INTRODUCTION The fundamentals of efficiency for production and metabolic stress in lactating dair... more INTRODUCTION The fundamentals of efficiency for production and metabolic stress in lactating dairy cows involve the interplay of energy expenditure and energy sources during lactation. Both milk yield and dietary intake, their amounts and compositions, can be recorded readily, at least on experimental farms, but body reserves of a living lactating cow cannot be measured. Body reserves is also a function of amount, or weight, and composition, or condition. Weight can be measured, but condition can be only approximated. Body condition score (BCS) is used to approximate the body condition of a dairy cow, with its crudeness unknown because of its subjectivity. It reflects largely adipose tissue stores and not protein reserves, but this is only speculation. Ultrasound measure of muscle (UTM) and backfat (UTBF) may be more objective measures, but indicators of exact what aspects of body reserves remain unknown. We in Denmark are in the process of attempting to profile body energy state of...
Tidligere eksperimentelle undersogelser har vist at en oget anvendelse af grovfoder kan give anle... more Tidligere eksperimentelle undersogelser har vist at en oget anvendelse af grovfoder kan give anledning til en forskellig rangering af genotyper indenfor en race, dvs. at udvaelgelsen af de bedste avlsdyr vil afhaenge af i hvilket produktionssystem koerne skal producere. Derfor er der gennemfort analyser af data fra kvaegdatabasen til afklaring af om der er forskel i den indbyrdes rangering af avlsvaerdi for maelkeydelse, sundhed og reproduktion afhaengig af om koerne star i okologiske eller konventionelle besaetninger. Undersogelsen viste ingen forskel i rangering af avlstyrene afhaengig af produktionssystem, men det kan ikke udelukkes at en yderlig forskel i fodring mv. mellem de to systemer vil aendre pa resultatet.
The aim of this study was to investigate if social genetic effects for average daily gain (ADG) i... more The aim of this study was to investigate if social genetic effects for average daily gain (ADG) in pigs depend on group size. Records included 119,919 pigs from 13 nucleus Landrace herds in Denmark. Pigs entered the performance test at ~30 kg and were assigned to pens containing between 8 to 15 pigs. Each pen had approximately the same stocking density. A total of 10,803 groups of pigs were included. The ADG from 30 kg to the end of the test (~94 kg) was 1012 g per day. ADG was analysed both separately for each of the eight different group sizes (8 to 15), and on the whole data, including all group sizes. Variance components were first estimated using a classical animal model including the fixed effect of sex, contemporary compartment, along with age and age squared at end of the test as covariates in addition to random effects of animal, group and litter. Thereafter variance components were estimated using a social genetic model, which in addition to the effects included in the cla...
DMU is a package directed towards applications in quantitative genetics, and it implements powerf... more DMU is a package directed towards applications in quantitative genetics, and it implements powerful tools to estimate variance components and fixed effects (BLUE) and to predict random effects (BLUP). Most of the development of DMU has been in response to the needs in research projects in applied quantitative animal genetics along a period extending for more than 25 years. Indeed, DMU has been the main tool for statistical inference (both estimation and prediction) in the Danish animal breeding research. Moreover, DMU has been used in routine genetic evaluation of cattle, sheep, mink and horse in Denmark, and in several other countries. This led to a package implementing an ample range of statistical methods and computation algorithms, which not only implement high performance methods for specific project-related problems, but also are of general applicability in quantitative genetics.
Four breeds are represented within the Danish dairy cattle population. These are Red Danes, Danis... more Four breeds are represented within the Danish dairy cattle population. These are Red Danes, Danish Holsteins, Danish Jerseys, and Danish Red Holsteins. The Danish Red Holsteins account for one percent of the purebred Danish dairy cattle whereas Red Danes, Danish Holsteins and Danish Jerseys account for approximately 10, 76, and 13 percent, respectively. Canadian studies have shown that covariance parameters are different across breeds (Schaeffer et al., 2000).
