E. Kalm | Christian-Albrechts-Universität zu Kiel (original) (raw)

Papers by E. Kalm

Journal of Animal Breeding and Genetics, 2000

ABSTRACT A previously published data-set with observations on supernumerary teats (hyperthelia) i... more ABSTRACT A previously published data-set with observations on supernumerary teats (hyperthelia) in dual-purpose Simmental was reanalysed by The data comprised 537 unrelated animals and 614 members of 27 paternal half-sib families with known phenotype of each sire. The frequency of hyperthelia was 58% in unrelated animals, 51% in families with unaffected sire, and 73% in families with affected sires. Six different cases of single-gene inheritance were considered. The highest log likelihood was obtained for additive inheritance and for a recessive pattern with 100% penetrance for recessive homozygotes and 32% for both other genotypes. Estimates for the gene frequency of the favourable allele were 0.34 and 0.29, respectively. Simple dominance or recessiveness with full or incomplete penetrance could be excluded. The possibility of finding paternal half-sib families with a heterozygous sire as a resource for a mapping experiment seem to be good in German Simmental.

Archives Animal Breeding, 2002

From 1997 to 1999 1005 new born German Holstein calves were investigated for the incidence of sup... more From 1997 to 1999 1005 new born German Holstein calves were investigated for the incidence of supernumerary teats. Age at inspection varied from 1 to 4 weeks. In total 110 affected calves (20 male and 90 female) and their 21 sires were genotyped for five chromosome 3 microsatellites. The average size of half-sib families was 5.2 ranging from 2 to 17. A non-parametric multipoint linkage analysis showed no evidence for linkage.

Small Ruminant Research, 2008

Reproductive records of 5373 Lori-Bakhtiari ewes were collected from a research flock at the Lori... more Reproductive records of 5373 Lori-Bakhtiari ewes were collected from a research flock at the Lori-Bakhtiari sheep breeding station during 1989–2005. Genetic parameters were estimated for six basic and six composite traits. The basic traits were conception rate (CR), total number of lambs born (NLB), number of lambs born alive (NLBA), number of lambs alive at weaning (NLAW), litter mean weight

Archives Animal Breeding, 2001

Title of the paper: Genetic analysis of the course of individual growth and feed intake of group-... more Title of the paper: Genetic analysis of the course of individual growth and feed intake of group-penned Performance tested boars Objective ofthe study was to analyse the course of feed intake and growth of 661 boars of three lines (259, 208, and 194 animals of lines 3, 4, and 8, respectively) during an age dependent Performance test between the lOO" 1 and 170 day of age. Individual feed intake ofthe group-penned animals was recorded by electronic feeding stations during the first, third, fifth, seventh, and ninth week on test. Additionally, each animal was weighted in biweekly intervalls. A second order polynomial and a third order polynomial were individually fitted on feed intake and live weight. From these curves, individual information about daily feed intake, daily gain, and food conversion ratio were derived for five periods of 12 days and for the entire period. Genetic parameters were estimated simultaneously using a multiple trait animal model. Heritabilities of h 2 = .50, .55, .40, and .39 for traits of entire test period were found for backfat thickness, daily gain, daily feed intake, and food conversion ratio, respectively. Estimated heritabilities for each test period from one to five were h 2 = .50, .56, .54, .50, and .37 for daily gain, h 2 = .18, .43, .46, .45, and .38 for daily feed intake, and h 2 = .34, .42, .46, .44, and .39 for food conversion. The genetic correlation between daily gain and food conversion in period one (r g =-.84) was significantly different from correlations between these traits in the following periods (r g =-.32 to-.51). Genetic correlations between daily gain and daily feed intake in each period were r g = .56 to .42 from first to last period. Except of first period (r g =-.11), the genetic associations between food conversion and daily feed intake for periods were similar (r g = .52 to .56). The genetic associations indicate, that a high feed intake in the beginning of the fattening period is desirable, while afterwards a more reduced feed intake should be achieved to improve efficiency of fattening Performance. In order to optimise fattening Performance, the use of part test information from growth rate and feed intake is necessary.

Archives Animal Breeding, 2000

The present study deals with estimation of genetic parameter for purebred and crossbred Performan... more The present study deals with estimation of genetic parameter for purebred and crossbred Performance of live born piglets, in order to choose the optimal selection method. Data sets of two pure breeds, line L03 and L04, with 5,422 sows, a two line crossbred, L303, with 3,553 sows and a three line crossbred, L350, with 3,609 sows of a North-German breeding Company were recorded. Estimated genetic correlation between purebred and crossbred Performance were rg = 0.59 and 0.40 for reciprocal crosses L03xL04 and L04xL03, respectively. Further investigations showed that the genetic correlation is influenced by genotype-environment interactions between a nucleus farm and a farm on production level. Full-sib effects showed a proportion of FS = 0.06 on the phenotypic variance of litter size. They were confounded with additive genetic variance and permanent environment variance, when full-sib effects were neglected. The percentage of equal selected purebred sires of line L03 were 80% when 30% ...

