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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. Statistical tests were then performed using different and complementary methods based on either site frequency (FST and Median homozygosity) or haplotype (iHS and XP-EHH). The results from candidate regions on chromosome 5 and X revealed clear evidence of selection with the derived haplotypes that was consistent with selection to near fixation for the haplotypes affecting fat tail size in the fat tail breed. An analysis of the candidate region on chromosome 7 indicated that selection differentiated the beneficial alleles between breeds and homozygosity has increased in the thin tail breed which also had the ancestral haplotype. These results enabled us to confirm the signature of selection in these regions and refine the critical intervals from 113 kb, 201 kb, and 2831 kb to 28 kb, 142 kb, and 1006 kb on chromosome 5, 7, and X respectively. These regions contain several genes associated with fat metabolism or developmental processes consisting of TCF7 and PPP2CA (OAR5), PTGDR and NID2 (OAR7), AR, EBP, CACNA1F, HSD17B10,SLC35A2, BMP15, WDR13, and RBM3 (OAR X), and each of which could potentially be the actual target of selection. The study of core haplotypes alleles in our regions of interest also supported the hypothesis that the first domesticated sheep were thin tailed, and that fat tail animals were developed later. Overall, our results provide a comprehensive assessment of how and where selection has affected the patterns of variation in candidate regions associated with fat deposition in thin and fat tail sheep breeds.

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. For each defined healthy and sick group, 133 samples from 13,276 genotyped dairy cows were selected based on mastitis random residual effects. Grouping was done to infer selection signatures based on XP-EHH statistic. The results revealed that for the top 0.01 percentile of the obtained XP-EHH values, five genomic regions on chromosomes 8, 11, 12, 14 and 26 of the control group, and four regions on chromosomes 3, 4 (two regions) and 22 of the case group, have been under selection. Also, consideration of the top 0.1 percentile of the XP-EHH values, clarified 21 and 15 selective sweeps in the control and case group, respectively. This study identified some genomic regions containing potential candidate genes associated with resistance and susceptibility to mastitis, immune system and inflammation, milk traits, udder morphology and different types of cancers. In addition, these regions overlap with some quantitative trait loci linked to clinical mastitis, immunoglobulin levels, somatic cell score, udder traits, milk fat and protein, milk yield, milking speed and veterinary treatments. It is noteworthy that we found two regions in the healthy group (on chromosomes 12 and 14) with strong signals, which were not described previously. It is likely that future research could link these identified genomic regions to mastitis. The results of the current study contribute to the identification of causal mutations, genomic regions and genes affecting mastitis incidence in dairy cows.

Background Fatness related traits are economically very important in sheep production and are associated with serious diseases in humans. The fat tail is a phenotype that divides domesticated sheep 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 hitchhiking approach. Results Zel (thin tail) and Lori-Bakhtiari (fat tail) breed samples that had previously been run on the Illumina Ovine 50k BeadChip, were genotyped with a denser set of SNPs in the three candidate regions using a Sequenom Mass ARRAY platform. Statistical tests were then performed using different and complementary methods based on either site frequency (FST and Median homozygosity) or haplotype (iHS and XP-EHH). Results from candidate regions on chromosome 5 and X revealed clear evidence of selection with the derived haplotypes that were consistent with selection to near fixation for the haplotypes affecting fat tail size in the fat tail breed. Analysis of the candidate region on chromosome 7 indicated that selection differentiated the beneficial alleles between breeds and homozygosity has increased in the thin tail breed which also had the ancestral haplotype. These results enabled us to confirm the signature of selection in these regions and refine the critical intervals from 113kb, 201kb and 2,831kb to 28kb, 142kb and 1,006kb on chromosome 5, 7 and X respectively. These regions contain several genes associated with fat metabolism or developmental processes consisting TCF7 and PPP2CA (OAR5), PTGDR and NID2 (OAR7), AR, EBP, CACNA1F, HSD15B, SLC35A2, BMP15, WDR13 and RBM3 (OAR X), each of which could potentially be the actual target of selection. Study of core haplotypes alleles in our regions of interest also supported the hypothesis that the first domesticated sheep were thin tailed and fat tail animals were developed later. Conclusions Our results provide a comprehensive assessment of how and where selection has affected the patterns of variation in candidate regions associated with fat deposition in thin and fat tail sheep breeds. The hitchhiking mapping approach in this study was novel in the sense that most of the exploratory genome scan studies in domestic animals have not clarified the signal from the candidate regions, probably due to the lack of suitable genomic resources.

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. Both Persian breeds were discriminated from the Thoroughbred. Pairwise FST between the two Persian samples (0.013) was significantly greater than zero and several fold less than those found between the Thoroughbred and Kurdish (0.052) or Thoroughbred and Persian Arabian (0.057). Cluster analysis assuming three genetic clusters assigned the Kurdish horse and Thoroughbred to distinct clusters (0.942 in cluster 2 and 0.953 in cluster 3 respectively); the Persian Arabian was not in a distinct cluster (0.519 in cluster 1), demonstrating shared ancestry or recent admixture with the Kurdish breed. Diversity as quantified by expected heterozygosity was the highest in the Kurdish horse (0.342), followed by the Persian Arabian (0.328) and the Thoroughbred (0.326). Analysis of Molecular Variance showed that 4.47% of the genetic variation was present among populations (PFIS) were not significantly different from zero in any of the populations. Analysis of individual inbreeding based on runs of homozygosity using a larger SNP set suggested greater diversity in both the Kurdish and Persian Arabian than in the Thoroughbred. These results have implications for developing conservation strategies to achieve sound breeding goals while maintaining genetic diversity.

