Sebastian Mucha

Estimation of genomic breeding values for milk yield in UK dairy goats

The objective of this study was to estimate genomic breeding values for milk yield in crossbred dairy goats. The research was based on data provided by 2 commercial goat farms in the UK comprising 590,409 milk yield records on 14,453 dairy goats kidding between 1987 and 2013. The population was created by crossing 3 breeds: Alpine, Saanen, and Toggenburg. In each generation the best performing animals were selected for breeding, and as a result, a synthetic breed was created. The pedigree file contained 30,139 individuals, of which 2,799 were founders. The data set contained test-day records of milk yield, lactation number, farm, age at kidding, and year and season of kidding. Data on milk composition was unavailable. In total 1,960 animals were genotyped with the Illumina 50K caprine chip. Two methods for estimation of genomic breeding value were compared-BLUP at the single nucleotide polymorphism level (BLUP-SNP) and single-step BLUP. The highest accuracy of 0.61 was obtained with single-step BLUP, and the lowest (0.36) with BLUP-SNP. Linkage disequilibrium (r(2), the squared correlation of the alleles at 2 loci) at 50 kb (distance between 2 SNP) was 0.18. This is the first attempt to implement genomic selection in UK dairy goats. Results indicate that the single-step method provides the highest accuracy for populations with a small number of genotyped individuals, where the number of genotyped males is low and females are predominant in the reference population.

Estimation of genetic parameters for milk yield across lactations in mixed-breed dairy goats

Currently, breeding values for dairy goats in the United Kingdom are not estimated and selection is based only on phenotypes. Several studies from other countries have applied various methodologies to estimate breeding values for milk yield in dairy goats. However, most of the previous analyses were based on relatively small data sets, which might have affected the accuracy of the parameter estimates. The objective of this study was to estimate genetic parameters for milk yield in crossbred dairy goats in lactations 1 to 4. The research was based on data provided by 2 commercial goat farms in the United Kingdom comprising 390,482 milk yield records on 13,591 dairy goats kidding between 1987 and 2012. The population was created by crossing 3 breeds: Alpine, Saanen, and Toggenburg. In each generation, the best-performing animals were selected for breeding and, as a result, a synthetic breed was created. The pedigree file contained 28,184 individuals, of which 2,414 were founders. The data set contained test-day records of milk yield, lactation number, farm, age at kidding, and year and season of kidding. Data on milk composition was unavailable. Covariance components were estimated with the average information REML algorithm in the ASReml package (VSN International Ltd., Hemel Hempstead, UK). A random regression animal model for milk yield with fixed effects of herd test day, year-season, and age at kidding was used. Heritability was the highest at 200 and 250d in milk (DIM), reaching 0.45 in the first lactation and between 0.34 and 0.25 in subsequent lactations. After 300 DIM, the heritability started decreasing to 0.23 and 0.10 at 400 DIM in the first and subsequent lactations, respectively. Genetic correlation between milk yield in the first and subsequent lactations was between 0.16 and 0.88. This study found that milk yields in first and subsequent lactations are highly correlated, both at the genetic and phenotypic level. Estimates of heritability for milk yield were higher than most of the values reported in the literature, although they were in the range reported in this species. This should facilitate genetic improvement for the population studied as part of a broader multi-trait breeding program.

Genetic parameters of linear conformation type traits and their relationship with milk yield throughout lactation in mixed-breed dairy goats

Conformation traits are of interest to many dairy goat breeders not only as descriptive traits in their own right, but also because of their influence on production, longevity, and profitability. If these traits are to be considered for inclusion in future dairy goat breeding programs, relationships between them and production traits such as milk yield must be considered. With the increased use of regression models to estimate genetic parameters, an opportunity now exists to investigate correlations between conformation traits and milk yield throughout lactation in more detail. The aims of this study were therefore to (1) estimate genetic parameters for conformation traits in a population of crossbred dairy goats, (2) estimate correlations between all conformation traits, and (3) assess the relationship between conformation traits and milk yield throughout lactation. No information on milk composition was available. Data were collected from goats based on 2 commercial goat farms during August and September in 2013 and 2014. Ten conformation traits, relating to udder, teat, leg, and feet characteristics, were scored on a linear scale (1-9). The overall data set comprised data available for 4,229 goats, all in their first lactation. The population of goats used in the study was created using random crossings between 3 breeds: British Alpine, Saanen, and Toggenburg. In each generation, the best performing animals were selected for breeding, leading to the formation of a synthetic breed. The pedigree file used in the analyses contained sire and dam information for a total of 30,139 individuals. The models fitted relevant fixed and random effects. Heritability estimates for the conformation traits were low to moderate, ranging from 0.02 to 0.38. A range of positive and negative phenotypic and genetic correlations between the traits were observed, with the highest correlations found between udder depth and udder attachment (0.78), teat angle and teat placement (0.70), and back legs and back feet (0.64). The genetic correlations estimated between conformation traits and milk yield across the first lactation demonstrated changes during this period. The majority of correlations estimated between milk yield and the udder and teat traits were negative. Therefore, future breeding programs would benefit from including these traits to ensure that selection for increased productivity is not accompanied by any unwanted change in functional fitness.

Genome-wide association study of conformation and milk yield in mixed-breed dairy goats

Identification of genetic markers that affect economically important traits is of high value from a biological point of view, enabling the targeting of candidate genes and providing practical benefits for the industry such as wide-scale genomic selection. This study is one of the first to investigate the genetic background of economically important traits in dairy goats using the caprine 50K single nucleotide polymorphism (SNP) chip. The aim of the project was to perform a genome-wide association study for milk yield and conformation of udder, teat, and feet and legs. A total of 137,235 milk yield records on 4,563 goats each scored for 10 conformation traits were available. Out of these, 2,381 goats were genotyped with the Illumina Caprine 50K BeadChip (Illumina Inc., San Diego, CA). A range of pseudo-phenotypes were used including deregressed breeding values and pseudo-estimated breeding values. Genome-wide association studies were performed using the multi-locus mixed model (MLMM) algorithm implemented in SNP & Variation Suite v7.7.8 (Golden Helix Inc., Bozeman, MT). A genome-wise significant [-log10(P-value) > 5.95] SNP for milk yield was identified on chromosome 19, with additional chromosome-wise significant (-log10(P-value) > 4.46] SNP on chromosomes 4, 8, 14, and 29. Three genome-wise significant SNP for conformation of udder attachment, udder depth, and front legs were identified on chromosome 19, and chromosome-wise SNP were found on chromosomes 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, and 27. The proportion of variance explained by the significant SNP was between 0.4 and 7.0% for milk yield and between 0.1 and 13.8% for conformation traits. This study is the first attempt to identify SNP associated with milk yield and conformation in dairy goats. Two genome-wise significant SNP for milk yield and 3 SNP for conformation of udder attachment, udder depth, and front legs were found. Our results suggest that conformation traits have a polygenic background because, for most of them, we did not identify any quantitative trait loci with major effect.