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B Heringstad - One of the best experts on this subject based on the ideXlab platform.

  • expression analysis of candidate genes for chronic subclinical mastitis in Norwegian Red cattle
    Journal of Dairy Science, 2020
    Co-Authors: E Kirsanova, B Heringstad, Preben Boysen, G M Johansen, Anna Lewandowskasabat, Ingrid Olsaker
    Abstract:

    Chronic subclinical mastitis (SCM) is characterized by a long-term inflammation in the udder with high somatic cell count (SCC) in milk. Previously, several novel alternative SCM traits for Norwegian Red (NR) cattle have been defined to improve breeding strategies against chronic SCM. Quantitative trait loci and candidate genes affecting chronic SCM in NR have been identified. The aim of this study was to analyze the expression profiles of 14 selected candidate genes (RAD17, ACOT2, ACOT4, FOS, CXCL1, CXCL8, CCNB1, CDK7, TGFB3, SEL1L, STAT4, C6, GLI2, and SLC18A2). Twenty healthy NR cows with official genomic estimated breeding values (GEBV) for lactation average somatic cell scores (LSCS) were selected. Ten cows had high GEBV for LSCS (cows with low probability to have high SCC in milk during lactation) and 10 cows had low GEBV for LSCS (cows with high probability of having high SCC in milk). We isolated RNA from unstimulated peripheral blood mononuclear cells from these. Two out of the 14 analyzed genes showed significantly different results between groups. The group with high GEBV for LSCS displayed significantly higher expression of the CXCL1 gene than the low GEBV group. Grouping by lactation stage revealed significant differential expression of the FOS gene, with higher expression in early lactation (2-3 mo after calving) compaRed with late lactation (7-8 mo after calving). In addition, flow cytometry was performed on the peripheral blood mononuclear cells samples to analyze if number and type of isolated cells influenced the gene expression in the groups. The results in the current study provide identified genes that can be consideRed as possible candidate genes for chronic SCM in NR cows.

  • differences in sperm functionality and intracellular metabolites in Norwegian Red bulls of contrasting fertility
    Theriogenology, 2020
    Co-Authors: Birgitte Narud, B Heringstad, Geir Klinkenberg, Abdolrahman Khezri, Teklu Tewoldebrhan Zeremichael, Elseberit Stenseth, Anna Nordborg, Tonje Husby Haukaas, J M Morrell, Froydis Deinboll Myromslien
    Abstract:

    Abstract In the dairy breeding industry, pRediction of bull fertility in artificial insemination (AI) is important for efficient and economically sustainable production. However, it is challenging to identify bulls with superior fertility applying conventional in vitro sperm assays. In the present study, sperm functionality was investigated to identify a multivariate model that could pRedict fertility. Two groups of young Norwegian Red bulls were selected, one with inferior fertility (18 bulls) and one with superior fertility (19 bulls) based on non-return rate after 56 days (NR56). Frozen-thawed semen doses were analysed for sperm chromatin integrity, viability, acrosome integrity, motility, and ATP content. A targeted approach was used to study intracellular concentrations of amino acids and trace elements in viable sperm cells. Significant differences between the two groups of bulls were observed, both for sperm functional attributes and intracellular concentrations of metabolites. Pearson correlation analyses indicated a negative relationship between NR56 and chromatin integrity parameters, DNA fragmentation index (DFI) and high DNA stainability (HDS). Several motility parameters correlated positively with NR56. The concentrations of cysteine and glutamic acid in sperm cells correlated negatively with NR56, while the concentrations of aspartic acid, leucine and serine showed a positive NR56-correlation. The sperm intracellular concentrations of the trace elements Fe, Al and Zn, correlated negatively with NR56. Correlations were observed between several sperm parameters and metabolites. Stepwise multiple regression analysis indicated that the best pRedictor of NR56 was a model containing %DFI, together with the intracellular sperm concentration of aspartic acid, Fe and Zn. This model explained 59% of the variability in NR56.

  • genetic correlations between body weight daily weight gain and semen characteristic traits in young Norwegian Red bulls
    Journal of Dairy Science, 2020
    Co-Authors: H B Olsen, B Heringstad, G Klemetsdal
    Abstract:

    ABSTRACT The aim of this study was to estimate genetic parameters for body weight (BW) at 150 d (Bw_150d), and 330 d (Bw_330d) of age and average daily weight gain (Dwg), and to estimate genetic correlations between these traits and semen characteristic traits: volume; concentration (Conc); motility in fresh, 24-h, and 48-h samples (Mot0h, Mot24h, Mot48h); and sperm defects. Data were collected at the performance test station of young Norwegian Red bulls from 2002 to 2012, before selection of bulls for artificial insemination. The weight and growth data consisted of observations for 3,209 bulls, and andrology information was available for up to 2,034 of these bulls. Genetic parameters were estimated using linear animal models. Models for BW and growth traits included the group and year the bull left the station and the pen they occupied during weighing (group-year-pen) and parity of their dam as fixed effects. Models for andrology traits had group-year, age in months (11 to 15), and the interaction between ejaculate number and days since previous collection included as fixed effects. Estimated heritability was 0.14 for Bw_150d, 0.26 for Bw_330d, and 0.34 for Dwg; the estimated genetic correlations among these traits were all favorable. Both BW traits correlated favorably with all the semen characteristic traits (0.20 to 0.76), whereas Dwg was favorably correlated with volume, Mot24h, Mot48h, and sperm defects, and unfavorably correlated with Conc (−0.25) and Mot0h (−0.53). Our results indicate that the genetic correlations between weight and growth traits and semen characteristics depend on the age of the bulls. Although most genetic correlations were favorable, selection for higher daily weight gain between 150 and 330 d might explain the slight negative genetic trends observed for semen characteristics in young Norwegian Red bulls.

