This review focuses on current understanding of prenatal, prepubertal and post-pubertal development of the male reproductive system of cattle. The critical developmental events occur during the first 3 to 4 months of gestation and the first ~6 to 9 months after birth. The Wilms Tumor-1 and SRY proteins play critical roles in early development and differentiation of the fetal testis, which in turn drives gestational development of the entire male reproductive system. The hypothalamic–pituitary–gonadal axis matures earlier in the bovine fetus than other domestic species with descent of the testes into the scrotum occurring around the 4th month of gestation. An array of congenital abnormalities affecting the reproductive system of bulls has been reported and most are considered to be heritable, although the mode of inheritance in most cases has not been fully defined. Early postnatal detection of most of these abnormalities is problematic as clinical signs are generally not expressed until after puberty. Development of genomic markers for these abnormalities would enable early culling of affected calves in seedstock herds. The postnatal early sustained increase in lutenising hormone secretion cues the rapid growth of the testes in the bull calf leading to the onset of puberty. There is good evidence that both genetic and environmental factors, in particular postnatal nutrition, control or influence development and maturation of the reproductive system. For example, in Bos taurus genotypes which have had sustained genetic selection pressure applied for fertility, and where young bulls are managed on a moderate to high plane of nutrition puberty typically occurs at 8 to 12 months of age. However, in many Bos indicus genotypes where there has been little selection pressure for fertility and where young bulls are reared on a low plane of nutrition, puberty typically occurs between 15 to 17 months. Our understanding of the control and expression of sexual behavior in bulls is limited, particularly in B. indicus genotypes.

The role of herbivorous livestock in supporting the sustainability of the farming systems in which they are found is complex and sometimes conflicting. In Sub-Saharan Africa (SSA), the integration of livestock into farming systems is important for sustainable agriculture as the recycling of nutrients for crop production through returns of animal manure is a central element of the dominant mixed crop-livestock systems. Sustainable agriculture has been widely advocated as the main practical pathway to address the challenge of meeting the food needs of the rapidly growing population in SSA while safeguarding the needs of future generations. The objective of this paper is to review the state of knowledge of the role of herbivores in sustainable intensification of key farming systems in SSA. The pathways to sustainable agriculture in SSA include intensification of production and livelihood diversification. Sustainable agricultural practices in SSA have focused on intensification practices which aim to increase the output : input ratio through increasing use of inputs, introduction of new inputs or use of existing inputs in a new way. Intensification of livestock production can occur through increased and improved fodder availability, genetic production gains, improved crop residue use and better nutrient recycling of manure. Livestock deliver many ‘goods’ in smallholder farming systems in SSA including improving food and nutrition security, increased recycling of organic matter and nutrients and the associated soil fertility amendments, adding value to crop residues by turning them into nutrient-rich foods, income generation and animal traction. Narratives on livestock ‘bads’ or negative environmental consequences have been largely shaped by the production conditions in the Global North but livestock production in SSA is a different story. In SSA, livestock are an integral component of mixed farming systems and they play key roles in supporting the livelihoods of much of the rural population. None-the-less, the environmental consequences of livestock production on the continent cannot be ignored. To enhance agricultural sustainability in SSA, the challenge is to optimize livestock’s role in the farming systems by maximizing livestock ‘goods’ while minimizing the ‘bads’. This can be through better integration of livestock into the farming systems, efficient nutrient management systems, and provision of necessary policy and institutional support.

The Brangus breed was developed to combine the superior characteristics of both of its founder breeds, Angus and Brahman. It combines the high adaptability to tropical and subtropical environments, disease resistance, and overall hardiness of Zebu cattle with the reproductive potential and carcass quality of Angus. It is known that the major histocompatibility complex (MHC, also known as bovine leucocyte antigen: BoLA), located on chromosome 23, encodes several genes involved in the adaptive immune response and may be responsible for adaptation to harsh environments. The objective of this work was to evaluate whether the local breed ancestry percentages in the BoLA locus of a Brangus population diverged from the estimated genome-wide proportions and to identify signatures of positive selection in this genomic region. For this, 167 animals (100 Brangus, 45 Angus and 22 Brahman) were genotyped using a high-density single nucleotide polymorphism array. The local ancestry analysis showed that more than half of the haplotypes (55.0%) shared a Brahman origin. This value was significantly different from the global genome-wide proportion estimated by cluster analysis (34.7% Brahman), and the proportion expected by pedigree (37.5% Brahman). The analysis of selection signatures by genetic differentiation (Fst) and extended haplotype homozygosity-based methods (iHS and Rsb) revealed 10 and seven candidate regions, respectively. The analysis of the genes located within these candidate regions showed mainly genes involved in immune response-related pathway, while other genes and pathways were also observed (cell surface signalling pathways, membrane proteins and ion-binding proteins). Our results suggest that the BoLA region of Brangus cattle may have been enriched with Brahman haplotypes as a consequence of selection processes to promote adaptation to subtropical environments.

