The role of the bovine growth hormone receptor and prolactin receptor genes in milk, fat and protein production in Finnish Ayrshire dairy cattle

We herein report new evidence that the QTL effect on chromosome 20 in Finnish Ayrshire can be explained by variation in two distinct genes, growth hormone receptor (GHR) and prolactin receptor (PRLR). In a previous study in Holstein-Friesian dairy cattle an F279Y polymorphism in the transmembrane domain of GHR was found to be associated with an effect on milk yield and composition. The result of our multimarker regression analysis suggests that in Finnish Ayrshire two QTL segregate on the chromosomal region including GHR and PRLR. By sequencing the coding sequences of GHR and PRLR and the sequence of three GHR promoters from the pooled samples of individuals of known QTL genotype, we identified two substitutions that were associated with milk production traits: the previously reported F-to-Y substitution in the transmembrane domain of GHR and an S-to-N substitution in the signal peptide of PRLR. The results provide strong evidence that the effect of PRLR S18N polymorphism is distinct from the GHR F279Y effect. In particular, the GHR F279Y has the highest influence on protein percentage and fat percentage while PRLR S18N markedly influences protein and fat yield. Furthermore, an interaction between the two loci is suggested.

Evidence for heterogeneity in recombination in the human pseudoautosomal region: high resolution analysis by sperm typing and radiation-hybrid mapping

Accurate genetic and physical maps for the human pseudoautosomal region were constructed by use of sperm typing and high-resolution radiation-hybrid mapping. PCR analysis of 1,912 sperm was done with a manual, single-sperm isolation method. Data on four donors show highly significant linkage heterogeneity among individuals. The most significant difference was observed in a marker interval located in the middle of the Xp/Yp pseudoautosomal region, where one donor showed a particularly high recombination fraction. Longitudinal models were fitted to the data to test whether linkage heterogeneity among donors was significant for multiple intervals across the region. The results indicated that increased recombination in particular individuals and regions is compensated for by reduced recombination in neighboring intervals. To investigate correspondence between physical and genetic distances within the region, we constructed a high-resolution radiation-hybrid map containing 29 markers. The recombination fraction per unit of physical distance varies between regions ranging from 13- to 70-fold greater than the genome-average rate.

Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross

The primary goal of this study was to localize quantitative trait loci (QTL) affecting meat quality traits in swine. In total, 42 traits were scored on 305 F2 individuals from a commercial slaughter pig cross in Norway. F1 and F2 individuals were genotyped for 29 markers on Chromosomes (Chrs) 4, 6, and 7, since previous studies had revealed QTL affecting meat quality traits on these chromosomes. The most evident result was detection of a QTL affecting amount of intramuscular fat on Chr 6. The QTL might also influence tenderness, whereas no effect was observed for back-fat thickness. Additionally, suggestive evidence for QTL affecting other meat quality traits was found on Chr 4 and Chr 7.

Review of alignment and SNP calling algorithms for next-generation sequencing data

Application of the massive parallel sequencing technology has become one of the most important issues in life sciences. Therefore, it was crucial to develop bioinformatics tools for next-generation sequencing (NGS) data processing. Currently, two of the most significant tasks include alignment to a reference genome and detection of single nucleotide polymorphisms (SNPs). In many types of genomic analyses, great numbers of reads need to be mapped to the reference genome; therefore, selection of the aligner is an essential step in NGS pipelines. Two main algorithms-suffix tries and hash tables-have been introduced for this purpose. Suffix array-based aligners are memory-efficient and work faster than hash-based aligners, but they are less accurate. In contrast, hash table algorithms tend to be slower, but more sensitive. SNP and genotype callers may also be divided into two main different approaches: heuristic and probabilistic methods. A variety of software has been subsequently developed over the past several years. In this paper, we briefly review the current development of NGS data processing algorithms and present the available software.