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 − 8), 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). Besides, 69 genes were identified for valeric acid (n = 18), PME per kg milk (n = 4) and PME per kg fat (n = 47) that were located within 1 Mb of significant SNPs. Based on the gene ontology (GO) term analysis, six promising candidate genes were significantly clustered in organelle organization (GO:0004984, p = 3.9 × 10− 2) for valeric acid, and 17 candidate genes significantly clustered in olfactory receptors activity (GO:0004984, p = 4 × 10− 10) for PME traits. Annotation results revealed 31 quantitative trait loci (QTLs) for milk yield and its components, body weight, and residual feed intake within 1 Mb of significant SNPs. Conclusions Our results identified 33 SNPs associated with PME and valeric acid traits, as well as 17 olfactory receptors activity genes for PME traits related to feed intake and preference. Identified SNPs were close to 31 QTLs for milk yield and its components, body weight, and residual feed intake traits. In addition, these traits had high correlations with PME trait. Overall, our findings suggest that marker-assisted and genomic selection could be used to improve the difficult and expensive-to-measure phenotypes such as PME. Moreover, prediction of methane emission by VFA indicators could be useful for increasing the size of reference population required in genome-wide association studies and genomic selection.

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. Milking times, herd, age of recording, year, and month of recording were included as fixed effects in the model. Additive genetic and permanent environmental random effects for the lactation curve were taken into account by applying orthogonal Legendre polynomials of the fourth order in the model. The lowest and highest additive genetic variances were estimated at the beginning and end of lactation, respectively. Permanent environmental variance was higher at both extremes. Residual variance was lowest at the middle of the lactation and contrarily, heritability increased during this period. Maximum heritability was found during the 12th lactation stage (0.213±0.007). Genetic, permanent, and phenotypic correlations among test-days decreased as the interval between consecutive test-days increased. A relatively large data set was used in this study; therefore, the estimated (co)variance components for random regression coefficients could be used for national genetic evaluation of dairy cattle in Iran.

The body weight is an economically important trait in sheep. We performed a genomewide association study using Ovine 50 K SNP chip to identify the genes and chromosome regions associated with body weight in Baluchi sheep. A total of 96 blood samples from two herds along with data on weight at birth (BW), weaning (WW), six month (SMW) and yearling (YW) were collected. Markers were tested for association based on linear regression using the PLINK software. Thirteen different SNP markers reached 5% Bonferroni chromosome-wide significance levels. In this study we detected one SNP with genomewide significance effect on yearling weight on chromosome 8. All significant SNPs at chromosome-wide significance level were within or close to known ovine genes. The SNP at genomewide significance level was within gene SYNE1. Thus, we suggest more investigation to prove these genes as candidate genes for body weight traits in sheep. Growth traits are economically important traits for sheep. Mapping of quantitative trait loci (QTL) is an appropriate approach and provides useful information for marker assisted selection (MAS) and gene-based selection in sheep breeding strategies. Relatively few number of QTLs have been reported in sheep. The current release (February 2014) of the Sheep QTLdb (http://www.animalgenome.org/cgi-bin/ QTLdb) contains 129 QTLs for growth traits reported from a genomic study based on marker-QTL linkage analysis. QTL mapping using linkage map QTLs to large confidence intervals on the genome. As a result, use of QTL in MAS is complicated. It would be possible to exploit linkage disequilibrium (LD) to map QTL if dense markers were available. With the advent of next-generation sequencing

There is a growing interest in odd- and branched-chain fatty acids (OBCFA) in milk following reports that several branched-chain fatty acids (FA) have health promoting effects, and certain milk OBCFA could serve as a biomarker to assess ruminal function. Twenty-four Holstein cows were fed 3 low-forage diets containing 30 g/kg of dry matter of prilled palm fat (PPF), sunflower oil (SO), or an equal mixture of both fats (experiment 1) or 3 diets containing 30 g/kg of dry matter of SO with a forage-to-concentrate ratio of 39:61, 44:56, or 48:52 (Experiment 2); diets were fed to investigate milk OBCFA composition and to explore the relationships between ruminal VFA and milk OBCFA using principal component analysis. Including SO in diets decreased yields of milk 13:0 anteiso, 15:0 anteiso, 15:0, 17:0, cis-9 15:1, and cis-9 17:1 compared with PPF. The molar proportion of ruminal propionate was the lowest and the yields of milk 14:0 iso and 16:0 iso were the greatest with the diet containing both fat supplements. Replacing concentrate with forages linearly increased ruminal acetate and yields of milk 13:0 iso, 14:0 iso, 15:0 iso, 16:0 iso, 17:0 iso, 13:0 anteiso, 15:0 anteiso, 15:0, 17:0, cis-9 15:1, and cis-9 17:1. The principal component analysis revealed that ruminal molar proportion of acetate related to concentrations of milk iso FA containing

