Prediction of key milk biomarkers in dairy cows through milk mid-infrared spectra and international collaborations

At the individual cow level, suboptimum fertility, mastitis, negative energy balance, and ketosis are major issues in dairy farming. These problems are widespread on dairy farms and have an important economic impact. The objectives of this study were (1) to assess the potential of milk mid-infrared (MIR) spectra to predict key biomarkers of energy deficit (citrate, isocitrate, glucose-6 phosphate [glucose-6P], free glucose), ketosis (β-hydroxybutyrate [BHB] and acetone), mastitis (N-acetyl-β-d-glucosaminidase activity [NAGase] and lactate dehydrogenase), and fertility (progesterone); (2) to test alternative methodologies to partial least squares (PLS) regression to better account for the specific asymmetric distribution of the biomarkers; and (3) to create robust models by merging large datasets from 5 international or national projects. Benefiting from this international collaboration, the dataset comprised a total of 9,143 milk samples from 3,758 cows located in 589 herds across 10 countries and represented 7 breeds. The samples were analyzed by reference chemistry for biomarker contents, whereas the MIR analyses were performed on 30 instruments from different models and brands, with spectra harmonized into a common format. Four quantitative methodologies were evaluated to address the strongly skewed distribution of some biomarkers. Partial least squares regression was used as the reference basis, and compared with a random modification of distribution associated with PLS (random-downsampling-PLS), an optimized modification of distribution associated with PLS (KennardStone-downsampling-PLS), and support vector machine (SVM). When the ability of MIR to predict biomarkers was too low for quantification, different qualitative methodologies were tested to discriminate low versus high values of biomarkers. For each biomarker, 20% of the herds were randomly removed within all countries to be used as the validation dataset. The remaining 80% of herds were used as the calibration dataset. In calibration, the 3 alternative methodologies outperform the PLS performances for the majority of biomarkers. However, in the external herd validation, PLS provided the best results for isocitrate, glucose-6P, free glucose, and lactate dehydrogenase (coefficient of determination in external herd validation [R2v] = 0.48, 0.58, 0.28, and 0.24, respectively). For other molecules, PLS-random-downsampling and PLS-KennardStone-downsampling outperformed PLS in the majority of cases, but the best results were provided by SVM for citrate, BHB, acetone, NAGase, and progesterone (R2v = 0.94, 0.58, 0.76, 0.68, and 0.15, respectively). Hence, PLS and SVM based on the entire dataset provided the best results for normal and skewed distributions, respectively. Complementary to the quantitative methods, the qualitative discriminant models enabled the discrimination of high and low values for BHB, acetone, and NAGase with a global accuracy around 90%, and glucose-6P with an accuracy of 83%. In conclusion, MIR spectra of milk can enable quantitative screening of citrate as a biomarker of energy deficit and discrimination of low and high values of BHB, acetone, and NAGase, as biomarkers of ketosis and mastitis. Finally, progesterone could not be predicted with sufficient accuracy from milk MIR spectra to be further considered. Consequently, MIR spectrometry can bring valuable information regarding the occurrence of energy deficit, ketosis, and mastitis in dairy cows, which in turn have major influences on their fertility and survival.

Genome-wide SNP analysis clearly distinguished the Belarusian Red cattle from other European cattle breeds

Local breeds can serve as an important source of genetic variability in domestic animal species. This study aimed to assess the genetic diversity and population structure of Belarusian Red cattle and their differentiation from other European cattle populations based on genome-wide SNP genotypes. Twenty pedigree-recorded non-closely related cows of Belarusian Red cattle were genotyped using the Illumina BovineHD BeadChip. Genotypes of 22 other European cattle breeds were included in the study for comparison. A total of 28 562 SNPs passed through the quality control checks and were selected for analysis. The Belarusian Red cattle displayed a moderate level of genetic variability (_U H_E  = 0.341, H_O  = 0.368), and the highest heterozygote excess (_U F_IS  = -0.066), among the studied breeds; this reflects the contribution of multiple breeds to their formation. The principal component analysis, F_ST -based Neighbor-Net tree and Admixture clustering, clearly distinguished the Belarusian Red cattle from the other European cattle breeds. Moreover, the presence of ancestral genomic components of Danish Red and Brown Swiss breeds were clearly visible, which agrees with the breed's history and its recent development. Our study highlights the importance of maintaining the specific genomic components, which makes a significant contribution to the global genetic diversity in the modern population of Belarusian Red cattle, allowing us to consider them a valuable national genetic resource. Our research results will be useful for the development of conservation programs for this local cattle breed.