Hypoxia strongly affects embryonic development during the pre-hatch period. This study was conducted to investigate the effects of oxygen supplementation (O) and a 38.5°C high temperature (HT) at high altitude (HA, 1720 m) on morphological traits during a pre-hatch period and on relative fluctuating asymmetry (relative FA) and allometric growth during an early post-hatch period in broilers. A total of 720 eggs were obtained from a 45-week-old Ross 308 broiler breeder flock raised at sea level (2 m). The eggs were divided into six incubation condition (IC) groups and were incubated at HA. O groups were exposed to 23.5% O2 for 1 h daily from either days 0 to 11 (O0–11), days 12 to 21 (O12–21) or days 18 to 21 (O18–21) of incubation. HT groups were exposed to 38.5°C daily from either days 12 to 21 (HT12–21) or days 18 to 21 (HT18–21) of incubation. A control was maintained at 37.8°C and 21% O2. The hatched chicks were raised for 6 days at HA. Embryo/chick and beak lengths and head diameter were measured during pre- and post-hatch periods. The face, middle toe and shank lengths were measured for each chick. The relative asymmetry (RA), mean RA (MRA) and allometric growth of the lengths were computed and the existence of FA was demonstrated. The IC significantly affected the embryo length, with embryos of the O0–11 group shorter than embryos of the other O groups. Chicks were longer in the O and HT groups than those in the control, except for the O0–11. We found significant interactions between the IC and each development period for beak length. During the post-hatch period, the head diameter of the O0-11 was significantly smaller than that of the other groups, but not in O12–21. The interactions among IC, age and sex were significant for the RA of the face and middle toe lengths and for MRA. All the examined bilateral traits were evaluated as allometric growth. The FA for bilateral traits was determined in both sexes. The right (R) – left (L) and IR-Ll were the lowest in females for face length and in males for shank length from the O18–21 and in males for middle toe length from the O0–11 and HT18–21 groups. Therefore, the effects of factors such as HT and O2 could mitigate the adverse effects of HA-induced hypoxia on optimal developmental stability of bilateral traits of broiler.

In ovo feeding (IOF) of l-arginine (Arg) can affect growth performance of broilers, but the response of IOF of Arg on breast muscle growth is unclear, and the mechanism involved in protein deposition remains unknown. Hense, this experiment was conducted to evaluate the effects of IOF of Arg on breast muscle growth and protein-deposited signalling in post-hatch broilers. A total of 720 fertile eggs were collected from 34-week-old Arbor Acres breeder hens and distributed to three treatments: (1) non-injected control group; (2) 7.5 g/l (w/v) NaCl diluent-injected control group; (3) 0.6 mg Arg/egg solution-injected group. At 17.5 days of incubation, fertile eggs were injected 0.6 ml solutions into the amnion of the injected groups. Upon hatching, 80 male chicks were randomly assigned to eight replicates of 10 birds each and fed ad libitum for 21 days. The results indicated that IOF of Arg increased relative breast muscle weight compared with those of control groups at hatch, 3-, 7- and 21-day post-hatch (P<0.05). In the Arg-injected group, the plasma total protein and albumen concentrations were higher at 7- and 21-day post-hatch than those of control groups (P<0.05). The alanine aminotransferase activity in Arg group was higher at hatch than that of control groups (P<0.05). The levels of triiodothyronine at four time points and thyroxine hormones at hatch, 7- and 21-day post-hatch in Arg group were higher than those of control groups (P<0.05). In addition, IOF of Arg increased the amino acid concentrations of breast muscle at hatch, 7- and 21-day post-hatch (P<0.05). In ovo feeding of Arg also enhanced mammalian target of rapamycin, ribosomal protein S6 kinase-1 and eIF4E-bindingprotein-1 messenger RNA expression levels at hatch compared with those of control groups (P<0.05). It was concluded that IOF of Arg treatment improved breast muscle growth, which might be associated with the enhancement of protein deposition.