  • ovarian follicular response to oestrous synchronisation and induction of ovulation in Norwegian Red cattle
    Acta Veterinaria Scandinavica, 2020
    Co-Authors: Halldor Felde Berg, B Heringstad, Vilde Granne Kvale, Knut Ingolf Dragset, Andres Waldmann, Erik Ropstad, Anne Hege Almkristiansen, Elisabeth Kommisrud
    Abstract:

    Oestrous synchronisation of cattle has been widely applied to accomplish simultaneous ovulation in animals and facilitate timed artificial insemination. The main aim of this study was to investigate the ovarian follicular growth and ovulatory response to oestrus and ovulation synchronisation in Norwegian Red heifers and cows. Oestrous cycles in 34 heifers and 10 cows from 4 herds were synchronised with two PGF2α analogue treatments 11 days apart, followed by GnRH analogue treatment for induction of ovulation. Thereafter, the ovaries were examined by ultrasonography at 3 h intervals until ovulation. The luteolytic effect of the PGF2α analogue was verified in 9 of 10 cows by progesterone contents in milk. Maximum physical activity of the cows occurRed on average 69 h after PGF2α analogue treatment. An ovulatory response was recorded in 95.5% (42/44) of the animals. A significant difference in follicle size at ovulation was found between 2 of the herds. Animals with medium sized and large follicles and heifers aged > 16 months ovulated earlier than other animals. The applied sequence of treatments in the study was shown to be effective in synchronizing and inducing ovulation within a relatively narrow time interval in the Norwegian Red heifers and cows, consistent with findings in other cattle breeds.

  • identification of candidate genes affecting chronic subclinical mastitis in Norwegian Red cattle combining genome wide association study topologically associated domains and pathway enrichment analysis
    Animal Genetics, 2020
    Co-Authors: E Kirsanova, B Heringstad, Anna Lewandowskasabat, Ingrid Olsaker
    Abstract:

    : The aim of this study was to identify genes associated with chronic subclinical mastitis (SCM) in Norwegian Red (NR) cattle. Twelve SCM traits defined based on fixed threshold for test-day somatic cell count (SCC) were, together with lactation-average somatic cell score (LSCS) used for association and pathway enrichment analyses. A GWAS was performed on 3795 genotyped NR bulls with 777K SNP data and phenotypic information from 7 300 847 test-day SCC observations from 3 543 764 cows. At 5% chromosome-wide significance level 36 unique SNP were detected to be associated with one or more of the traits. These SNPs were analysed for linked genes using genomic positions of topologically associated domains (TAD). For the SCM traits with SCC >50 000 and >100 000 cells/ml on two test-days in a row and LSCS, the same top significant genes were identified - checkpoint clamp loader component (RAD17) and cyclin B1 (CCNB1). The SCM traits with SCC >250 000, 300 000, 350 000 or 400 000 cells/ml on two test-days in a row and D400 (number of days before the first case with SCC >400 000 cells/ml) displayed similar top significant genes: acyl-CoA thioesterase 2 and 4 (ACOT2; ACOT4). For the traits SCM200_3 (SCC >200 000 cells/ml on three test-days in a row) and SCM150, SCM200 (SCC >150 000; 200 000 cells/ml on two test-days in a row) a group of chemokine (C-X-C motif) ligand genes and the Fos proto-oncogene, AP-1 transcription factor subunit (FOS) gene, were identified. Further functional studies of these identified candidate genes are necessary to clarify their actual role in development of chronic SCM in NR cattle.

G Klemetsdal - One of the best experts on this subject based on the ideXlab platform.

  • genetic correlations between body weight daily weight gain and semen characteristic traits in young Norwegian Red bulls
    Journal of Dairy Science, 2020
    Co-Authors: H B Olsen, B Heringstad, G Klemetsdal
    Abstract:

    ABSTRACT The aim of this study was to estimate genetic parameters for body weight (BW) at 150 d (Bw_150d), and 330 d (Bw_330d) of age and average daily weight gain (Dwg), and to estimate genetic correlations between these traits and semen characteristic traits: volume; concentration (Conc); motility in fresh, 24-h, and 48-h samples (Mot0h, Mot24h, Mot48h); and sperm defects. Data were collected at the performance test station of young Norwegian Red bulls from 2002 to 2012, before selection of bulls for artificial insemination. The weight and growth data consisted of observations for 3,209 bulls, and andrology information was available for up to 2,034 of these bulls. Genetic parameters were estimated using linear animal models. Models for BW and growth traits included the group and year the bull left the station and the pen they occupied during weighing (group-year-pen) and parity of their dam as fixed effects. Models for andrology traits had group-year, age in months (11 to 15), and the interaction between ejaculate number and days since previous collection included as fixed effects. Estimated heritability was 0.14 for Bw_150d, 0.26 for Bw_330d, and 0.34 for Dwg; the estimated genetic correlations among these traits were all favorable. Both BW traits correlated favorably with all the semen characteristic traits (0.20 to 0.76), whereas Dwg was favorably correlated with volume, Mot24h, Mot48h, and sperm defects, and unfavorably correlated with Conc (−0.25) and Mot0h (−0.53). Our results indicate that the genetic correlations between weight and growth traits and semen characteristics depend on the age of the bulls. Although most genetic correlations were favorable, selection for higher daily weight gain between 150 and 330 d might explain the slight negative genetic trends observed for semen characteristics in young Norwegian Red bulls.