An amendment to this paper has been published and can be accessed via a link at the top of the pa... more An amendment to this paper has been published and can be accessed via a link at the top of the paper.
The objective of this study was to investigate genetic variation and genotype by environment (G ×... more The objective of this study was to investigate genetic variation and genotype by environment (G × E) interactions for fertility (including age at first calving and calving interval), somatic cell score (SCS), and milk production traits for Iranian Holsteins. Different environments were defined based on the climatic zones (cold, semi-cold, and moderate) and considering the herd location. Data were collected between 2003 and 2018 by the National Animal Breeding Center of Iran (Karaj). Variance and covariance components and genetic correlations were estimated using 2 different models, which were analyzed using Bayesian methods. For both models, performance of traits in each climate were considered as different traits. Fertility traits were analyzed using a trivariate model. Furthermore, SCS and production traits were analyzed using trivariate random regression models (records in different climate zones considered as different traits). For the fertility traits, the largest estimates of heritability were observed in cold climate. Fertility performance was always better in cold environment. Genetic correlations between climatic zones ranged from 0.85 to 0.94. For daily measurements of SCS and production traits, heritability ranged from 0.031 to 0.037 and 0.069 to 0.209, respectively. Genetic variances were the highest in the semi-cold and moderate climates for the SCS and production traits, respectively. Furthermore, across the studied climates, 305-d genetic correlation ranged from 0.756 to 0.884 for SCS and from 0.925 to 0.957 for the production traits. The structure of genetic correlation within each climate indicated a negative correlation between early and late lactation for SCS, especially in the cold climate and for milk production in the moderate climate. For fat percentage, in all climatic zones, the lowest genetic correlations were observed between early and mid-lactation. In addition, for protein production in the cold climate, a negative correlation was observed between early and late lactation. Results indicated heterogeneous variance components for all the studied traits across various climatic zones. Estimated genetic correlations for SCS revealed that the genetic expression of animals may vary by climatic zone. Results indicated the existence of G × E interaction due to the climatic condition, only for SCS. Therefore, in Iranian Holsteins, the effect of G × E interactions should not be neglected, especially for SCS, as different sires might be optimal for use in different climatic zones.
Background The traditional way to estimate variance components (VC) is based on the animal model ... more Background The traditional way to estimate variance components (VC) is based on the animal model using a pedigree-based relationship matrix (A) (A-AM). After genomic selection was introduced into breeding programs, it was anticipated that VC estimates from A-AM would be biased because the effect of selection based on genomic information is not captured. The single-step method (H-AM), which uses an H matrix as (co)variance matrix, can be used as an alternative to estimate VC. Here, we compared VC estimates from A-AM and H-AM and investigated the effect of genomic selection, genotyping strategy and genotyping proportion on the estimation of VC from the two methods, by analyzing a dataset from a commercial broiler line and a simulated dataset that mimicked the broiler population. Results VC estimates from H-AM were severely overestimated with a high proportion of selective genotyping, and overestimation increased as proportion of genotyping increased in the analysis of both commercial ...
Background Physical removal of individuals from groups causes reductions in group sizes and chang... more Background Physical removal of individuals from groups causes reductions in group sizes and changes in group composition, which may affect the predictive ability of estimates of indirect genetic effects of animals on phenotypes of group mates. We hypothesized that including indirect genetic effects of culled animals and of animals without phenotypes in the analysis affects estimates of genetic parameters, improves predictive ability, and reduces bias of predicted breeding values. We tested this by applying different editing procedures, i.e. omission of individuals or groups from the data, and genetic models, i.e. a classical and an indirect genetic model (IGM) without or with weighting of indirect genetic effects based on the relative proportion of time spent in the pen or space allowance. Data consisted of average daily gain for 123,567 pigs in 11,111 groups, from which 3% of individuals in 25% of groups were prematurely removed from the group. Results The estimate of total heritab...