Archives Animal Breeding, 2001

The objectives of this study were the analysis of the effect of driver on racing Performances of ... more The objectives of this study were the analysis of the effect of driver on racing Performances of trotters and development of a genetic model in order to estimate genetic parameters for German trotters. Data on 6,611 trotters with 163,322 records during 1997 and 1999 were analysed with a repeatability animal model using each individual start of trotters and pedigree information of up to 11 generations (13,202 horses). Besides the driver effect, the genetic model included year-season, age and sex of trotter, racing track, distance and condition of race track as fixed effects as well as additive genetic and permanent environmental effects as random effects. Traits analysed were Square root. of rank at finish, racing time per km and the logarithms of earnings per start. Ignoring the effect of driver resulted in an overestimation of heritability of 60, 24 and 44% for rank at finish, racing time and earnings, respectively, which shows the necessity to include the driver effect in the mode...

Animal Genetics, 2001

The results of genotypic data contributed to the International Society of Animal Genetics (ISAG) ... more The results of genotypic data contributed to the International Society of Animal Genetics (ISAG) Bovine Chromosome 11 (BTA11) Workshop are presented. Six laboratories contributed a total of 26 199 informative meioses from 80 loci. Thirty-six loci were typed by at least two independent laboratories and were used to construct a consensus linkage map of the chromosome. The remaining loci were subsequently incorporated into a comprehensive map. The sex-averaged consensus map covered 128.9 cM. The female consensus map was 101.2 cM, while the male consensus map was 129.8 cM. The comprehensive sex-averaged map was 134.2 cM and the average genetic distance between loci was 1.72 cM.

Journal of dairy science, 2006

Data from 3,200 Holstein cows from 3 commercial dairy farms in Germany were used to estimate heri... more Data from 3,200 Holstein cows from 3 commercial dairy farms in Germany were used to estimate heritabilities and breeding values for liability to udder diseases (UD), fertility diseases (FD), metabolic diseases (MD), and claw and leg diseases (CLD) using single-trait threshold sire models. A total of 92,722 medical treatments recorded from 1998 to 2003 were included in the analysis. Approximate genetic correlations between persistency of milk yield, fat yield, protein yield, and persistency of milk energy yield and liability to the health traits were calculated based on correlations between EBV. Posterior means of heritability of liability ranged from 0.05 to 0.08 for UD, from 0.04 to 0.07 for FD, from 0.08 to 0.12 for MD, and from 0.04 to 0.07 for CLD. Approximate genetic correlations of the disease traits with the persistency traits were favorable, except for MD in all lactations, which were unfavorable, and UD, which were around zero. Highest correlations in the range of 0.13 to 0...

Poultry Science, 2007

Variance components and breeding values were estimated for 3 reproductive traits in a pure line o... more Variance components and breeding values were estimated for 3 reproductive traits in a pure line of White Leghorn laying hens. The traits were proportion of fertile eggs of eggs set, proportion of first quality chicks of eggs set, and proportion of first-quality chicks of fertile eggs. A total of 3,020 hens were tested up to 3 times over a period of 7 d. For the definition of the traits, each egg was scored for each trait either as 0 or 1. To account for the binomial distribution of the data, a Bayesian animal threshold model implemented in a Gibbs sampler was

Meat Science, 2011

The aim of the research was to gain a better understanding of the genomic regulation of meat qual... more The aim of the research was to gain a better understanding of the genomic regulation of meat quality by investigating individual and epistatic QTL in a three-generation full-sib population (Pietrain × crossbred dam line). In total, 386 animals were genotyped for 96 markers. Analysed traits included pH, reflectance value, conductivity, and meat colour. Thirteen significant individual QTL were identified. The most significant QTL were detected on SSC1 and SSC9 for pH, on SSC4 for meat colour, and on SSC8 for conductivity, accounting for 3.4% to 4.7% of the phenotypic variance. Nine significant epistatic QTL pairs were detected accounting for between 5.7% and 10.9% of the phenotypic variance. Epistatic QTL pairs showing the largest effects were for reflectance value between two locations of SSC4, and for pH between SSC10 and SSC13, explaining 9.5% and 10.9% of the phenotypic variance, respectively. This study indicates that meat quality traits are influenced by numerous QTL as well as a complex network of interactions.

Livestock Science, 2011

Numerous quantitative trait loci (QTL) have been identified for growth and feed intake in pigs, h... more Numerous quantitative trait loci (QTL) have been identified for growth and feed intake in pigs, however, there are currently no reports of interactions between QTL (epistasis) for these traits at different stages of growth. A genomic scan for epistatic QTL was conducted on animals from a three generation full-sib population, created by crossing Pietrain sires with a crossbred dam line. All types of two-locus interactions were fitted in the model using Cockerham's decomposition, by regressing on a linear combination of the individual QTL origin probabilities. This study is the first to report epistatic QTL for growth, feed intake and chemical body composition in pigs. Eighteen significant epistatic QTL pairs were identified, seven affecting growth, six affecting feed intake or food conversion ratio, and five affecting chemical body composition. Most interacting QTL resided on different chromosomes; only two were located on the same chromosome. The identified QTL pairs explained substantial proportions of the phenotypic variance, from 5% to 10.3%. All types of digenic epistatic effects were identified with the additive-by-additive effect being the most prevalent. These findings suggest that epistasis is important in the genomic regulation of growth, feed intake and chemical body composition. Furthermore, interactions occur between different pairs of epistatic QTL for the same trait depending on the growth stage, increasing the complexity of genomic networks. This agrees with studies on gene expression levels which showed that those are time and tissue dependent.