  • genetic analysis of semen characteristic traits in young Norwegian Red bulls
    Journal of Dairy Science, 2020
    Co-Authors: H B Olsen, B Heringstad, G Klemetsdal
    Abstract:

    ABSTRACT The aim of this study was to estimate genetic parameters and genetic trends for male fertility in Norwegian Red bulls. We analyzed data on semen characteristics traits collected at the performance test station of young bulls from 1994 to 2016, in an andrology test used to ensure acceptable semen quality before being selected as an artificial insemination bull. Traits included were volume, concentration, and motility (percentage of moving sperm cells) in fresh samples and after storing for 24 and 48 h, and sperm defects. The data consisted of 14,972 ejaculates from 3,927 young (11–15 mo) Norwegian Red bulls. Genetic parameters were estimated using bivariate linear animal models that included age in months, group-year, and collection-group (main effect of the interaction between ejaculate number and interval between collections) as fixed effects, and test-day and additive genetic and permanent environment effect of the bull as random effects. Considerable genetic coefficients of variation were found for concentration and volume, with lower values for motility. Estimated heritabilities ranged from 0.02 and 0.03 (for sperm defects and motility in fresh samples) to 0.14 (volume and concentration measuRed on a continuous scale). All estimated genetic correlations were favorable, but the genetic correlations between volume and concentration and volume and sperm defects were not significantly different from zero. The genetic correlations between concentration and motility traits ranged from 0.53 to 0.83, and those between volume and the motility traits were between 0.24 and 0.57. All traits showed a slightly unfavorable genetic trend. Our results indicate that selection of bulls with better sperm quality is possible.

  • detection of runs of homozygosity in Norwegian Red density criteria and genotyping quality control
    Acta Agriculturae Scandinavica Section A-animal Science, 2017
    Co-Authors: Borghild Hillestad, Harald Grove, Dag Inge Vage, John Woolliams, T H E Meuwissen, Solomon Antwi Boison, G Klemetsdal
    Abstract:

    ABSTRACTRuns of homozygosity (ROH) are long, homozygote segments of an individual’s genome, traceable to the parents and might be identical by descent. Due to the lack of standards for quality control of genotyping and criteria to define ROH, Norwegian Red was used to find the effects of SNP density, genotyping quality control and ROH criteria on the detection of ROH. A total of 384 bulls were genotyped with the Illumina HD-chip containing 777,962 SNP markers. A total of 22 data subsets were derived to examine the effects of SNP density, quality control of genotyping and ROH criteria. ROH was detected by PLINK. High SNP density led to increased resolution, fewer false-positive ROH segment, and made it possible to detect shorter ROH. Considering the ROH criteria, we demonstrated that allowing for heterozygote SNP could generate false positives. Furthermore, genotyping quality control should be tuned towards keeping as many SNP as possible, also low minor allele frequency SNP, as otherwise many ROH segments...

  • the relationship between Norwegian Red heifer growth and their first lactation test day milk yield a field study
    Journal of Dairy Science, 2017
    Co-Authors: Kristin S Storli, G Klemetsdal, H Volden, Ragnar Salte
    Abstract:

    ABSTRACT Today's Norwegian Red (NR) is markedly different from the one that existed 25 yr ago due to the continuous genetic improvement of economically important traits. Still, current national recommendations on replacement heifer rearing largely are based on results from Danish studies from the late 1980s to the mid 1990s. The objectives of the present study were to gain information on (1) growth and growth profiles of modern NR replacement heifers in commercial dairy herds and (2) how growth during the rearing period affects the heifers' milk yield during their first lactation. To this end, we conducted a field study on 5 high-producing and 5 low-producing commercial dairy farms from each of 3 geographical regions in Norway. On these 30 farms, we combined repeated onsite registrations of growth on all available females from newborn to calving with registrations deriving from the Norwegian Dairy Herd Recording System. Each herd was visited 6 to 8 times over a period of 2 yr. At each visit, heart girth circumference on all available young females was measuRed. Registrations were made on a total of 3,110 heifers. After imposing restrictions on the data, growth parameters were estimated based on information from 536 animals, whereas 350 of these animals had the requiRed information needed to estimate the relationship between growth and test-day milk yield. Our findings pointed toward an optimal ADG of 830 g/d from 10 to 15 mo of age that would optimize first-lactation yield of heifers in an average Norwegian dairy herd. The optimum will likely increase from selection over time. Utilizing simple proportionality, the ADG between 5 and 10 mo of age ideally should be 879 g/d, taking into account the fact that animal growth rate is higher at low ages and that a high prepubertal growth rate had no negative effect on first-lactation yield. When such a rearing practice is used to meet the requirements of today's genetically improved NR heifer, heifers can both optimize production in their first lactation and enter the milking herd earlier than the current average age of 24.8 mo.