1Department of Animal Science, Laboratory for Molecular Genetics Animal Biotechnology, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, Sari, Iran 2Department of Animal Sciences, Faculty of Agronomy Sciences, College of Agriculture Natural Resources, University of Tehran, Karaj, Iran 3Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07 Uppsala, Sweden

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. Results The total of 16,607 probe sets, which represented 11,397 genes, with unique Entrez ID were consolidated into 32 co-expression modules that contained between 29 and 2569 probe sets. All of the identified modules showed strong functional enrichment for gene ontology (GO) terms and Reactome pathways. For example, modules with important biological functions such as response to virus, response to bacteria, energy metabolism, cell signaling and cell cycle have been identified. Moreover, gene co-expression networks using “guilt-by-association” principle have been used to predict the potential function of 132 genes with no functional annotation. Four unknown Hub genes were identified in modules highly enriched for GO terms related to leukocyte activation (LOC509513), RNA processing (LOC100848208), nucleic acid metabolic process (LOC100850151) and organic-acid metabolic process (MGC137211). Such highly connected genes should be investigated more closely as they likely to have key regulatory roles. Conclusions We have demonstrated that the CGCN and its corresponding regulons provides rich information for experimental biologists to design experiments, interpret experimental results, and develop novel hypothesis on gene function in this poorly annotated genome. The network is publicly accessible at http://www.animalgenome.org/cgi-bin/host/reecylab/d. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3176-2) contains supplementary material, which is available to authorized users.

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. The number of transcripts in the identified modules varied in response to different infections. Fourteen modules showed a strong functional enrichment for specific GO/pathway terms related to “immune system process” (71%), “metabolic process” (71%), “growth and developmental process” (64%) and “signaling pathways” (50%), which demonstrated the close interconnection between these biological pathways in response to different infections. The largest module in the network had several over-represented GO/pathway terms related to different aspects of lipid metabolism and genes in this module were down-regulated for the most part during various infections. Significant negative correlations between this module’s eigengene values, three immune related modules in the network, and close interconnection between their hub genes, might indicate the potential co-regulation of these modules during different infections in bovine. In addition, the potential function of 93 genes with no functional annotation was inferred based on neighbor analysis and functional uniformity among associated genes. Several hypothetical genes were differentially expressed during experimental infections, which might indicate their important role in cattle response to different infections. Conclusions We identified several biological pathways involved in immune response to different infections in cattle. These findings provide rich information for experimental biologists to design experiments, interpret experimental results, and develop novel hypothesis on immune response to different infections in cattle. Electronic supplementary material The online version of this article (10.1186/s12865-017-0238-4) contains supplementary material, which is available to authorized users.

The objectives of this study were to quantify the errors in economic values (EVs) for traits affected by cost or price thresholds when skewed or kurtotic distributions of varying degree are assumed to be normal and when data with a normal distribution is subject to censoring. EVs were estimated for a continuous trait with dichotomous economic implications because of a price premium or penalty arising from a threshold ranging between -4 and 4 standard deviations from the mean. In order to evaluate the impacts of skewness, positive and negative excess kurtosis, standard skew normal, Pearson and the raised cosine distributions were used, respectively. For the various evaluable levels of skewness and kurtosis, the results showed that EVs can be underestimated or overestimated by more than 100% when price determining thresholds fall within a range from the mean that might be expected in practice. Estimates of EVs were very sensitive to censoring or missing data. In contrast to practical genetic evaluation, economic evaluation is very sensitive to lack of normality and missing data. Although in some special situations, the presence of multiple thresholds may attenuate the combined effect of errors at each threshold point, in practical situations there is a tendency for a few key thresholds to dominate the EV, and there are many situations where errors could be compounded across multiple thresholds. In the development of breeding objectives for non-normal continuous traits influenced by value thresholds, it is necessary to select a transformation that will resolve problems of non-normality or consider alternative methods that are less sensitive to non-normality.

An experiment was conducted to investigate the effect of short-term selection for 4 week breast weight (4wk BRW), and to estimate genetic parameters of body weight, and carcass traits. A selection (S) line and control (C) line was randomly selected from a base population. Data were collected over two consecutive hatches for four generations. A total of 1 135 records from 156 sires and 218 dams were used to estimate the genetic parameters. The genetic improvement of 4wk BRW was 3.5, 2.7 and 0.6 g in generation 2, 3 and 4, respectively. The estimated heritability by using pedigree information was 0.35±0.06. There were a significant difference for BW, and carcass weights but not for carcass percent components between lines (P

A stochastic bio-economic model has been used to determine the effects of new reproductive technologies over a 15-year period. A strategy of using conventional artificial insemination (AI) or embryo transfer (ET) using two sex-controlled embryos at different conception rates (CRs) and herd sizes resulted in a 24 state model. The genetic means of AI population increased over the years, and the genetic means of milk production for all of the embryo strategies were greater than those of AI. In addition, the genetic means of milk yield using different embryo-based scenarios in the expanding herds were greater than those for the fixed herds. The net profit of using sexed ET in the expanding herds was greater (P < 0.05) than that of fixed size herds. In general, there was a roughly consistent trend in net profit per cow for sexed ET strategies in the expanding herds over the years, but there was an increasing trend in net profit per cow for sexed ET strategies in the fixed herds over the years. Medium to high CRs for ET and the use of sex-controlled embryo systems, especially for induction of twin births to produce dairy replacements, will be critical elements of a system that produces significant numbers of female calves. The greater number of female calves produced in the sex-controlled scenarios allows the farmer to select animals with the best genetic potential as dairy replacement heifers; therefore, the rate of genetic gain increased in the dairy herd. Results of sensitivity analyses showed that a significant decrease in the production costs and increase in the ET performance are essential for embryo-based technologies to be profitable.

