Herbivores are found in a variety of ecosystems all over the world. Permanent pastures and meadows cover about 25% of global land. We currently count one domesticated herbivore for two people in the world and the number is growing. Production systems and products are highly diverse. This high diversity is the result of thousands of years of natural selection and human-controlled breeding, as well as migration and trade. Because of the high diversity of domestic herbivore genetic resources, herders have been able to live in regions where no alternative for income generation exists. Meat and milk from domestic herbivores provide 16% and 8% of the global protein and kilocalorie consumption, respectively. They also provide a variety of essential micronutrients but can contribute to overweight and obesity when consumed in excess. Domestic herbivores also make significant contribution to food security through the production of manure, draught power and transport and the generation of income at household and national level. They have a key role to play in women’s empowerment and gender equality, both in rural and urban areas.

Demand for meat and milk is increasing because of population growth, rising incomes and urbanisation. This trend is expected to continue, especially in Latin America, South Asia and China. The sustainable development of domestic herbivore production needs to address the feed/food and the efficiency of herbivores in turning forages into protein. It also needs to address the contribution of herbivores to greenhouse gas emissions, especially of ruminants through enteric fermentation, and their mitigation potential, including through carbon sequestration. Animal genetic resources have a key role to play in mitigating and adapting to climate change. The role of ruminants in the circular bioeconomy needs to be enhanced, promoting the use of by-products and waste as livestock feed and the recycling of manure for energy and nutrients. Finally, the role of domestic herbivores in providing secure livelihoods and economic opportunities for millions of smallholder farmers and pastoralists needs to be enhanced. The sustainable development of the sector therefore requires adequate policies, and there are already a variety of mechanisms available, including regulations, cross-compliance systems, payments for environmental services and research and development. Priority areas for policy makers should be aligned with the global framework of the Sustainable Development Goals and include: (i) food security and nutrition, (ii) economic development and livelihoods, (iii) animal and human health and finally, (iv) environment, climate and natural resources.

The origins and phylogeny of different sheep breeds has been widely studied using polymorphisms within the mitochondrial hypervariable region. However, little is known about the mitochondrial DNA (mtDNA) content and phylogeny based on mtDNA protein-coding genes. In this study, we assessed the phylogeny and copy number of the mtDNA in eight indigenous (population size, n=184) and three introduced (n=66) sheep breeds in China based on five mitochondrial coding genes (COX1, COX2, ATP8, ATP6 and COX3). The mean haplotype and nucleotide diversities were 0.944 and 0.00322, respectively. We identified a correlation between the lineages distribution and the genetic distance, whereby Valley-type Tibetan sheep had a closer genetic relationship with introduced breeds (Dorper, Poll Dorset and Suffolk) than with other indigenous breeds. Similarly, the Median-joining profile of haplotypes revealed the distribution of clusters according to genetic differences. Moreover, copy number analysis based on the five mitochondrial coding genes was affected by the genetic distance combining with genetic phylogeny; we also identified obvious non-synonymous mutations in ATP6 between the different levels of copy number expressions. These results imply that differences in mitogenomic compositions resulting from geographical separation lead to differences in mitochondrial function.

Compared with conventional identification methods, DNA-based genetic approaches such as single nucleotide polymorphisms (SNPs) and satellites are much more reliable for pig identification and meat traceability. In this study, multiallelic amplification fragments with multiple SNPs, incorporating the advantages of both SNPs and microsatellites, were explored for the first time for pig identification and meat traceability. Primer pairs for multiallelic fragments and their optimal SNPs were successfully selected and used for identification of individuals from Suzhong and Duroc populations. Meanwhile, the combined panel of the above mentioned primer pairs together with their optimal SNPs for Suzhong and/or Duroc pigs were validated for identification of the hybrids (Suzhong×Duroc). Therefore, we have successfully selected multiallelic amplification fragments with multiple SNPs to identify pigs and their meat samples from Suzhong, Duroc or their hybrids. Our study demonstrates that our method is more powerful for pig identification or meat traceability than SNPs or microsatellites.