From farmers to livestock keepers: a typology of cattle production systems in south-western Burkina Faso

Cattle production is an essential livelihood strategy in south-western Burkina Faso. Although having a distinct cultural role and known to be resistant against African animal trypanosomosis, the Lobi taurine cattle breed is endangered due to its low market value. As the first step in preservation efforts, our study aimed to develop a typology of production systems at the farm level. We used a structured questionnaire and focus group discussions for collecting data on household characteristics, socioeconomic activities, livestock, and access to services. The sample comprised 169 households in three communities. The analytical strategy included factor analysis of mixed data and hierarchical clustering. We identified four distinct types of cattle production systems: (1) sedentary Lobi farms, (2) sedentary crossbreed farms, (3) semi-transhumant Fulani zebu farms, and (4) transhumant Fulani zebu farms. Significant factors in developing this typology were the farmers’ ethnic group, crop diversity, cattle herd size, cattle herd composition, number of small ruminants, and livestock management strategies. Across all production systems, men were considered being primary decision-makers in cattle production, with women, herders, and children being responsible for specific tasks. All identified production systems are increasingly confronting disease pressure and scarcity of water and land. Future efforts in preservation and breeding will need to respond to these trends in the agroecosystem, integrate risk management measures, and resonate with the specific needs of the different household members involved in cattle rearing.

Evaluation of increased feed supply and different fattening strategies for an Ethiopian sheep population by system dynamics modelling

Context The productivity of Ethiopian smallholder farms is considered to be low owing to different factors such as feed shortage, lack of breeding strategies, disease prevalence and missing marketing strategies. Aim The main objective of the study was to develop a dynamic, stochastic herd model by adopting system dynamic modelling methodology for evaluation of the effect of increased feed availability (forage production) in combination with different fattening strategies on herd dynamics and profitability of an Ethiopian sheep population. Methods Forage production utilising part of smallholder farmers’ cropland was built into a dynamic simulation model. Two alternative feed-supply systems were evaluated: turning 25% and 50% of the current cropland into area used for forage production. The simulation period was 20 years, the first 10 years representing the baseline fattening scenario (culled rams fattened). For the last 10 years, genetic selection was introduced and two scenarios were evaluated: fattening of culled rams (Scenario I) and fattening of young rams (Scenario II). Key results Increasing the feed supply resulted in an increase to the herd size when the model balanced dry matter supply and demand of the herd. Fattening of young rams (Scenario II) with genetic selection was significantly more profitable than the baseline and Scenario I in both of the simulated alternative feed-supply systems. This can be used for regular cash generation, which might reduce disposal of animals at lower price in cases of need for emergency cash. Conclusions Overall, the simulation model demonstrates that production of improved forage crops should be combined with selective breeding and an appropriate finishing strategy. The competition for resources (land and labour) with crop production, forage seed shortage and extended family size are other challenges raised by smallholder farmers for the feasibility of the two alternative feed-supply systems.

Association of missense variants in GDF9 with litter size in Entlebucher Mountain dogs

In the past two decades, average litter size (ALS) in Entlebucher Mountain dogs decreased by approximately 0.8 puppies. We conducted a GWAS for ALS using the single-step methodology to take advantage of 1632 pedigree records, 892 phenotypes and 372 genotypes (173 662 markers) for which only 12% of the dogs had both phenotypes and genotypes available. Our analysis revealed associations towards the growth differentiation factor 9 gene (GDF9), which is known to regulate oocyte maturation. The trait heritability was estimated at 43.1%, from which approximately 15% was accountable by the GDF9 locus alone. Therefore, markers flanking GDF9 explained approximately 6.5% of the variance in ALS. Analysis of WGSs revealed two missense substitutions in GDF9, one of which (g.11:21147009G>A) affected a highly conserved nucleotide in vertebrates. The derived allele A was validated in 111 dogs and shown to be associated with decreased ALS (-0.75 ± 0.22 puppies per litter). The variant was further predicted to cause a proline to serine substitution. The affected residue was immediately followed by a six-residue deletion that is fixed in the canine species but absent in non-canids. We further confirmed that the deletion is prevalent in the Canidae family by sequencing three species of wild canids. Since canids uniquely ovulate oocytes at the prophase stage of the first meiotic division, requiring maturation in the oviduct, we conjecture that the amino acid substitution and the six-residue deletion of GDF9 may serve as a model for insights into the dynamics of oocyte maturation in canids.