Comparison of random regression test-day models for Polish Black and White cattle

Test-day milk yields of first-lactation Black and White cows were used to select the model for routine genetic evaluation of dairy cattle in Poland. The population of Polish Black and White cows is characterized by small herd size, low level of production, and relatively early peak of lactation. Several random regression models for first-lactation milk yield were initially compared using the "percentage of squared bias" criterion and the correlations between true and predicted breeding values. Models with random herd-test-date effects, fixed age-season and herd-year curves, and random additive genetic and permanent environmental curves (Legendre polynomials of different orders were used for all regressions) were chosen for further studies. Additional comparisons included analyses of the residuals and shapes of variance curves in days in milk. The low production level and early peak of lactation of the breed required the use of Legendre polynomials of order 5 to describe age-season lactation curves. For the other curves, Legendre polynomials of order 3 satisfactorily described daily milk yield variation. Fitting third-order polynomials for the permanent environmental effect made it possible to adequately account for heterogeneous residual variance at different stages of lactation.

Evidence for individual and between-family variability of the recombination rate in cattle

We have conducted a study based on single sperm typing in a family design to assess patterns of variability of the male recombination rate in cattle. 2214 sperm of 37 bulls were typed for 11 loci on bovine Chromosomes (Chrs) 6, 23, and the sex chromosomes. Statistically significant individual variability of the recombination rate was observed for one interval in the pseudoautosomal region (PAR) of the bovine sex chromosomes; one marker interval on bovine Chr 23 exhibited individual variability that was close to significance. Thirty-five of the bulls were members of six paternal halfsib groups, and highly significant variability between families was found for one interval in the PAR. This variability may be due to DNA sequence differences in the PAR or to a genetic control of the recombination activity in this region. It is demonstrated that differences in the recombination rate of the magnitude observed in the present study may have a considerable impact on the power of QTL mapping experiments as well as on the sustainability of marker-assisted selection strategies.

Statistical modeling of candidate gene effects on milk production traits in dairy cattle

A major objective of dairy cattle genomic research is to identify genes underlying the variability of milk production traits that could be useful in breeding programs. The candidate gene approach provides tools for searching for causative polymorphisms affecting quantitative traits. Genes with a possible effect on milk traits in cattle can be involved in different physiological pathways, such as triglyceride synthesis [acyl-CoA:diacylglycerol acyltransferase 1 gene (DGAT1)], fat secretion from the mammary epithelial tissue (butyrophilin), or entire-body energy homeostasis regulation (leptin and leptin receptor). In this study, based on data from 252 Black and White bulls from the active Polish dairy population, effects and potential interactions of 9 single nucleotide polymorphisms in the butyrophilin, DGAT1, leptin, and leptin receptor genes were investigated. Additionally, the effect of the number of additive, dominance, and epistatic genetic effects fitted into the model on the estimates of model parameters and model selection was illustrated. Phenotypic records were daughter yield deviations for milk, fat, and protein yields, obtained from a routine national genetic evaluation. Out of all the analyzed polymorphisms, DGAT1 K232A had a much larger effect on milk traits than the other single nucleotide polymorphisms considered. Estimates of the additive genetic effect of K232A expressed as half of the difference between Lys- and Ala-encoding variants were -107.4 kg of milk, 5.4 kg of fat, and -1.6 kg of protein at first parity, as well as -120 kg of milk and 6.8 kg of fat at second parity. In terms of model selection, it was demonstrated that the modified version of Bayesian information criterion selects models with the parameterization reflecting the genetic background of the analyzed trait, while the Bayesian information criterion chooses models that are too highly parameterized.

Evaluating markers in selected genes for association with functional longevity of dairy cattle

Background

Longevity expressed as the number of days between birth and death is a trait of great importance for both human and animal populations. In our analysis we use dairy cattle to demonstrate how the association of Single Nucleotide Polymorphisms (SNPs) located within selected genes with longevity can be modeled. Such an approach can be extended to any genotyped population with time to endpoint information available. Our study is focused on selected genes in order to answer the question whether genes, known to be involved into the physiological determination of milk production, also influence individual's survival.