Nutrition is a major factor that regulates ruminant milk components, particularly its fatty acid (FA) composition, which is an important determinant of milk nutritional quality. In the mammary gland, milk component biosynthesis involves a large number of genes under nutritional regulation that are not well understood. Thus, the objective of the present study was to evaluate the effects of extruded linseeds (EL) alone or in combination with fish oil (ELFO) on goat mammary gene expression. In total, 14 goats were fed one of the following three diets: a natural grassland hay basal diet (CTRL) alone, CTRL supplemented with 530 g/day of EL, or 340 g/day of EL plus 39 g/day of fish oil (ELFO). Mammary secretory tissues were collected after slaughter on day 28, to determine the expression of 14 lipogenic genes and five lipogenic enzyme activities and transcriptomic profiles. The mRNA abundance decreased for SCD1 (P<0.1) with ELFO v. CTRL, and for AZGP1 (P<0.1) and ACSBG1 (P<0.05) decreased with EL v. ELFO and the CTRL diets (only for ACSBG1), respectively. Transcriptomic analyses performed using a bovine microarray revealed 344 and 314 differentially expressed genes (DEG) in the EL and ELFO diets, respectively, compared with the CTRL diet, with 76 common DEGs. In total, 21 and 27 DEGs were involved in lipid metabolism and transport class in the EL and ELFO v. the CTRL diets, respectively, with eight common genes (ALDH3B1, ALDH18A1, DGKD1, ENPP1, IL7, NSMAF, PI4KA and SERINC5) down-regulated by these two treatments. In EL v. CTRL diets, a gene network related to lipid metabolism and transport was detected. Although this network was not detected in the ELFO v. CTRL analysis, five genes known to be involved in lipid metabolism and transport were up-regulated (SREBF1, PPARG and GPX4) or down-regulated (FABP1 and ENPP6) by ELFO. The protein metabolism and transport biological processes were largely altered by both EL and ELFO v. CTRL diets without changes in major milk protein secretion. Amino acid metabolism was highlighted as an enriched network by Ingenuity Pathway Analysis and was similar to cellular growth and proliferation function. Two regulation networks centered on the estrogen receptor (ESR1) and a transcriptional factor (SP1) were identified in EL and ELFO v. CTRL diets. In conclusion, these results show that these two supplemented diets, which largely changed milk FA composition, had more effects on mRNA linked to protein metabolism and transport pathways than to lipid metabolism, and could affect mammary remodeling.

Litter size has a great impact on the profit of swine producers. Uterine development is an important determinant of reproduction efficiency and could hence affect litter size. Chinese Erhualian pig is one of the most prolific breeds in the world, even though large phenotypic variation in litter size was observed within Erhualian sows. To dissect the genetic basis of the phenotypic variation, we herein conducted genome-wide association studies for total number born and number born alive (NBA) of Erhualian sows. In total, one significant single nucleotide polymorphism (SNP) (P<1.78e−06) and 11 suggestive SNPs (P<3.57e−05) were identified on 10 chromosomes, confirming seven previously reported quantitative trait loci (QTL) and uncovering six QTL for litter size or uterus length. One locus on Sus scrofa chromosome (SSC) 13 (79.28 to 90.43 Mb) harbored a cluster of suggestive SNPs associated with multiparous NBA. The SNP (rs81447100) within this region was confirmed to be significantly (P<0.05) associated with litter size in Erhualian (n=313), Sutai (n=173) and Yorkshire (n=488) populations. Retinol binding protein 2 and retinol binding protein 1 functionally related to the development of uterus were located in a region of 2 Mb around rs81447100. Moreover, four genes related to embryo implantation and development were also detected around other significant SNPs. Taken together, our findings provide a potential marker (rs81447100) for the genetic improvement of litter size not only in Chinese Erhualian pigs but also in European commercial pig breeds like Yorkshire, and would facilitate the final identification of causative variant(s) underlying the effect of SSC13 QTL on litter size.