  • selection responses for disease resistance in two selection experiments with Norwegian Red cows
    Journal of Dairy Science, 2007
    Co-Authors: B Heringstad, G Klemetsdal, T Steine
    Abstract:

    Genetic trends for clinical mastitis (CM), ketosis (KET), retained placenta (RP), and 305-d protein yield (PY305) were calculated for 2 Norwegian dairy cattle selection experiments. The first experiment, accomplished from 1978 to 1989, included groups selected for high (HMP) and low milk production (LMP). The second experiment started in 1989 and included selection for high protein yield (HPY) and low mastitis frequency (LCM). In both experiments proven sires from the active breeding program of Norwegian Red were used as sires. To take into account that selection of sires was external to the experiment, all available data from the Norwegian Red population, including disease records for 2.7 million first-lactation cows, were analyzed with a multivariate animal model. Estimated breeding values for cows in the experiments were extracted from this analysis to calculate genetic trends in the selection groups. Genetic trends for PY305 were, as expected, positive for the HMP and HPY groups, and negative for LMP and LCM. The HMP group showed increasing genetic trends for all 3 diseases, arguably a correlated response after selection for increased milk production, whereas the LCM group showed decreasing genetic trends for CM, KET, and RP. The genetic trends for KET and RP in the LCM group are most likely correlated responses after selection against CM. After 5 cow-generations the genetic difference between HPY and LCM was 10 percentage units CM, 1.5 percentage units KET, and 0.5 percentage units RP.

Daniel Gianola - One of the best experts on this subject based on the ideXlab platform.

  • inferring relationships between health and fertility in Norwegian Red cows using recursive models
    Journal of Dairy Science, 2009
    Co-Authors: B Heringstad, Daniel Gianola, Xiaolin Wu
    Abstract:

    Health and fertility are complex traits, and the phenotype for one trait may affect the phenotype of one or more other traits. For instance, disease in early lactation may impair a cow's ability to show estrus and to conceive after insemination. The objectives of the present study were to explore phenotypic and genetic relationships among health and fertility traits in Norwegian Red cows using a recursive effects model, which allows disentangling causal effects of phenotypes from the genetic and environmental correlations among traits. Records of interval from calving to first insemination (CFI), nonreturn rate within 56 d after first insemination (NR56), clinical mastitis (CM), ketosis (KET), and retained placenta from 55,568 first-lactation daughters of 1,577 Norwegian Red sires were analyzed. Trivariate recursive Gaussian-threshold models were used to analyze the 2 fertility traits (CFI and NR56) together with 1 disease trait in each analysis. The estimated structural coefficients of the recursive models imply that presence of KET or retained placenta lengthened CFI, whereas causal effects from CM to fertility were negligible. Recursive effects of disease on NR56, and of CFI on NR56, were all close to zero. Genetic correlations between health and fertility traits were low or moderate. The strongest genetic correlation was between KET and CFI (0.29), whereas genetic correlations between CM and NR56 and between CFI and NR56 were nil. In general, selection against disease is expected to slightly improve fertility (shorter CFI and higher NR56) as a correlated response and vice versa. The present results suggest that the use of structural-equation models, such as the one used here, may enhance our understanding of complex relationships among traits.

  • assessment of poisson logit and linear models for genetic analysis of clinical mastitis in Norwegian Red cows
    Journal of Dairy Science, 2009
    Co-Authors: Ana I Vazquez, Daniel Gianola, Douglas M Bates, K A Weigel, B Heringstad
    Abstract:

    Abstract Clinical mastitis is typically coded as presence/absence during some period of exposure, and records are analyzed with linear or binary data models. Because presence includes cows with multiple episodes, there is loss of information when a count is treated as a binary response. The Poisson model is designed for counting random variables, and although it is used extensively in epidemiology of mastitis, it has rarely been used for studying the genetics of mastitis. Many models have been proposed for genetic analysis of mastitis, but they have not been formally compaRed. The main goal of this study was to compare linear (Gaussian), Bernoulli (with logit link), and Poisson models for the purpose of genetic evaluation of sires for mastitis in dairy cattle. The response variables were clinical mastitis (CM; 0, 1) and number of CM cases (NCM; 0, 1, 2, …). Data consisted of records on 36,178 first-lactation daughters of 245 Norwegian Red sires distributed over 5,286 herds. PRedictive ability of models was assessed via a 3-fold cross-validation using mean squaRed error of pRediction (MSEP) as the end-point. Between-sire variance estimates for NCM were 0.065 in Poisson and 0.007 in the linear model. For CM the between-sire variance was 0.093 in logit and 0.003 in the linear model. The ratio between herd and sire variances for the models with NCM response was 4.6 and 3.5 for Poisson and linear, respectively, and for model for CM was 3.7 in both logit and linear models. The MSEP for all cows was similar. However, within healthy animals, MSEP was 0.085 (Poisson), 0.090 (linear for NCM), 0.053 (logit), and 0.056 (linear for CM). For mastitic animals the MSEP values were 1.206 (Poisson), 1.185 (linear for NCM response), 1.333 (logit), and 1.319 (linear for CM response). The models for count variables had a better performance when pRedicting diseased animals and also had a similar performance between them. Logit and linear models for CM had better pRedictive ability for healthy cows and had a similar performance between them.