Genome-wide mapping of the dominance effects based on breed ancestry for semen traits in admixed Swiss Fleckvieh bulls

Heterosis is the beneficial deviation of crossbred progeny from the average of parental lines for a particular trait. Heterosis is due to nonadditive genetic effects with dominance and epistatic components. Recent advances in genotyping technology have encouraged researchers to estimate and scan heterosis components for a range of traits in crossbred populations, applying various definitions of such components. In this study, we defined the intralocus (dominance) component of heterosis using local genetic ancestry and performed genome-wide association analysis for admixed Swiss Fleckvieh bulls and their parental populations, Red Holstein Friesian and Swiss Simmental, for semen traits. A linear mixed model for 41,824 SNP, including SNP additive genetic, breed additive, and breed dominance effects on 1,178 bulls (148 Red Holstein Friesian, 213 Swiss Simmental, and 817 Swiss Fleckvieh) with a total of 43,782 measurements was performed. In total, 19 significant regions for breed dominance were identified for volume (2 regions on Bos taurus autosome 10 and 22) and percentage of live spermatozoa (17 regions on Bos taurus autosome 3, 4, 5, 7, 13, 14, and 17), and genes associated with spermatogenesis, sperm motility, and male fertility traits were located there. No significant region for breed dominance was detected for total number of spermatozoa. The signals for breed dominance were relatively wide, most likely due to limited numbers of recombination events in a small number of generations (10-15 generations) of crossbreeding in the recent Swiss Fleckvieh composite.

Genome-wide association study and heritability estimate for ectopic ureters in Entlebucher mountain dogs

An ectopic ureter is a congenital anomaly which may lead to urinary incontinence and without a surgical intervention even to end-stage kidney disease. A genetic component contributes to the development of this anomaly in Entlebucher mountain dogs (EMD); however, its nature remains unclear. Using the Illumina CanineHD bead chip, a case-control genome-wide association study was performed to identify SNPs associated with the trait. Six loci on canine chromosomes 3, 17, 27 and 30 were identified with 16 significantly associated SNPs. There was no single outstanding SNP associated with the phenotype, and the association signals were not close to known genes involved in human congenital anomalies of the kidney or lower urinary tract. Additional research will be necessary to elucidate the potential role of the associated genes in the development of ectopic ureters in the EMD breed.

Effects of breed proportion and components of heterosis for semen traits in a composite cattle breed

The aim of this study was to estimate the non-additive genetic effects of the dominance component of heterosis as well as epistatic loss on semen traits in admixed Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF) cattle. Heterosis is the additional gain in productivity or fitness of cross-bred progeny over the mid-purebred parental populations. Intralocus gene interaction usually has a positive effect, while epistatic loss generally reduces productivity or fitness due to lack of evolutionarily established interactions of genes from different breeds. Genotypic data on 38,205 SNP of 818 admixed, as well as 148 RHF and 213 SI bulls as the parental breeds were used to predict breed origin of alleles. The genomewide locus-specific breed ancestries of individuals were used to calculate effects of breed difference as well as the dominance component of heterosis, while proxies for two definitions of epistatic loss were derived from 100,000 random pairs of loci. The average Holstein Friesian ancestry in admixed bulls was estimated 0.82. Results of fitting different linear mixed models showed including the dominance component of heterosis considerably improved the model adequacy for three of the four traits. Inclusion of epistatic loss increased the accuracy of the models only for our new definition of the epistatic effect for two traits, while the other definition was so highly correlated with the dominance component that statistical separation was impossible.