Intramuscular fat (IMF) content and composition are relevant for the meat industry due to their effect on human health and meat organoleptic properties. A divergent selection experiment for IMF of Longissimus dorsi (LD) muscle was performed in rabbits during eight generations. The aim of this study is to estimate the correlated responses to selection for IMF on the fatty acid composition of LD. Response to selection for IMF was 0.34 g/100 g of LD, representing 2.4 phenotypic SD of the trait. High-IMF line showed 9.20% more monounsaturated fatty acids (MUFA) and 0.39%, 9.97% and 10.3% less n-3, n-6 and polyunsaturated fatty acids (PUFA), respectively, than low-IMF line. The main MUFA and PUFA individual fatty acids followed a similar pattern, except for C18:3n-3 that was greater in the high-IMF line. We did not observe differences between lines for the percentage of total saturated fatty acids, although high-IMF line showed greater C14:0 and C16:0 and lower C18:0 percentages than low-IMF line. Heritability estimates were generally high for all fatty acids percentages, ranging from 0.43 to 0.59 with a SD around 0.08, showing an important genetic component on these traits. Genetic correlations between IMF and LD fatty acid percentages were strong and positive for C14:0, C16:1, C18:1n-9, and MUFA, ranging from 0.88 to 0.97, and strong and negative for C18:0, C18:2n-6, C20:4n-6, n-6 and PUFA, ranging from −0.83 to −0.91. These correlations were accurately estimated, with SD ranging from 0.02 to 0.06. The genetic correlations between IMF and other fatty acids were estimated with lower accuracy. In general, phenotypic and genetic correlations were of the same order. Our experiment shows that selection for IMF strongly affects the fatty acid composition of meat, due the high heritabilities of fatty acids and their high genetic correlations with IMF.

The uptake of genomic selection (GS) by the swine industry is still limited by the costs of genotyping. A feasible alternative to overcome this challenge is to genotype animals using an affordable low-density (LD) single nucleotide polymorphism (SNP) chip panel followed by accurate imputation to a high-density panel. Therefore, the main objective of this study was to screen incremental densities of LD panels in order to systematically identify one that balances the tradeoffs among imputation accuracy, prediction accuracy of genomic estimated breeding values (GEBVs), and genotype density (directly associated with genotyping costs). Genotypes using the Illumina Porcine60K BeadChip were available for 1378 Duroc (DU), 2361 Landrace (LA) and 3192 Yorkshire (YO) pigs. In addition, pseudo-phenotypes (de-regressed estimated breeding values) for five economically important traits were provided for the analysis. The reference population for genotyping imputation consisted of 931 DU, 1631 LA and 2103 YO animals and the remainder individuals were included in the validation population of each breed. A LD panel of 3000 evenly spaced SNPs (LD3K) yielded high imputation accuracy rates: 93.78% (DU), 97.07% (LA) and 97.00% (YO) and high correlations (>0.97) between the predicted GEBVs using the actual 60 K SNP genotypes and the imputed 60 K SNP genotypes for all traits and breeds. The imputation accuracy was influenced by the reference population size as well as the amount of parental genotype information available in the reference population. However, parental genotype information became less important when the LD panel had at least 3000 SNPs. The correlation of the GEBVs directly increased with an increase in imputation accuracy. When genotype information for both parents was available, a panel of 300 SNPs (imputed to 60 K) yielded GEBV predictions highly correlated (⩾0.90) with genomic predictions obtained based on the true 60 K panel, for all traits and breeds. For a small reference population size with no parents on reference population, it is recommended the use of a panel at least as dense as the LD3K and, when there are two parents in the reference population, a panel as small as the LD300 might be a feasible option. These findings are of great importance for the development of LD panels for swine in order to reduce genotyping costs, increase the uptake of GS and, therefore, optimize the profitability of the swine industry.

This study investigated the potential application of genomic selection under a multi-breed scheme in the Spanish autochthonous beef cattle populations using a simulation study that replicates the structure of linkage disequilibrium obtained from a sample of 25 triplets of sire/dam/offspring per population and using the BovineHD Beadchip. Purebred and combined reference sets were used for the genomic evaluation and several scenarios of different genetic architecture of the trait were investigated. The single-breed evaluations yielded the highest within-breed accuracies. Across breed accuracies were found low but positive on average confirming the genetic connectedness between the populations. If the same genotyping effort is split in several populations, the accuracies were lower when compared with single-breed evaluation, but showed a small advantage over small-sized purebred reference sets over the accuracies of subsequent generations. Besides, the genetic architecture of the trait did not show any relevant effect on the accuracy with the exception of rare variants, which yielded slightly lower results and higher loss of predictive ability over the generations.