Livestock Production Science, 2003

The use of feed intake behaviour traits, obtained from electronic feeding stations, and feed inta... more The use of feed intake behaviour traits, obtained from electronic feeding stations, and feed intake curve parameters to genetically improve performance traits was analysed. Daily feed intake and feed intake behaviour of 5601 group-penned boars of two dam lines were recorded by electronic feeders in weeks 1, 3, 5, 7 and 9 during 10 weeks (100–170 d) on performance test.

Livestock Production Science, 2003

The objective of this study was to find the best function and covariance structure to estimate fe... more The objective of this study was to find the best function and covariance structure to estimate feed intake pattern in growing pigs for breeding purposes in order to optimise the feed intake curve corresponding to lean growth rate. Daily feed intake from 81 group-housed pigs was ...

Livestock Production Science, 2003

The objective of this study was the development of a genetic statistical method for longitudinal ... more The objective of this study was the development of a genetic statistical method for longitudinal data of daily feed intake in growing pigs using random regression models (RRM) in order to change the pattern of feed intake by selection. Besides a quadratic RRM for additive genetic effects, different combinations of covariance structures for permanent environmental effects using RRM and for temporary residual effects were fitted to individual information from 5245 boars (2938 of line 3, 2307 of line 4) in order to obtain the best fitting model for daily feed intake recorded during a test period of 10 weeks. Based on Akaike’s Information Criterion, the parsimonious model included a constant diagonal covariance structure for the permanent environmental effects and a heterogeneous autoregressive-moving-average structure of order (1,1) for temporary residual effects. Estimates of the autocorrelation were 0.80 (line 3) and 0.81 (line 4) and estimates of the moving-average components were 0.15 (line 3) and 0.11 (line 4). Estimates of heritabilities were low and increased from 0.02 to 0.06 during the test, with the highest estimates in the seventh week on test. The low heritabilities were only due to a higher residual variance when using individual daily records of feed intake, whereas additive genetic variances (0.01 to 0.04 kg2) were similar to estimates using average records of feed intake. Genetic correlations between intercept and linear regression coefficients were positive within 0.57 and 0.55, those between intercept and quadratic regression coefficients were negative within −0.77 and −0.89, and those between linear and quadratic coefficients were within −0.48 and −0.61 for lines 3 and 4, respectively, indicating the opportunity for changing the feed intake pattern. Additionally, eigenfunctions obtained from the additive genetic (co)variance matrix indicated that a genetic change in feed intake pattern is achievable, e.g. the second major eigenfunction, which explained about 10% of the additive genetic variation, allowed selection for a high increase in feed intake at the beginning of the test period and for reduced feed intake at the end of the test period in order to improve feed efficiency.

Livestock Production Science, 2002

... Means and standard errors of R 2 , Durbin Watson Statistics (DBW) and residual standard devia... more ... Means and standard errors of R 2 , Durbin Watson Statistics (DBW) and residual standard deviations (RSDs) are presented in Table 5. The DBW statistic indicated no significant autocorrelation of the residuals for all functions. ...

Livestock Production Science, 1996

Voluntary feed intake, feed intake pattern and performance traits were recorded on 3188 group hou... more Voluntary feed intake, feed intake pattern and performance traits were recorded on 3188 group housed boars of Landrace and Large White tested from day 100 to day 170. Measurements of feed intake and feed intake behaviour were obtained by electronic feed dispensers (ACEMO) under ad libitum conditions. Heritabilities of feed intake in periods 1 to 5 and over the entire test period were estimated to be 0.16, 0.24, 0.30, 0.27, 0.26, and 0.22, respectively. The maximum heritability of daily feed intake in the third time period on test corresponds to about 130 days of age at about 85 kg of weight. Daily feed intake in this period showed a high genetic correlation with the average feed intake over the whole performance test (rg = 0.91). Estimates of genetic correlations between daily feed intake and feed conversion ratio, residual feed intake, average daily gain or backfat thickness were 0.04, 0.97, 0.62 and 0.42, respectively. Boars feed intake activities decreased over time while time per day in the feeder was almost constant. Traits of feed intake behaviour as feeding rate, feed intake/visit, number of visits, time per visit, and time per day in the feeder showed high heritabilities of 0.44, 0.51, 0.43, 0.42, and 0.43, respectively, but genetic correlations with performance and carcass traits were generally low. One exception was the behavioural trait time per day in the feeder with its moderate genetic correlations to daily feed intake (rg = 0.44) and average daily gain on test (rg = 0.32). Selection for lean growth will improve lean growth feed efficiency as indicated by the negative correlation of −0.47. But more efficient may be the use of the component traits, lean content, daily feed intake and daily gain in particular of the most informative test period.