Livestock farming systems provide multiple benefits to humans: protein-rich diets that contribute to food security, employment and rural economies, capital stock and draught power in many developing countries and cultural landscape all around the world. Despite these positive contributions to society, livestock is also the centre of many controversies as regards to its environmental impacts, animal welfare and health outcomes related to excessive meat consumption. Here, we review the potentials of sustainable intensification (SI) and agroecology (AE) in the design of sustainable ruminant farming systems. We analyse the two frameworks in a historical perspective and show that they are underpinned by different values and worldviews about food consumption patterns, the role of technology and our relationship with nature. Proponents of SI see the increase in animal protein demand as inevitable and therefore aim at increasing production from existing farmland to limit further encroachment into remaining natural ecosystems. Sustainable intensification can thus be seen as an efficiency-oriented framework that benefits from all forms of technological development. Proponents of AE appear more open to dietary shifts towards less animal protein consumption to rebalance the whole food system. Agroecology promotes system redesign, benefits from functional diversity and aims at providing regulating and cultural services. We analyse the main criticisms of the two frameworks: Is SI sustainable? How much can AE contribute to feeding the world? Indeed, in SI, social justice has long lacked attention notably with respect to resource allocation within and between generations. It is only recently that some of its proponents have indicated that there is room to include more diversified systems and food-system transformation perspectives and to build socially fair governance systems. As no space is available for agricultural land expansion in many areas, agroecological approaches that emphasise the importance of local production should also focus more on yield increases from agricultural land. Our view is that new technologies and strict certifications offer opportunities for scaling-up agroecological systems. We stress that the key issue for making digital science part of the agroecological transition is that it remains at a low cost and is thus accessible to smallholder farmers. We conclude that SI and AE could converge for a better future by adopting transformative approaches in the search for ecologically benign, socially fair and economically viable ruminant farming systems.

Spermatogenesis is a finely regulated process of germ cell multiplication and differentiation leading to the production of spermatozoa in the seminiferous tubules. Spermatogenesis can be divided into three parts: spermatocytogenesis, meiosis and spermiogenesis. During spermatocytogenesis, germ cells engage in a cycle of several mitotic divisions that increases the yield of spermatogenesis and to renew stem cells and produce spermatogonia and primary spermatocytes. Meiosis involves duplication and exchange of genetic material and two cell divisions that reduce the chromosome number and yield four haploid round spermatids. Spermiogenesis involves the differentiation of round spermatids into fully mature spermatozoa released into the lumin of seminiferous tubules. The seminiferous epithelium is composed of several generations of germ cells due to the fact that new generations of sperm cells engage in the spermatogenic process without waiting for the preceding generations to have completed their evolution and to have disappeared as spermatozoa into the lumen of the tubules. In bulls, the duration of the seminiferous epithelium cycle is 13.5 days. The total duration of spermatogenesis is 61 days, that is 4.5 times the duration of the cycle of the seminiferous epithelium. The spermatogenetic wave is used to describe the spatial arrangement of cell associations along the tubules. Several theories have been described to explain the renewal of spermatogonia. Depending on the model, there are five or six spermatogonial mitoses explaining the renewal of stem cells and the proliferation of spermatogonia. Daily sperm production and germ cell degeneration can be quantified from numbers of germ cells in various steps of development throughout spermatogenesis. Bulls have a lower efficiency of spermatogenesis than most species examined, but higher than that of humans.