System dynamics modeling in designing breeding schemes: The case of Menz sheep in Ethiopian highlands

A comprehensive dynamic simulation model was developed to describe a community-based breeding program for the Menz sheep population of Ethiopia. Selection of male and female animals based on their own and maternal performance was simulated. The breeding goal traits were 6-mo weight, preweaning survival, and fertility rate. The model input data were obtained from the flock book, questionnaires, and references. The simulation model used a mix of deterministic and stochastic procedures to model the complex system. In the baseline scenario, the proportion of selected male and female animals varied between 20 and 30% and between 70 and 80%, respectively. A reasonable annual genetic gain was predicted for the breeding goal traits at the village level. For 6-mo weight and preweaning survival rate, the annual genetic gain varied from 0.213 to 0.214 kg and 0.255 to 0.256%, respectively. For fertility rate, an annual genetic gain of 0.063% was obtained. The predicted rate of inbreeding per year was between 0.094 and 0.116%. Furthermore, a scenario analysis was conducted by varying the proportions of selected animals. Annual genetic gains of 0.230 kg, 0.277%, and 0.069% were obtained for 6-mo weight, preweaning survival rate, and fertility rate, respectively, when the proportion of selected male and female animals decreased by 10%. The annual genetic gains decreased to 0.198 kg, 0.236%, and 0.059%, respectively, when the selection proportion of male and female animals increased by 10%. The lowest rate of inbreeding per year, ranging from 0.065 to 0.079%, was achieved when the selection proportion of selected male and female animals increased. The model is relevant for the step-by-step evaluation of more than one round of selection. It is flexible and usage driven. The model is a valuable tool to design different population structures and can be easily expanded to adopt different breeding strategies. Hence, the system dynamics modeling approach is a potential tool to describe complex breeding programs.

Whole genome SNP scanning of snow sheep (Ovis nivicola)

This is the first report performing the whole genome SNP scanning of snow sheep (Ovis nivicola). Samples of snow sheep (n = 18) collected in six different regions of the Republic of Sakha (Yakutia) from 64° to 71° N. For SNP genotyping, we applied Ovine 50K SNP BeadChip (Illumina, United States), designed for domestic sheep. The total number of genotyped SNPs (call rate 90%) was 47796 (88.1% of total SNPs), wherein 1006 SNPs were polymorphic (2.1%). Principal component analysis (PCA) showed the clear differentiation within the species O. nivicola: studied individuals were distributed among five distinct arrays corresponding to the geographical locations of sampling points. Our results demonstrate that the DNA chip designed for domestic sheep can be successfully used to study the allele pool and the genetic structure of snow sheep populations.

Locus-specific ancestry to detect recent response to selection in admixed Swiss Fleckvieh cattle

Identification of selection signatures is one of the current endeavors of evolutionary genetics. Admixed populations may be used to infer post-admixture selection. We calculated local ancestry for Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF), to infer such signals. Illumina Bovine SNP50 BeadChip data for 300 admixed, 88 SI and 97 RHF bulls were used. The average RHF ancestry across the whole genome was 0.70. To identify regions with high deviation from average, we considered two significance thresholds, based on a permutation test and extreme deviation from normal distribution. Regions on chromosomes 13 (46.3-47.3 Mb) and 18 (18.7-25.9 Mb) passed both thresholds in the direction of increased SI. Extended haplotype homozygosity within (iHS) and between (Rsb) populations was calculated to explore additional patterns of pre- and post-admixture selection signals. The Rsb score of admixed and SI was significant in a wide region of chromosome 18 (6.6-24.6 Mb) overlapped with one area of strong local ancestry deviation. FTO, with pleiotropic effect on milk and fertility, NOD2 on dairy and NKD1 and SALL1 on fertility traits are located there. Genetic differentiation of RHF and SI (F_st ), an alternative indicator of pre-admixture selection in pure populations, was calculated. No considerable overlap of peaks of local ancestry deviations and F_st was observed. We found two regions with significant signatures of post-admixture selection in this very young composite, applying comparatively stringent significance thresholds. The signals cover relatively large genomic areas and did not allow pinpointing of the gene(s) responsible for the apparent shift in ancestry proportions.

The use of coancestry based on shared segments for maintaining genetic diversity

We have evaluated the use of genomic coancestry coefficients based on shared segments for the maintenance of genetic diversity through optimal contributions methodology for populations of three different Austrian cattle breeds. This coancestry measure has been compared with the genomic coancestry coefficient calculated on a SNP-by-SNP basis and with pedigree-based coancestry. The regressions of the shared segments coancestry on the other two coefficients suggest that the former mainly reflect Identity By Descent but with the advantage over pedigree-based coancestry of providing the realized Identity By Descent rather than an expectation. The effective population size estimated from the rate of coancestry based on shared segments was very similar to those obtained with the other coefficients and of small magnitude (from 26.24 to 111.90). This result highlights the importance of implementing active management strategies to control the increase of inbreeding and the loss of genetic diversity in livestock breeds, even when the population size is reasonably large. One problem for the implementation of coancestry based on shared segments is the need of estimating the gametic phases of the SNPs which, given the techniques used to obtain the genotypes, are a priori unknown. This study shows, through computer simulations, that using estimates of gametic phases for computing coancestry based on shared segments does not lead to a significant loss in the diversity maintained. This has been shown to be true even when the size of the population is very small as it is usually the case in populations subjected to conservation programmes.

