The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data.

BACKGROUND: Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. METHODS: Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright's F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations. RESULTS: The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs. CONCLUSION: African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations.

Genetic evaluation of test-day milk yields from smallholder dairy production systems in Kenya using genomic relationships.

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.

How many markers are enough? Factors influencing parentage testing in different livestock populations.

Reliability of parentage test panels is usually based on its power to exclude wrong parentage assignments based on allele frequencies. We evaluated the rates of false exclusions and inclusions in parentage assignments, and how these results are affected by allele frequencies, panel sizes and the number of allowed mismatches. We also evaluated the reliability of parentage testing by comparing populations with distinct genetic backgrounds using pure and composite families of cattle and sheep. Allowing for 1% genotype mismatches in true parent-offspring relations provided the best compromise between false-positive and false-negative assignments. Pure breeds needed at least 200-210 single-nucleotide polymorphism (SNP) markers to correctly assign relations, but between 700 and 890 markers to avoid assigning incorrect relationships. Composite breeds needed between 220 (sheep) and 500 (cattle) markers for correct assignment; 680 (cattle) to 4400 (sheep) SNPs were needed to eliminate false-positive assignments. Allowing 0% genotype mismatches decreased false-positive but increased false-negative assignments, whilst a higher threshold of 2% showed the opposite effects. Panels with high minor allele frequencies (0.35-0.45) provided the best chance for correct parentage resolutions requiring fewer markers. Further, we propose that a dynamic threshold would allow adapting to population specific error rates. A comparison to the performance of the official International Society for Animal Genetics SNP panel for cattle and a recently published SNP panel for sheep showed that randomly selected markers performed only slightly worse for the applied parentage test based on opposing homozygotes. This suggests that even with carefully selected panels, only marginal assignment improvements are obtainable for a particular number of SNPs. The main point for improvement is the number of markers used. We recommend using at least 200 SNP markers for parentage testing if the aim is to reduce false-negative results. To fully exclude false positives at least 700 markers are required.

Performance of different SNP panels for parentage testing in two East Asian cattle breeds.

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.

Genomewide study and validation of markers associated with production traits in German Landrace boars.

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 cm(2), P < 0.0001; validation study: 0.35 cm(2), 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.

Characterization of CD4+ subpopulations and CD25+ cells in ileal lymphatic tissue of weaned piglets infected with Salmonella Typhimurium with or without Enterococus faecium feeding.

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.

Genome-wide associations for investigating time-dependent genetic effects for milk production traits in dairy cattle.

Phenotypic variation in milk production traits has been described over the course of a lactation as well as between different parities. The objective of this study was to investigate whether variation in production is affected by different loci across lactations. A genome-wide association study (GWAS) using a 50-k SNP chip was conducted in 152 divergent German Holstein Friesian cows to test for association with milk production traits over different lactations. The first four lactations were analysed regarding milk yield, fat, protein, lactose, milk urea nitrogen yield and content as well as somatic cell score. Two approaches were used: (i) Wilmink curve parameters were used to assess the genetic effects over the course of a lactation and (ii) test-day yield deviations (YD) were used as a normative approach for a GWAS. The significant effects were largest for markers affecting curve parameters for which there was a statistical power <0.8 of detection even in this small design. While significant markers for YDs were detected in this study, the power to detect effects of a similar magnitude was only 0.11, suggesting that many loci may have been missed with this approach in the present design. Furthermore, all significant effects were specific for a single lactation, leading to the conclusion that the variance explained by a certain locus changes from lactation to lactation. We confirm the common evidence that most production traits vary in the degree of persistency after the peak as a result of genetic influence.

Lactation curve models for estimating gene effects over a timeline.

The effects of genes are commonly estimated using random regression models based on test-day data and only give a general gene effect. Alternatively, lactation curve models can be used to estimate biological and environmental effects, or to predict missing test-day data and perform breeding value estimation. This study combines lactation curve models and estimation of gene effects to represent gene effects in different stages of lactation. The lactation curve models used were based on the Wood, Wilmink, and Ali and Schaeffer models. A random regression test-day model was used to compare estimated gene effects with the results of commonly used models. The well-characterized DGAT1 gene with known effects on milk yield, milk fat, and milk protein production was chosen to test this new approach in a Holstein-Friesian dairy cattle population. The K232A polymorphism and the promoter VNTR (variable number of tandem repeats) of the DGAT1 gene were used. All lactation curve models predicted the production curves sufficiently. Nevertheless, for predicting genotype effects, the Wilmink curve indicated the closest fit to the data. This study shows that the characteristic gene effects for DGAT1 genotypes occur after lactation d 40, which might be explained by a link to other genes affecting metabolic traits. Furthermore, allele substitution effects of allele K of the K232A locus showed that the typical effect of low milk and protein yield is due mainly to a lower overall production level, whereas the higher fat and protein content is reached by increased production toward its peak and fat yield is increased because of a higher production after this peak. Predicting gene effects with production curves gives better insight into the timeline of gene effects. This can be used to form genetic groups, in addition to feeding groups, for managing livestock populations in a more effective way.