Ruminal in situ incubations are widely used to assess the nutritional value of feedstuffs for ruminants. In in situ methods, feed samples are ruminally incubated in indigestible bags over a predefined timespan and the disappearance of nutrients from the bags is recorded. To describe the degradation of specific nutrients, information on the concentration of feed samples and undegraded feed after in situ incubation (‘bag residues’) is needed. For cereal and pea grains, CP and starch (ST) analyses are of interest. The numerous analyses of residues following ruminal incubation contribute greatly to the substantial investments in labour and money, and faster methods would be beneficial. Therefore, calibrations were developed to estimate CP and ST concentrations in grains and bag residues following in situ incubations by using their near-infrared spectra recorded from 680 to 2500 nm. The samples comprised rye, triticale, barley, wheat, and maize grains (20 genotypes each), and 15 durum wheat and 13 pea grains. In addition, residues after ruminal incubation were included (at least from four samples per species for various incubation times). To establish CP and ST calibrations, 620 and 610 samples (grains and bag residues after incubation, respectively) were chemically analysed for their CP and ST concentration. Calibrations using wavelengths from 1250 to 2450 nm and the first derivative of the spectra produced the best results (R2Validation=0.99 for CP and ST; standard error of prediction=0.47 and 2.10% DM for CP and ST, respectively). Hence, CP and ST concentration in cereal grains and peas and their bag residues could be predicted with high precision by NIRS for use in in situ studies. No differences were found between the effective ruminal degradation calculated from NIRS estimations and those calculated from chemical analyses (P>0.70). Calibrations were also calculated to predict ruminal degradation kinetics of cereal grains from the spectra of ground grains. Estimation of the effective ruminal degradation of CP and ST from the near-infrared spectra of cereal grains showed promising results (R2>0.90), but the database needs to be extended to obtain more stable calibrations for routine use.

Dietary interventions are a common practice in the poultry industry to promote optimal performance and health of animals. Here, we aim at assessing the influence of supplementing broiler diets with dry whey powder (DWP) and whey protein concentrate (WPC) on nutrient coefficient of apparent ileal digestibility (CAID) and productive performance. Cecal microbiota composition was also determined using Illumina amplicon sequencing. Dietary treatments were control diet (no supplementation of DWP or WPC), 60-DWP (60 g/kg of DWP), and 80-WPC (80 g/kg of WPC). One-day-old male broilers were randomly assigned to one of three treatments, and housed in floor pens. In Trial 1, 90 1-day-old chicks were allocated to three pens/treatment, with 10 birds/pen, during 21 days for CAID evaluation. Diet 60-DWP increased Ca CAID (P=0.041), while diet 80-WPC improved Ca and P CAID (P<0.001 and 0.002, respectively) when compared with control diet. In Trial 2, 810 one-day-old chicks were allocated to nine pens/treatment, with 30 birds/pen, during 42 days. Feeding chickens with 60-DWP and 80-WPC increased their BW, average daily gain (ADG) and feed intake (FI) during the starter (P<0.001 for all variables) and grower-finisher periods (P<0.001 for BW and FI, and P=0.048 for ADG), and during the entire feeding period (P<0.05), when compared with control diet. Diets 60-DWP and 80-WPC reduced the feed conversion ratio of chickens during the starter period (P<0.001 and 0.003, respectively), while 60-DWP reduced this parameter during the entire feeding period (P=0.048), when compared to control diet. At day 42, cecal microbial communities of chickens that were fed with 60-DWP and 80-WPC differed from those fed with control diet (R=0.776, P=0.008; and R=0.740, P=0.008, respectively). The abundance of Bacteroides fragilis, Bacteroides spp., Escherichia coli/Shigella flexneri and Megamonas furniformis increased when 60-DWP and 80-WPC diets were offered, while the presence of Helicobacter pullorum decreased. Lactobacillus salivarius consistently increased in chickens with better feed conversion ratio, which were those fed with 60-DWP. The results obtained in the present study indicate that growth of chickens is improved by DWP and WPC supplementation because of a higher mineral digestibility, increased feed intake and modulation of cecal microbiota communities.

Until recently, the main selection focus in UK dairy goats has been on milk yield. To develop a selection index suitably weighted for a variety of traits, it is important to understand the genetic relationships between production, health and fertility traits. This study focussed on three aspects of reproduction that are of interest to goat breeders. (1) Out of season (OOS) kidding ability: goats are highly seasonal breeders so achieving consistent, year-round dairy production presents a challenge. It may be possible to select for extended or shifted breeding cycles, however, there are no published studies on the genetic basis of seasonal kidding ability, and a genetic correlation with milk production in dairy goats; (2) age at first kidding (AFK): a reduced AFK offers the opportunity for more rapid genetic improvement, as well as reducing the amount of time and resources required to raise the animals to producing age; (3) pseudopregnancy (PPG): as it is difficult to diagnose pregnancy within 30 days of mating, high herd levels of PPG could add a significant delay in breeding replacement animals, or commencing a new lactation. Using records from 9546 goats, the objective of this study was to investigate the genetic relationships between the reproductive traits described above, and the production traits 520-day milk yield (MY520), lifetime milk yield (MYLife) and lifetime number of days in milk (DIMLife). The ‘out of season’ phenotype was defined as week of kidding relative to the 4 weeks of the year where the highest average number of births occur. Incidences of PPG that occurred during the first lactation were used as cases, while goats with none were assigned as controls. Relevant fixed and random effects were fitted in the models. In line with other reproduction traits, heritability estimates were low ranging from 0.08 to 0.11. A negative genetic correlation was found between AFK and MY520 (−0.22±0.10), whereas a positive genetic correlation was found between PPG and DIMLife (0.58±0.11). Pseudopregnancy and OOS were positively genetically correlated (0.36±0.15). All other genetic correlations were very low. The results of this study indicate that selection for the reproductive traits analysed is feasible, without adversely affecting MYLife.