GRAIN: a computer program to calculate ancestral and partial inbreeding coefficients using a gene dropping approach

GRain is freely available software intended to enable and promote testing of hypotheses with respect to purging and heterogeneity of inbreeding depression. The program is based on a stochastic approach, the gene dropping method, and calculates various coefficients from large and complex pedigrees. GRain calculates, together with the 'classical' inbreeding coefficient, ancestral inbreeding coefficients proposed by Ballou, (1997) J. Hered., 88, 169 and Kalinowski et al., (2000) Conserv. Biol., 14, 1375 as well as an ancestral history coefficient (AHC ), defined here for the first time. AHC is defined as the number that tells how many times during pedigree segregation (gene dropping) a randomly taken allele has been in IBD status. Furthermore, GRain enables testing of heterogeneity and/or purging of inbreeding depression with respect to different founders/ancestors by calculating partial coefficients for all previously obtained coefficients.

The Survival Kit: software to analyze survival data including possibly correlated random effects

The Survival Kit is a Fortran 90 Software intended for survival analysis using proportional hazards models and their extension to frailty models with a single response time. The hazard function is described as the product of a baseline hazard function and a positive (exponential) function of possibly time-dependent fixed and random covariates. Stratified Cox, grouped data and Weibull models can be used. Random effects can be either log-gamma or normally distributed and can account for a pedigree structure. Variance parameters are estimated in a Bayesian context. It is possible to account for the correlated nature of two random effects either by specifying a known correlation coefficient or estimating it from the data. An R interface of the Survival Kit provides a user friendly way to run the software.

Estimates of autozygosity derived from runs of homozygosity: empirical evidence from selected cattle populations

Using genome-wide SNP data, we calculated genomic inbreeding coefficients (FROH  > 1  Mb , FROH  > 2 Mb , FROH  > 8 Mb and FROH  > 16 Mb ) derived from runs of homozygosity (ROH) of different lengths (>1, >2, >8 and > 16 Mb) as well as from levels of homozygosity (FHOM ). We compared these values of inbreeding coefficients with those calculated from pedigrees (FPED ) of 1422 bulls comprising Brown Swiss (304), Fleckvieh (502), Norwegian Red (499) and Tyrol Grey (117) cattle breeds. For all four breeds, population inbreeding levels estimated by the genomic inbreeding coefficients FROH  > 8 Mb and FROH  > 16 Mb were similar to the levels estimated from pedigrees. The lowest values were obtained for Fleckvieh (FPED  = 0.014, FROH  > 8 Mb  = 0.019 and FROH  > 16 Mb  = 0.008); the highest, for Brown Swiss (FPED  = 0.048, FROH  > 8 Mb  = 0.074 and FROH  > 16 Mb  = 0.037). In contrast, inbreeding estimates based on the genomic coefficients FROH  > 1 Mb and FROH  > 2 Mb were considerably higher than pedigree-derived estimates. Standard deviations of genomic inbreeding coefficients were, on average, 1.3-1.7-fold higher than those obtained from pedigrees. Pearson correlations between genomic and pedigree inbreeding coefficients ranged from 0.50 to 0.62 in Norwegian Red (lowest correlations) and from 0.64 to 0.72 in Tyrol Grey (highest correlations). We conclude that the proportion of the genome present in ROH provides a good indication of inbreeding levels and that analysis based on ROH length can indicate the relative amounts of autozygosity due to recent and remote ancestors.

