Genome-wide association study for milking speed in Fleckvieh cattle.

Milking speed is an important trait influencing udder health of dairy cows as well as labor efficiency. Yet, it has received little attention in genomic association studies. The main objective of this study was to determine regions and genes on the genome with a potential effect on milking speed in Fleckvieh (dual purpose Simmental) cattle. Genome-wide association studies were conducted using de-regressed breeding values of bulls as phenotypes. Six SNP on 4 autosomes were significantly associated with milking speed for additive effects. Significant regions on BTA4 and BTA19 correspond with findings for other dairy cattle breeds. Based on the observation of Fleckvieh breed managers, variation of milking speed in batches of daughters of some bulls is much higher than in daughter groups of other bulls. This difference in within family variation may be caused by transmission of alternative alleles of bulls being heterozygous for a gene affecting milking speed. To check on this, we considered standard deviation of yield deviations in milking speed of half-sib daughters as a new trait and performed GWAS for dominance effects. One signal on BTA5 passed the genome wide Bonferroni threshold that corresponded to the significant signal from standard GWAS on de-regressed breeding values. The key conclusion of this study is that several strong genomic signals were found for milking speed in Fleckvieh cattle and that the strongest of them are supported by similar findings in Brown Swiss and Holstein Friesian cattle. Milking speed is a complex trait whose sub-processes have not yet been elucidated in detail. Hence, it remains a challenge to link the associated regions on the genome with causal genes and their functions.

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 (ß-hydroxybutyrate [BHB] and acetone), mastitis (N-acetyl-ß-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 HE  = 0.341, HO  = 0.368), and the highest heterozygote excess (U FIS  = -0.066), among the studied breeds; this reflects the contribution of multiple breeds to their formation. The principal component analysis, FST -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.

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.

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.

A complex structural variant at the KIT locus in cattle with the Pinzgauer spotting pattern.

A specific white spotting phenotype, termed finching or line-backed spotting, is known for all Pinzgauer cattle and occurs occasionally in Tux-Zillertaler cattle, two Austrian breeds. The so-called Pinzgauer spotting is inherited as an autosomal incompletely dominant trait. A genome-wide association study using 27 white spotted and 16 solid-coloured Tux-Zillertaler cattle, based on 777k SNP data, revealed a strong signal on chromosome 6 at the KIT locus. Haplotype analyses defined a critical interval of 122 kb downstream of the KIT coding region. Whole-genome sequencing of a Pinzgauer cattle and comparison to 338 control genomes revealed a complex structural variant consisting of a 9.4-kb deletion and an inversely inserted duplication of 1.5 kb fused to a 310-kb duplicated segment from chromosome 4. A diagnostic PCR was developed for straightforward genotyping of carriers for this structural variant (KITPINZ ) and confirmed that the variant allele was present in all Pinzgauer and most of the white spotted Tux-Zillertaler cattle. In addition, we detected the variant in all Slovenian Cika, British Gloucester and Spanish Berrenda en negro cattle with similar spotting patterns. Interestingly, the KITPINZ variant occurs in some white spotted animals of the Swiss breeds Evolèner and Eringer. The introgression of the KITPINZ variant confirms admixture and the reported historical relationship of these short-headed breeds with Austrian Tux-Zillertaler and suggests a mutation event, occurring before breed formation.

Genetic associations of lactose and its ratios to other milk solids with health traits in Austrian Fleckvieh cows.