Results

Generally, the highest risk differences among animals with different genotypes are observed for polymorphisms located within the leptin gene. The polymorphism with a highest effect on functional longevity is LEP-R25C, for which the relative risk of culling for cows with genotype CC is 3.14 times higher than for the heterozygous animals. Apart from LEP-R25C, also FF homozygotes at the LEP-Y7F substitution attribute 3.64 times higher risk of culling than the YY homozygotes and VV homozygotes at LEP-A80V have 1.83 times higher risk of culling than AA homozygotes. Differences in risks between genotypes of polymorphisms within the other genes (the butyrophilin subfamily 1 member A1 gene, BTN1A1; the acyl-CoA:diacylglycerol acyltransferase 1 gene, DGAT1; the leptin receptor gene, LEPR; the ATP-binding cassette sub-family G member 2, ABCG2) are much smaller.

Conclusions

Our results indicate association between LEP and longevity and are very well supported by results of other studies related to dairy cattle. In view of the growing importance of functional traits in dairy cattle, LEP polymorphisms should be considered as markers supporting selection decisions. Furthermore, since the relationship between both LEP polymorphism and its protein product with longevity in humans is well documented, with our result we were able to demonstrate that livestock with its detailed records of family structure, genetic, and environmental factors as well as extensive trait recording can be a good model organism for research aspects related to humans.

Parity-dependent association between TNF-α and LTF gene polymorphisms and clinical mastitis in dairy cattle

BACKGROUND

One major problem in dairy cattle husbandry is the prevalence of udder infections. In today's breeding programmes, top priority is being given to making animal evaluation more cost-effective and reliable and less time-consuming. We proposed tumor necrosis factor α (TNF-α), lactoferrin (LTF) and macrophage-expressed lysozyme (mLYZ) genes as potential DNA markers in the improvement of immunity to mastitis.This study included 588 Polish Holstein-Friesian cows kept on one farm located in the north-western region of Poland. All clinical cases of mastitis in the herd under study were recorded by a qualified veterinarian employed by the farm. The following indicators were applied to determine udder immunity to mastitis in the cows under study: morbidity rate (MR), duration of mastitis (DM) and extent of mastitis (EM). TNF-α, mLYZ and LTF genotypes were identified by real-time PCR method, using SimpleProbe technology. Due to the very low frequency of mLYZ allele T, the gene was excluded from further analysis.A statistical analysis of associations between TNF-α and LTF genes and immunity to mastitis were performed using three models: 1) a parity-averaged model including only additive effects of the genes; 2) a parity-averaged model including both additive and epistatic effects of the genes; and 3) a parity-specific model including only additive effects of the genes.

RESULTS

With the first and second models it was revealed that the genes effects on the applied indicators of immunity to mastitis were non-significant whereas with the third one the effects were found to be statistically significant. Particularly noteworthy was the finding that the effects of TNF-α and LTF varied depending on age (parity). The alleles which were linked to high immunity to mastitis in lower parities appeared to be less favourable in higher parities.

CONCLUSIONS

These interactions might be related to inflamm-ageing, that is an increased susceptibility to infection due to immune system deregulation that progresses with age. Such pattern of interactions makes it impossible to use the genes in question in marker-assisted selection aimed at reducing heritable susceptibility to mastitis. This is because the immune mechanisms behind resistance to infections proved to be too complex.

Multivariate mixed inheritance models for QTL detection on porcine chromosome 6

A series of multivariate mixed-inheritance models is fitted to the data from an outbred-line pig cross commercially used in Norway. Each model accommodates information on polygenic (co)variances between F2 individuals and their F1 parents across the five traits through incorporation of a random animal effect. Considered traits relate to meat quality and are chosen following up the results from a previous evaluation, in which a putative quantitative trait locus (QTL) was identified on chromosome six that affects the amount of intramuscular fat (IMF), meat percentage, meat tenderness and smell intensity (Grindflek et al., 2001). An additional trait included in the model, based on results of other studies, is the backfat thickness. The analysed material comprises data scored for 305 F2 individuals, whereas marker information is available for F1 and F2 generations. Based on the results of the multivariate analysis with the mixed-inheritance model, it was possible to conclude that the evidence for QTLs for meat percentage, meat tenderness and smell intensity in the study of Grindflek et al. (2001) do not represent separate QTLs, but is caused by the fact that the applied pre-adjustment of trait values for polygenic effects failed properly to remove the polygenic variation. The QTL effect on IMF on chromosome six was confirmed.

