Detection of the important chromosomal regions determining production traits in meat-type chicken using entropy analysis.

1. The objective of this study was to indicate the most informative chromosomal regions and candidate genes connected to body weight at 36 d, body weight at 39 d, body weight changes between 39 and 46 d, feed intake between 39 and 46 d and feed conversion ratio of meat-type chicken based on genomic data using entropy analysis. 2. Data contained information about 862 genotyped individuals from a Cobb commercial line using 60K Illumina iSelect chicken array and information from 42 770 Single Nucleotide Polymorphisms (SNPs). Entropy analysis was employed to detect important chromosomal regions determining the target traits. Locations of genes within the designated regions on each chromosome and for each trait were verified using the Ensembl genome database. 3. The most informative SNPs were located on chromosomes 1, 2, 4, 8, 12 and Z, whereas clusters of the most informative pairs of SNPs connected to all recorded traits were located on chromosomes 1, 2, 3, 4, 6, 12, 20 and Z. The identified chromosomal localisations overlap with genes functionally connected to the nervous system and gastrointestinal tract.

Genetic evaluation of laying performance in the Zatorska goose: contribution to the conservation programme.

1. The aim of the study was to estimate the heritability of the laying performance in the cumulative and partial production of eggs and predict the breeding values of native Zatorska geese in a conservation programme using Best Linear Unbiased Prediction (BLUP) methodology. Second, the trajectory of the egg production curve was examined. 2. The data contain information about the laying performance of 1831 individuals in the first year of laying. To describe the trajectory of the laying performance, 10 mathematical models were tested. For the genetic parameter estimation of egg production, data from 1038 birds were used with a production higher than 20 eggs during the first season of laying. 3. The analysis of egg production was based on single and multi-trait models. Heritability, genetic and phenotypic correlations between phases of the laying performance as well as breeding values were estimated. 4. The best adaptation to the goose egg laying curve was the Ali and Schaeffer model. The estimates of heritability were 0.20 (0.06 SE) using the single-trait model and ranged from 0.12 to 0.24 using the multi-trait model. 5. The results suggest that the BLUP method can support the conservation programme.

Inbreeding rate and genetic structure of cat populations in Poland.

The objective of the study was to analyze effective population size and inbreeding level in populations of cat breeds registered in the Polish Studbook. The Association of Purebred Cat Breeders in Poland provided access to pedigrees of 26725 cats from seven breeds. The most frequent breed was Persian, however increasing tendency in numbers of registered animals from other breeds was recorded in later years. Although the percentage of inbred individuals was increasing over time, mating of close relatives was avoided by most of the breeders, and the average inbreeding coefficient exceeded 5% only for Siberian and Russian breeds. Current analysis suggests that the Polish pedigree cat populations are not threatened by negative effects of inbreeding.

Estimation of genetic parameters for monthly egg production in laying hens based on random regression models.

Heritability and genetic correlations of monthly egg production under random regression models were estimated. Three layer lines (A22, A88, K66) in six consecutive generations were analysed. A22 (13,770 recorded hens) and A88 (13,950 recorded hens) are maternal lines of Rhode Island White birds selected on egg production and shell colour; K66 (9,351 recorded birds) is a paternal line of Rhode Island Red birds selected on egg weight. Eight models with different orders of Legendre polynomials were applied. Adequacy of the models was checked by the Akaike Information Criterion. According to the most adequate model including second order Legendre polynomials for fixed effects and third order for additive genetic and permanent environmental effects, relatively high heritabilities were estimated in the first (h2=0.3) and final (h2 above 0.3) periods of production with a substantial decrease in heritability during the egg production peak. Methodology based on random regression animal models can be recommended for genetic evaluation of laying hens.

Mixed model studies on inheritance of reproductive traits in laying hens - a Bayesian approach.