  • short communication genetic analysis of respiratory disease in Norwegian Red calves
    Journal of Dairy Science, 2008
    Co-Authors: B Heringstad, Yumei Chang, Daniel Gianola, O Osteras
    Abstract:

    A genetic analysis of respiratory disease (RD) in Norwegian Red calves was conducted. This is the first genetic study of calf diseases based on data from the Norwegian health recording system, and RD was chosen because it is the most frequent disease in calves. Records on absence or presence of RD before 180 d of age for 250,212 calves (progeny of 728 Norwegian Red artificial insemination sires) were analyzed with a threshold model. A total of 0.7% of the calves had veterinary treatment of RD before 180 d of age. Heritability of RD in the underlying scale was 0.05, with a 95% cRedibility interval from 0.02 to 0.09. The "worst" sire had a pRedicted probability of RD that was more than twice as high as that of the "best" one (1.15 vs. 0.44%). Their 95% cRedibility intervals for pRedicted probability of RD, however, overlapped. With improved and more extensive recording of calf diseases, the precision in genetic evaluation of sires could increase considerably. The frequency of RD is very low in the Norwegian Red population at present, so there is not much scope for genetic improvement. However, this study indicates that reasonably precise genetic evaluation of sires for resistance to RD could be feasible.

  • a zero inflated poisson model for genetic analysis of the number of mastitis cases in Norwegian Red cows
    Journal of Dairy Science, 2007
    Co-Authors: Mariana Rodriguesmotta, B Heringstad, Daniel Gianola, G J M Rosa, Yumei Chang
    Abstract:

    The objective was to extend a zero-inflated Poisson (ZIP) model to account for correlated genetic effects, and to use this model to analyze the number of clinical mastitis cases in Norwegian Red cows. The ZIP model is suitable for analysis of count data containing an excess of zeros relative to what is expected from Poisson sampling. A ZIP model was developed and compaRed with a corresponding Poisson model. The Poisson parameter followed a hierarchical structure, and a residual term accounting for overdispersion was included. In both models, the Poisson parameter was regressed 1) on the year, month, and age at first calving; 2) on the logarithm of the number of days elapsed from calving to the end of first lactation; and c) on herd and sire effects. Herd and sire effects were assigned normal prior distributions in a Bayesian analysis, corresponding to a random effects treatment in a frequentist analysis. An analysis of residuals favoRed the Poisson model when there were 2 or more cases of mastitis during first lactation, with very small differences between the ZIP and Poisson models at 0 and 1 cases. However, the residual assessment was not satisfactory for either of the models. The ZIP model, on the other hand, had a better pRedictive ability than the corresponding Poisson model. Posterior means of the sire, herd, and residual variances in the ZIP model (log scale) were 0.09, 0.37, and 0.36, respectively, highlighting the importance of herds as a source of variation in clinical mastitis. The correlation between sire rankings from the ZIP and Poisson models was 0.98. A weaker correlation would be expected in a population with more severe inflation at zero than the present one. The estimate of the perfect state probability p was 0.32, indicating that 32% of the animals would be in the perfect state, either because they are resistant or because they were not exposed to mastitis.

  • genetic analysis of calving difficulty and stillbirth in Norwegian Red cows
    Journal of Dairy Science, 2007
    Co-Authors: B Heringstad, Morten Svendsen, Yumei Chang, Daniel Gianola
    Abstract:

    Abstract The objectives of this study were to infer genetic parameters for stillbirth (SB) and calving difficulty (CD) and to evaluate phenotypic and genetic change for these traits in the Norwegian Red breed. Stillbirth is recorded as a binary trait and calving difficulty has 3 categories: 1) easy calving, 2) slight problems, and 3) difficult calving. The overall mean frequency of SB in Norwegian Red was 3% at first calving and 1.5% for second and later calvings; mean frequency of the category “difficult calving” was 2 to 3% for heifers and 1% for cows at second and later calvings. Mean stillbirth rate has remained unchanged from 1978 to 2004. The proportion of the category “difficult calving” has not changed over the years, but the “slight problems” category increased from 4 to 7% for heifers and from 2 to 3% for cows. A total of 528,475 first-calving records were analyzed with a Bayesian bivariate sire-maternal grandsire threshold liability model. Posterior means of direct and maternal heritabilities were 0.13 and 0.09 for CD, and 0.07 and 0.08 for SB, respectively. Strong genetic correlations were found between direct SB and direct CD (0.79), and between maternal SB and maternal CD (0.62), whereas all genetic correlations between direct and maternal effects within or between traits were close to zero. These positive correlations are favorable in the sense that selection for one of the traits would result in a favorable selection response for the second trait. No genetic correlations between direct and maternal effects imply that bulls should be evaluated both as sire of the calf (direct) and sire of the cow (maternal). No genetic change for SB was found, and a slight genetic improvement for CD was detected.

Sigbjorn Lien - One of the best experts on this subject based on the ideXlab platform.