The genetic correlations (ra) of milk lactose percentage (LP), lactose yield (LY), and ratios of LP to other milk solids with udder, metabolic, and fertility disorders have not been assessed in dairy cattle so far. To evaluate the potential role of milk lactose as indicator of cow health, 142,285 lactation records of 84,289 Austrian Fleckvieh cows were analyzed with univariate and bivariate animal models. Milk traits were on a 150-d basis and health traits were coded as binary (0/1). Other than LP and LY, 3 new phenotypes were defined and included in the present study, namely the lactose-to-fat, lactose-to-protein, and lactose-to-solids ratios. The most heritable trait was LP (0.566 ± 0.008) and heritability of LY was much lower (0.145 ± 0.005). Heritability estimates close to 0.50 were assessed for the ratios. The frequency of health disorders was higher in multiparous cows yielding milk with low LP (≤4.553%) compared with cows yielding milk with high LP (≥5.045%). Heritabilities of health traits were in the expected ranges, with the highest estimate for ovarian cysts (CYS; 0.037 ± 0.004) and the lowest for retained placenta (0.005 ± 0.001). Mastitis (MAS) genetically correlated with LY (0.518 ± 0.057); considering that the amount of synthesized lactose is the key regulator of milk volume, this result confirmed that high-producing cows are more genetically susceptible to MAS than low-producing animals. Similar to MAS, ketosis (KET) was also positively genetically associated with LY (0.420 ± 0.077) and a weak and unfavorable ra between KET and lactose-to-protein ratio was estimated (0.159 ± 0.077). The ra of LY with milk fever (MFV) and CYS were approximately 0.20. The ra of LP with MAS, KET, and MFV were negative (-0.142 on average), supporting the idea that LP is a potential health indicator. Genetic correlations between health traits ranged from zero (retained placenta with MAS and CYS) to 0.463 ± 0.090 (MAS and MFV). Results of the present study suggest that LP has potentiality to be used as indicator trait to improve udder health in Austrian Fleckvieh population.

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.

The use of mid-infrared spectrometry to estimate the ration composition of lactating dairy cows.

The composition of cow milk is strongly affected by the feeding regimen. Because milk components are routinely determined using mid-infrared (MIR) spectrometry, MIR spectra could also be used to estimate an animal's ration composition. The objective of this study was to determine whether and how well amounts of dry matter intake and the proportions of concentrates, hay, grass silage, maize silage, and pasture in the total ration can be estimated using MIR spectra at an individual animal level. A total of 10,200 milk samples and sets of feed intake data were collected from 90 dairy cows at 2 experimental farms of the Agricultural Research and Education Centre in Raumberg-Gumpenstein, Austria. For each run of analysis, the data set was split into a calibration and a validation data set in a 40:60 ratio. Estimated ration compositions were calculated using a partial least squares regression and then compared with the respective observed ration compositions. In separate analyses, the factors milk yield and concentrate intake were included as additional predictors. To evaluate accuracy, the coefficient of determination (R2) and ratio to performance deviation were used. The highest R2 values (for kg of dry matter intake/for % of ration) for the individual feedstuffs were as follows: pasture, 0.63/0.66; grass silage, 0.32/0.43; concentrate intake, 0.39/0.34; maize silage, 0.32/0.33; and hay, 0.15/0.16. Estimation of groups of feedstuffs (forages, energy-dense feedstuffs) mostly resulted in R2 values >0.50. Including the parameters milk yield or concentrate intake improved R2 values by up to 0.21, with an average improvement of 0.04. The results of this study indicate that not all ration components may be estimated equally accurately. Even if some estimates are good on average, there may be strong deviations between estimated and observed values in individual data sets, and therefore individual estimates should not be overemphasized. Further research including pooled samples (e.g., bulk milk, farm samples) or variations in ration composition is called for.

Accuracy of genomic predictions in Gyr (Bos indicus) dairy cattle.