The objective of this study was to develop a method for calculating economic values of clinical mastitis (CM) and somatic cell score (SCS) for inclusion in a dairy cattle breeding goal in the context of a country where farm production and economic data are scarce. In order to calculate the costs and derive economic values for SCS, a new model, 'milk collection method', has been developed and was compared with the Meijering model with individual and average SCS distributions. For the population, estimated economic values using the milk collection method were 1.3 and 2.4 times higher than those of Meijering method with average and individual SCS, respectively. The milk collection method needs no assumptions about normality of the distribution of SCS and because of a lack of normality in Iranian data for SCS, the Meijering method resulted in economic values that were biased downwards. Failing to account for the fact that milk price penalties for SCS are applied at milk collection rather than individual cow level resulted in a further large downward bias in the economic value of SCS. When the distribution of data is unknown or difficult to approximate or when a transformation to normality is not straightforward, the milk collection method would be preferable. Inclusion of SCS and CM in the breeding goal for Iranian dairy cattle is justified based on these results. The model to calculate mastitis costs proposed here could be used to estimate economic values for CM in other developing countries where farm production and economic data are generally poor.

The objectives of this study were to estimate economic values (EVs) for three production traits (milk, fat and protein yields) and longevity and to develop a national selection index. The proposed Iranian selection index was compared with selection indices of three other countries in the world. A simple and appropriate model was used to describe the Holstein dairy cattle industry under an Iranian production system. Production parameters and economic data were collected from two Holstein dairy farms in Tehran province. The EVs were estimated at farm level for three breeding perspectives (maximized profit, minimized costs, and economic efficiency) and two restrictions in production system (fixed herd size and fixed total input). The average absolute EVs on profit perspective and herd size restriction for milk, fat, and protein yields (based on $/kg) and longevity ($/month) were 0.11, 0.89, -0.20, and 6.20, respectively. The average absolute EVs under minimized costs per unit of product interest for milk, fat, protein yields and longevity were -0.30, -3.43, 0.88 and -20.40, respectively. The average absolute EVs under maximized economic efficiency for milk, fat and protein yields and longevity were 0.34, 2.73, -0.99 and 36.33, respectively. Relative emphasis for three production traits and longevity were 59.7, 14.3, -3.0 and 23.1, respectively. The comparison of the proposed Iranian index with those countries where most of the semen and embryos are imported points out that developing a national selection index to improve cow profitability and optimum generic trends is necessary. Sensitivity analysis indicated that the influence of milk payment changes on EVs was the greatest as its influence on fat and protein EVs is substantial. EVs for milk and fat yields, with respect to price changes (milk, feed and non-feed), were the least sensitive and most sensitive, respectively.

Functional analysis of the red module. Over-represented GO/pathway terms were grouped based on kappa statistics. The size of each category within a pie chart represents the number of included terms. Only the most significant GO/terms within groups were labeled. GO/pathway terms are represented as nodes, and the node size represents the term enrichment significance, while the edges represent significant similarity between categories. (A) Representative biological processes interactions among module genes. (B) Representative molecular function interactions among module genes. (C) Representative Ractome analysis interactions among module genes. (PDF 2606Â kb)

(A) Frequency of combined interaction scores from the String database [21] and (B) Frequency of TOM connectivity in BGCN. (PDF 648Â kb)

Functional analysis of the light green module genes. Over-represented GO/pathway terms were grouped based on kappa statistics. The size of each category within a pie chart represents the number of included terms. Only the most significant GO/terms within groups were labeled. GO/pathway terms are represented as nodes, and the node size represents the term enrichment significance, while the edges represent significant similarity between categories. (A) Representative biological processes interactions among module genes. (B) Representative molecular function interactions among module genes. (C) Representative Ractome analysis interactions among module genes. (PDF 2605Â kb)

Functional analysis of the red module genes. Over-represented GO/pathway terms were grouped based on kappa statistics. The size of each category within a pie chart represents the number of included terms. Only the most significant GO/terms within groups were labeled. GO/pathway terms are represented as nodes, and the node size represents the term enrichment significance, while the edges represent significant similarity between categories. (A) Representative biological processes interactions among module genes. (B) Representative molecular function interactions among module genes. (C) Representative Ractome analysis interactions among module genes. (PDF 3753Â kb)