Livestock Production Science, 2005

Two different statistical models considering racetrack or individual race as fixed effect were co... more Two different statistical models considering racetrack or individual race as fixed effect were compared, regarding genetic parameters and by using cross validation. Data for variance component estimation consisted of 48,942 performance observations from 4249 trotters. Variance components for the traits square root of rank at finish, racing time per km, and log of earnings per race were estimated by REML using two multiple trait animal models involving different racetracks or individual races. When including each individual race instead of racetracks in the statistical model, heritabilities increased from 0.05 to 0.07, 0.19 to 0.23, and 0.08 to 0.09 for square root of rank at finish, racing time per km, and log of earnings per race, respectively. Genetic and phenotypic correlations among traits increased also after consideration of individual races. Square root of rank at finish, as well as racing time per km and log of earnings per race, was highly genetically correlated with −0.99 and −0.88. The two statistical models were compared on the basis of their predictive ability by using cross validation. Data for these analyses consisted of 706,082 observations from 21,363 trotters. Randomly eliminated performance observations were predicted by cumulation of fixed and random effects obtained from estimation of breeding values for both models. Estimates for racing time showed lower bias and mean square error (MSE) when considering individual races instead of racetracks. Also, the correlation between predicted and true phenotypic value increased from 0.85 to 0.92. Estimates for square root of rank at finish were unbiased, but with a higher MSE when considering individual race effect. A similar high bias and MSE with both models were obtained for log of earnings. In order to avoid bias in estimation of genetic parameters and breeding values for racing time and square root of rank at finish, inclusion of each individual race in the statistical model was recommended.

Journal of Animal Science, 2010

The present study focused on the identification of epistatic QTL pairs for body composition trait... more The present study focused on the identification of epistatic QTL pairs for body composition traits (carcass cut, lean tissue, and fat tissue weights) measured at slaughter weight (140 kg of BW) in a 3-generation full-sib population developed by crossing Pietrain sires with a crossbred dam line. Depending on the trait, phenotypic observations were available for 306 to 315 F(2) animals. For the QTL analysis, 386 animals were genotyped for 88 molecular markers covering chromosomes SSC1, SSC2, SSC4, SSC6, SSC7, SSC8, SSC9, SSC10, SSC13, and SSC14. In total, 23 significant epistatic QTL pairs were identified, with the additive x additive genetic interaction being the most prevalent. Epistatic QTL were identified across all chromosomes except for SSC13, and epistatic QTL pairs accounted for between 5.8 and 10.2% of the phenotypic variance. Seven epistatic QTL pairs were between QTL that resided on the same chromosome, and 16 were between QTL that resided on different chromosomes. Sus scrofa chromosome 1, SSC2, SSC4, SSC6, SSC8, and SSC9 harbored the greatest number of epistatic QTL. The epistatic QTL pair with the greatest effect was for the entire loin weight between 2 locations on SSC7, explaining 10.2% of the phenotypic variance. Epistatic associations were identified between regions of the genome that contain the IGF-2 or melanocortin-4 receptor genes, with QTL residing in other genomic locations. Quantitative trait loci in the region of the melanocortin-4 receptor gene and on SSC7 showed significant positive dominance effects for entire belly weight, which were offset by negative dominance x dominance interactions between these QTL. In contrast, the QTL in the region of the IGF-2 gene showed significant negative dominance effects for entire ham weight, which were largely overcompensated for by positive additive x dominance genetic effects with a QTL on SSC9. The study shows that epistasis is of great importance for the genomic regulation of body composition in pigs and contributes substantially to the variation in complex traits.

Journal of Animal Breeding and Genetics, 2003

The factors leading to the bias of quantitative trait loci (QTL) effect estimates were investigat... more The factors leading to the bias of quantitative trait loci (QTL) effect estimates were investigated by simulating paternal half-sib families. An upward bias was found in nearly all simulated configurations when only significant replicates were considered. This bias was a function of the experimental power of detecting a QTL (increased bias when power decreased) and was attributed to biased sampling. Three non-parametric bootstrap schemes were tested to re-estimate bias-reduced QTL effects. The classical bootstrap bias corrected re-estimate and the permutation bootstrap bias corrected re-estimate failed to reduce the bias substantially. With the 0.368-bootstrap the entire data set was repeatedly split into an estimation set formed by the bootstrap sample and into an independent test set formed by progeny not found in the estimation set. The size of the test set is asymptotically 0.368 times the number of progeny. The estimation set was used for calibration (i.e. estimating QTL position), and the test set was used for validation (i.e. estimating QTL effect at the particular position). The 0.368bootstrap re-estimate was the mean effect estimate from validation from all bootstrap runs. The 0.368bootstrap produced on average significantly less biased QTL effects which showed reduced mean square errors compared with the original estimates. It was relatively robust against biased sampling.

