Genetic variations between indigenous fat-tailed sheep populations

Blood samples were collected from a total 816 sheep of both sexes in three Iranian fat-tailed breeds (Sangsari, Makoei, indigenous sheep on firoozkouh mountain) serum, plasma and erythrocyte were separated and were frozen at -20°C. Variation in their blood proteins, albumin, haemoglobin and transferrin were examined to characterize the breeds and to obtain genetic relationship among them. Only transferrin was polymorphic in all breeds investigated; while albumin was monomorphic for S allele and haemoglobin was fixed for the B allele in three breeds.Keywords: Sangsari, makoei, firoozkouhi, fat-tailed, albumin, transferrin, haemoglobinAfrican Journal of Biotechnology Vol. 9(36), pp. 5993-5996, 6 September, 201

Genome Diversity and the Origin of the Arabian Horse

The Arabian horse, one of the world\u27s oldest breeds of any domesticated animal, is characterized by natural beauty, graceful movement, athletic endurance, and, as a result of its development in the arid Middle East, the ability to thrive in a hot, dry environment. Here we studied 378 Arabian horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing to examine hypotheses about genomic diversity, population structure, and the relationship of the Arabian to other horse breeds. We identified a high degree of genetic variation and complex ancestry in Arabian horses from the Middle East region. Also, contrary to popular belief, we could detect no significant genomic contribution of the Arabian breed to the Thoroughbred racehorse, including Y chromosome ancestry. However, we found strong evidence for recent interbreeding of Thoroughbreds with Arabians used for flat-racing competitions. Genetic signatures suggestive of selective sweeps across the Arabian breed contain candidate genes for combating oxidative damage during exercise, and within the Straight Egyptian subgroup, for facial morphology. Overall, our data support an origin of the Arabian horse in the Middle East, no evidence for reduced global genetic diversity across the breed, and unique genetic adaptations for both physiology and conformation

Evaluation of the effect of adding different levels of n-3 fatty acids to the Bioxcell® extender on freezing ability of goat semen

The objective of this study was to investigate adding different levels of a n-3 fatty acid source to the Bioxcell® extender on freezing ability of goat semen. Six mature Mahabadi bucks were selected and semen was collected using an artificial vagina. Semen samples were pooled together and divided into four equal groups, after evaluating for qualitative characteristics. Treatment groups were supplemented by 0, 0.1, 1 and10 ng/ml levels of n-3 fatty acid, respectively. The rates of motility, progressive motility, viability and sperm abnormality were evaluated and recovery rate was calculated. Data were analyzed using proc GLM of SAS. Percentage of motility and recovery rate were significantly higher in 10 ng/ml group than the other groups.  Percentage of progressive motility was significantly higher in 10 and 0.1ng/ml than the other groups. Percentage of viability was significantly lower in 1ng/ml group than the other groups. Percentage of abnormality was not significant between the levels of n-3 fatty acid. The results indicated that adding of 10 ng/ml n-3 fatty acids to extender could improve freezing ability of goat semen

Underlying functional genomics of fat deposition in adipose tissue

The objective of this study was to gain insight into the underlying mechanisms of fat deposition. Two sheep breeds with large fat-tail (Lori-Bakhtiari) and with thin-tail (Zel) were used as models. To determine important and key candidate lipid metabolism related genes, comparative genomic approaches were employed. Gene expression profiles of adipose tissues were analyzed in human, pig, and cattle by express sequence tag (EST) analysis. EST analysis determined 65, 102 and 125 transcripts in human, pig and cattle respectively with at least 10 fold over-expression in the adipose tissue. Based on our comparative functional genomic analysis, seven genes were more abundant and common in investigated mammalian adipose tissues promising a conserved novel gene network in mammalian lipid metabolism. The candidate genes including fatty acid binding protein 4 (FABP4), fatty acid synthase (FASN), Stearoyl-CoA desaturase (SCD) and Lipoprotein lipase (LPL) were selected for further gene expression investigation within two sheep breeds. The real time PCR results showed that among the genes tested, FABP4 was expressed at higher levels than the others. The expression of FABP4 was significantly higher in the fat-tail of Lori-Bakhtiari than in the fat-tail and visceral adipose tissues of Zel (P<0.05). The findings suggest that the FABP4 gene expression in the fat-tail is an important index of fat deposition.Mohammad Reza Bakhtiarizadeh, Mohammad Moradi-Shahrbabak, Esmaeil Ebrahimi