In this study, direct and maternal heritabilities were estimated for growth traits and carcass characteristics in Lori-Bakhtiari sheep. Data for birth weight (BW; n=5826), weaning weight (WW; n=5408), body weight at six months of age (6MW; n=4237), body weight at slaughter (SW; n=396), cold carcass weight (CCW; n=291), lean weight (LW; n=204), bone weight (WB; n=291), fat weight (WF; n=204) and fat-tail weight (FTW; n=396) were used to estimate the heritabilities. The data for first three traits had been collected during seventeen years, 1990 to 2006, while for other traits had been collected during six years, 2000 to 2006. Genetic parameters including both direct and maternal genetic effects were estimated using multivariate animal models, and a Derivative Free Restricted Maximum Likelihood (DFREML) approach. The direct heritability for BW, WW, 6MW, SW, CCW, LW, WB, WF and FTW were 0.30 ? 0.03, 0.13 ? 0.03, 0.20 ? 0.03, 0.24 ? 0.06, 0.16 ? 0.06, 0.16 ? 0.06, 0.20 ? 0.11, 0.23 ? 0.11, and 0.27 ? 0.11, respectively. Maternal heritability estimates were 0.22, 0.17, 0.06, 0.10, 0.09, 0.15, 0.26, 0.06 and 0.07 for BW, WW, 6MW, SW, CCW, LW, WB, WF and FTW, respectively. Consequently, genetic progress is possible for growth traits and carcass composition by selection.

Genetic profiles of Iranian Holstein young bulls at the national artificial insemination station were determined on the basis of individual genotypes at 13 ISAG's recommended microsatellites, the most useful markers of choice for parentage identification. In the present study a total of 119 individuals were genotyped at 13 microsatellite loci and for possible parent-offspring combinations. A high level of genetic variation was evident within the investigated individuals as assessed from various genetic diversity measures. The mean number of observed alleles per microsatellite marker was 9.15 and the number of effective alleles as usual was less than the observed values (4.03). The average observed and expected heterozygosity values were 0.612 and 0.898, respectively. The mean polymorphic information content (PIC) value (0.694) further reflected a high level of genetic variability. The average exclusion of probability (PE) of the 13 markers was 0.520, ranging from 0.389 to 0.788. The combined exclusion of probability was 0.999, when 13 microsatellite loci were used for analysis in the individual identification system. Inbreeding was calculated as the difference between observed and expected heterozygosity. Observed homozygosity was less than expected which reflects inbreeding of -3.7% indicating that there are genetic differences between bull-sires and bull-dams used to produce young bulls. The results obtained from this study demonstrate that the microsatellite DNA markers used in the present DNA typing are useful and sufficient for individual identification and parentage verification without accurate pedigree information. (Asian-Aust. J. Anim. Sci. 2006. Vol 19, No. 4 : 463-467)

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). The fertility index (FI1) that included INS and DFS had the greatest genetic gain for INS (−0.39 insemination), DFS (−7.47 days), and profit ($4.3) per generation. Genetic gain for profit, DFS, and INS including only DO showed slight differences regarding FI1. A selection index that included only INS (DFS) presented the larger (smaller) genetic gains for INS and smaller (larger) for DFS, which were −0.40 (−0.034) and −0.975 (−11.18) inseminations and days, respectively. The result of this study showed that recording INS and DFS are preferable traits for including in a fertility subindex. DO can be used in the absence of other fertility traits. © 2014, Springer Science+Business Media Dordrecht.

On the basis of the potential benefits to human health there is an increased interest in producing milk containing lower-saturated fatty acid (SFA) and higher unsaturated fatty acid (FA) concentrations, including cis-9 18:1 and cis-9, trans-11-conjugated linoleic acid (CLA). Twenty-four multiparous Holstein cows were used in two experiments according to a completely randomized block design, with 21-day periods to examine the effects of incremental replacement of prilled palm fat (PALM) with sunflower oil (SFO) in high-concentrate diets containing 30 g/kg dry matter (DM) of supplemental fat (Experiment 1) or increases in the forage-to-concentrate (F : C) ratio from 39 : 61 to 48 : 52 of diets containing 30 g/kg DM of SFO (Experiment 2) on milk production, digestibility and milk FA composition. Replacing PALM with SFO had no effect on DM intake, but tended to increase organic matter digestibility, yields of milk, protein and lactose, and decreased linearly milk fat content. Substituting SFO for PALM decreased linearly milk fat 8:0 to 16:0 and cis-9 16:1, and increased linearly 18:0, cis-9 18:1, trans-18:1 (��4 to 16), 18:2 and CLA concentrations. Increases in the F : C ratio of diets containing SFO had no effect on intake, yields of milk, milk protein or milk lactose, lowered milk protein content in a quadratic manner, and increased linearly NDF digestion and milk fat secretion. Replacing concentrates with forages in diets containing SFO increased milk fat 4:0 to 10:0 concentrations in a linear or quadratic manner, decreased linearly cis-9 16:1, trans-6 to -10 18:1, 18:2n-6, trans-7, cis-9 CLA, trans-9, cis-11 CLA and trans-10, cis-12 CLA, without altering milk fat 14:0 to 16:0, trans-11 18:1, cis-9, trans-11 CLA or 18:3n-3 concentrations. In conclusion, replacing prilled palm fat on with SFO in high-concentrate diets had no adverse effects on intake or milk production, other than decreasing milk fat content, but lowered milk fat medium-chain SFA and increased trans FA and polyunsaturated FA concentrations. Increases in the proportion of forage in diets containing SFO increased milk fat synthesis, elevated short-chain SFA and lowered trans FA concentrations, without altering milk polyunsaturated FA content. Changes in fat yield on high-concentrate diets containing SFO varied between experiments and individual animals, with decreases in milk fat secretion being associated with increases in milk fat trans-10 18:1, trans-10, cis-12 CLA and trans-9, cis-11 CLA concentrations.

