Genome-wide scan for selective sweeps identifies novel loci associated with resistance to mastitis in German Holstein cattle.

Domestication and selection significantly changed phenotypic and behavioural traits in modern domestic animals. In this study, to identify the genomic regions associated with mastitis, genomic data of German Holstein dairy cattle were analysed. The samples were genotyped using the Bovine 50 K SNP chip.

Hitchhiking Mapping of Candidate Regions Associated with Fat Deposition in Iranian Thin and Fat Tail Sheep Breeds Suggests New Insights into Molecular Aspects of Fat Tail Selection.

The fat tail is a phenotype that divides indigenous Iranian sheep genetic resources into two major groups. The objective of the present study is to refine the map location of candidate regions associated with fat deposition, obtained via two separate whole genome scans contrasting thin and fat tail breeds, and to determine the nature of the selection occurring in these regions using a hitchhiking approach. Zel (thin tail) and Lori-Bakhtiari (fat tail) breed samples that had previously been run on the Illumina Ovine 50 k BeadChip, were genotyped with a denser set of SNPs in the three candidate regions using a Sequenom Mass ARRAY platform.

Genetic structure analysis in several populations of cattle using SNP genotypes.

Parameters such as effective population size (Ne), runs of homozygosity (ROH), and inbreeding based on ROH (FROH) can give new insight into the level of genetic diversity for the population under selection. This research aimed to measure the extent of linkage disequilibrium (LD), effective population size (Ne), Haplotype Block Structure, and runs of homozygosity (ROHs) in several populations of cattle using SNP genotypes. In this study, that the average decreased with the increasing distance of SNP pairs.

Genomic comparisons of Persian Kurdish, Persian Arabian and American Thoroughbred horse populations.

The present research aimed to characterize the Persian Kurdish horse population relative to the Persian Arabian and American Thoroughbred populations using genome-wide SNP data. Fifty-eight Kurdish, 38 Persian Arabian and 83 Thoroughbred horses were genotyped across 670,796 markers. After quality control and pruning to eliminate linkage disequilibrium between loci which resulted in 13,554 SNPs in 52 Kurdish, 24 Persian Arabian and 58 Thoroughbred horses, the Kurdish horses were generally distinguished from the Persian Arabian samples by Principal Component Analyses, cluster analyses and calculation of pairwise FST.

Genome-wide association studies for methane emission and ruminal volatile fatty acids using Holstein cattle sequence data.

Background: Methane emission by ruminants has contributed considerably to the global warming and understanding the genomic architecture of methane production may help livestock producers to reduce the methane emission from the livestock production system. The goal of our study was to identify genomic regions affecting the predicted methane emission (PME) from volatile fatty acids (VFAs) indicators and VFA traits using imputed whole-genome sequence data in Iranian Holstein cattle.

Results: Based on the significant-association threshold (p < 5 × 10), 33 single nucleotide polymorphisms (SNPs) were detected for PME per kg milk (n = 2), PME per kg fat (n = 14), and valeric acid (n = 17).

Exploring novel single nucleotide polymorphisms and haplotypes of the diacylglycerol O-acyltransferase 1 (DGAT1) gene and their effects on protein structure in Iranian buffalo.

Background: Diacylglycerol O-acyltransferase 1 (DGAT1) plays a key role in the synthesis of triglycerides. Recent studies have shown that a transition mutation resulting in substitutions of guanine by adenine in the DGAT1 gene in cattle has considerable effects on milk yield and composition. Currently, there is no systematic research reporting on the utilization of this gene segment in Iranian buffalo (Bubalus bubalis).

Cattle infection response network and its functional modules.

Background: Weighted Gene Co-expression Network analysis, a powerful technique used to extract co-expressed gene pattern from mRNA expression data, was constructed to infer common immune strategies used by cattle in response to five different bacterial species (Escherichia coli, Mycobacterium avium, Mycobacterium bovis, Salmonella and Staphylococcus aureus) and a protozoa (Trypanosoma Congolense) using 604 publicly available gene expression microarrays from 12 cattle infection experiments.