Impact of dominance and epistasis on the genetic make-up of simulated populations under selection: a model development

SUMMARY

A two-locus genetic model was used to simulate different levels of additive, dominance, and additive-by-additive genetic effects. The character under phenotypic selection was controlled by 30 pairs of diallelic loci, located on different chromosomes. Initial gene frequencies were set to 0.5 for all loci and the recombination probability was 0.20 between adjacent loci. The broad-sense heritability was varied at levels of 0.03, 0.30, and 0.60. After building up a random mating population with 200 males and 400 females, the phenotypic best individuals per year were selected over 200 years (approx. 35 overlapping generations), keeping the population size constant. The results of the simulations showed extreme differences between eight models with the same initial heritability, but different amounts of additive, dominance, and additive-by-additive variance components. A model with additive, dominance, and additive-by-additive variance at the same initial magnitude, and negative dominance and positive additive-by-additive effect, led to the highest genetic response in the long term for all heritabilities simulated. The additive model showed the best selection advance in the short term. Some of the initial dominance and additive-by-additive variance was converted to additive genetic variance during the selection period, which in turn contributed to the selection response. ZUSAMMENFASSUNG: Auswirkungen von Dominanz and Epistasie auf den genetischen Aufbau von simulierten Populationen unter Selektion: Eine Modellentwicklung Ein 2-Locus-Genmodell wurde zur Simulation verschiedener Ausprägungen von additiven, Dominanz und additiv mal additiv genetischen Effekten verwendet. Das Merkmal under phänotypischer Selektion wurde von 30 diallelen Locuspaaren auf verschiedenen Chromosomen kontrolliert. Die Anfangsgenfrequenz wurde für alle Loci mit 0.5 angenommen und die Rekombinationsrate betrug 0.20 zwischen benachbarten Loci. Die Heritabilität im weiteren Sinn wurde zwischen 0.03, 0.30 und 0.60 variiert. Nach dem Aufbau einer Population durch Zufallspaarung von 200 männlichen und 400 weiblichen Individuen wurden die phänotypisch besten Individuen pro Jahr unter Konstanthaltung der Populationsgröße über einen Zeitraum von 200 Jahren (ca. 35 überlappende Generationen) selektiert. Die Ergebnisse der Simulationen zeigten extreme Unterschiede zwischen den acht Modellen mit der gleichen Anfangsheritabilität aber verschiedenen Anteilen von additiven, Dominanz und additiv mal additiven Varianzkomponenten. Ein Modell mit zu Beginn gleich hoher additiver, Dominanz und additiv mal additiver Varianz und negativem Dominanz- und positivem additiv mal additiven Effekt führte bei allen simulierten Heritabilitäten langfristig zum höchsten Selektionserfolg. Kurzfristig zeigte das additive Modell den höchsten Selektionsfortschritt. Ein Teil der Anfangs-Dominanz- und -Additiv mal additiv-Varianz wurde während der Selektionsperiode in additive Varianz umgewandelt, die wiederum zum Selektionserfolg beitrug.

Prediction of breed composition in an admixed cattle population

Swiss Fleckvieh was established in 1970 as a composite of Simmental (SI) and Red Holstein Friesian (RHF) cattle. Breed composition is currently reported based on pedigree information. Information on a large number of molecular markers potentially provides more accurate information. For the analysis, we used Illumina BovineSNP50 Genotyping Beadchip data for 90 pure SI, 100 pure RHF and 305 admixed bulls. The scope of the study was to compare the performance of hidden Markov models, as implemented in structure software, with methods conventionally used in genomic selection [BayesB, partial least squares regression (PLSR), least absolute shrinkage and selection operator (LASSO) variable selection)] for predicting breed composition. We checked the performance of algorithms for a set of 40 492 single nucleotide polymorphisms (SNPs), subsets of evenly distributed SNPs and subsets with different allele frequencies in the pure populations, using F(ST) as an indicator. Key results are correlations of admixture levels estimated with the various algorithms with admixture based on pedigree information. For the full set, PLSR, BayesB and structure performed in a very similar manner (correlations of 0.97), whereas the correlation of LASSO and pedigree admixture was lower (0.93). With decreasing number of SNPs, correlations decreased substantially only for 5% or 1% of all SNPs. With SNPs chosen according to F(ST) , results were similar to results obtained with the full set. Only when using 96 and 48 SNPs with the highest F(ST) , correlations dropped to 0.92 and 0.90 respectively. Reducing the number of pure animals in training sets to 50, 20 and 10 each did not cause a drop in the correlation with pedigree admixture.