Estimation of Quantitative Trait Loci Parameters for Milk Production Traits in German Holstein Dairy Cattle Population

The main objective of this study was to estimate the proportion of total genetic variance attributed to a quantitative trait locus (QTL) on Bos taurus autosome 6 (BTA6) for milk production traits in the German Holstein dairy cattle population. The analyzed chromosomal region on BTA6 spanned approximately 70 cM, and contained 6 microsatellite markers. Milk production data were obtained from routine genetic evaluation for 4500 genotyped German Holstein bulls. Technical aspects related to the estimation of model parameters for a large data set from routine genotype recording were outlined. A fixed QTL model and a random QTL model were introduced to incorporate marker information into parameter estimation and genetic evaluation. Estimated QTL variances, expressed as the ratio of QTL to polygenic variances, were 0.04, 0.03, and 0.07 for milk yield; 0.06, 0.08, and 0.14 for fat yield; and 0.04, 0.04, and 0.11 for protein yield, in the first 3 parities, respectively. The estimated QTL positions, expressed as distances from the leftmost marker DIK82, were 18, 31, and 17 cM for milk yield; 25, 17, and 9 cM for fat yield; and 16, 30, and 17 cM for protein yield in the 3 respective parities. Because the data for the parameter estimation well represented the current population of active German Holstein bulls, the QTL parameter estimates have been used in routine marker-assisted genetic evaluation for German Holsteins.

Fine mapping of a QTL for intramuscular fat on porcine chromosome 6 using combined linkage and linkage disequilibrium mapping

In this study data from a commercial Norwegian slaughter pig cross was analysed to confirm a previous reported quantitative trait locus (QTL) affecting intramuscular fat (IMF) on porcine chromosome 6. The data consisted of an old experiment, in which the QTL was previously detected, and new experimental data from the Norwegian slaughter pig cross. The old and new experimental data were analysed separately and together. A previously described method combining linkage and linkage disequilibrium analysis (LDLA) was used for the analysis, but this method assumes that all animals are descendants from a common base population, which is not realistic in a cross between different breeds. An adjusted version of the method, able to distinguish between different breeds in the cross, is presented here. Using the LDLA method, we were not able to confirm the QTL in the old experimental data, because the genetic variance could be explained by the polygenic effect. Analysis from the new experimental data did however detect the QTL, and analysing the data from both experiments together gave highly significant results for a QTL (p < 0.001) between markers SW1355 and SW1823. The main conclusion is therefore that the previously reported QTL for IMF on porcine chromosome 6 was confirmed within a 8.7-cM confidence interval.

Sex ratio distortion in bovine sperm correlates to recombination in the pseudoautosomal region

A total of 2122 single sperm from 35 bulls belonging to six different paternal half-sib groups were analysed with respect to two markers in the bovine pseudoautosomal region (PAR) and sex-specific loci on the X and Y chromosomes, respectively. A segregation ratio significantly different from 1:1 was observed in a test over all families, with a higher proportion of X-bearing gametes (53.5%). The analysis of recombination conducted separately for X- and Y-bearing sperm showed that X-bearing sperm cells possess highly significant individual and between-family variability in recombination rate, whereas Y-bearing sperm show linkage homogeneity. To test whether the two phenomena are related, different logistic regression models were fitted to the data. The results show that sex ratio significantly correlates with changes in recombination rate among X-bearing but not among Y-bearing sperm. Different hypotheses to explain these observations are discussed.