Journal of Animal Breeding and Genetics, 2001

ABSTRACT

Journal of Animal Breeding and Genetics, 2000

ABSTRACT A previously published data-set with observations on supernumerary teats (hyperthelia) i... more ABSTRACT A previously published data-set with observations on supernumerary teats (hyperthelia) in dual-purpose Simmental was reanalysed by The data comprised 537 unrelated animals and 614 members of 27 paternal half-sib families with known phenotype of each sire. The frequency of hyperthelia was 58% in unrelated animals, 51% in families with unaffected sire, and 73% in families with affected sires. Six different cases of single-gene inheritance were considered. The highest log likelihood was obtained for additive inheritance and for a recessive pattern with 100% penetrance for recessive homozygotes and 32% for both other genotypes. Estimates for the gene frequency of the favourable allele were 0.34 and 0.29, respectively. Simple dominance or recessiveness with full or incomplete penetrance could be excluded. The possibility of finding paternal half-sib families with a heterozygous sire as a resource for a mapping experiment seem to be good in German Simmental.

Archives Animal Breeding, 2002

From 1997 to 1999 1005 new born German Holstein calves were investigated for the incidence of sup... more From 1997 to 1999 1005 new born German Holstein calves were investigated for the incidence of supernumerary teats. Age at inspection varied from 1 to 4 weeks. In total 110 affected calves (20 male and 90 female) and their 21 sires were genotyped for five chromosome 3 microsatellites. The average size of half-sib families was 5.2 ranging from 2 to 17. A non-parametric multipoint linkage analysis showed no evidence for linkage.

Small Ruminant Research, 2008

Reproductive records of 5373 Lori-Bakhtiari ewes were collected from a research flock at the Lori... more Reproductive records of 5373 Lori-Bakhtiari ewes were collected from a research flock at the Lori-Bakhtiari sheep breeding station during 1989–2005. Genetic parameters were estimated for six basic and six composite traits. The basic traits were conception rate (CR), total number of lambs born (NLB), number of lambs born alive (NLBA), number of lambs alive at weaning (NLAW), litter mean weight

Archives Animal Breeding, 2001

Title of the paper: Genetic analysis of the course of individual growth and feed intake of group-... more Title of the paper: Genetic analysis of the course of individual growth and feed intake of group-penned Performance tested boars Objective ofthe study was to analyse the course of feed intake and growth of 661 boars of three lines (259, 208, and 194 animals of lines 3, 4, and 8, respectively) during an age dependent Performance test between the lOO" 1 and 170 day of age. Individual feed intake ofthe group-penned animals was recorded by electronic feeding stations during the first, third, fifth, seventh, and ninth week on test. Additionally, each animal was weighted in biweekly intervalls. A second order polynomial and a third order polynomial were individually fitted on feed intake and live weight. From these curves, individual information about daily feed intake, daily gain, and food conversion ratio were derived for five periods of 12 days and for the entire period. Genetic parameters were estimated simultaneously using a multiple trait animal model. Heritabilities of h 2 = .50, .55, .40, and .39 for traits of entire test period were found for backfat thickness, daily gain, daily feed intake, and food conversion ratio, respectively. Estimated heritabilities for each test period from one to five were h 2 = .50, .56, .54, .50, and .37 for daily gain, h 2 = .18, .43, .46, .45, and .38 for daily feed intake, and h 2 = .34, .42, .46, .44, and .39 for food conversion. The genetic correlation between daily gain and food conversion in period one (r g =-.84) was significantly different from correlations between these traits in the following periods (r g =-.32 to-.51). Genetic correlations between daily gain and daily feed intake in each period were r g = .56 to .42 from first to last period. Except of first period (r g =-.11), the genetic associations between food conversion and daily feed intake for periods were similar (r g = .52 to .56). The genetic associations indicate, that a high feed intake in the beginning of the fattening period is desirable, while afterwards a more reduced feed intake should be achieved to improve efficiency of fattening Performance. In order to optimise fattening Performance, the use of part test information from growth rate and feed intake is necessary.

Archives Animal Breeding, 2000

The present study deals with estimation of genetic parameter for purebred and crossbred Performan... more The present study deals with estimation of genetic parameter for purebred and crossbred Performance of live born piglets, in order to choose the optimal selection method. Data sets of two pure breeds, line L03 and L04, with 5,422 sows, a two line crossbred, L303, with 3,553 sows and a three line crossbred, L350, with 3,609 sows of a North-German breeding Company were recorded. Estimated genetic correlation between purebred and crossbred Performance were rg = 0.59 and 0.40 for reciprocal crosses L03xL04 and L04xL03, respectively. Further investigations showed that the genetic correlation is influenced by genotype-environment interactions between a nucleus farm and a farm on production level. Full-sib effects showed a proportion of FS = 0.06 on the phenotypic variance of litter size. They were confounded with additive genetic variance and permanent environment variance, when full-sib effects were neglected. The percentage of equal selected purebred sires of line L03 were 80% when 30% ...

