Dissection of X chromosome dosage compensation for quantitative traits in sheep using different statistical models.

Since males and females have different number of X chromosome, different mechanisms have evolved to equalize dosage of gene products from the X chromosome between XX females and XY males. The aim of this study was to study X chromosome dosage compensation for growth rate (GR), Kleiber ratio (KR), efficiency of growth (EF) and relative growth rate (RGR) in Zandi sheep. A two steps procedure was adopted to analysis data.

Parent of origin genetic effects on milk production traits in a population of Iranian Holstein cows.

The aim was to estimate the relative contribution of imprinting effects from both paternal and maternal sides to phenotypic variation in milk production traits including 305 days milk yield (MY), average daily milk production (ADM), fat percentage (F%), protein percentage (P%), 305 days fat yield (FY), 305 days protein yield (PY), ratio of fat percentage to protein percentage (F:P) and somatic cell score (SCS) in Iranian Holstein cows. To do this, each trait was analysed with a series of four animal models, which were identical for fixed and additive genetic effects but differed for combinations of paternal and maternal imprinting effects. The log-likelihood ratio test (LRT) and Akaike's information criteria (AIC) were used to select the best model for each trait.

Accelerating imputation of missing genotypes using parallel computing.

Owing to massive jump in DNA technology, large-scale genomic datasets, including valuable information, have become available. While this is a prodigious opportunity, and it can also be a big challenge because analysing these large datasets with current computers and software tools is very difficult and may take days or even weeks to complete. Novel approaches such as parallel computing have been suggested to deal with these large datasets.

Relative contribution of Imprinting, X chromosome and Litter effects to phenotypic variation in economic traits of sheep.

Data on Zandi sheep were analysed to quantify maternal and paternal imprinting, X chromosome and litter effects' contribution to phenotypic variation in birth weight (BW), weaning weight (WW), growth rate (GR), Kleiber ratio (KR), efficiency of growth (EF) and relative growth rate (RGR). To this end, a two-step approach was adopted. In the first step, each trait was analysed with a series of 16 animal models, which were identical for fixed and autosomal additive genetic effects but differed for combinations of maternal permanent environmental, maternal genetic, X chromosome and litter effects.

Comparison of regression tree-based methods in genomic selection.

The aim of this study was to compare the predictive performance of tree-based methods including regression tree (RT), random forest (RF) and Boosting (BT) in genomic selection. To do this, a genome comprised of five chromosomes was simulated for 1000 individuals on which 5000 single-nucleotide polymorphisms were evenly distributed. Comparison of methods was made in different scenarios of genetic architecture (number of QTL and distribution of QTL effects) and heritability level (0.

Assessing the performance of a novel method for genomic selectio:rrBLUP-method6.

The aim of this study was to compare the predictive performance of ridge regression best linear unbiased prediction-method 6 (rrBLUPm6) with well-known genomic selection methods (rrBLUP, GBLUP and BayesA) in terms of accuracy of prediction, computing time and memory requirement. The impact of the genetic architecture and heritability on the accuracy of genomic evaluation was also studied. To this end, a genome was simulated which consisted of five chromosomes, one Morgan each, on which 5000 biallelic singlenucleotide polymorphisms (SNP) were distributed.

The relation between the genetic architecture of quantitative traits and long-term genetic response.

The genetic architecture of a quantitative trait refers to the number of genetic variants, allele frequencies, and effect sizes of variants that affect a trait and their mode of gene action. This study was conducted to investigate the effect of four shapes of allelic frequency distributions (constant, uniform, L-shaped and U-shaped) and different number of trait-affecting loci (50, 100, 200, 500) on allelic frequency changes, long term genetic response, and maintaining genetic variance. To this end, a population of 440 individuals composed of 40 males and 400 females as well as a genome of 200 cM consisting of two chromosomes and with a mutation rate of 2.

Change in genetic size of small-closed populations: Lessons from a domestic mammal population.

The aim of this study was to monitor changes in genetic size of a small-closed population of Iranian Zandi sheep, by using pedigree information from animals born between 1991 and 2005. The genetic size was assessed by using measures based on the probability of identity-by-descend of genes (coancestry, f, and effective population size, N(e) ), as well as measures based on probability of gene origin (effective number of founders, f(e) , effective number of founder genomes, f(g) , and effective number of non-founder genomes, f(ne) ). Average coancestry, or the degree of genetic similarity of individuals, increased from 0.