Landscape of copy number variations in Bos taurus: individual - and inter-breed variability

Background

The number of studies of Copy Number Variation in cattle has increased in recent years. This has been prompted by the increased availability of data on polymorphisms and their relationship with phenotypes. In addition, livestock species are good models for some human phenotypes. In the present study, we described the landscape of CNV driven genetic variation in a large population of 146 individuals representing 13 cattle breeds, using whole genome DNA sequence.

Results

A highly significant variation among all individuals and within each breed was observed in the number of duplications (P < 10⁻¹⁵) and in the number of deletions (P < 10⁻¹⁵). We also observed significant differences between breeds for duplication (P = 0.01932) and deletion (P = 0.01006) counts. The same variation CNV length - inter-individual and inter-breed differences were significant for duplications (P < 10⁻¹⁵) and deletions (P < 10⁻¹⁵). Moreover, breed-specific variants were identified, with the largest proportion of breed-specific duplications (9.57%) found for Fleckvieh and breed-specific deletions found for Brown Swiss (5.00%). Such breed-specific CNVs were predominantly located in intragenic regions, however in Simmental, one deletion present in five individuals was found in the coding sequence of a novel gene ENSBTAG00000000688 on chromosome 18. In Brown Swiss, Norwegian Red and Simmental breed-specific deletions were located within KIT and MC1R genes, which are responsible for a coat colour. The functional annotation of coding regions underlying the breed-specific CNVs showed that in Norwegian Red, Guernsey, and Simmental significantly under- and overrepresented GO terms were related to chemical stimulus involved in sensory perception of smell and the KEGG pathways for olfactory transduction. In addition, specifically for the Norwegian Red breed, the dopaminergic synapse KEGG pathway was significantly enriched within deleted parts of the genome.

Conclusions

The CNV landscape in Bos taurus genome revealed by this study was highly complex, with inter-breed differences, but also a significant variation within breeds. The former, may explain some of the phenotypic differences among analysed breeds, and the latter contributes to within-breed variation available for selection.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4815-6) contains supplementary material, which is available to authorized users.

Fitting and validating the genomic evaluation model to Polish Holstein-Friesian cattle

The aim of the study was to fit the genomic evaluation model to Polish Holstein-Friesian dairy cattle. A training data set for the estimation of additive effects of single nucleotide polymorphisms (SNPs) consisted of 1227 Polish Holstein-Friesian bulls. Genotypes were obtained by the use of Illumina BovineSNP50 Genotyping BeadChip. Altogether 29 traits were considered: milk-, fat- and protein- yields, somatic cell score, four female fertility traits, and 21 traits describing conformation. The prediction of direct genomic values was based on a mixed model containing deregressed national proofs as a dependent variable and random SNP effects as independent variables. The correlations between direct genomic values and conventional estimated breeding values estimated for the whole data set were overall very high and varied between 0.98 for production traits and 0.78 for non return rates for cows. For the validation data set of 232 bulls the corresponding correlations were 0.38 for milk-, 0.37 for protein-, and 0.32 for fat yields, while the correlations between genomic enhanced breeding values and conventional estimated breeding values for the four traits were: 0.43, 0.44, 0.31, and 0.35. This model was able to pass the interbull validation criteria for genomic selection, which indicates that it is realistic to implement genomic selection in Polish Holstein-Friesian cattle.

The assessment of inter-individual variation of whole-genome DNA sequence in 32 cows

Despite the growing number of sequenced bovine genomes, the knowledge of the population-wide variation of sequences remains limited. In many studies, statistical methodology was not applied in order to relate findings in the sequenced samples to a population-wide level. Our goal was to assess the population-wide variation in DNA sequence based on whole-genome sequences of 32 Holstein-Friesian cows. The number of SNPs significantly varied across individuals. The number of identified SNPs increased with coverage, following a logarithmic curve. A total of 15,272,427 SNPs were identified, 99.16 % of them being bi-allelic. Missense SNPs were classified into three categories based on their genomic location: housekeeping genes, genes undergoing strong selection, and genes neutral to selection. The number of missense SNPs was significantly higher within genes neutral to selection than in the other two categories. The number of variants located within 3'UTR and 5'UTR regions was also significantly different across gene families. Moreover, the number of insertions and deletions differed significantly among cows varying between 261,712 and 330,103 insertions and from 271,398 to 343,649 deletions. Results not only demonstrate inter-individual variation in the number of SNPs and indels but also show that the number of missense SNPs differs across genes representing different functional backgrounds.