An isotope dose technique was utilized (i) to determine endogenous amino acid (AA) and protein losses and (ii) to propose adjusted values for AA requirements. The endogenous flow rate was calculated from the pool of enrichment in plasma AA, assuming similitude to enrichment of endogenous AA. In experiment 1, chicks were orally administered D4-lysine at 2% of estimated lysine intake from 16 to 24 days to find the isotopic steady state of the atom percent excess (APE) of lysine for plasma and jejunal and ileal digesta. The APE of D4-lysine in plasma, jejunal digesta and ileal digesta reached the isotopic steady state at 5.5, 3.4 and 2.0 days, respectively, by using the broken-line model. It was assumed that the isotopic steady state at 5 days identified for D4-lysine is also representative for the 15N-labeled AA. In experiment 2, chicks were fed diets from 1 to 21 days with increasing levels of fat (6%, 8%, 12%, 13% extract ether), protein (26%, 28.5%, 31% CP) or fiber (14%, 16%, 18% NDF) by adding poultry fat, soybean meal, blended animal protein or barley. Chicks were orally administered 15N-threonine, 15N-cysteine, 15N-methionine, 15N-lysine and 15N-leucine at 2% of estimated daily intake for 5 days from 17 to 21 days of age. Dietary nutrients influenced endogenous losses (EL), where dietary fat stimulated EL of lysine (P=0.06), leucine and protein (P=0.07); dietary protein enhanced EL of leucine and protein; and finally the dietary fiber increased EL of leucine. Dietary nutrients also affected apparent ileal digestibility (AID). Dietary fat increased AID of cysteine but decreased AID of lysine. Dietary protein reduced AID of protein, threonine, lysine and leucine, and similarly dietary fiber decreased AID of protein, threonine, methionine, lysine and leucine. In contrast, dietary fat or protein did not affect real ileal digestibility (RID) of protein and AA except threonine and leucine. The dietary fiber reduced the RID of protein, threonine and leucine. This indicate that variations of some endogenous AA and protein losses due to dietary nutrients almost eliminates the effects of RID, and thus the EL coming from the body should be utilized to adjust the AA requirement instead of changing the true digestible nutrients of ingredients. The present data suggest that 5 days’ feeding labeled AA was enough to reach the isotopic steady state and AA requirements should be adjusted when additional dietary protein, fat or fiber is fed.

Genetic improvement, without control of inbreeding, can go to loss of genetic variability, reducing the potential for genetic gains in the domestic populations. The aim of this study was to analyze the population structure and the inbreeding depression in Campolina horses. Phenotype information from 43 465 individuals was analyzed, data provided by the Campolina Breeders Association. A pedigree file containing 107 951 horses was used to connected the phenotyped individuals. The inbreeding coefficient was performed by use of the diagonal of the relationship matrix and the genealogical parameters were computed using proper softwares. The effective population size was estimated based on the rate of inbreeding and census information, and the stratification of the population was verified by the average relationship coefficient between animals born in different regions of Brazil. The effects of inbreeding on morphological traits were made by the use of inbreeding coefficient as a covariate in the model of random regression. The inbreeding coefficient increased from 1990 on, impacting effective population size and, consequently, shrinking genetic variability. The paternal inbreeding was greater than maternal, which may be attributed to the preference for inbred animals in reproduction. The average genetic relationship coefficient of animals born in different states was lower than individuals born within the same state. The increase in the inbreeding coefficient was negatively associated with all studied traits, showing the importance to avoid genetic losses in the long term. Although results do not indicate a severe narrowing of the population until the present date, the average relationship coefficient shows signs of increase, which could cause a drastic reduction in genetic variability if inbred mating is not successfully controlled in the Campolina horse population.

Despite single nucleotide polymorphism (SNP) availability and frequent cost reduction has allowed genome-wide association studies even in complex traits as tick resistance, the use of this information source in SNP by environment interaction context is unknown for many economically important traits in cattle. We aimed at identifying putative genomic regions explaining differences in tick resistance in Hereford and Braford cattle under SNP by environment point of view as well as to identify candidate genes derived from outliers/significant markers. The environment was defined as contemporary group means of tick counts, since they seemed to be the most appropriate entities to describe the environmental gradient in beef cattle. A total of 4363 animals having tick counts (n=10 673) originated from 197 sires and 3966 dams were used. Genotypes were acquired on 3591 of these cattle. From top 1% SNPs (410) having the greatest effects in each environment, 75 were consistently relevant in all environments, which indicated SNP by environment interaction. The outliers/significant SNPs were mapped on chromosomes 1, 2, 5, 6, 7, 9, 11, 13, 14, 15, 16, 18, 21, 23, 24, 26 and 28, and potential candidate genes were detected across environments. The presence of SNP by environment interaction for tick resistance indicates that genetic expression of resistance depends upon tick burden. Markers with major portion of genetic variance explained across environments appeared to be close to genes with different direct or indirect functions related to immune system, inflammatory process and mechanisms of tissue destruction/repair, such as energy metabolism and cell differentiation.