Archives Animal Breeding, 2001

The objectives of this study were the analysis of the effect of driver on racing Performances of ... more The objectives of this study were the analysis of the effect of driver on racing Performances of trotters and development of a genetic model in order to estimate genetic parameters for German trotters. Data on 6,611 trotters with 163,322 records during 1997 and 1999 were analysed with a repeatability animal model using each individual start of trotters and pedigree information of up to 11 generations (13,202 horses). Besides the driver effect, the genetic model included year-season, age and sex of trotter, racing track, distance and condition of race track as fixed effects as well as additive genetic and permanent environmental effects as random effects. Traits analysed were Square root. of rank at finish, racing time per km and the logarithms of earnings per start. Ignoring the effect of driver resulted in an overestimation of heritability of 60, 24 and 44% for rank at finish, racing time and earnings, respectively, which shows the necessity to include the driver effect in the mode...

Animal Genetics, 2001

The results of genotypic data contributed to the International Society of Animal Genetics (ISAG) ... more The results of genotypic data contributed to the International Society of Animal Genetics (ISAG) Bovine Chromosome 11 (BTA11) Workshop are presented. Six laboratories contributed a total of 26 199 informative meioses from 80 loci. Thirty-six loci were typed by at least two independent laboratories and were used to construct a consensus linkage map of the chromosome. The remaining loci were subsequently incorporated into a comprehensive map. The sex-averaged consensus map covered 128.9 cM. The female consensus map was 101.2 cM, while the male consensus map was 129.8 cM. The comprehensive sex-averaged map was 134.2 cM and the average genetic distance between loci was 1.72 cM.

Journal of dairy science, 2006

Data from 3,200 Holstein cows from 3 commercial dairy farms in Germany were used to estimate heri... more Data from 3,200 Holstein cows from 3 commercial dairy farms in Germany were used to estimate heritabilities and breeding values for liability to udder diseases (UD), fertility diseases (FD), metabolic diseases (MD), and claw and leg diseases (CLD) using single-trait threshold sire models. A total of 92,722 medical treatments recorded from 1998 to 2003 were included in the analysis. Approximate genetic correlations between persistency of milk yield, fat yield, protein yield, and persistency of milk energy yield and liability to the health traits were calculated based on correlations between EBV. Posterior means of heritability of liability ranged from 0.05 to 0.08 for UD, from 0.04 to 0.07 for FD, from 0.08 to 0.12 for MD, and from 0.04 to 0.07 for CLD. Approximate genetic correlations of the disease traits with the persistency traits were favorable, except for MD in all lactations, which were unfavorable, and UD, which were around zero. Highest correlations in the range of 0.13 to 0...

Poultry Science, 2007

Variance components and breeding values were estimated for 3 reproductive traits in a pure line o... more Variance components and breeding values were estimated for 3 reproductive traits in a pure line of White Leghorn laying hens. The traits were proportion of fertile eggs of eggs set, proportion of first quality chicks of eggs set, and proportion of first-quality chicks of fertile eggs. A total of 3,020 hens were tested up to 3 times over a period of 7 d. For the definition of the traits, each egg was scored for each trait either as 0 or 1. To account for the binomial distribution of the data, a Bayesian animal threshold model implemented in a Gibbs sampler was

Meat Science, 2011

The aim of the research was to gain a better understanding of the genomic regulation of meat qual... more The aim of the research was to gain a better understanding of the genomic regulation of meat quality by investigating individual and epistatic QTL in a three-generation full-sib population (Pietrain × crossbred dam line). In total, 386 animals were genotyped for 96 markers. Analysed traits included pH, reflectance value, conductivity, and meat colour. Thirteen significant individual QTL were identified. The most significant QTL were detected on SSC1 and SSC9 for pH, on SSC4 for meat colour, and on SSC8 for conductivity, accounting for 3.4% to 4.7% of the phenotypic variance. Nine significant epistatic QTL pairs were detected accounting for between 5.7% and 10.9% of the phenotypic variance. Epistatic QTL pairs showing the largest effects were for reflectance value between two locations of SSC4, and for pH between SSC10 and SSC13, explaining 9.5% and 10.9% of the phenotypic variance, respectively. This study indicates that meat quality traits are influenced by numerous QTL as well as a complex network of interactions.

Livestock Science, 2011

Numerous quantitative trait loci (QTL) have been identified for growth and feed intake in pigs, h... more Numerous quantitative trait loci (QTL) have been identified for growth and feed intake in pigs, however, there are currently no reports of interactions between QTL (epistasis) for these traits at different stages of growth. A genomic scan for epistatic QTL was conducted on animals from a three generation full-sib population, created by crossing Pietrain sires with a crossbred dam line. All types of two-locus interactions were fitted in the model using Cockerham's decomposition, by regressing on a linear combination of the individual QTL origin probabilities. This study is the first to report epistatic QTL for growth, feed intake and chemical body composition in pigs. Eighteen significant epistatic QTL pairs were identified, seven affecting growth, six affecting feed intake or food conversion ratio, and five affecting chemical body composition. Most interacting QTL resided on different chromosomes; only two were located on the same chromosome. The identified QTL pairs explained substantial proportions of the phenotypic variance, from 5% to 10.3%. All types of digenic epistatic effects were identified with the additive-by-additive effect being the most prevalent. These findings suggest that epistasis is important in the genomic regulation of growth, feed intake and chemical body composition. Furthermore, interactions occur between different pairs of epistatic QTL for the same trait depending on the growth stage, increasing the complexity of genomic networks. This agrees with studies on gene expression levels which showed that those are time and tissue dependent.