Efficient reproductive performance is an important prerequisite for sustainable dairy production systems. Moreover, reproductive performance has become one of the most important functional traits in the dairy cattle industry, because of its economic importance, as well as its effect on animal welfare. The objective of present study was to evaluate the consequence of alternative selection strategies to improve fertility performance of Holstein cows in Iran. The traits milk production (. M), number of inseminations per conception (INS), days from calving to first insemination (DFS), maternal calving difficulty (MCD) and direct calving difficulty (DCD) were included in an aggregate genotype (. H). The selection indices in each strategy were a different combination of fertility traits and milk production. Although fertility traits were included in the aggregate genotype, in the first selection strategy, in which selection was based on milk production, unfavorable genetic gain for fertility traits occurred. In the second strategy, in which genetic gain for milk production was restricted to zero, in comparison to the other strategies, the genetic gains for profit and fertility traits were lowest and highest, respectively. In the third strategy, in which genetic gain for fertility traits was restricted to zero, the genetic gains for milk production and profit differed little compared to the first strategy. Favorable genetic gains were obtained for both fertility traits and milk production in the fourth strategy, in which proportional restriction was used. Although the genetic gain for milk production in this strategy was lower than in the first strategy, genetic gain for profit showed slightly differed. © 2012 Elsevier B.V.

Neuropeptide Y (NPY) and gonadotrophin-releasing hormone receptor (GnRHR) are two candidate genes with a wide variety of physiological functions in growth and especially in reproduction processes. We examined the association of one SNP from each of these genes with growth- and egg production-related traits in Mazandaran native chickens. Two hundred and six individuals were genotyped by PCR-RFLP. Marker-trait association analyses were performed using both breeding value and phenotypic information. The data came from 18 successive generations of selection at a Mazandaran native chicken breeding station in Iran. Data were analyzed with a univariate animal model in an ASREML procedure to estimate breeding values of the birds for these traits. Two alleles were found for both genes, A and a alleles for GnRHR, with frequencies of 0.614 and 0.386, B and b alleles for NPY, with frequencies of 0.780 and 0.221, respectively. The additive genetic effects of the GnRHR gene on egg number and egg mass were significant. Also, body weight at sexual maturity was significantly influenced by the NPY gene. We conclude that GnRHR and NPY genes are associated with egg production and growth traits, respectively.

Stochastic simulation was used for studying the impacts of sexed semen on genetic progress and reproductive performance of dairy cows. Three strategies were compared: WSS (use unsexed semen in cows and heifers), SSH (use sexed semen in heifers and unsexed semen in cows) and SSCH (use sexed semen in both cows and heifers). Conception rate (CR) of unsexed semen was considered to be 35% and 65% in cows and heifers, respectively. CR of sexed semen was considered to be 15 (20% in cows and 50% in heifers), 10, 5 and 0 percentage points lower than unsexed semen. Thus, four subschemes were compared under SSCH (SSCH15, SSCH10, SSCH5, SSCH0) and SSH (SSH15, SSH10, SSH5, SSH0). Moreover, the effect was studied in four distinct paths of selection: active sires (AS), young bulls (YB), bull dams (BD) and milking cows (CW). The average genetic superiority of CW was 12% and 9.5% in SSCH15 and SSH15 strategies relative to a base scheme, respectively. The average genetic superiority of CW was 19% and 10.5% in SSCH0 and SSH0, respectively. Regression analysis showed that genetic superiority of CW increased significantly, that is, 0.5% and 0.1% per every 1% increase in CR in SSCH and SSH, respectively. The result showed that there is a significant difference between genetic superiority of cows in SSCH and SSH schemes. Widespread and limited use of sexed semen in commercial dairy herds resulted in a large genetic advantage in CW. The genetic advantage of gender control was minimal in the selection paths of AS, YB and BD. Open days and services per conception reached to 153 v. 125 days and 5 v. 2.86 under SSCH15 compared with WSS. The age at first calving increased from 774 to 790 days in SSH15 and SSCH15 strategies. Mean of parities decreased to 2.26 v. 2.42 by using sexed semen. The widespread use of sexed semen increased the age average of cows in all parities. Sexed semen increased selection intensity in the CW path, and this contributed to the genetic merit of future cows. On the other hand, sexed semen had a negative effect on the reproductive performance of dairy cows. Generally, although the effect of widespread use of sexed semen (SSCH) on genetic progress is significantly more than limited use of sexed semen (SSH), SSCH decreased reproductive performance of dairy herds dramatically, and this suggests that SSH scenarios might be more appropriate in animal breeding programs. Finally, to make a decision of which schemes are more convenient, it is necessary to compare the economic aspects of schemes.