Segregation analyses performed for many livestock species indicate a mixed inheritance model of reproductive traits. Additionally, depending on the population, a given trait can be determined by a number of genes with large effects. Genetic backgrounds of hatch-ability and fertility in poultry are still not known sufficiently. The objectives of this study are to verify the hypothesis on segregation of single genes (1 vs. 2) affecting fertility and hatchability and to estimate a heritability of these traits. Records from 2,040 and 2,015 dams from full-pedigreed strains of Rhode Island Red (R33) and New Hampshire (N88) from a pedigree farm were analyzed. The percentage of fertilized eggs and the percentage of the eggs hatched of fertilized eggs were registered for dams only. Fertility was checked by candling on the eighth day of incubation. To obtain a binomial phenotypic scale, 10 eggs per dam were included into the analysis. Animal single-trait threshold models were used for the analysis of data. The first model included the effects of 2 single genes, 2 fixed effects of year and season, additive polygenic effects, and permanent environmental effects. In the second model, only 1 single gene effect was included. Additionally, the analysis based on the polygenic threshold model was also performed. The Gibbs sampling procedure was used. The significance of single gene effects was verified by highest posterior density regions. The obtained results clearly gave evidence for the segregation of 1 major gene for hatchability in strain R33. Furthermore, the mixed inheritance model can also be suggested for fertility in this strain. After the analysis, the polygenic heritabilities were very low (<0.11), whereas major polygenic heritability ranged from 0.05 to 0.12.

Genetic and permanent environmental variability of twinning in Thoroughbred horses estimated via three threshold models.

Twinning is a serious problem in Thoroughbred horses, as most of the multiple pregnancies are miscarried and live foals present lower performance values. The aim of this study was to estimate the heritability and repeatability of twinning in Thoroughbred horses. A total of 12648 pregnancies of 2033 Thoroughbred mares born between 1929 and 1994 in 11 studs were included. The analysis was performed by the use of AI-REML algorithm under three threshold animal models. The first model included effects of stud, mare's birth period and interaction between them as fixed. The second model included the interaction between the stud and mare's birth period as random, whereas in the third model stud effects were also treated as random. The models were compared based on the deviances. Phenotypic and genetic trends were evaluated as well. The twinning rate was 3.5%. The study involved 443 twins and two triplets. Heritability estimates varied from 0.24 (model III) to 0.29 (model I), whereas repeatability estimates ranged from 0.33 (model I) to 0.34 (model III). The fluctuations of average annual genetic effects may result from segregation of the major gene in the population.

Bayesian segregation analysis of production traits in two strains of laying chickens.

A bayesian marker-free segregation analysis was applied to search for evidence of segregating genes affecting production traits in two strains of laying hens under long-term selection. The study used data from 6 generations of Leghorn (H77) and New Hampshire (N88) breeding nuclei. Estimation of marginal posterior means of variance components and parameters of a single autosomal locus was performed by use of the Gibbs sampler. The results showed evidence for a mixed major gene: -polygenic inheritance of BW and age at sexual maturity (ASM) in both strains. Single genes affecting BW and ASM explained one-third of the genetic variance. For ASM large overdominance effect at single locus was estimated. Initial egg production (IEP) and average egg weight (EW) showed a polygenic model of inheritance. The polygenic heritability estimates for BW, ASM, IEP, and EW were 0.32, 0.25, 0.23, and 0.08 in Strain H77 and 0.25, 0.24, 0.11, and 0.38 in Strain N88, respectively.

Analysis of single gene multitrait effects in livestock by the use of Gibbs sampling.

The paper presents a method of multivariate data analysis described by a model which involves fixed effects, additive polygenic individual effects and the effects of a major gene. To find the estimates of model parameters, the maximization of likelihood function method is applied. The maximum of likelihood function is computed by the use of the Gibbs sampling approach. In this approach, following the conditional posterior distributions, values of all unknown parameters are generated. On the basis of the obtained samples the marginal posterior densities as well as the estimates of fixed effects, gene frequency, genotypic values, major gene, polygenic and error (co)variances are calculated. A numerical example, supplemented to theoretical considerations, deals with data simulated according to the considered model.