Mastitis can prove expensive in sheep reared for meat production due to costs associated with treatment methods, poor lamb growth and premature culling of ewes. The most commonly used method to detect mastitis, in dairy systems, is somatic cell counts. However, in many meat-producing sheep flocks ewes are not routinely handled, thus regular milk sampling is not always possible. It is, therefore, worthwhile to investigate alternative phenotypes, such as those associated with udder conformation and methods of evaluating somatic cell counts in the milk, such as the California Mastitis Test. The main objectives of this study were therefore: (a) to estimate genetic parameters of traits relating to mastitis and udder conformation in a meat sheep breed; (b) estimate the level of association between somatic cell counts and the California Mastitis Test and (c) assess the relationships between mastitis and both udder conformation and lamb live weights. Data were collected from Texel ewes based on 29 flocks, throughout the UK, during 2015 and 2016. The ewes were scored twice each year, at mid- and late-lactation. Eight different conformation traits, relating to udder and teat characteristics, and milk samples were recorded. The data set comprised of data available for 2957 ewes. The pedigree file used contained sire and dam information for 31 775 individuals. The animal models used fitted relevant fixed and random effects. Heritability estimates for traits relating to mastitis (somatic cell score and the California Mastitis Test), ranged from 0.08 to 0.11 and 0.07 to 0.11, respectively. High genetic correlations were observed between somatic cell score and the California Mastitis Test (0.76 to 0.98), indicating the California Mastitis Test to be worthwhile for assessing infection levels, particularly at mid-lactation. The strongest correlations observed between the mastitis traits and the udder conformation traits were associated with udder depth (0.61 to 0.75) also at mid-lactation. Negative phenotypic correlations were estimated between mastitis and the weight of lamb reared by the ewe (−0.15 to −0.23), suggesting that lamb weights fell as infection levels rose. Genetic correlations were not significantly different from zero. Reducing mastitis will lead to improvements in flock productivity and the health and welfare of the animals. It will also improve the efficiency of production and the resilience to disease challenge. The economic benefits, therefore, of these results combined could be substantial not only in this breed but also in the overall meat sheep industry.

Goats have played a key role as source of nourishment for humans in their expansion all over the world in long land and sea trips. This has guaranteed a place for this species in the important and rapid episode of livestock expansion triggered by Columbus’ arrival in the Americas in the late 1400s. The aims of this study are to provide a comprehensive perspective on genetic diversity in American goat populations and to assess their origins and evolutionary trajectories. This was achieved by combining data from autosomal neutral genetic markers obtained in more than two thousand samples that encompass a wide range of Iberian, African and Creole goat breeds. In general, even though Creole populations differ clearly from each other, they lack a strong geographical pattern of differentiation, such that populations of different admixed ancestry share relatively close locations throughout the large geographical range included in this study. Important Iberian signatures were detected in most Creole populations studied, and many of them, particularly the Cuban Creole, also revealed an important contribution of African breeds. On the other hand, the Brazilian breeds showed a particular genetic structure and were clearly separated from the other Creole populations, with some influence from Cape Verde goats. These results provide a comprehensive characterisation of the present structure of goat genetic diversity, and a dissection of the Iberian and African influences that gave origin to different Creole caprine breeds, disentangling an important part of their evolutionary history. Creole breeds constitute an important reservoir of genetic diversity that justifies the development of appropriate management systems aimed at improving performance without loss of genomic diversity.