Results: A total of 14,999 transcripts that were differentially expressed (DE) in at least three different infection experiments were consolidated into 15 modules that contained between 43 and 4441 transcripts. The high number of shared DE transcripts between the different types of infections indicated that there were potentially common immune strategies used in response to these infections.

Large-scale gene co-expression network as a source of functional annotation for cattle genes.

Background: Genome sequencing and subsequent gene annotation of genomes has led to the elucidation of many genes, but in vertebrates the actual number of protein coding genes are very consistent across species (~20,000). Seven years after sequencing the cattle genome, there are still genes that have limited annotation and the function of many genes are still not understood, or partly understood at best. Based on the assumption that genes with similar patterns of expression across a vast array of tissues and experimental conditions are likely to encode proteins with related functions or participate within a given pathway, we constructed a genome-wide Cattle Gene Co-expression Network (CGCN) using 72 microarray datasets that contained a total of 1470 Affymetrix Genechip Bovine Genome Arrays that were retrieved from either NCBI GEO or EBI ArrayExpress.

Random Regression Models Using Legendre Polynomials to Estimate Genetic Parameters for Test-day Milk Protein Yields in Iranian Holstein Dairy Cattle.

The objective of this study was to estimate the genetic parameters of milk protein yields in Iranian Holstein dairy cattle. A total of 1,112,082 test-day milk protein yield records of 167,269 first lactation Holstein cows, calved from 1990 to 2010, were analyzed. Estimates of the variance components, heritability, and genetic correlations for milk protein yields were obtained using a random regression test-day model.

Effect of ethanol induced mild stress on post-thawed bull sperm quality.

This study was performed to investigate the effect of sub-lethal exposure of bull semen to ethanol on the post-thaw spermatozoa quality. Semen samples (n=24, 6 ejaculates/bull) from 4 Holstein bulls were collected and pooled. Pooled samples were divided into 4 equal parts and each part was frozen after being diluted with Optidyl® extender containing 0 (O-E0), 0.

Fertility subindex for improving fertility performance in Iranian Holstein cows.

Different fertility indices were constructed for improving fertility performance in Iranian Holstein dairy cows. Number of inseminations per conception and days from calving to first insemination, each weighted by its economic value, were included as breeding goals in the aggregate genotype definition. Different fertility indices (FI) were constructed with different combinations of available fertility traits: number of inseminations to conception (INS), days from calving to first service (DFS), interval between first and last insemination (IFL), and days open (DO).

Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition.

Background: Identification of genomic regions that have been targets of selection for phenotypic traits is one of the most important and challenging areas of research in animal genetics. However, currently there are relatively few genomic regions identified that have been subject to positive selection. In this study, a genome-wide scan using ~50,000 Single Nucleotide Polymorphisms (SNPs) was performed in an attempt to identify genomic regions associated with fat deposition in fat-tail breeds.

Estimation of genetic parameters for body weight and egg production traits in Mazandaran native chicken.

Native chicken breeding station of Mazandaran was established in 1988 with two main objectives: genetic improvement through selection programs and dissemination of indigenous Mazandarani birds. (Co)variance components and genetic parameters for economically important traits were estimated using (bi) univariate animal models with ASREML procedure in Mazandarani native chicken. The data were from 18 generations of selection (1988-2009).

Bio-economic evaluation of the use of sexed semen at different conception rates and herd sizes in Holstein populations.

A stochastic bio-economic model was used to determine the effects of applying artificial insemination (AI) with conventional or sexed semen at different conception rates and herd sizes on the genetic progress of productive trait and net profit over a 15-year period. The genetic means of the cattle population was predicted to increase over the years and the rate of genetic progress in the population program using sexed semen was significantly greater than the rate of progress in the population using conventional semen. The theoretical genetic gain was greater than the realized genetic gain for milk yield for all the AI scenarios.

Effect of the threshold nature of traits on heritability estimates obtained by linear model.

In this research we used stochastic method to simulate litter size data under assumption that the phenotype of the trait of interest is categorically distributed with a liability of normally distributed background effect. For the phenotypic categorical measurements, normal distribution of liability was assumed. Analysis was conducted by DFREML for phenotypic categorical data set.