  • genome wide association mapping in Norwegian Red cattle identifies quantitative trait loci for fertility and milk production on bta12
    Animal Genetics, 2011
    Co-Authors: H G Olsen, Morten Svendsen, Matthew Peter Kent, Ben J Hayes, Torfinn Nome, A G Larsgard, Sigbjorn Lien
    Abstract:

    Reproductive performance is a critical trait in dairy cattle. Poor reproductive performance leads to prolonged calving intervals, higher culling rates and extra expenses related to multiple inseminations, veterinary treatments and replacements. Genetic gain for improved reproduction through traditional selection is often slow because of low heritability and negative correlations with production traits. Detection of DNA markers associated with improved reproductive performance through genome-wide association studies could lead to genetic gain that is more balanced between fertility and production. Norwegian Red cattle are well suited for such studies, as very large numbers of detailed reproduction records are available. We conducted a genome-wide association study for non-return rate, fertility treatments and retained placenta using almost 1 million records on these traits and 17 343 genome-wide single-nucleotide polymorphisms. Genotyping costs were minimized by genotyping the sires of the cows recorded and by using daughter averages as phenotypes. The genotyped sires were assigned to either a discovery or a validation population. Associations were only consideRed to be validated if they were significant in both groups. Strong associations were found and validated on chromosomes 1, 5, 8, 9, 11 and 12. Several of these were highly supported by findings in other studies. The most important result was an association for non-return rate in heifers in a region of BTA12 where several associations for milk production traits have previously been found. Subsequent fine-mapping verified the presence of a quantitative trait loci (QTL) having opposing effects on non-return rate and milk production at 18 Mb. The other reproduction QTL did not have pleiotropic effects on milk production, and these are therefore of considerable interest for use in marker-assisted selection.

  • molecular characterization of a long range haplotype affecting protein yield and mastitis susceptibility in Norwegian Red cattle
    BMC Genetics, 2011
    Co-Authors: Marte Sodeland, Morten Svendsen, Harald Grove, Matthew Peter Kent, Ben J Hayes, Simon Taylor, Sigbjorn Lien
    Abstract:

    Previous fine mapping studies in Norwegian Red cattle (NRC) in the region 86-90.4 Mb on Bos taurus chromosome 6 (BTA6) has revealed a quantitative trait locus (QTL) for protein yield (PY) around 88 Mb and a QTL for clinical mastitis (CM) around 90 Mb. The close proximity of these QTLs may partly explain the unfavorable genetic correlation between these two traits in NRC. A long range haplotype covering this region was introduced into the NRC population through the importation of a Holstein-Friesian bull (1606 Frasse) from Sweden in the 1970s. It has been suggested that this haplotype has a favorable effect on milk protein content but an unfavorable effect on mastitis susceptibility. Selective breeding for milk production traits is likely to have increased the frequency of this haplotype in the NRC population. Association mapping for PY and CM in NRC was performed using genotypes from 556 SNPs throughout the region 86-97 Mb on BTA6 and daughter-yield-deviations (DYDs) from 2601 bulls made available from the Norwegian dairy herd recording system. Highest test scores for PY were found for single-nucleotide polymorphisms (SNPs) within and surrounding the genes CSN2 and CSN1S2, coding for the β-casein and αS2-casein proteins. High coverage re-sequencing by high throughput sequencing technology enabled molecular characterization of a long range haplotype from 1606 Frasse encompassing these two genes. Haplotype analysis of a large number of descendants from this bull indicated that the haplotype was not markedly disrupted by recombination in this region. The haplotype was associated with both increased milk protein content and increased susceptibility to mastitis, which might explain parts of the observed genetic correlation between PY and CM in NRC. Plausible causal polymorphisms affecting PY were detected in the promoter region and in the 5'-flanking UTR of CSN1S2. These polymorphisms could affect transcription or translation of CSN1S2 and thereby affect the amount of αS2-casein in milk. Highest test scores for CM were found in the region 89-91 Mb on BTA6, very close to a cluster of genes coding for CXC chemokines. Expression levels of some of these CXC chemokines have previously been shown to increase in bovine mammary gland cell lines after exposure to bacterial cell wall components. Molecular characterization of the long range haplotype from the Holstein-Friesian bull 1606 Frasse, imported into NRC in the 1970s, revealed polymorphisms that could affect transcription or translation of the casein gene CSN1S2. Sires with this haplotype had daughters with significantly elevated milk protein content and selection for milk production traits is likely to have increased the frequency of this haplotype in the NRC population. The haplotype was also associated with increased mastitis susceptibility, which might explain parts of the genetic correlation between PY and CM in NRC.

  • Genome‐wide association mapping in Norwegian Red cattle identifies quantitative trait loci for fertility and milk production on BTA12
    Animal Genetics, 2011
    Co-Authors: H G Olsen, M Svendsen, Matthew Peter Kent, Ben J Hayes, Torfinn Nome, A G Larsgard, Sigbjorn Lien
    Abstract:

    Reproductive performance is a critical trait in dairy cattle. Poor reproductive performance leads to prolonged calving intervals, higher culling rates and extra expenses related to multiple inseminations, veterinary treatments and replacements. Genetic gain for improved reproduction through traditional selection is often slow because of low heritability and negative correlations with production traits. Detection of DNA markers associated with improved reproductive performance through genome-wide association studies could lead to genetic gain that is more balanced between fertility and production. Norwegian Red cattle are well suited for such studies, as very large numbers of detailed reproduction records are available. We conducted a genome-wide association study for non-return rate, fertility treatments and retained placenta using almost 1 million records on these traits and 17 343 genome-wide single-nucleotide polymorphisms. Genotyping costs were minimized by genotyping the sires of the cows recorded and by using daughter averages as phenotypes. The genotyped sires were assigned to either a discovery or a validation population. Associations were only consideRed to be validated if they were significant in both groups. Strong associations were found and validated on chromosomes 1, 5, 8, 9, 11 and 12. Several of these were highly supported by findings in other studies. The most important result was an association for non-return rate in heifers in a region of BTA12 where several associations for milk production traits have previously been found. Subsequent fine-mapping verified the presence of a quantitative trait loci (QTL) having opposing effects on non-return rate and milk production at 18 Mb. The other reproduction QTL did not have pleiotropic effects on milk production, and these are therefore of considerable interest for use in marker-assisted selection.