A methodological framework was presented for deriving weightings to be applied in selection indexes to account for the impact genetic change in traits will have on greenhouse gas emissions intensities (EIs). Although the emission component of the breeding goal was defined as the ratio of total emissions relative to a weighted combination of farm outputs, the resulting trait-weighting factors can be applied as linear weightings in a way that augments any existing breeding objective before consideration of EI. Calculus was used to define the parameters and assumptions required to link each trait change to the expected changes in EI for an animal production system. Four key components were identified. The potential impact of the trait on relative numbers of emitting animals per breeding female first has a direct effect on emission output but, second, also has a dilution effect from the extra output associated with the extra animals. Third, each genetic trait can potentially change the amount of emissions generated per animal and, finally, the potential impact of the trait on product output is accounted for. Emission intensity weightings derived from this equation require further modifications to integrate them into an existing breeding objective. These include accounting for different timing and frequency of trait expressions as well as a weighting factor to determine the degree of selection emphasis that is diverted away from improving farm profitability in order to achieve gains in EI. The methodology was demonstrated using a simple application to dairy cattle breeding in Ireland to quantify gains in EI reduction from existing genetic trends in milk production as well as in fertility and survival traits. Most gains were identified as coming through the dilution effect of genetic increases in milk protein per cow, although gains from genetic improvements in survival by reducing emissions from herd replacements were also significant. Emission intensities in the Irish dairy industry were estimated to be reduced by ~5% in the last 10 years because of genetic trends in production, fertility and survival traits, and a further 15% reduction was projected over the next 15 years because of an observed acceleration of genetic trends.

The objective of this study was to investigate the association of single nucleotide polymorphisms (SNPs) with birth weight, weight gain from birth to weaning and from weaning to yearling, yearling height and cow weight in Nelore cattle. Data from 5064 animals participating in the DeltaGen and PAINT breeding programs were used. The animals were genotyped with a panel of 777 962 SNPs (Illumina BovineHD BeadChip) and 412 993 SNPs remained after quality control analysis of the genomic data. A genome-wide association study was performed using a single-step methodology. The analyses were processed with the BLUPF90 family of programs. When applied to a genome-wide association studies, the single-step GBLUP methodology is an iterative process that estimates weights for the SNPs. The weights of SNPs were included in all analyses by iteratively applying the single-step GBLUP methodology and repeated twice so that the effect of the SNP and the effect of the animal were recalculated in order to increase the weight of SNPs with large effects and to reduce the weight of those with small effects. The genome-wide association results are reported based on the proportion of variance explained by windows of 50 adjacent SNPs. Considering the two iterations, only windows with an additive genetic variance >1.5% were presented in the results. Associations were observed with birth weight on BTA 14, with weight gain from birth to weaning on BTA 5 and 29, with weight gain from weaning to yearling on BTA 11, and with yearling height on BTA 8, showing the genes TMEM68 (transmembrane protein 8B) associated with birth weight and yearling height, XKR4 (XK, Kell blood group complex subunit-related family, member 4) associated with birth weight, NPR2 (natriuretic peptide receptor B) associated with yearling height, and REG3G (regenerating islet-derived 3-gamma) associated with weight gain from weaning to yearling. These genes play an important role in feed intake, weight gain and the regulation of skeletal growth.

The growing request for healthier fatty acid composition of animal products is raising the necessity of a deeper knowledge of the main factors controlling fatty acids storage in muscle and backfat. Perilipin (PLIN) 5, and the whole Perilipin family, seem to play a crucial role in the regulation of lipids deposition as code for proteins coating intracellular lipid droplets surface. Nevertheless, the knowledge of these genes in pig is still incomplete. The present research was aimed at investigating in different pig breeds the PLIN5 gene, analysing its expression level and the associations of the variability in its downstream gene region with pork meat and carcass quality traits. Moreover, the PLIN5 protein localisation in porcine skeletal muscle was investigated through immunofluorescence, resulting to be widespread in Semimembranosus muscle (SM) myofibers. The identified single nucleotide polymorphism (SNP) rs327694326 (NC_010444.4:g.74314701T>C) located in PLIN5 downstream region was analysed in different pig populations, represented by 512 Italian Large White (ILW) pigs, 300 Italian Duroc (IDU) samples, 100 Italian Landrace, 100 Pietrain and 60 pigs belonging to three Italian native breeds (20 samples of Cinta Senese, 20 Calabrese and 20 Casertana pigs). The C allele was found in ILW, IDU and Pietrain pigs. In ILW pigs this SNP showed results indicating a possible association with oleic and cis-vaccenic fatty acid contents in backfat tissue. Furthermore, as PLINs are known to regulate lipases activity, we tested if the rs327694326 SNP was associated with differences in Hormone-sensitive lipase (LIPE) gene expression levels. In SM of ILW pigs, PLIN5 C allele was associated with significantly lower LIPE transcription levels than T allele (P=0.02 for Student’s t test of TT v. CT samples, P<0.0001 for TT v. CC pigs), whereas in IDU breed no significant difference was noticed in LIPE transcription levels between TT and TC animals. The results may suggest that variations in the PLIN5 sequence may be linked to LIPE expression through a still poorly known regulative molecular process.