Livestock Production Science, 2003

The use of feed intake behaviour traits, obtained from electronic feeding stations, and feed inta... more The use of feed intake behaviour traits, obtained from electronic feeding stations, and feed intake curve parameters to genetically improve performance traits was analysed. Daily feed intake and feed intake behaviour of 5601 group-penned boars of two dam lines were recorded by electronic feeders in weeks 1, 3, 5, 7 and 9 during 10 weeks (100–170 d) on performance test.

Livestock Production Science, 2003

The objective of this study was to find the best function and covariance structure to estimate fe... more The objective of this study was to find the best function and covariance structure to estimate feed intake pattern in growing pigs for breeding purposes in order to optimise the feed intake curve corresponding to lean growth rate. Daily feed intake from 81 group-housed pigs was ...

Livestock Production Science, 2003

The objective of this study was the development of a genetic statistical method for longitudinal ... more The objective of this study was the development of a genetic statistical method for longitudinal data of daily feed intake in growing pigs using random regression models (RRM) in order to change the pattern of feed intake by selection. Besides a quadratic RRM for additive genetic effects, different combinations of covariance structures for permanent environmental effects using RRM and for temporary residual effects were fitted to individual information from 5245 boars (2938 of line 3, 2307 of line 4) in order to obtain the best fitting model for daily feed intake recorded during a test period of 10 weeks. Based on Akaike’s Information Criterion, the parsimonious model included a constant diagonal covariance structure for the permanent environmental effects and a heterogeneous autoregressive-moving-average structure of order (1,1) for temporary residual effects. Estimates of the autocorrelation were 0.80 (line 3) and 0.81 (line 4) and estimates of the moving-average components were 0.15 (line 3) and 0.11 (line 4). Estimates of heritabilities were low and increased from 0.02 to 0.06 during the test, with the highest estimates in the seventh week on test. The low heritabilities were only due to a higher residual variance when using individual daily records of feed intake, whereas additive genetic variances (0.01 to 0.04 kg2) were similar to estimates using average records of feed intake. Genetic correlations between intercept and linear regression coefficients were positive within 0.57 and 0.55, those between intercept and quadratic regression coefficients were negative within −0.77 and −0.89, and those between linear and quadratic coefficients were within −0.48 and −0.61 for lines 3 and 4, respectively, indicating the opportunity for changing the feed intake pattern. Additionally, eigenfunctions obtained from the additive genetic (co)variance matrix indicated that a genetic change in feed intake pattern is achievable, e.g. the second major eigenfunction, which explained about 10% of the additive genetic variation, allowed selection for a high increase in feed intake at the beginning of the test period and for reduced feed intake at the end of the test period in order to improve feed efficiency.

Livestock Production Science, 2002

... Means and standard errors of R 2 , Durbin Watson Statistics (DBW) and residual standard devia... more ... Means and standard errors of R 2 , Durbin Watson Statistics (DBW) and residual standard deviations (RSDs) are presented in Table 5. The DBW statistic indicated no significant autocorrelation of the residuals for all functions. ...

Livestock Production Science, 1996

Voluntary feed intake, feed intake pattern and performance traits were recorded on 3188 group hou... more Voluntary feed intake, feed intake pattern and performance traits were recorded on 3188 group housed boars of Landrace and Large White tested from day 100 to day 170. Measurements of feed intake and feed intake behaviour were obtained by electronic feed dispensers (ACEMO) under ad libitum conditions. Heritabilities of feed intake in periods 1 to 5 and over the entire test period were estimated to be 0.16, 0.24, 0.30, 0.27, 0.26, and 0.22, respectively. The maximum heritability of daily feed intake in the third time period on test corresponds to about 130 days of age at about 85 kg of weight. Daily feed intake in this period showed a high genetic correlation with the average feed intake over the whole performance test (rg = 0.91). Estimates of genetic correlations between daily feed intake and feed conversion ratio, residual feed intake, average daily gain or backfat thickness were 0.04, 0.97, 0.62 and 0.42, respectively. Boars feed intake activities decreased over time while time per day in the feeder was almost constant. Traits of feed intake behaviour as feeding rate, feed intake/visit, number of visits, time per visit, and time per day in the feeder showed high heritabilities of 0.44, 0.51, 0.43, 0.42, and 0.43, respectively, but genetic correlations with performance and carcass traits were generally low. One exception was the behavioural trait time per day in the feeder with its moderate genetic correlations to daily feed intake (rg = 0.44) and average daily gain on test (rg = 0.32). Selection for lean growth will improve lean growth feed efficiency as indicated by the negative correlation of −0.47. But more efficient may be the use of the component traits, lean content, daily feed intake and daily gain in particular of the most informative test period.