  • recent and historical recombination in the admixed Norwegian Red cattle breed
    BMC Genomics, 2011
    Co-Authors: Marte Sodeland, Harald Grove, Matthew Peter Kent, Ben J Hayes, Sigbjorn Lien
    Abstract:

    Comparison of recent patterns of recombination derived from linkage maps to historical patterns of recombination from linkage disequilibrium (LD) could help identify genomic regions affected by strong artificial selection, appearing as Reduced recent recombination. Norwegian Red cattle (NRF) make an interesting case study for investigating these patterns as it is an admixed breed with an extensively recorded pedigree. NRF have been under strong artificial selection for traits such as milk and meat production, fertility and health. While measures of LD is also crucial for determining the number of markers requiRed for association mapping studies, estimates of recombination rate can be used to assess quality of genomic assemblies. A dataset containing more than 17,000 genome-wide distributed SNPs and 2600 animals was used to assess recombination rates and LD in NRF. Although low LD measuRed by r2 was observed in NRF relative to some of the breeds from which this breed originates, reports from breeds other than those assessed in this study have described more rapid decline in r2 at short distances than what was found in NRF. Rate of decline in r2 for NRF suggested that to obtain an expected r2 between markers and a causal polymorphism of at least 0.5 for genome-wide association studies, approximately one SNP every 15 kb or a total of 200,000 SNPs would be requiRed. For well known quantitative trait loci (QTLs) for milk production traits on Bos Taurus chromosomes 1, 6 and 20, map length based on historic recombination was greater than map length based on recent recombination in NRF. Further, positions for 130 previously unpositioned contigs from assembly of the bovine genome sequence (Btau_4.0) found using comparative sequence analysis were validated by linkage analysis, and 28% of these positions corresponded to extreme values of population recombination rate. While LD is Reduced in NRF compaRed to some of the breeds from which this admixed breed originated, it is elevated over short distances compaRed to some other cattle breeds. Genomic regions in NRF where map length based on historic recombination was greater than map length based on recent recombination coincided with some well known QTL regions for milk production traits. Linkage analysis in combination with comparative sequence analysis and detection of regions with extreme values of population recombination rate proved to be valuable for detecting problematic regions in the Btau_4.0 genome assembly.

  • the accuracy of genomic selection in Norwegian Red cattle assessed by cross validation
    Genetics, 2009
    Co-Authors: Tu Luan, Morten Svendsen, Sigbjorn Lien, John Woolliams, Matthew Peter Kent, Theo H E Meuwissen
    Abstract:

    Genomic Selection (GS) is a newly developed tool for the estimation of breeding values for quantitative traits through the use of dense markers covering the whole genome. For a successful application of GS, accuracy of the pRediction of genomewide breeding value (GW-EBV) is a key issue to consider. Here we investigated the accuracy and possible bias of GW-EBV pRediction, using real bovine SNP genotyping (18,991 SNPs) and phenotypic data of 500 Norwegian Red bulls. The study was performed on milk yield, fat yield, protein yield, first lactation mastitis traits, and calving ease. Three methods, best linear unbiased pRediction (G-BLUP), Bayesian statistics (BayesB), and a mixture model approach (MIXTURE), were used to estimate marker effects, and their accuracy and bias were estimated by using cross-validation. The accuracies of the GW-EBV pRediction were found to vary widely between 0.12 and 0.62. G-BLUP gave overall the highest accuracy. We observed a strong relationship between the accuracy of the pRediction and the heritability of the trait. GW-EBV pRediction for production traits with high heritability achieved higher accuracy and also lower bias than health traits with low heritability. To achieve a similar accuracy for the health traits probably more records will be needed.

Yumei Chang - One of the best experts on this subject based on the ideXlab platform.

  • short communication genetic analysis of respiratory disease in Norwegian Red calves
    Journal of Dairy Science, 2008
    Co-Authors: B Heringstad, Yumei Chang, Daniel Gianola, O Osteras
    Abstract:

    A genetic analysis of respiratory disease (RD) in Norwegian Red calves was conducted. This is the first genetic study of calf diseases based on data from the Norwegian health recording system, and RD was chosen because it is the most frequent disease in calves. Records on absence or presence of RD before 180 d of age for 250,212 calves (progeny of 728 Norwegian Red artificial insemination sires) were analyzed with a threshold model. A total of 0.7% of the calves had veterinary treatment of RD before 180 d of age. Heritability of RD in the underlying scale was 0.05, with a 95% cRedibility interval from 0.02 to 0.09. The "worst" sire had a pRedicted probability of RD that was more than twice as high as that of the "best" one (1.15 vs. 0.44%). Their 95% cRedibility intervals for pRedicted probability of RD, however, overlapped. With improved and more extensive recording of calf diseases, the precision in genetic evaluation of sires could increase considerably. The frequency of RD is very low in the Norwegian Red population at present, so there is not much scope for genetic improvement. However, this study indicates that reasonably precise genetic evaluation of sires for resistance to RD could be feasible.