Autosomal markers and mtDNA have been used in horse phylogenetic studies. These studies display evolutionary events that happened in both sexes or only in females. It is necessary to investigate genetic diversity in Y-specific markers for clarifying contribution of males in horse domestication. The Y chromosome, excluding the pseudoautosomal region, is inherited as a single nonrecombinant unit and, therefore, it warrants that mutational events in patrilines are preserved as single haplotypes. Six Yspecific microsatellites were used to study patrilineal genetic variation in 405 male horses from 8 Iranian native horse breeds, one wild population and an exotic breed. These markers displayed no variation in all populations. The lack of polymorphisms could be as a result of lower contribution of stallions to the gene pools of the domestic horses compared to the mares because a sex bias is towards females due to a special breeding strategy (in which a few selected stallions mate with many mares each), a strong tendency to upgrade many breeds by crossing between champion stallions from particular breeds and mares from different breeds; also due to a bias in the early utilization of male horses as food source, a bias towards stallions in migrations and lack of detailed maps on horse Y chromosome.Key words: Iranian horse breeds, microsatellite, patriline, polymorphism, Y chromosome.

Trait-by-trait and multiple trait bioeconomic modeling were used to derive farm-specific economic weights (EW) for a wide range of traits under different production and economic circumstances to define breeding objectives for Holstein dairy cattle in Iran. Production parameters and economic data were gathered on 10 dairy farms from March 2008 to February 2010. The EW (economic values multiplied by gene expressions, in US dollars per unit of trait per calf born from sires of self-replacing females in planning horizon of 20 yr) were estimated to be $0.15 per kilogram of milk yield; $1.36 per kilogram of fat yield; −$1.02 per kilogram of protein yield; $4.59 per month of longevity; −$1.22 per kilogram of mature cow weight; −$105.67 for combined somatic cell score and clinical mastitis; −$1.35 and −$0.28 for percentage direct and maternal calving difficulties, respectively; −$3.98 for percentage direct stillbirth; −$0.76 per day of age at first calving; −$0.72 per calving interval day; and $0.91 for percentage 56-d nonreturn rate on averages across investigated farms. The coefficient of variation of economic weights across the 10 farms was lowest for direct calving difficulty and highest for calving interval. The proposed Iranian selection index was compared with selection indices of major countries exporting semen to Iran. Average relative emphasis for production, durability, and health and reproduction, across all exporter countries, was 41, 37.5, and 21.5%, respectively, whereas the respective values were 50, 14, and 36% for the Iranian index. Significant differences in selection indices may potentially decrease the utility of importation of semen as a means of achieving sustainable genetic progress in Iran. Results obtained in this study provide important information about economic values of traits that can be used to improve the Iranian national progeny testing program as well as importation rules for semen to Iran.

Linear and threshold animal models were used to estimate genetic parameters for reproductive traits in Iranian Holstein cows. Reproductive traits included days from calving to first service (DFS), number of inseminations to conception (INS), calving interval (CI), days open (DO), and interval between first and last insemination (IFL), pregnancy rate (PR), and success to first insemination (SF). A total of 72,124 records in parity 1 to 6 from 27,113 cows from 1981 to 2007 were used. Estimated heritabilities for reproductive traits were low (below 0.1); SF (0.029) had the lowest and DO and PR had the highest (0.076) heritability. Heritabilities obtained for interval traits were higher than those for categorical and binary traits. Strong genetic correlations were estimated between fertility traits. The results from current study show that fertility is a complex trait and several measurements related to fertility should be combined in a fertility index for selection purposes. © 2011 Elsevier B.V.

Calving records from the Animal Breeding Center of Iran, collected from January 1991 to December 2007 and comprising 1,163,594 Holstein calving events from 2,552 herds, were analyzed using a linear animal model, linear sire model, threshold animal model, and threshold sire model to estimate variance components, heritabilities, genetic correlations, and genetic trends for twinning rate in the first, second, and third parities. The overall twinning rate was 3.01%. Mean incidence of twins increased from first to fourth and later parities: 1.10, 3.20, 4.22, and 4.50%, respectively. For first-parity cows, a maximum frequency of twinning was observed from January through April (1.36%), and second- and third-parity cows showed peaks from July to September (at 3.35 and 4.55%, respectively). The phenotypic rate of twinning decreased from 1991 to 2007 for the first, second, and third parities. Sire predicted transmitting abilities were estimated using linear sire model and threshold sire model analyses. Sire transmitting abilities for twinning rate in the first, second, and third parities ranged from -0.30 to 0.42, -0.32 to 0.31, and -0.27 to 0.30, respectively. Heritability estimates of twinning rate for parities 1, 2, and 3 ranged from 1.66 to 10.6%, 1.35 to 9.0%, and 1.10 to 7.3%, respectively, using different models for analysis. Heritability estimates for twinning rate, obtained from the analysis of threshold models, were greater than the estimates of linear models. Solutions for age at calving for the first, second, and third parities demonstrated that cows older at calving were more likely to have twins. Genetic correlations for twinning rate between parities 2 and 3 were greater than correlations between parities 1 and 2 and between parities 1 and 3. There was a slightly increasing trend for twinning rate in parities 1, 2, and 3 over time with the analysis of linear animal and linear sire models, but the trend for twinning rate in parities 1, 2, and 3 with threshold animal model analysis was decreased over the years. There was a significant decreasing trend for twinning rate in parities 1 and 2 over time with the threshold sire model analysis, but the genetic trend for twinning rate in parity 3 with this model of analysis was significant and positive. In general, there were increasing genetic trends for twinning rate from parities 1 through 3 using different models of analysis.