Sheep are an important part of the global agricultural economy. Growth and meat production traits are significant economic traits in sheep. The Texel breed is the most popular terminal sire breed in the UK, mainly selected for muscle growth and lean carcasses. This is a study based on a genome-wide association approach that investigates the links between some economically important traits, including computed tomography (CT) measurements, and molecular polymorphisms in UK Texel sheep. Our main aim was to identify single nucleotide polymorphisms (SNP) associated with growth, carcass, health and welfare traits of the Texel sheep breed. This study used data from 384 Texel rams. Data comprised ten traits, including two CT measured traits. The phenotypic data were placed in four categories: growth traits, carcass traits, health traits and welfare traits. De-regressed estimated breeding values (EBV) for these traits together with sire genotypes derived with the Ovine 50 K SNP array of Illumina were jointly analysed in a genome wide association analysis. Eight novel chromosome-wise significant associations were found for carcass, growth, health and welfare traits. Three significant markers were intronic variants and the remainder intergenic variants. This study is a first step to search for genomic regions controlling CT-based productivity traits related to body and carcass composition in a terminal sire sheep breed using a 50 K SNP genome-wide array. Results are important for the further development of strategies to identify causal variants associated with CT measures and other commercial traits in sheep. Independent studies are needed to confirm these results and identify candidate genes for the studied traits.

Weaning of piglets is associated with important changes in gut structure and function resulting from stressful events such as separation from the sow, moving to a new facility and dietary transition from a liquid to a solid feed. This may result in post-weaning diarrhoea and a decrease in feed intake and growth. In humans, the cyanobacterium Spirulina platensis (SP) and the freshwater microalga Chlorella vulgaris (CV) are known for their beneficial health effects. This study aimed to determine the effects of early oral administration of Spirulina and Chlorella in piglets on mucosal architecture and cytokine expression in the intestine around weaning, and consequences on growth performance and diarrhoea incidence. The experiment was conducted on 108 suckling piglets of 14 days of age (initial BW=4.9±0.7 kg) and weaned at 28 days of age (day 0). Animals received orally 385 mg/kg BW per day of SP or CV, or water (negative control (NC)) during 4 weeks from day −14 to day 14 and their growth performance was measured daily. After weaning, growth, feed intake and diarrhoea incidence were measured daily. Intestinal morphology and functionality were assessed at day −1, day 2, and day 14. During the suckling period, average daily gain (ADG) in SP piglets was higher, resulting in a higher weaning BW compared to NC and CV piglets (P<0.05). No significant difference between treatments was observed for ADG, average daily feed intake, and gain to feed (G : F) ratio after weaning, but the extent of growth retardation after weaning was the lowest in piglets supplemented with Chlorella (P<0.01). Supplementation with Spirulina reduced diarrhoea incidence by 50% from day 0 to day 14 (P<0.05). Mucosal architecture at the jejunum was unaffected by Spirulina or Chlorella administration (P>0.10). Shorter ileal villi were measured in SP and CV piglets than in NC piglets (P<0.05). Cytokine expression did not differ between treatments in response to weaning. At day 14, IL-8 expression in the ileum was higher in SP piglets, while IL-1β expression in the jejunum was higher in CV piglets (P<0.05). This study shows that Spirulina administration around weaning alleviates diarrhoea in weaned piglets, without marked modulation of local inflammation.

