The imprinted gene DIO3 is a candidate gene for litter size in pigs.

Genomic imprinting is an important epigenetic phenomenon, which on the phenotypic level can be detected by the difference between the two heterozygote classes of a gene. Imprinted genes are important in both the development of the placenta and the embryo, and we hypothesized that imprinted genes might be involved in female fertility traits. We therefore performed an association study for imprinted genes related to female fertility traits in two commercial pig populations.

Long-term response to genomic selection: effects of estimation method and reference population structure for different genetic architectures.

Background: Genomic selection has become an important tool in the genetic improvement of animals and plants. The objective of this study was to investigate the impacts of breeding value estimation method, reference population structure, and trait genetic architecture, on long-term response to genomic selection without updating marker effects.

Methods: Three methods were used to estimate genomic breeding values: a BLUP method with relationships estimated from genome-wide markers (GBLUP), a Bayesian method, and a partial least squares regression method (PLSR).

Partial least square regression applied to the QTLMAS 2010 dataset.

Background: Partial least square regression (PLSR) was used to analyze the data of the QTLMAS 2010 workshop to identify genomic regions affecting either one of the two traits and to estimate breeding values. PLSR was appropriate for these data because it enabled to simultaneously fit several traits to the markers.

Results: A preliminary analysis showed phenotypic and genetic correlations between the two traits.

QTLMAS 2009: simulated dataset.

Background: The simulation of the data for the QTLMAS 2009 Workshop is described. Objective was to simulate observations from a growth curve which was influenced by a number of QTL.

Results: The data consisted of markers, phenotypes and pedigree.

Comparison of analyses of the QTLMAS XIII common dataset. II: QTL analysis.

Background: Five participants of the QTL-MAS 2009 workshop applied QTL analyses to the workshop common data set which contained a time-related trait: cumulative yield. Underlying the trait were 18 QTLs for three parameters of a logistic growth curve that was used for simulating the trait.

Methods: Different statistical models and methods were employed to detect QTLs and estimate position and effect sizes of QTLs.

Comparison of analyses of the QTLMAS XIII common dataset. I: genomic selection.

Background: Genomic selection, the use of markers across the whole genome, receives increasing amounts of attention and is having more and more impact on breeding programs. Development of statistical and computational methods to estimate breeding values based on markers is a very active area of research. A simulated dataset was analyzed by participants of the QTLMAS XIII workshop, allowing a comparison of the ability of different methods to estimate genomic breeding values.

Sensitivity of methods for estimating breeding values using genetic markers to the number of QTL and distribution of QTL variance.

The objective of this simulation study was to compare the effect of the number of QTL and distribution of QTL variance on the accuracy of breeding values estimated with genomewide markers (MEBV). Three distinct methods were used to calculate MEBV: a Bayesian Method (BM), Least Angle Regression (LARS) and Partial Least Square Regression (PLSR). The accuracy of MEBV calculated with BM and LARS decreased when the number of simulated QTL increased.

Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken.

Background: The chicken (Gallus gallus), like most avian species, has a very distinct karyotype consisting of many micro- and a few macrochromosomes. While it is known that recombination frequencies are much higher for micro- as compared to macrochromosomes, there is limited information on differences in linkage disequilibrium (LD) and haplotype diversity between these two classes of chromosomes. In this study, LD and haplotype diversity were systematically characterized in 371 birds from eight chicken populations (commercial lines, fancy breeds, and red jungle fowl) across macro- and microchromosomes.

Haplotype inference in crossbred populations without pedigree information.

Background: Current methods for haplotype inference without pedigree information assume random mating populations. In animal and plant breeding, however, mating is often not random. A particular form of nonrandom mating occurs when parental individuals of opposite sex originate from distinct populations.

Biochemical pathways analysis of microarray results: regulation of myogenesis in pigs.

Background: Combining microarray results and biological pathway information will add insight into biological processes. Pathway information is widely available in databases through the internet. Mammalian muscle formation has been previously studied using microarray technology in pigs because these animals are an interesting animal model for muscle formation due to selection for increased muscle mass.