Efforts to improve dairy production in smallholder farming systems of East Africa over the past decade have had limited impact because of the lack of records on performance to guide targeted breeding programs. Estimates of genetic parameters in these systems are lacking. Using data generated through a project (“Germplasm for Dairy Development in East Africa”) in Kenya and a genomic relationship matrix from genotypic records, we examined the potential impact of different models handling contemporary groups or herd effects on estimates of genetic parameters using a fixed regression model (FRM) for test-day (TD) milk yields, and the covariance structure for TD milk yield at various stages of lactation for animals using a random regression model (RRM). Models in which herd groups were defined using production levels derived from the data fitted the data better than those in which herds were grouped depending on management practices or were random. Lactation curves obtained for animals under different production categories did not display the typical peak yield characteristic of improved dairy systems in developed countries. Heritability estimates for TD milk yields using the FRM varied greatly with the definition of contemporary herd groups, ranging from 0.05 ± 0.03 to 0.27 ± 0.05 (mean ± standard error). The analysis using the RRM fitted the data better than the FRM. The heritability estimates for specific TD yields obtained by the RRM were higher than those obtained by the FRM. Genetic correlations between TD yields were high and positive for measures within short consecutive intervals but decreased as the intervals between TD increased beyond 60 d and became negative with intervals of more than 5 mo. The magnitude of the genetic correlation estimates among TD records indicates that using TD milk records beyond a 60-d interval as repeated measures of the same trait for genetic evaluation of animals on smallholder farms would not be optimal. Although each individual smallholder farmer retains only a few animals, using the genomic relationship between animals to link the large number of farmers operating under specified environments provides a sufficiently large herd-group for which a breeding program could be developed.

The International Society for Animal Genetics (ISAG) proposed a panel of single nucleotide polymorphisms (SNPs) for parentage testing in cattle (a core panel of 100 SNPs and an additional list of 100 SNPs). However, markers specific to East Asian taurine cattle breeds were not included, and no information is available as to whether the ISAG panel performs adequately for these breeds. We tested ISAG's core (100 SNP) and full (200 SNP) panels on two East Asian taurine breeds: the Korean Hanwoo and the Japanese Wagyu, the latter from the Australian herd. Even though the power of exclusion was high at 0.99 for both ISAG panels, the core panel performed poorly with 3.01% false-positive assignments in the Hanwoo population and 3.57% in the Wagyu. The full ISAG panel identified all sire-offspring relations correctly in both populations with 0.02% of relations wrongly excluded in the Hanwoo population. Based on these results, we created and tested two population-specific marker panels: one for the Wagyu population, which showed no false-positive assignments with either 100 or 200 SNPs, and a second panel for the Hanwoo, which still had some false-positive assignments with 100 SNPs but no false positives using 200 SNPs. In conclusion, for parentage assignment in East Asian cattle breeds, only the full ISAG panel is adequate for parentage testing. If fewer markers should be used, it is advisable to use population-specific markers rather than the ISAG panel.