Livestock Production Science, 2005

Two different statistical models considering racetrack or individual race as fixed effect were co... more Two different statistical models considering racetrack or individual race as fixed effect were compared, regarding genetic parameters and by using cross validation. Data for variance component estimation consisted of 48,942 performance observations from 4249 trotters. Variance components for the traits square root of rank at finish, racing time per km, and log of earnings per race were estimated by REML using two multiple trait animal models involving different racetracks or individual races. When including each individual race instead of racetracks in the statistical model, heritabilities increased from 0.05 to 0.07, 0.19 to 0.23, and 0.08 to 0.09 for square root of rank at finish, racing time per km, and log of earnings per race, respectively. Genetic and phenotypic correlations among traits increased also after consideration of individual races. Square root of rank at finish, as well as racing time per km and log of earnings per race, was highly genetically correlated with −0.99 and −0.88. The two statistical models were compared on the basis of their predictive ability by using cross validation. Data for these analyses consisted of 706,082 observations from 21,363 trotters. Randomly eliminated performance observations were predicted by cumulation of fixed and random effects obtained from estimation of breeding values for both models. Estimates for racing time showed lower bias and mean square error (MSE) when considering individual races instead of racetracks. Also, the correlation between predicted and true phenotypic value increased from 0.85 to 0.92. Estimates for square root of rank at finish were unbiased, but with a higher MSE when considering individual race effect. A similar high bias and MSE with both models were obtained for log of earnings. In order to avoid bias in estimation of genetic parameters and breeding values for racing time and square root of rank at finish, inclusion of each individual race in the statistical model was recommended.

Journal of Animal Science, 2010

The present study focused on the identification of epistatic QTL pairs for body composition trait... more The present study focused on the identification of epistatic QTL pairs for body composition traits (carcass cut, lean tissue, and fat tissue weights) measured at slaughter weight (140 kg of BW) in a 3-generation full-sib population developed by crossing Pietrain sires with a crossbred dam line. Depending on the trait, phenotypic observations were available for 306 to 315 F(2) animals. For the QTL analysis, 386 animals were genotyped for 88 molecular markers covering chromosomes SSC1, SSC2, SSC4, SSC6, SSC7, SSC8, SSC9, SSC10, SSC13, and SSC14. In total, 23 significant epistatic QTL pairs were identified, with the additive x additive genetic interaction being the most prevalent. Epistatic QTL were identified across all chromosomes except for SSC13, and epistatic QTL pairs accounted for between 5.8 and 10.2% of the phenotypic variance. Seven epistatic QTL pairs were between QTL that resided on the same chromosome, and 16 were between QTL that resided on different chromosomes. Sus scrofa chromosome 1, SSC2, SSC4, SSC6, SSC8, and SSC9 harbored the greatest number of epistatic QTL. The epistatic QTL pair with the greatest effect was for the entire loin weight between 2 locations on SSC7, explaining 10.2% of the phenotypic variance. Epistatic associations were identified between regions of the genome that contain the IGF-2 or melanocortin-4 receptor genes, with QTL residing in other genomic locations. Quantitative trait loci in the region of the melanocortin-4 receptor gene and on SSC7 showed significant positive dominance effects for entire belly weight, which were offset by negative dominance x dominance interactions between these QTL. In contrast, the QTL in the region of the IGF-2 gene showed significant negative dominance effects for entire ham weight, which were largely overcompensated for by positive additive x dominance genetic effects with a QTL on SSC9. The study shows that epistasis is of great importance for the genomic regulation of body composition in pigs and contributes substantially to the variation in complex traits.

Journal of Animal Breeding and Genetics, 2003

The factors leading to the bias of quantitative trait loci (QTL) effect estimates were investigat... more The factors leading to the bias of quantitative trait loci (QTL) effect estimates were investigated by simulating paternal half-sib families. An upward bias was found in nearly all simulated configurations when only significant replicates were considered. This bias was a function of the experimental power of detecting a QTL (increased bias when power decreased) and was attributed to biased sampling. Three non-parametric bootstrap schemes were tested to re-estimate bias-reduced QTL effects. The classical bootstrap bias corrected re-estimate and the permutation bootstrap bias corrected re-estimate failed to reduce the bias substantially. With the 0.368-bootstrap the entire data set was repeatedly split into an estimation set formed by the bootstrap sample and into an independent test set formed by progeny not found in the estimation set. The size of the test set is asymptotically 0.368 times the number of progeny. The estimation set was used for calibration (i.e. estimating QTL position), and the test set was used for validation (i.e. estimating QTL effect at the particular position). The 0.368bootstrap re-estimate was the mean effect estimate from validation from all bootstrap runs. The 0.368bootstrap produced on average significantly less biased QTL effects which showed reduced mean square errors compared with the original estimates. It was relatively robust against biased sampling.

Journal of Animal Breeding and Genetics, 2001

ABSTRACT