Accuracy of imputation of single-nucleotide polymorphism marker genotypes for water buffaloes (Bubalus bubalis) using different reference population sizes and imputation tools

The accuracy of genotype imputation from a customized low-density to a moderate-density single-nucleotide polymorphism marker panel was tested in Italian Mediterranean buffalo using different sizes of reference populations (RP) and imputation programs. Masked genotypes were imputed using Beagle, minimac and FImpute. The accuracy of predicted genotypes was assessed by the percentage of correctly imputed genotypes. As expected, overall imputation accuracy was better for larger RP sizes. However, increasing the RP size from small to intermediate (i.e., from 42 to 202) resulted in a greater improvement in imputation accuracy compared to increasing the RP size from intermediate to large (i.e., from 202 to 736). The percentage of correctly imputed genotypes was 97.3%, 97.9% and 98.0% for minimac, Beagle and FImpute, respectively, using 736 reference individuals. The accuracy of imputation tended to decrease for high minor-allele frequency of imputed genotypes especially when the RP size was small. The variation in accuracy with increasing RP size was highest for Beagle and lowest for minimac. The accuracy of imputation was larger when the genomic relationship between the reference and the target populations was higher for all three imputation software tools used in this study. The trend of increasing imputation accuracy with genomic relationship was strongest when the RP size was small. Our results indicate that imputation of genotypes from a low to a moderate density panel (i.e., 10K to 90K) is a valid option to reduce the cost of genotyping for genomic evaluation in Italian Mediterranean buffalo.Seyed Mohammad Ghoreishifar, Hossein Moradi-Shahrbabak, Mohammad Moradi-Shahrbabak, Ezequiel L.Nicolazzi, John L.Williams, Daniela Iamartino, Ardeshir Nejati-Javarem

Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology

Abstract not availableMohammad Reza Bakhtiarizadeh, Mohammad Moradi-Shahrbabak, Mansour Ebrahimi, Esmaeil Ebrahimi

Accounting for heterogeneity of phenotypic variance in Iranian Holstein test-day milk yield records

First lactation milk yield data consisting of 1,576,102 test-day records for 221,862 Iranian Holstein cows having lactations between 1983 and 2008 were used to study the existence and effect of heterogeneity of variance (HOV) on estimated breeding values and the performance of random regression models (RRMs) with different orders of fit. A pre-correction method based on phenotypic variance, assuming equal heritability for different levels of herd-test date classes and a genetic correlation of one between them, was used to correct for HOV. RRMs with Legendre polynomial functions were used to analyze adjusted and unadjusted records. Some re-ranking of animals occurred from the adjustment, but the correction method only had slight effects on the overall ranking and rank correlations of animals. Data correction had considerable effects on top animals, such that 10% and 17% of top sires and dams, respectively, were replaced from the list of top 1% animals when compared to the homogeneous variance scenario. Application of the adjustment method resulted in slightly higher heritabilities, which may be due to the more accurate estimation of additive genetic effects when HOV is considered. An index consisting of different comparison criteria was used to investigate the effect of HOV on fitting orders of Legendre polynomials and to compare RRMs. In general, the rank of models was improved by increasing the order of fit, but models with smaller orders of fit and correction for HOV performed better than models with higher orders of fit without correction for variance heterogeneity. The results of this research indicate that the accuracy of estimated breeding values may be increased and the genetic progress of the herds could be affected by accounting for HOV as part of genetic evaluations in Iran