We present results from a genomewide association study (GWAS) and a single-marker association study. The GWAS was performed with the Illumina PorcineSNP60 BeadChip from which 5 markers were selected for a validation analysis. Genetic effects were estimated for feed intake, weight gain, and traits of fat and muscle tissue in German Landrace boars kept on performance test stations. The GWAS was performed in a population of 288 boars and the validation study for another 432 boars. No statistically significant effect was found in the GWAS after adjusting for multiple testing. Effects of 2 markers, which were significant genomewide before correction for multiple testing (P < 0.00005), could be confirmed in the validation study. The major allele of marker ALGA0056781 on SSC1 was positively associated with both higher weight gain and fat deposition. The effect on live-weight gain was 2.25 g/d in the GWAS (P=0.0003) and 3.73 g/d in the validation study (P=0.01) and for back fat thickness was 0.15 mm in the GWAS (P < 0.0001) and 0.20 mm in the validation study (P=0.02). The marker had similar effects on test-day weight gain (GWAS: 3.85 g/d, P=0.001; validation study: 6.80 g/d, P=0.003) and back fat area (GWAS: 0.27 ㎠ , P < 0.0001; validation study: 0.35 ㎠ , P=0.03). Marker ASGA0056782 on SSC13 was associated with live-weight gain. The major allele had negative effects in both studies (GWAS: -4.88 g/d, P < 0.0001; validation study: -3.75 g/d, P=0.02). The effects of these 2 markers would have been excluded based on the GWAS alone but were shown to be significantly trait associated in the validation study indicating a false-negative result. The G protein-coupled receptor 126 (GPR126) gene approximately 200 kb downstream of marker ALGA0001781 was shown to be associated with human height and therefore might explain the association with weight gain in pigs. Several traits were affected in an economically desired direction by the minor allele of the markers, pointing to the possibility of improvement through further selection.

African taurine cattle populations are widely distributed in humid and sub-humid zones of West and Central Africa. We assessed the genetic structure and differentiation within and across 8 African Bos taurus populations: 4 N’Dama populations (N’Dama, N’Dama1, N’Dama2, N’Dama3), Lagunaire, Lagune, Somba, and Baoule. A total of 38k autosomal SNPs were used for principal component analyses (PCA), estimation of pairwise FST values and within population heterozygosity (FIS), and neighbour-joining (NJ) tree construction. The first PC clearly differentiated Lagune and Lagunaire from N’Dama; PC2 separated Lagunaire, Lagune and one N’Dama population from the rest of taurine breeds; and PC3 separated N’Dama3 from Somba and Baoule. Estimates of pairwise FST values among the majority of populations ranged from 0.03 to 0.149, indicating low to moderate genetic differentiations, while a high genetic divergence between N’Dama3 and Lagune (FST =0.178), and N’Dama3 and Lagunaire (FST =0.168) was observed. No genetic subdivision was found between N’Dama and N’Dama1, and Lagune and Lagunaire. A higher heterozygosity (FIS value from -0.011 to 0.025) was found in N’Dama, N’Dama1, N’Dama2, Lagune, Lagunaire, and Baoule breeds. The NJ tree clearly separated Lagune and Lagunaire as well as Somba and Baoule with a 100% and around 31% bootstrap value, respectively, from the other taurine populations. We highlighted that African taurine populations are diverse and genetic differences between sampling locations exists even within a breed. Therefore, choice of an African taurine breed to anchor African indigenous breeds should be carefully considered.

Background: This study focused on the dynamics of genome-wide effects on five milk production and eight fertility traits as well as genetic correlations between the traits. For 2,405 Holstein Friesian bulls, estimated breeding values (EBVs) were used. The production traits were additionally assessed in 10-day intervals over the first 60 lactation days, as this stage is physiologically the most crucial time in milk production. Results: SNPs significantly affecting the EBVs of the production traits could be separated into three groups according to the development of the size of allele effects over time: 1) increasing effects for all traits; 2) decreasing effects for all traits; and 3) increasing effects for all traits except fat yield. Most of the significant markers were found within 22 haplotypes spanning on average 135,338 bp. The DGAT1 region showed high density of significant markers, and thus, haplotype blocks. Further functional candidate genes are proposed for haplotype blocks of significant SNPs (KLHL8, SICLEC12, AGPAT6 and NID1). Negative genetic correlations were found between yield and fertility traits, whilst content traits showed positive correlations with some fertility traits. Genetic correlations became stronger with progressing lactation. When correlations were estimated within genotype classes, correlations were on average 0.1 units weaker between production and fertility traits when the yield increasing allele was present in the genotype. Conclusions: This study provides insight into the expression of genetic effects during early lactation and suggests possible biological explanations for the presented time-dependent effects. Even though only three markers were found with effects on fertility, the direction of genetic correlations within genotype classes between production and fertility traits suggests that alleles increasing the milk production do not affect fertility in a more negative way compared to the decreasing allele.