Genomic regions under high selective pressure present specific runs of homozygosity (ROH), which provide valuable information on the genetic mechanisms underlying the adaptation to environment imposed challenges. In broiler chickens, the adaptation to conventional production systems in tropical environments lead the animals with favorable genotypes to be naturally selected, increasing the frequency of these alleles in the next generations. In this study, ~1400 chickens from a paternal broiler line were genotyped with the 600 K Affymetrix® Axiom® high-density (HD) genotyping array for estimation of linkage disequilibrium (LD), effective population size (Ne), inbreeding and ROH. The average LD between adjacent single nucleotide polymorphisms (SNPs) in all autosomes was 0.37, and the LD decay was higher in microchromosomes followed by intermediate and macrochromosomes. The Ne of the ancestral population was high and declined over time maintaining a sufficient number of animals to keep the inbreeding coefficient of this population at low levels. The ROH analysis revealed genomic regions that harbor genes associated with homeostasis maintenance and immune system mechanisms, which may have been selected in response to heat stress. Our results give a comprehensive insight into the relationship between shared ROH regions and putative regions related to survival and production traits in a paternal broiler line selected for over 20 years. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the chicken genome.

Selection in native local breeds needs great carefulness due to the small population size and the risk of inbreeding. Furthermore, most breeds are dual-purpose, and milk and beef attitudes are antagonistic. For preservation purposes functional traits need to be considered. Focusing on the small local Rendena cattle, this study aimed to analyse the genetic correlations among milk, beef and udder health traits and the response to selection predicted under different scenarios. The study considered milk, fat and protein yields (MY), factor scores for udder volume (UV), conformation (UC) and muscularity obtained from type traits scored on primiparous cows, and performance test traits (PT) measured on young bulls at test station: average daily gain, in vivo SEUROP fleshiness, in vivo dressing percentage. Somatic cell score (SCS) was considered as a functional trait, with a possibility of restricting its genetic gain to zero. The study considered 281 497 MY test-day data collected on 16 974 cows, and data from linear type evaluation on 11 992 primiparous cows for factor scores. The PT data were recorded on 1428 young bulls, and SCS obtained from cell counts at milk recording. Bi-trait restricted maximum likelihood animal model analyses were performed to assess genetic parameters. Heritability varied from 0.157 (fat) to 0.442 (dressing percentage). Udder volume and MY resulted positively genetically correlated (average correlation 0.427), whereas the low-negative genetic correlation between MY and UC (−0.141) suggested a negative impact of milk gain on udder form. Beef traits of factor muscularity and PT showed medium-high favourable genetic correlations (from 0.357 to 0.984), excluding a null correlation between daily gain and muscularity. The genetic correlation MY v. muscularity was unfavourable (−0.328 on average), whereas null correlations were found in MY v. PT, apart from fat v. dressing percentage (−0.151). Somatic cell score showed low unfavourable correlations with protein (0.111) and UV (0.092), and favourable correlations with UC (−0.193). Response to selection in different scenarios indicated a good balanced gain for milk and beef when standardized economic weights of 0.66 and 0.34 are given to the two attitudes, and SCS genetic gain is restricted. Current genetic trends (MY and PT increasing, but muscularity lessening) reflect a stronger selection for milk, suggesting a slight progressive change towards a milk conformation. Aiming to preserve the dual-purpose characteristics of a breed, proper breeding policies taking into account the genetic relationships among traits and including functional traits should be applied in local dual-purpose populations.