  • a zero inflated poisson model for genetic analysis of the number of mastitis cases in Norwegian Red cows
    Journal of Dairy Science, 2007
    Co-Authors: Mariana Rodriguesmotta, B Heringstad, Daniel Gianola, G J M Rosa, Yumei Chang
    Abstract:

    The objective was to extend a zero-inflated Poisson (ZIP) model to account for correlated genetic effects, and to use this model to analyze the number of clinical mastitis cases in Norwegian Red cows. The ZIP model is suitable for analysis of count data containing an excess of zeros relative to what is expected from Poisson sampling. A ZIP model was developed and compaRed with a corresponding Poisson model. The Poisson parameter followed a hierarchical structure, and a residual term accounting for overdispersion was included. In both models, the Poisson parameter was regressed 1) on the year, month, and age at first calving; 2) on the logarithm of the number of days elapsed from calving to the end of first lactation; and c) on herd and sire effects. Herd and sire effects were assigned normal prior distributions in a Bayesian analysis, corresponding to a random effects treatment in a frequentist analysis. An analysis of residuals favoRed the Poisson model when there were 2 or more cases of mastitis during first lactation, with very small differences between the ZIP and Poisson models at 0 and 1 cases. However, the residual assessment was not satisfactory for either of the models. The ZIP model, on the other hand, had a better pRedictive ability than the corresponding Poisson model. Posterior means of the sire, herd, and residual variances in the ZIP model (log scale) were 0.09, 0.37, and 0.36, respectively, highlighting the importance of herds as a source of variation in clinical mastitis. The correlation between sire rankings from the ZIP and Poisson models was 0.98. A weaker correlation would be expected in a population with more severe inflation at zero than the present one. The estimate of the perfect state probability p was 0.32, indicating that 32% of the animals would be in the perfect state, either because they are resistant or because they were not exposed to mastitis.

  • genetic analysis of calving difficulty and stillbirth in Norwegian Red cows
    Journal of Dairy Science, 2007
    Co-Authors: B Heringstad, Morten Svendsen, Yumei Chang, Daniel Gianola
    Abstract:

    Abstract The objectives of this study were to infer genetic parameters for stillbirth (SB) and calving difficulty (CD) and to evaluate phenotypic and genetic change for these traits in the Norwegian Red breed. Stillbirth is recorded as a binary trait and calving difficulty has 3 categories: 1) easy calving, 2) slight problems, and 3) difficult calving. The overall mean frequency of SB in Norwegian Red was 3% at first calving and 1.5% for second and later calvings; mean frequency of the category “difficult calving” was 2 to 3% for heifers and 1% for cows at second and later calvings. Mean stillbirth rate has remained unchanged from 1978 to 2004. The proportion of the category “difficult calving” has not changed over the years, but the “slight problems” category increased from 4 to 7% for heifers and from 2 to 3% for cows. A total of 528,475 first-calving records were analyzed with a Bayesian bivariate sire-maternal grandsire threshold liability model. Posterior means of direct and maternal heritabilities were 0.13 and 0.09 for CD, and 0.07 and 0.08 for SB, respectively. Strong genetic correlations were found between direct SB and direct CD (0.79), and between maternal SB and maternal CD (0.62), whereas all genetic correlations between direct and maternal effects within or between traits were close to zero. These positive correlations are favorable in the sense that selection for one of the traits would result in a favorable selection response for the second trait. No genetic correlations between direct and maternal effects imply that bulls should be evaluated both as sire of the calf (direct) and sire of the cow (maternal). No genetic change for SB was found, and a slight genetic improvement for CD was detected.

  • A periodic analysis of longitudinal binary responses: a case study of clinical mastitis in Norwegian Red cows
    Genetics Selection Evolution, 2007
    Co-Authors: Yumei Chang, Bjørg Heringstad, Daniel Gianola, Gunnar Klemetsdal
    Abstract:

    A Bayesian procedure for analyzing longitudinal binary responses using a periodic cosine function was developed. It was assumed that, after adjustment for "seasonal" effects, the oscillation of the underlying latent variables for longitudinal binary responses was a stationary series. Based on this assumption, a single dimension sinusoidal analysis of longitudinal binary responses using the Gibbs sampling and Metropolis algorithms was implemented in a study of clinical mastitis records of Norwegian Red cows taken over five lactations.

  • short communication genetic analysis of nonreturn rate and mastitis in first lactation Norwegian Red cows
    Journal of Dairy Science, 2006
    Co-Authors: B Heringstad, Yumei Chang, Daniel Gianola, I M Andersenranberg
    Abstract:

    Abstract Associations between clinical mastitis (CM) and nonreturn rate within 56 d after first insemination (NR56) were examined in Norwegian Red (NRF) cows. Records on absence or presence of CM within each of the intervals, −30 to 30, 31 to 150, and 151 to 300 d after first calving, and records on NR56 for 620,492 first-lactation daughters of 3,064 NRF sires were analyzed with a Bayesian multivariate threshold liability model. Point estimates of genetic correlations between NR56 and the 3 CM traits were between −0.05 and −0.02. Residual correlations were close to zero, and correlations between herd-5-yr effects on NR56 and CM in the 3 lactation intervals ranged from −0.15 to −0.17. It appears that CM and NR56 in first lactation are independent traits.