumption during lactation, measured both by weighing SM and by calculation using the regression equation, was greater in litters where there were supernumerary piglets compared to functional teats (<strong>IS</strong>), than in litters where there were no supernumerary piglets (<strong>S</strong>). Litter weight at each timepoint was greater for IS litters than for S litters, but average piglet weight was lower. Piglets with very high duration of SM visits/d during the final week of lactation were lightest at weaning, and at d 54 postweaning, with the lowest postweaning average daily gain (<strong>ADG)</strong>. Piglets suckling posterior teats had a higher duration of SM visits/d than piglets suckling anterior teats, throughout lactation. Piglets observed as non-sucklers on d 14 had the highest du/d throughout the suckling period and were lightest at weaning. The SM DM feed conversion ratio for non-suckling pigs predicted using the regression equation was 0.88. This was higher than the predicted 0.70 for piglets suckling sow milk, indicating lower efficiency of piglet growth from SM. This may be due to reduced fat and protein content of SM compared to sow’s milk; therefore, further investigation of the composition of SM and refinement of the formulation is warranted. Validation of the methodology employed to estimate SM consumption from the duration of SM visits/d is also necessary.</div></div>","PeriodicalId":50789,"journal":{"name":"Animal","volume":"20 1","pages":"Article 101737"},"PeriodicalIF":4.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145935988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.animal.2025.101743
M. Cupido , S. Mullan , L. Boyle , K. O’Driscoll
The welfare of commercial pigs, especially concerning the reduction of tail biting, is an ongoing topical issue in current farming systems. Inadequate space allowance and lack of suitable loose material have been identified as two of the main risk factors for tail biting in pigs. This study evaluated the effectiveness of four manipulable loose materials (Straw, Haylage, Hay, and Grass) in reducing tail biting in pigs reared in pens containing either 8, 10, or 12 pigs (weaner: 0.62, 0.49, 0.41 m2/pig; finisher: 1.24, 1.00, 0.83 m2/pig, respectively). Although the study design conflates stocking density, space allowance, and feeder space, making it impossible to evaluate each factor independently, this confound allows for on-farm application. At weaning (approx. 4 weeks), forty-seven litters with undocked tails were assigned as litter groups to enrichment and stocking density treatments using a 4 × 3 experimental design. The fully slatted pens were equipped with single−space feeders. Manipulable materials were provided ad lib via a mesh rack hung on the front wall of the pen. Pens were observed twice daily for any indication of tail biting. Lesion scoring at the individual pig level was performed weekly. Pig behaviour was observed at the group level directly every fortnight, and by video on four occasions (1, 6, 10, and 18 weeks postweaning). Weights were taken one day prior to weaning, 63 days postweaning, and at 22 weeks of age, at which time pigs were slaughtered. Carcass characteristics were obtained from the slaughterhouse. Greater space per pig benefited welfare, as indicated by physical and behavioural measurements. Pigs stocked in groups of 8 and 10 displayed significantly less aggressive and damaging behaviour, fewer and more manageable tail biting outbreaks, and had more undamaged tails than pigs in groups of 12. In addition, pigs in lower−stocked pens were heavier at the end of their lives, creating potential to sell pigs earlier. Interestingly, the type of loose material had no significant impact on most measures, but pigs provided with grass engaged significantly more with the rack than those with other loose materials, and had fewer, more manageable tail biting outbreaks. This study contributes to existing research that suggests the current European Union legal minimum requirement for space allowance should be increased to improve pig welfare, reduce damaging behaviour, and tail biting outbreaks in pigs, especially with undocked tails.