Testing candidate gene effects on milk production traits in dairy cattle under various parameterizations and modes of inheritance

The major objectives of this study were 1) to assess the statistical properties of models commonly used for the estimation of single nucleotide polymorphism (SNP) effects under the assumption of various modes of inheritance and various parameterizations of SNP genotypes using simulated data, and 2) to compare effects of the selected polymorphisms located within butyrophilin (BTN1A1), diacylglycerol acyltransferase 1 (DGAT1), leptin (LEP), and leptin receptor (LEPR) candidate genes on milk production traits using data from 2 dairy cattle breeds (190 Jersey cows and 475 Polish Holstein-Friesian cows). Simulation results showed that type I error and power were not dependent on the assumed parameterization, but differences were observed regarding confidence intervals of estimated SNP effects. In the presence of epistasis, correct confidence intervals for all (epistatic and nonepistatic) SNP and all modes of inheritance were provided only by the parameterization proposed by C. H. Kao and Z. B. Zeng in 2002. However, if no dominance effect was included in the model, confidence intervals for SNP effects were correct for all parameterizations. Results based on real data showed that for both breeds the additive effects of polymorphisms were generally similar, except for LEPR, which had a different allele associated with increased fat content in Holstein-Friesians than in Jerseys. In both breeds, DGAT1 had the largest additive effect of the polymorphisms considered, but its effect on most milk traits was more pronounced in Jerseys than in Holstein-Friesians. Evidence of epistasis was found between LEPR and DGAT1, as well as between LEPR and BTN1A1, but only for milk content traits and only in the Holstein-Friesian breed. There was also more evidence for dominance in the Holstein-Friesian breed than in the Jersey breed.

Identification and annotation of breed-specific single nucleotide polymorphisms in Bos taurus genomes

In Bos taurus the universality of the reference genome is biased towards genetic variation represented by only two related individuals representing the same Hereford breed. Therefore, results of genetic analyses based on this reference may not be reliable. The 1000 Bull Genomes resource allows for identification of breed-specific polymorphisms and for the construction of breed-specific reference genomes. Whole-genome sequences or 936 bulls allowed us to construct seven breed specific reference genomes of Bos taurus for Angus, Brown Swiss, Fleckvieh, Hereford, Jersey, Limousin and Simmental. In order to identify breed-specific variants all detected SNPs were filtered within-breed to satisfy criteria of the number of missing genotypes not higher than 7% and the alternative allele frequency equal to unity. The highest number of breed-specific SNPs was identified for Jersey (130,070) and the lowest—for the Simmental breed (197). Such breed-specific polymorphisms were annotated to coding regions overlapping with 78 genes in Angus, 140 in Brown Swiss, 132 in Fleckvieh, 100 in Hereford, 643 in Jersey, 10 in Limousin and no genes in Simmental. For most of the breeds, the majority of breed-specific variants from coding regions was synonymous. However, most of Fleckvieh-specific and Hereford-specific polymorphisms were missense mutations. Since the identified variants are characteristic for the analysed breeds, they form the basis of phenotypic differences observed between them, which result from different breeding programmes. Breed-specific reference genomes can enhance the accuracy of SNP driven inferences such as Genome-wide Association Studies or SNP genotype imputation.