INTRODUCTION The fundamentals of efficiency for production and metabolic stress in lactating dair... more INTRODUCTION The fundamentals of efficiency for production and metabolic stress in lactating dairy cows involve the interplay of energy expenditure and energy sources during lactation. Both milk yield and dietary intake, their amounts and compositions, can be recorded readily, at least on experimental farms, but body reserves of a living lactating cow cannot be measured. Body reserves is also a function of amount, or weight, and composition, or condition. Weight can be measured, but condition can be only approximated. Body condition score (BCS) is used to approximate the body condition of a dairy cow, with its crudeness unknown because of its subjectivity. It reflects largely adipose tissue stores and not protein reserves, but this is only speculation. Ultrasound measure of muscle (UTM) and backfat (UTBF) may be more objective measures, but indicators of exact what aspects of body reserves remain unknown. We in Denmark are in the process of attempting to profile body energy state of...
Tidligere eksperimentelle undersogelser har vist at en oget anvendelse af grovfoder kan give anle... more Tidligere eksperimentelle undersogelser har vist at en oget anvendelse af grovfoder kan give anledning til en forskellig rangering af genotyper indenfor en race, dvs. at udvaelgelsen af de bedste avlsdyr vil afhaenge af i hvilket produktionssystem koerne skal producere. Derfor er der gennemfort analyser af data fra kvaegdatabasen til afklaring af om der er forskel i den indbyrdes rangering af avlsvaerdi for maelkeydelse, sundhed og reproduktion afhaengig af om koerne star i okologiske eller konventionelle besaetninger. Undersogelsen viste ingen forskel i rangering af avlstyrene afhaengig af produktionssystem, men det kan ikke udelukkes at en yderlig forskel i fodring mv. mellem de to systemer vil aendre pa resultatet.
The aim of this study was to investigate if social genetic effects for average daily gain (ADG) i... more The aim of this study was to investigate if social genetic effects for average daily gain (ADG) in pigs depend on group size. Records included 119,919 pigs from 13 nucleus Landrace herds in Denmark. Pigs entered the performance test at ~30 kg and were assigned to pens containing between 8 to 15 pigs. Each pen had approximately the same stocking density. A total of 10,803 groups of pigs were included. The ADG from 30 kg to the end of the test (~94 kg) was 1012 g per day. ADG was analysed both separately for each of the eight different group sizes (8 to 15), and on the whole data, including all group sizes. Variance components were first estimated using a classical animal model including the fixed effect of sex, contemporary compartment, along with age and age squared at end of the test as covariates in addition to random effects of animal, group and litter. Thereafter variance components were estimated using a social genetic model, which in addition to the effects included in the cla...
DMU is a package directed towards applications in quantitative genetics, and it implements powerf... more DMU is a package directed towards applications in quantitative genetics, and it implements powerful tools to estimate variance components and fixed effects (BLUE) and to predict random effects (BLUP). Most of the development of DMU has been in response to the needs in research projects in applied quantitative animal genetics along a period extending for more than 25 years. Indeed, DMU has been the main tool for statistical inference (both estimation and prediction) in the Danish animal breeding research. Moreover, DMU has been used in routine genetic evaluation of cattle, sheep, mink and horse in Denmark, and in several other countries. This led to a package implementing an ample range of statistical methods and computation algorithms, which not only implement high performance methods for specific project-related problems, but also are of general applicability in quantitative genetics.
Four breeds are represented within the Danish dairy cattle population. These are Red Danes, Danis... more Four breeds are represented within the Danish dairy cattle population. These are Red Danes, Danish Holsteins, Danish Jerseys, and Danish Red Holsteins. The Danish Red Holsteins account for one percent of the purebred Danish dairy cattle whereas Red Danes, Danish Holsteins and Danish Jerseys account for approximately 10, 76, and 13 percent, respectively. Canadian studies have shown that covariance parameters are different across breeds (Schaeffer et al., 2000).