{"title":"Evaluating loose materials and space allowance to improve welfare in commercial weaner and finisher pigs","authors":"M. Cupido , S. Mullan , L. Boyle , K. O’Driscoll","doi":"10.1016/j.animal.2025.101743","DOIUrl":"10.1016/j.animal.2025.101743","url":null,"abstract":"<div><div>The welfare of commercial pigs, especially concerning the reduction of tail biting, is an ongoing topical issue in current farming systems. Inadequate space allowance and lack of suitable loose material have been identified as two of the main risk factors for tail biting in pigs. This study evaluated the effectiveness of four manipulable loose materials (Straw, Haylage, Hay, and Grass) in reducing tail biting in pigs reared in pens containing either 8, 10, or 12 pigs (weaner: 0.62, 0.49, 0.41 m<sup>2</sup>/pig; finisher: 1.24, 1.00, 0.83 m<sup>2</sup>/pig, respectively). Although the study design conflates stocking density, space allowance, and feeder space, making it impossible to evaluate each factor independently, this confound allows for on-farm application. At weaning (approx. 4 weeks), forty-seven litters with undocked tails were assigned as litter groups to enrichment and stocking density treatments using a 4 × 3 experimental design. The fully slatted pens were equipped with single−space feeders. Manipulable materials were provided <em>ad lib</em> via a mesh rack hung on the front wall of the pen. Pens were observed twice daily for any indication of tail biting. Lesion scoring at the individual pig level was performed weekly. Pig behaviour was observed at the group level directly every fortnight, and by video on four occasions (1, 6, 10, and 18 weeks postweaning). Weights were taken one day prior to weaning, 63 days postweaning, and at 22 weeks of age, at which time pigs were slaughtered. Carcass characteristics were obtained from the slaughterhouse. Greater space per pig benefited welfare, as indicated by physical and behavioural measurements. Pigs stocked in groups of 8 and 10 displayed significantly less aggressive and damaging behaviour, fewer and more manageable tail biting outbreaks, and had more undamaged tails than pigs in groups of 12. In addition, pigs in lower−stocked pens were heavier at the end of their lives, creating potential to sell pigs earlier. Interestingly, the type of loose material had no significant impact on most measures, but pigs provided with grass engaged significantly more with the rack than those with other loose materials, and had fewer, more manageable tail biting outbreaks. This study contributes to existing research that suggests the current European Union legal minimum requirement for space allowance should be increased to improve pig welfare, reduce damaging behaviour, and tail biting outbreaks in pigs, especially with undocked tails.</div></div>","PeriodicalId":50789,"journal":{"name":"Animal","volume":"20 1","pages":"Article 101743"},"PeriodicalIF":4.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145939259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.animal.2025.101732
A. Bionda , A. Negro , M. Barbato , L. Liotta , S. Grande , P. Crepaldi
Italy hosts a rich biodiversity of local goat breeds, shaped by its wide variety of climates, landscapes, and traditional farming systems, making the preservation of these locally adapted populations critical for maintaining genetic resources. This study aimed to explore the genomic biodiversity of Italian goats, track recent temporal changes through comparison with samples collected about two decades ago, and investigate the genomic mechanisms underlying environmental adaptation, as well as identify hotspots of possible climatic vulnerability. Demographic data over the last 15 years show that only five breeds are currently considered not at risk of extinction according to FAO criteria, while 22 breeds are classified as critical or formally extinct (no registered animals in 2024). Medium-density single-nucleotide polymorphism (SNP) data from 685 goats representing 31 populations were analysed for population structure, genomic background, and genetic diversity. Comparison with historical samples revealed changes over time, exemplified by Bianca Monticellana and Capestrina, which now display a highly similar and uniform genetic background and higher inbreeding. Genomic analyses revealed a clear separation between northern and central-southern breeds, with northern populations exhibiting more distinct genomic backgrounds while central-southern populations are generally more admixed. Landscape genomic analyses were conducted on a subset of 693 goats from 32 populations, using latent factor mixed model and partial redundancy analysis approaches together with present and projected (SSPs 2–4.5 and 5–8.5, 2080–2100) climatic variables from WorldClim 2.1. A total of 468 SNPs were identified as putatively adaptive, including five detected by both methods, encompassing genes such as KPNA1, PARP9, and LRP8. Genomic offset analyses highlighted vulnerable areas in the northern fringes of the Alpine region, the eastern Po Valley (unsampled due to limited presence of local goat populations), and the Murgia-Gargano region of Apulia, home to the Garganica breed. Overall, these results reveal the impact of breeding practices and environmental pressures on Italian goat genomes, provide insights into adaptive genetic variation of goat species, and identify populations and regions at greatest risk, emphasising the need for targeted conservation and management strategies to preserve this unique component of livestock biodiversity.