Runs of homozygosity (ROH) are widely used as predictors of whole-genome inbreeding levels in cattle. They identify regions that have an unfavorable effect on a phenotype when homozygous, but also identify the genes associated with traits of economic interest present in these regions. Here, the distribution of ROH islands and enriched genes within these regions in four dairy cattle breeds were investigated. Cinisara (71), Modicana (72), Reggiana (168) and Italian Holstein (96) individuals were genotyped using the 50K v2 Illumina BeadChip. The genomic regions most commonly associated with ROHs were identified by selecting the top 1% of the single nucleotide polymorphisms (SNPs) most commonly observed in the ROH of each breed. In total, 11 genomic regions were identified in Cinisara and Italian Holstein, and eight in Modicana and Reggiana, indicating an increased ROH frequency level. Generally, ROH islands differed between breeds. The most homozygous region (>45% of individuals with ROH) was found in Modicana on chromosome 6 within a quantitative trail locus affecting milk fat and protein concentrations. We identified between 126 and 347 genes within ROH islands, which are involved in multiple signaling and signal transduction pathways in a wide variety of biological processes. The gene ontology enrichment provided information on possible molecular functions, biological processes and cellular components under selection related to milk production, reproduction, immune response and resistance/susceptibility to infection and diseases. Thus, scanning the genome for ROH could be an alternative strategy to detect genomic regions and genes related to important economic traits.

Longer-lived cows tend to be more profitable and the stayability trait is a selection criterion correlated to longevity. An alternative to the traditional approach to evaluate stayability is its definition based on consecutive calvings, whose main advantage is the more accurate evaluation of young bulls. However, no study using this alternative approach has been conducted for Zebu breeds. Therefore, the objective of this study was to compare linear random regression models to fit stayability to consecutive calvings of Guzerá, Nelore and Tabapuã cows and to estimate genetic parameters for this trait in the respective breeds. Data up to the eighth calving were used. The models included the fixed effects of age at first calving and year-season of birth of the cow and the random effects of contemporary group, additive genetic, permanent environmental and residual. Random regressions were modeled by orthogonal Legendre polynomials of order 1 to 4 (2 to 5 coefficients) for contemporary group, additive genetic and permanent environmental effects. Using Deviance Information Criterion as the selection criterion, the model with 4 regression coefficients for each effect was the most adequate for the Nelore and Tabapuã breeds and the model with 5 coefficients is recommended for the Guzerá breed. For Guzerá, heritabilities ranged from 0.05 to 0.08, showing a quadratic trend with a peak between the fourth and sixth calving. For the Nelore and Tabapuã breeds, the estimates ranged from 0.03 to 0.07 and from 0.03 to 0.08, respectively, and increased with increasing calving number. The additive genetic correlations exhibited a similar trend among breeds and were higher for stayability between closer calvings. Even between more distant calvings (second v. eighth), stayability showed a moderate to high genetic correlation, which was 0.77, 0.57 and 0.79 for the Guzerá, Nelore and Tabapuã breeds, respectively. For Guzerá, when the models with 4 or 5 regression coefficients were compared, the rank correlations between predicted breeding values for the intercept were always higher than 0.99, indicating the possibility of practical application of the least parameterized model. In conclusion, the model with 4 random regression coefficients is recommended for the genetic evaluation of stayability to consecutive calvings in Zebu cattle.

Two highly pathogenic avian influenza (HPAI) outbreaks have affected commercial egg production flocks in the American continent in recent years; a H7N3 outbreak in Mexico in 2012 that caused 70% to 85% mortality and a H5N2 outbreak in the United States in 2015 with over 99% mortality. Blood samples were obtained from survivors of each outbreak and from age and genetics matched non-affected controls. A total of 485 individuals (survivors and controls) were genotyped with a 600 k single nucleotide polymorphism (SNP) array to detect genomic regions that influenced the outcome of highly pathogenic influenza infection in the two outbreaks. A total of 420458 high quality, segregating SNPs were identified across all samples. Genetic differences between survivors and controls were analyzed using a logistic model, mixed models and a Bayesian variable selection approach. Several genomic regions potentially associated with resistance to HPAI were identified, after performing multidimensional scaling and adjustment for multiple testing. Analysis conducted within each outbreak identified different genomic regions for resistance to the two virus strains. The strongest signals for the Iowa H5N2 survivor samples were detected on chromosomes 1, 7, 9 and 15. Positional candidate genes were mainly coding for plasma membrane proteins with receptor activity and were also involved in immune response. Three regions with the strongest signal for the Mexico H7N3 samples were located on chromosomes 1 and 5. Neuronal cell surface, signal transduction and immune response proteins coding genes were located in the close proximity of these regions.