An amendment to this paper has been published and can be accessed via a link at the top of the pa... more An amendment to this paper has been published and can be accessed via a link at the top of the paper.
The objective of this study was to investigate genetic variation and genotype by environment (G ×... more The objective of this study was to investigate genetic variation and genotype by environment (G × E) interactions for fertility (including age at first calving and calving interval), somatic cell score (SCS), and milk production traits for Iranian Holsteins. Different environments were defined based on the climatic zones (cold, semi-cold, and moderate) and considering the herd location. Data were collected between 2003 and 2018 by the National Animal Breeding Center of Iran (Karaj). Variance and covariance components and genetic correlations were estimated using 2 different models, which were analyzed using Bayesian methods. For both models, performance of traits in each climate were considered as different traits. Fertility traits were analyzed using a trivariate model. Furthermore, SCS and production traits were analyzed using trivariate random regression models (records in different climate zones considered as different traits). For the fertility traits, the largest estimates of heritability were observed in cold climate. Fertility performance was always better in cold environment. Genetic correlations between climatic zones ranged from 0.85 to 0.94. For daily measurements of SCS and production traits, heritability ranged from 0.031 to 0.037 and 0.069 to 0.209, respectively. Genetic variances were the highest in the semi-cold and moderate climates for the SCS and production traits, respectively. Furthermore, across the studied climates, 305-d genetic correlation ranged from 0.756 to 0.884 for SCS and from 0.925 to 0.957 for the production traits. The structure of genetic correlation within each climate indicated a negative correlation between early and late lactation for SCS, especially in the cold climate and for milk production in the moderate climate. For fat percentage, in all climatic zones, the lowest genetic correlations were observed between early and mid-lactation. In addition, for protein production in the cold climate, a negative correlation was observed between early and late lactation. Results indicated heterogeneous variance components for all the studied traits across various climatic zones. Estimated genetic correlations for SCS revealed that the genetic expression of animals may vary by climatic zone. Results indicated the existence of G × E interaction due to the climatic condition, only for SCS. Therefore, in Iranian Holsteins, the effect of G × E interactions should not be neglected, especially for SCS, as different sires might be optimal for use in different climatic zones.
Background The traditional way to estimate variance components (VC) is based on the animal model ... more Background The traditional way to estimate variance components (VC) is based on the animal model using a pedigree-based relationship matrix (A) (A-AM). After genomic selection was introduced into breeding programs, it was anticipated that VC estimates from A-AM would be biased because the effect of selection based on genomic information is not captured. The single-step method (H-AM), which uses an H matrix as (co)variance matrix, can be used as an alternative to estimate VC. Here, we compared VC estimates from A-AM and H-AM and investigated the effect of genomic selection, genotyping strategy and genotyping proportion on the estimation of VC from the two methods, by analyzing a dataset from a commercial broiler line and a simulated dataset that mimicked the broiler population. Results VC estimates from H-AM were severely overestimated with a high proportion of selective genotyping, and overestimation increased as proportion of genotyping increased in the analysis of both commercial ...
Background Physical removal of individuals from groups causes reductions in group sizes and chang... more Background Physical removal of individuals from groups causes reductions in group sizes and changes in group composition, which may affect the predictive ability of estimates of indirect genetic effects of animals on phenotypes of group mates. We hypothesized that including indirect genetic effects of culled animals and of animals without phenotypes in the analysis affects estimates of genetic parameters, improves predictive ability, and reduces bias of predicted breeding values. We tested this by applying different editing procedures, i.e. omission of individuals or groups from the data, and genetic models, i.e. a classical and an indirect genetic model (IGM) without or with weighting of indirect genetic effects based on the relative proportion of time spent in the pen or space allowance. Data consisted of average daily gain for 123,567 pigs in 11,111 groups, from which 3% of individuals in 25% of groups were prematurely removed from the group. Results The estimate of total heritab...
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