{"title":"Spatio-temporal genomics of goats: recent evolution, adaptation, and future vulnerability","authors":"A. Bionda , A. Negro , M. Barbato , L. Liotta , S. Grande , P. Crepaldi","doi":"10.1016/j.animal.2025.101732","DOIUrl":"10.1016/j.animal.2025.101732","url":null,"abstract":"<div><div>Italy hosts a rich biodiversity of local goat breeds, shaped by its wide variety of climates, landscapes, and traditional farming systems, making the preservation of these locally adapted populations critical for maintaining genetic resources. This study aimed to explore the genomic biodiversity of Italian goats, track recent temporal changes through comparison with samples collected about two decades ago, and investigate the genomic mechanisms underlying environmental adaptation, as well as identify hotspots of possible climatic vulnerability. Demographic data over the last 15 years show that only five breeds are currently considered not at risk of extinction according to FAO criteria, while 22 breeds are classified as critical or formally extinct (no registered animals in 2024). Medium-density single-nucleotide polymorphism (<strong>SNP</strong>) data from 685 goats representing 31 populations were analysed for population structure, genomic background, and genetic diversity. Comparison with historical samples revealed changes over time, exemplified by Bianca Monticellana and Capestrina, which now display a highly similar and uniform genetic background and higher inbreeding. Genomic analyses revealed a clear separation between northern and central-southern breeds, with northern populations exhibiting more distinct genomic backgrounds while central-southern populations are generally more admixed. Landscape genomic analyses were conducted on a subset of 693 goats from 32 populations, using latent factor mixed model and partial redundancy analysis approaches together with present and projected (SSPs 2–4.5 and 5–8.5, 2080–2100) climatic variables from WorldClim 2.1. A total of 468 SNPs were identified as putatively adaptive, including five detected by both methods, encompassing genes such as <em>KPNA1</em>, <em>PARP9</em>, and <em>LRP8</em>. Genomic offset analyses highlighted vulnerable areas in the northern fringes of the Alpine region, the eastern Po Valley (unsampled due to limited presence of local goat populations), and the Murgia-Gargano region of Apulia, home to the Garganica breed. Overall, these results reveal the impact of breeding practices and environmental pressures on Italian goat genomes, provide insights into adaptive genetic variation of goat species, and identify populations and regions at greatest risk, emphasising the need for targeted conservation and management strategies to preserve this unique component of livestock biodiversity.</div></div>","PeriodicalId":50789,"journal":{"name":"Animal","volume":"20 1","pages":"Article 101732"},"PeriodicalIF":4.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145939260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.animal.2025.101734
M. Špinka , V. Sekyrová , Š. Hulmáková , A. Bennettová , G. Illmann
Farrowing crates drastically restrict behavioural opportunities for lactating sows. Temporary crating (TC) systems restrain the sow for the first few days after farrowing and then allow free sow movement in the farrowing pen for the rest of lactation. TC housing systems are promoted because they improve sow welfare in comparison with permanent crating (PC) systems that restrict the sow for the whole lactation. How TC affects piglet welfare is less well understood, as it may be associated with higher mortality by crushing but also with increased positive piglet behaviours. Specifically, it has not yet been investigated whether the free movement of the mother sow, all other things being equal, influences the play behaviour of her piglets. This study compared play behaviour in 10 litters housed in PC pens with 10 litters housed in TC pens shortly after the crate removal (Days 3–6 postpartum, Period 1) and then during the 4th week of lactation (Days 18–27 postpartum, Period 2). The only difference between the two treatments was the free sow movement in TC while all other parameters of the two housing systems (e.g., pen area, floor quality, bedding) were equal. Total play behaviour, piglet-piglet social play and piglet-sow play were substantially more frequent in the TC system in both Period 1 and Period 2. This is the first study to show that giving the sow the freedom of movement within a farrowing pen early in lactation promotes piglet play behaviour. Thus, temporary crating is superior to permanent crating not only in relation to sow welfare but also when it comes to aspects of piglet welfare.
{"title":"Temporary versus permanent crating: free movement of mother sow enhances piglet play behaviour","authors":"M. Špinka , V. Sekyrová , Š. Hulmáková , A. Bennettová , G. Illmann","doi":"10.1016/j.animal.2025.101734","DOIUrl":"10.1016/j.animal.2025.101734","url":null,"abstract":"<div><div>Farrowing crates drastically restrict behavioural opportunities for lactating sows. Temporary crating (<strong>TC</strong>) systems restrain the sow for the first few days after farrowing and then allow free sow movement in the farrowing pen for the rest of lactation. TC housing systems are promoted because they improve sow welfare in comparison with permanent crating (<strong>PC</strong>) systems that restrict the sow for the whole lactation. How TC affects piglet welfare is less well understood, as it may be associated with higher mortality by crushing but also with increased positive piglet behaviours. Specifically, it has not yet been investigated whether the free movement of the mother sow, all other things being equal, influences the play behaviour of her piglets. This study compared play behaviour in 10 litters housed in PC pens with 10 litters housed in TC pens shortly after the crate removal (Days 3–6 <em>postpartum</em>, Period 1) and then during the 4th week of lactation (Days 18–27 <em>postpartum</em>, Period 2). The only difference between the two treatments was the free sow movement in TC while all other parameters of the two housing systems (e.g., pen area, floor quality, bedding) were equal. Total play behaviour, piglet-piglet social play and piglet-sow play were substantially more frequent in the TC system in both Period 1 and Period 2. This is the first study to show that giving the sow the freedom of movement within a farrowing pen early in lactation promotes piglet play behaviour. Thus, temporary crating is superior to permanent crating not only in relation to sow welfare but also when it comes to aspects of piglet welfare.</div></div>","PeriodicalId":50789,"journal":{"name":"Animal","volume":"20 1","pages":"Article 101734"},"PeriodicalIF":4.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145884714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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