Early detection of karyotype abnormalities, including aneuploidy, could aid producers in identifying animals which, for example, would not be suitable candidate parents. Genome-wide genetic marker data in the form of single nucleotide polymorphisms (SNPs) are now being routinely generated on animals. The objective of the present study was to describe the statistics that could be generated from the allele intensity values from such SNP data to diagnose karyotype abnormalities; of particular interest was whether detection of aneuploidy was possible with both commonly used genotyping platforms in agricultural species, namely the Applied BiosystemsTM AxiomTM and the Illumina platform. The hypothesis was tested using a case study of a set of dizygotic X-chromosome monosomy 53,X sheep twins. Genome-wide SNP data were available from the Illumina platform (11 082 autosomal and 191 X-chromosome SNPs) on 1848 male and 8954 female sheep and available from the AxiomTM platform (11 128 autosomal and 68 X-chromosome SNPs) on 383 female sheep. Genotype allele intensity values, either as their original raw values or transformed to logarithm intensity ratio (LRR), were used to accurately diagnose two dizygotic (i.e. fraternal) twin 53,X sheep, both of which received their single X chromosome from their sire. This is the first reported case of 53,X dizygotic twins in any species. Relative to the X-chromosome SNP genotype mean allele intensity values of normal females, the mean allele intensity value of SNP genotypes on the X chromosome of the two females monosomic for the X chromosome was 7.45 to 12.4 standard deviations less, and were easily detectable using either the AxiomTM or Illumina genotype platform; the next lowest mean allele intensity value of a female was 4.71 or 3.3 standard deviations less than the population mean depending on the platform used. Both 53,X females could also be detected based on the genotype LRR although this was more easily detectable when comparing the mean LRR of the X chromosome of each female to the mean LRR of their respective autosomes. On autopsy, the ovaries of the two sheep were small for their age and evidence of prior ovulation was not appreciated. In both sheep, the density of primordial follicles in the ovarian cortex was lower than normally found in ovine ovaries and primary follicle development was not observed. Mammary gland development was very limited. Results substantiate previous studies in other species that aneuploidy can be readily detected using SNP genotype allele intensity values generally already available, and the approach proposed in the present study was agnostic to genotype platform.

Livestock guarding dogs are a valuable adjunct to the pastoral community. Having been traditionally selected for their working ability, they fulfil their function with minimal interaction or command from their human owners. In this study, the population structure and the genetic differentiation of three Italian livestock guardian breeds (Sila’s Dog, Maremma and Abruzzese Sheepdog and Mannara’s Dog) and three functionally and physically similar breeds (Cane Corso, Central Asian Shepherd Dog and Caucasian Shepherd Dog), totalling 179 dogs unrelated at the second generation, were investigated with 18 autosomal microsatellite markers. Values for the number of alleles per locus, observed and expected heterozygosity, Hardy–Weinberg Equilibrium, F stats, Nei’s and Reynold’s genetic distances, clustering and sub-population formation abilities and individual genetic structures were calculated. Our results show clear breed differentiation, whereby all the considered breeds show reasonable genetic variability despite small population sizes and variable selection schemes. These results provide meaningful data to stakeholders in specific breed and environmental conservation programmes.

Feed efficiency traits (FETs) are important economic indicators in poultry production. Because feed intake (FI) is a time-dependent variable, longitudinal models can provide insights into the genetic basis of FET variation over time. It is expected that the application of longitudinal models as part of genome-wide association (GWA) and genomic selection (i.e. genome-wide selection (GS)) studies will lead to an increase in accuracy of selection. Thus, the objectives of this study were to evaluate the accuracy of estimated breeding values (EBVs) based on pedigree as well as high-density single nucleotide polymorphism (SNP) genotypes, and to conduct a GWA study on longitudinal FI and residual feed intake (RFI) in a total of 312 chickens with phenotype and genotype in the F2 population. The GWA and GS studies reported in this paper were conducted using β-spline random regression models for FI and RFI traits in a chicken F2 population, with FI and BW recorded for each bird weekly between 2 and 10 weeks of age. A single SNP regression approach was used on spline coefficients for weekly FI and RFI traits, with results showing that two significant SNPs for FI occur in the synuclein (SNCAIP) gene. Results also show that these regions are significantly associated with the spline coefficients (q2) for 5- and 6-week-old birds, while GWA study results showed no SNP association with RFI in F2 chickens. Estimated breeding value predictions obtained using a pedigree-based best linear unbiased prediction (ABLUP) model were then compared with predictions based on genomic best linear unbiased prediction (GBLUP). The accuracy was measured as correlation between genomic EBV and EBV with the phenotypic value corrected for fixed effects divided by the square root of heritability. The regression of observed on predicted values was used to estimate bias of methods. Results show that prediction accuracies using GBLUP and ABLUP for the FI measured from 2nd to 10th week were between 0.06 and 0.46 and 0.03 and 0.37, respectively. These results demonstrate that genomic methods are able to increase the accuracy of predicted breeding values at later ages on the basis of both traits, and indicate that use of a longitudinal model can improve selection accuracy for the trajectory of traits in F2 chickens when compared with conventional methods.