Identification of candidate genes and mutations in QTL regions for immune responses in chicken

There are two categories of immune responses – innate and adaptive immunity – both having polygenic backgrounds and a significant environmental component. In our study, adaptive immunity was represented by the specific antibody response toward keyhole limpet hemocyanin (KLH); innate immunity was represented by natural antibodies toward lipopolysaccharide (LPS) and lipoteichoic acid (LTA). Defining genetic bases of immune responses leads from defining quantitative trait loci (QTL) toward a single mutation responsible for variation in the phenotypic trait. The goal of the reported study was to define candidate genes and mutations for the immune traits of interest in chicken by performing an association study of SNPs located in candidate genes defined in QTL regions. Candidate genes and SNPs in QTL regions were selected in silico. SNP association was based on a custom SNP panel, GoldenGate genotyping assay (Illumina) and two statistical models: random mixed model and CAR score. The most significant SNP for immune response toward KLH was located in the JMJD6 gene located on GGA18. Four SNPs in candidate genes FOXJ1 (GGA18), EPHB1 (GGA9), PTGER4 (GGAZ) and PRKCB (GGA14) showed association with natural antibodies for LPS. A single SNP in ITGB4 (GGA18) was associated with natural antibodies for LTA. All associated SNPs mentioned above showed additive effects.

The impact of single nucleotide polymorphism selection on prediction of genomewide breeding values

The study focuses on the impact of different sets of single nucleotide polymorphisms (SNPs) selected from the available data set on prediction of genomewide breeding values (GBVs) of animals. Correlations between breeding values estimated as additive polygenic effects (EBVs) and GBVs as well as correlations between true breeding values (TBVs) and GBVs are used as major criteria for the comparison of different SNP selection schemes and GBV estimation models.

The analysed data is the simulated data set from the XII QTL Workshop. In the analysis five different SNP data sets are considered. For prediction of EBVs a standard mixed animal model is applied, whereas GBVs are defined as the sum of additive effects of SNPs estimated for the different SNP data sets using model 1 with fixed SNPs effects, model 2 with fixed SNPs effects and a random additive polygenic effect, model 3 with a random effects of uncorrelated SNP genotypes.

The additive polygenic and residual variance components estimated by the EBV model amount to 1.36 and 3.12, respectively. Differences between models are expressed by comparing the ranking of individuals based on EBV and on GBV and by correlations. Among 100 individuals with the highest EBVs, depending on a model and a data set, there are only between 11 and 37 individuals with the highest GBVs. The highest correlation between GBV and EBV amounts to 0.787 and is observed for model 3 with 3,328 SNPs selected based on their minor allele frequency, the lowest correlation of 0.519 is attributed to model 2 with 300 SNPs. Correlations between GBV estimates obtained from different models with the same number of SNPs range between 0.916 and 0. 998, whereas correlations between different SNP data sets using the same model fall under 0.850.

These results indicate that successful application of high throughoutput SNP genotyping technologies for prediction of breeding values is a very promising approach, but before the method can be routinely applied further methodological improvements regarding model construction and SNP selection are required.

Detection of two QTL on chicken chromosome 14 for keyhole lymphet haemocyanin

A keyhole lymphet haemocyanin is an antigen which triggers Th1 type of immune response. A QTL for a primary immune response towards keyhole lymphet haemocyanin has been detected on chicken chromosome 14 in three populations. The results from the most recent population were inconsistent and varied depending on the applied QTL detection model. The major goal of the current study was the reanalysis of this data using a 2 QTL model. Additionally, in order to provide more accurate estimates of QTL effects and positions, epistasis between the QTL was considered as a potential important contributor to quantitative traits. Four statistical models were assumed: M1: A model assuming marginal additive effects of two QTL; M2: A model assuming marginal and epistatic additive effects of two QTL; M3: A model assuming marginal additive and dominance effects of two QTL; M4: A model assuming marginal additive and dominance effects of two QTL and all possible pairwise epistases. Two QTL with significant additive and dominance effects were detected on chicken chromosome 14 using model M3. One QTL was detected at 63 cM between MCW0123 and ROS0005, another at 76 cM between ROS0005 and MCW0225/NTN2Lsts1 (FDR = 0.0051). Modelling only additive effects resulted in a significantly worse fit. On the other hand, including epistatic effects did not improve fit significantly. The current study confirms previous reports of the QTL location on GGA14. A notable finding of this study is recognition of two closely related QTL for a keyhole lymphet haemocyanin response at the distal part of chicken chromosome 14.