Genomic selection may accelerate genetic progress in breeding programs of indicine breeds when compared with traditional selection methods. We present results of genomic predictions in Gyr (Bos indicus) dairy cattle of Brazil for milk yield (MY), fat yield (FY), protein yield (PY), and age at first calving using information from bulls and cows. Four different single nucleotide polymorphism (SNP) chips were studied. Additionally, the effect of the use of imputed data on genomic prediction accuracy was studied. A total of 474 bulls and 1,688 cows were genotyped with the Illumina BovineHD (HD; San Diego, CA) and BovineSNP50 (50K) chip, respectively. Genotypes of cows were imputed to HD using FImpute v2.2. After quality check of data, 496,606 markers remained. The HD markers present on the GeneSeek SGGP-20Ki (15,727; Lincoln, NE), 50K (22,152), and GeneSeek GGP-75Ki (65,018) were subset and used to assess the effect of lower SNP density on accuracy of prediction. Deregressed breeding values were used as pseudophenotypes for model training. Data were split into reference and validation to mimic a forward prediction scheme. The reference population consisted of animals whose birth year was ≤2004 and consisted of either only bulls (TR1) or a combination of bulls and dams (TR2), whereas the validation set consisted of younger bulls (born after 2004). Genomic BLUP was used to estimate genomic breeding values (GEBV) and reliability of GEBV (R2PEV) was based on the prediction error variance approach. Reliability of GEBV ranged from ∼0.46 (FY and PY) to 0.56 (MY) with TR1 and from 0.51 (PY) to 0.65 (MY) with TR2. When averaged across all traits, R2PEV were substantially higher (R2PEV of TR1 = 0.50 and TR2 = 0.57) compared with reliabilities of parent averages (0.35) computed from pedigree data and based on diagonals of the coefficient matrix (prediction error variance approach). Reliability was similar for all the 4 marker panels using either TR1 or TR2, except that imputed HD cow data set led to an inflation of reliability. Reliability of GEBV could be increased by enlarging the limited bull reference population with cow information. A reduced panel of ∼15K markers resulted in reliabilities similar to using HD markers. Reliability of GEBV could be increased by enlarging the limited bull reference population with cow information.

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 (Fst ), an alternative indicator of pre-admixture selection in pure populations, was calculated. No considerable overlap of peaks of local ancestry deviations and Fst 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.

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.

Strategies for single nucleotide polymorphism (SNP) genotyping to enhance genotype imputation in Gyr (Bos indicus) dairy cattle: Comparison of commercially available SNP chips.

Genotype imputation is widely used as a cost-effective strategy in genomic evaluation of cattle. Key determinants of imputation accuracies, such as linkage disequilibrium patterns, marker densities, and ascertainment bias, differ between Bos indicus and Bos taurus breeds. Consequently, there is a need to investigate effectiveness of genotype imputation in indicine breeds. Thus, the objective of the study was to investigate strategies and factors affecting the accuracy of genotype imputation in Gyr (Bos indicus) dairy cattle. Four imputation scenarios were studied using 471 sires and 1,644 dams genotyped on Illumina BovineHD (HD-777K; San Diego, CA) and BovineSNP50 (50K) chips, respectively. Scenarios were based on which reference high-density single nucleotide polymorphism (SNP) panel (HDP) should be adopted [HD-777K, 50K, and GeneSeek GGP-75Ki (Lincoln, NE)]. Depending on the scenario, validation animals had their genotypes masked for one of the lower-density panels: Illumina (3K, 7K, and 50K) and GeneSeek (SGGP-20Ki and GGP-75Ki). We randomly selected 171 sires as reference and 300 as validation for all the scenarios. Additionally, all sires were used as reference and the 1,644 dams were imputed for validation. Genotypes of 98 individuals with 4 and more offspring were completely masked and imputed. Imputation algorithms FImpute and Beagle v3.3 and v4 were used. Imputation accuracies were measured using the correlation and allelic correct rate. FImpute resulted in highest accuracies, whereas Beagle 3.3 gave the least-accurate imputations. Accuracies evaluated as correlation (allelic correct rate) ranged from 0.910 (0.942) to 0.961 (0.974) using 50K as HDP and with 3K (7K) as low-density panels. With GGP-75Ki as HDP, accuracies were moderate for 3K, 7K, and 50K, but high for SGGP-20Ki. The use of HD-777K as HDP resulted in accuracies of 0.888 (3K), 0.941 (7K), 0.980 (SGGP-20Ki), 0.982 (50K), and 0.993 (GGP-75Ki). Ungenotyped individuals were imputed with an average accuracy of 0.970. The average top 5 kinship coefficients between reference and imputed individuals was a strong predictor of imputation accuracy. FImpute was faster and used less memory than Beagle v4. Beagle v4 outperformed Beagle v3.3 in accuracy and speed of computation. A genotyping strategy that uses the HD-777K SNP chip as a reference panel and SGGP-20Ki as the lower-density SNP panel should be adopted as accuracy was high and similar to that of the 50K. However, the effect of using imputed HD-777K genotypes from the SGGP-20Ki on genomic evaluation is yet to be studied.