The aim of the present study was to test the effect of Enterococcus faecium NCIMB 10415 (E. faecium) on CD4+ T helper immune cell subpopulations and CD25+ cells in ileal lymphatic tissue after challenge with Salmonella (S.) Typhimurium DT 104. German Landrace piglets treated with E. faecium (n = 16) as a feed additive and untreated controls (n = 16) were challenged with S. Typhimurium 10 days after weaning. The expression of lineage specific T helper cell subtype master transcription factors on mRNA level was measured in the whole tissue of the gut associated lymphoid tissues (ileocecal mesenteric lymph node, ileum with Peyer’s patches and papilla ilealis) and in magnetically sorted T helper cells from blood and ileocecal mesenteric lymph nodes at two and 28 days post infection. CD25 protein expression of T helper cells was studied by flow cytometry in ileal Peyer’s patches, lymph nodes and blood. Distribution and morphology of CD25+ cells was demonstrated in situ by immunohistochemistry in paraffin embedded specimens of the ileum and the ileocecal mesenteric lymph nodes. The data provide evidence for a higher T helper 2 cell driven immune response in the control group compared to the E. faecium treated group (P < 0.05) in CD4+ magnetically sorted lymphocytes from the ileocecal mesenteric lymph nodes at two and 28 days post infection. We did not observe differences for CD25+ cells in immunohistochemistry and flow cytometry between E. faecium fed pigs and the control group, but provided a detailed description of the occurrence and morphology of these cells in the gut associate lymphoid tissues of piglets. In conclusion we suggest that (i) prolonged feeding with E. faecium can result in changes of the T helper cell response leading to a stronger infection with S. Typhimurium and (ii) that it is important to examine purified immune cells to be able to detect effects on T helper cell subpopulations.

Iranian cattle breeds are currently under-represented in studies regarding genetic variability and conservation effort even though they are settled in a region that is believed to be one of two ancient cattle domestication centres. This study provides first population genetic parameters for eight Iranian cattle breeds collected from across the entire country to highlight the necessity for conservation programs. High density genome-wide SNP chips were used. None of the Iranian breeds showed a decreased heterozygosity compared to outgroup breeds (Holstein, Jersey, and Brahman) and inbreeding coefficients were low. Nevertheless, estimated effective population sizes were <10 for the Mazandarani, Sarabi, and Kermani breeds and it is predicted that most of the genetic variability will be lost within 20-30 generations if no intervention measures are taken. Effective population size estimates varied between chromosomes with occasional extremely high values, especially for Najdi, Pars, and Kermani which have high proportions of indicine ancestry as represented by the Brahman outgroup.

Genetic diversity and breed proportions of Indian stud cattle India is the world's leading milk producer, however, average milk yield per animal is low. Most of India's cattle milk is produced by indigenous breeds, followed by crossbred cows. Crossbreeding intensified in the 1960s and 70s with a large influx of Holstein Friesian and Jersey bulls, and an increased use of artificial insemination. Based on genotypes generated from the 50K v2 BovineHD BeadChip assay, we analysed the genetic diversity and breed composition of 242 breeding cattle sampled from the BAIF breed herds, including indigenous, exotic dairy, and crossbred animals. We compared these animals to indigenous and animals used in smallholder systems in East Africa. Key findings were: confirmation that Indian Zebu breeds are pure Bos indicus in contrast to African Zebu and Sanga breeds, which are admixtures of Bos indicus and African Bos taurus; as found elsewhere, many apparently pure animals contain some admixture from imported breeds; crossbred animals exhibit a wider range of breed composition than intended, reflecting the lack of pedigree when sampling bull mothers from smallholder farms; breed composition of purebred and crossbred animals can in future be tested using SNP data, and only those meeting the desired composition retained for breeding.