Buffalo (Bubalus bubalis) is an important livestock species in many tropical and subtropical regions. In recent decades, the interest in buffalo’s milk have expanded and intensive buffalo farms start to emerge. However, breeding programs and population genetics information for this species is scarce or inexistent. The present study aims to test the suitability of the commercial high-density single nucleotide polymorphisms (SNP) genotyping panel, the Illumina BovineHD BeadChip, to estimate population genetics parameters, pedigree control and identification of common variants in major production candidate genes. From a total of 777 962 SNPs included in the panel, 20 479 were polymorphic in water buffalo at a call rate of 86% and an average expected heterozygosity (HE) of 0.306. From these, 357 were mapped within or around the flanking regions of several major candidate genes. A principal components analysis identified three different clusters, each representing pure swamp buffalo type, pure river buffalo type and admixed river buffalo. The hybrids between swamp and river buffalo were clearly identified as an intermediary cluster. The suitability of these SNPs data set for parentage and identity testing demonstrated that the combination of just 30 to 50 SNPs were enough to attain high probabilities of parentage exclusion (0.9999) in both types and identity (2.3×10−5 and 2.0×10−7) for river and swamp buffalo, respectively. Our analysis confirms the suitability of the BovineHD BeadChip to assess population structure, hybridization and identity of the water buffalo populations.

This experiment evaluated the impacts of supplementing a yeast-derived product (Celmanax; Church & Dwight Co., Inc., Princeton, NJ, USA) on productive and health responses of beef steers, and was divided into a preconditioning (days 4 to 30) and feedlot receiving phase (days 31 to 69). In all, 84 Angus × Hereford steers were weaned on day 0 (BW=245±2 kg; age=186±2 days), and maintained in a single group from days 0 to 3. On day 4, steers were allocated according to weaning BW and age to a 21-pen drylot (4 steers/pen). Pens were randomly assigned to (n=7 pens/treatment): (1) no Celmanax supplementation during the study, (2) Celmanax supplementation (14 g/steer daily; as-fed) from days 14 to 69 or (3) Celmanax supplementation (14 g/steer daily; as-fed) from days 31 to 69. Steers had free-choice access to grass-alfalfa hay, and were also offered a corn-based concentrate beginning on day 14. Celmanax was mixed daily with the concentrate. On day 30, steers were road-transported for 1500 km (24 h). On day 31, steers returned to their original pens for the 38-day feedlot receiving. Shrunk BW was recorded on days 4, 31 and 70. Feed intake was evaluated daily (days 14 to 69). Steers were observed daily (days 4 to 69) for bovine respiratory disease (BRD) signs. Blood samples were collected on days 14, 30, 31, 33, 35, 40, 45, 54 and 69, and analyzed for plasma cortisol, haptoglobin, IGF-I, and serum fatty acids. Preconditioning results were analyzed by comparing pens that received (CELM) or not (CONPC) Celmanax during the preconditioning phase. Feedlot receiving results were analyzed by comparing pens that received Celmanax from days 14 to 69 (CELPREC), days 31 to 69 (CELRECV) or no Celmanax supplementation (CON). During preconditioning, BRD incidence was less (P=0.03) in CELM v. CONPC. During feedlot receiving, average daily gain (ADG) (P=0.07) and feed efficiency (P=0.08) tended to be greater in CELPREC and CELRECV v. CON, whereas dry matter intake was similar (P⩾0.29) among treatments. No other treatment effects were detected (P⩾0.20). Collectively, Celmanax supplementation reduced BRD incidence during the 30-day preconditioning. Moreover, supplementing Celmanax tended to improve ADG and feed efficiency during the 38-day feedlot receiving, independently of whether supplementation began during preconditioning or after feedlot entry. These results suggest that Celmanax supplementation benefits preconditioning health and feedlot receiving performance in beef cattle.

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.