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.

Community-based livestock breeding programmes: essentials and examples.

Breeding programmes described as community-based (CBBP) typically relate to low-input systems with farmers having a common interest to improve and share their genetic resources. CBBPs are more frequent with keepers of small ruminants, in particular smallholders of local breeds, than with cattle, pigs or chickens with which farmers may have easier access to alternative programmes. Constraints that limit the adoption of conventional breeding technologies in low-input systems cover a range of organizational and technical aspects. The analysis of 8 CBBPs located in countries of Latin-America, Africa and Asia highlights the importance of bottom-up approaches and involvement of local institutions in the planning and implementation stages. The analysis also reveals a high dependence of these programmes on organizational, technical and financial support. Completely self-sustained CBBPs seem to be difficult to realize. There is a need to implement and document formal socio-economic evaluations of CBBPs to provide governments and other development agencies with the information necessary for creating sustainable CBBPs at larger scales.

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.

Diagnosis of asphyxiation in advanced decomposed corpses by using Oil-Red-O Stain and immunohistochemical technology.

BACKGROUND: The unambiguous diagnosis of asphyxiation is still a major challenge for the forensic pathologist, especially in terms of highly advanced decomposed corps. METHODOLOGY: In order to demonstrate asphyxiation particularly in profoundly putrid bodies we hypothesized that hypoxic stress is basically responsible for generalized fatty degeneration of visceral organs which can be detected by histological examination using a special staining technique referred to as Oil-Red-O Stain (Sudan III-red-B-stain). To test this hypothesis we examined different tissues (myocardium, liver, lung and kidney) of 107 people divided into 5 groups. These are: (i) 71 case-victims who were found in a truck and died most likely due to asphyxiation, whereby any other violent or natural cause of death was ruled out by postmortem examination; (ii) 10 barely decomposed positive-control-victims; (iii) 6 non-decomposed positive-control-victims; iv) 10 drowning non-decomposed positive-control victims, and v) 10 negative-control-victims. Apart from general histological special staining methods, an immunohistochemically approach as a case-control-study on lung tissues of same individuals was carried out by means of using two polyclonal rabbit-antibodies against (i) HIF-1-α (Hypoxia Inducing Factor-1 alpha) and (ii) SP-A (pulmonary surfactant-associated protein A) to detect both the transcription factor and pulmonary surfactants. The positive proof of already either of them gives evidence of death caused by hypoxia. RESULTS: Histological examination of myocardium, liver and kidney of the 71 case-victims and the 10 positive-control-victims using Oil-Red-O Stain showed a fatty degeneration of small droplet type; there was no evidence for fatty degeneration in tissues of the 10 negative-control-victims. These findings strongly indicate a causal association between oxygen deficiency and generalized fatty degeneration of viscera due to insufficient oxygen supply. In terms of methodology, this special staining technique seems to be very informative, even applicable on decomposed corps. Results of immunohistochemistry indicate that on the one hand the detection of HIF-1α is not possible to perform on (advanced) putrid bodies, whereas the verification of SP-A is still feasible on the other. CONCLUSION: Positive Oil-Red-O staining and the immunohistochemical detection of SP-A can serve as a serious hint for the diagnosis of asphyxia on putrid corpses, considering other circumstances of death that have been determined.