Korean Hanwoo cattle have been subjected to intensive artificial selection over the past four decades to improve meat production traits. Another three cattle varieties very closely related to Hanwoo reside in Korea (Jeju Black and Brindle) and in China (Yanbian). These breeds have not been part of a breeding scheme to improve production traits. Here, we compare the selected Hanwoo against these similar but presumed to be unselected populations to identify genomic regions that have been under recent selection pressure due to the breeding program. Rsb statistics were used to contrast the genomes of Hanwoo versus a pooled sample of the three unselected population (UN). We identified 37 significant SNPs (FDR corrected) in the HW/UN comparison and 21 known protein coding genes were within 1 MB to the identified SNPs. These genes were previously reported to affect traits important for meat production (14 genes), reproduction including mammary gland development (3 genes), coat color (2 genes), and genes affecting behavioral traits in a broader sense (2 genes). We subsequently sequenced (Illumina HiSeq 2000 platform) 10 individuals of the brown Hanwoo and the Chinese Yanbian to identify SNPs within the candidate genomic regions. Based on allele frequency differences, haplotype structures, and literature research, we singled out one non-synonymous SNP in the APP gene (APP: c.569C>T, Ala199Val) and predicted the mutational effect on the protein structure. We found that protein-protein interactions might be impaired due to increased exposed hydrophobic surfaces of the mutated protein. The APP gene has also been reported to affect meat tenderness in pigs and obesity in humans. Meat tenderness has been linked to intramuscular fat content, which is one of the main breeding goals for brown Hanwoo, potentially supporting a causal influence of the herein described nsSNP in the APP gene.

The aims of this study were to estimate the genotype and allele frequencies and genotype effects located in the Acyl-CoA: diacylglycerol acyltransferase 1 (DGAT1), Leptin (Lep/ob),Growth hormone receptor (GHR), Prolactin receptor (PRLR), and Kappa casein (CSN3) genes on milk yield, composition and somatic cell score (SCS) in German Holstein cows. The association analyses were based on data from 1380 German Holstein cows. The allele frequencies of the DGAT1 K232A were 44.2% and 55.8% for the Lysine and Alanine variant, respectively. The allele substitution effect for the Lysine variant was significantly increased the fat (0.30%, p < 0.0001), protein (0.08%, p < 0.0001) and casein contents (0.06%, p < 0.0001) and fat yield (9.13 kg, p < 0.0001). In contrast, the effect was negative on milk yield (-372.77 kg, p < 0.0001), protein yield (-6.32 kg, p < 0.0001), and lactose yield (-0.05 kg, p < 0.0001). With respect to the Mbo1-RFLP in the Lep gene, the allele A was the major allele with a frequency of 90.3%. The substitution effect of the minor allele B had a significant influence on fat yield (6.3 kg, p < 0.05). The frequency of the Phenylalanine allele of the GHR F279Y polymorphism was 83%. The allele substitution effect of the minor Tyrosine variant was 320 kg (p < 0.0001), 0.02 kg (p < 0.05), 0.07 kg (p < 0.0001), and 0.03% (p < 0.05) for milk, casein, and lactose yields, and lactose content, respectively. Negative effects were evident for fat (-0.12%, p < 0.0001), protein (-0.09%, p < 0.0001) and casein (-0.07%, p < 0.0001) contents. The Tyrosine variant of GHR F279Y was associated with lower SCS (p <0.05). For the PRLR S18N polymorphism, Serine was the major allele (76.7%). The Asparagine variant had a significant (p < 0.05) effect on the casein content (0.02%). For the CSN3 gene locus, the allele encoding the protein variant A was higher frequent (85.1%) and the minor Allele B was associated with protein (0.03%, p < 0.05) and casein contents (0.03%, p < 0.05). This study demonstrated that power of candidate gene analyses. The gene effects are considered in genome wide genomic selection programs.