Short communication: Genomic selection using a multi-breed, across-country reference population

Three breeds (Fleckvieh, Holstein, and Jersey) were included in a reference population, separately and together, to assess the accuracy of prediction of genomic breeding values in single-breed validation populations. The accuracy of genomic selection was defined as the correlation between estimated breeding values, calculated using phenotypic data, and genomic breeding values. The Holstein and Jersey populations were from Australia, whereas the Fleckvieh population (dual-purpose Simmental) was from Austria and Germany. Both a BLUP with a multi-breed genomic relationship matrix (GBLUP) and a Bayesian method (BayesA) were used to derive the prediction equations. The hypothesis tested was that having a multi-breed reference population increased the accuracy of genomic selection. Minimal advantage existed of either GBLUP or BayesA multi-breed genomic evaluations over single-breed evaluations. However, when the goal was to predict genomic breeding values for a breed with no individuals in the reference population, using 2 other breeds in the reference was generally better than only 1 breed.

Multiple paternal origins of domestic cattle revealed by Y-specific interspersed multilocus microsatellites

In this study, we show how Y-specific interspersed multilocus microsatellites, which are loci that yield several amplified bands differing in size from the same male individual and PCR reaction, are a powerful source of information for tracing the history of cattle. Our results confirm the existence of three main groups of sires, which are separated by evolutionary time and clearly predate domestication. These three groups are consistent with the haplogroups previously identified by Götherström et al. (2005) using five Y-specific segregating sites: Y1 and Y2 in taurine (Bos taurus) cattle and Y3 in zebu (Bos indicus) cattle. The zebu cattle cluster clearly originates from a domestication process that was geographically and temporally separated from that of taurine clusters. Our analyses further suggest that: (i) introgression of wild sire genetic material into domesticated herds may have a significant role in the formation of modern cattle, including the formation of the Y1 haplogroup; (ii) a putative domestication event in Africa probably included local Y2-like wild sires; (iii) the West African zebu cattle Y-chromosome may have partially originated from an ancient introgression of humped cattle into Africa; and (iv) the high genetic similarity among Asian zebu sires is consistent with a single domestication process.

Pedigree analysis in the Austrian Noriker draught horse: genetic diversity and the impact of breeding for coat colour on population structure

The pedigree of the current Austrian Noriker draught horse population comprising 2808 horses was traced back to the animals considered as founders of this breed. In total, the number of founders was 1991, the maximum pedigree length was 31 generations, with an average of 12.3 complete generations. Population structure in this autochthonous Austrian draught horse breed is defined by seven breeding regions (Carinthia, Lower Austria, Salzburg, Styria, Tyrol, Upper Austria and Vorarlberg) or through six coat colour groups (Bay, Black, Chestnut, Roan, Leopard, Tobiano). Average inbreeding coefficients within the breeding regions ranged from 4.5% to 5.5%; for the colour groups, the coefficients varied from 3.5% to 5.9%. Other measures of genetic variability like the effective number of founders, ancestors and founder genomes revealed a slightly different genetic background of the subpopulations. Average co-ancestries between and within breeding areas showed that the Salzburg population may be considered as the nucleus or original stock whereas all other subpopulations showed high relationship to horses from Salzburg. The target of draught horse breeding in the 21st century does not meet the breeding concept of maximizing genetic gains any more. Stabilizing selection takes place. In this study, we show that demographic factors as well as structure given by different coat colours helped to maintain genetic diversity in this endangered horse breed.

Design of a village breeding programme for a llama population in the High Andes of Bolivia

No national breeding programme for llamas is in place in Bolivia. Initiatives for genetic improvement are rarely found and are usually carried out by NGOs working in rural development or improvement of livestock production or research stations. Farmers in the Province of Ayopaya in the District of Cochabamba have formed a breeders' organization with the aim of improving fibre production. In this study, a detailed outline of a breeding programme with a focus on organizational and technical details is described. Facing constraints like illiteracy of farmers, bad infrastructure and lack of finances, a simple breeding programme is set up. The breeding goal is a higher fleece weight while keeping the fleece quality at the current high level. Greasy fleece weight and fibre diameter are identified as main selection criteria. Mass selection of males is carried out. Selected males are either exchanged between farmers and used in the herds or are kept during the mating season in a central mating station owned by the breeders' organization. Model calculations were carried out with the program zplan, which is based on a deterministic approach. zplan evaluates the genetic and economic efficiency of breeding strategies considering one cycle of selection. Scenarios with only intra-herd use, using only the central mating station or combinations of those were compared in terms of expected genetic gain and expected increase of inbreeding. Fastest genetic progress is achieved when the males are kept in a central mating station as the selection intensity is on a high level. Rates of inbreeding vary between 0.08 and 0.32% per generation.