The families of TGF-β proteins are the most important growth factors in the ovary for growth and differentiation of early ovarian follicles. Three related oocyte-derived members of the transforming growth factor-β superfamily, namely GDF9, BMP15 and BMPR-IB have been shown to be essential for follicular growth and ovulation. The aim of the present study was to detect the incidence of mutation in exon two of GDF9 as a major gene in the Shal sheep breed. Blood samples were collected from 239 sheep and genomic DNA was extracted using the modified salting-out method. The quantity and quality of extracted DNA was examined using spectrophotometery and gel electrophoresis, respectively. A fragment with the size of 139 bp from exon two of GDF9 gene (FecGH) was amplified using polymerase chain reaction (PCR) with a pair of specific primers. The amplified PCR products were digested with DdeI restriction enzyme. In the presence of mutations at this locus, the DdeI enzyme cannot recognize the restriction site. However, in the absence of mutations, the enzyme recognizes one restriction site and divides the amplified fragment into two fragments of 31 and 108 bp. In the present study only the wild type alleles were detected and all the samples showed the AA genotype. The analysis of polymorphism for GDF9 (FecGH) loci in Shal sheep indicates that the genetic factor responsible for twinning or multiple lambing rates is not related to reported mutated alleles at the GDF9 major gene in this breed. Therefore, we should attempt to detect other SNP for the GDF9 geneand/or other loci responsible for twining rate in this breed.Keywords: Sheep, Shal breed, twinning, GDF9, PCR-RFLP

Calving records of Holstein dairy cows from April 1998 to September 2006 comprising 16 herds with 104,572 calving events representing 4,045 twin births were used to evaluate reported twinning rate, calf sex ratio, stillbirth, and abortion rates in single and twin births. Overall, the reported twinning rate was 3.9%, and twinning increased with parity [1.1% for primiparous cows vs. 5.7% for cows in their fourth or greater lactation; odds ratio (OR) = 5.50]. Regardless of parity, the greatest twinning rate was observed when conception occurred in fall season from September to December (OR = 1.17). Calf stillbirth was greater after twin births, with 18.8% of twin calving events resulting in one or both calves as stillborn, compared with 4.0% for singleton births (OR = 7.58). Calf stillbirth for multiparous cows was 2.9% for single births and 18.0% for twin births (OR = 7.08), whereas for primiparous cows, stillbirth was 6.6% for singletons and 27.7% for twins (OR = 5.85). Calf sex ratios (male, M; female, F) were 52.4% M and 47.6% F for singleton calves and 28.2% MM, 48.9% MF, and 22.9% FF for twin calves. The mean abortion rate was 13.4%, with 13.8% for single births and 4.2% for twin births (OR = 1.22). Abortion rate for multiparous cows was 15.9% for single births and 4.0% for twin births (OR = 4.31), whereas for primiparous cows, abortion rate was 9.4% for single births and 5.4% for twin births (OR = 1.89). Although milk production, as a causative factor associated with twinning, increased in recent years, twinning rate decreased over the years.

Given the genotypes of parents and progeny, their haplotypes over several or many linked loci can be easily assigned by listing the allele type at each locus along the haplotype known to be from each parent. Only a small number (5-10) of progeny per family is usually needed to assign the parental and progeny haplotypes. Any gaps left in the haplotypes may be filled in from the assigned haplotypes of relatives. The process is facilitated by having multiple alleles at the loci and by using more linked loci in the haplotype and with more progeny from the mating. Crossover haplotypes in the progeny can be identified by their being unique or uncommon, and the crossover point can often be detected if the locus linkage map order is known. The haplotyping method applies to outbreeding populations in plants, animals and man, as well as to traditional experimental crosses of inbred lines. The method also applies to half-sib families, whether the genotypes of the mates are known or unknown. The haplotyping procedure is already used in linkage analysis but does not seem to have been published. It should be useful in teaching and in genetic applications of haplotypes.

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. This trait and its modification are very important in those countries grazing these breeds. Results Two independent experiments using either Iranian or Ovine HapMap genotyping data contrasted thin and fat tail breeds. Population differentiation using FST in Iranian thin and fat tail breeds revealed seven genomic regions. Almost all of these regions overlapped with QTLs that had previously been identified as affecting fat and carcass yield traits in beef and dairy cattle. Study of selection sweep signatures using FST in thin and fat tail breeds sampled from the Ovine HapMap project confirmed three of these regions located on Chromosomes 5, 7 and X. We found increased homozygosity in these regions in favour of fat tail breeds on chromosome 5 and X and in favour of thin tail breeds on chromosome 7. Conclusions In this study, we were able to identify three novel regions associated with fat deposition in thin and fat tail sheep breeds. Two of these were associated with an increase of homozygosity in the fat tail breeds which would be consistent with selection for mutations affecting fat tail size several thousand years after domestication.