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

A Morphometric Survey among Three Iranian Horse Breeds with Multivariate Analysis

Three Iranian horse breeds, Turkoman, Caspian, and Kurdish, are the most important Iranian horse breeds which are well known in all around of the world because of their beauty, versatility, great stamina, and  intelligence. Phenotypic characterization was used to identify and document the diversity within and between distinct breeds, based on their observable attributes. Phenotypic characterization and body biometric in 23 traits were measured in 191 purebred horses belonging to three breeds, i.e. Turkoman (70 horses), Kurdish (77 horses), and Caspian (44 horses).  Caspian breed was  sampled from the Provinces of Alborz and Gilan. Kurdish breed was sampled from the Provinces of Kurdistan, Kermanshah, and Hamadan. Turkoman breed was sampled from the Provinces of Golestan, Markazi, and Isfahan. Multivariate analysis of variance (MANOVA) was implemented. In addition, Canonical Discriminate Analysis (CDA), Principal Component Analysis (PCA), and Custer analysis were executed for assessing the relationship among the breeds. All statistical analysis was executed by SAS statistical program. The results of our investigation represented the breeds classification into 3 different classes (Caspian, Turkoman, and Kurdish) based on different morphometrical traits. Caspian breed with smaller size in most variables was detached clearly from the others with more distance than Kurdish and Turkoman breeds. The result showed that the most variably trait for classification was Hind Hoof Length. Adaptation with different environments causes difference in morphology and difference among breeds. We can identify and classify domestic population using PCA, CDA, and cluster analysis

Viunalikeviruses are environmentally common agents of horizontal gene transfer in pathogens and biocontrol bacteria.

Bacteriophages have been used as natural biocontrol and therapeutic agents, but also as biotechnological tools for bacterial engineering. We showed recently that the transducing bacteriophage ϕMAM1 is a ViI-like phage and a member of the new genus, 'Viunalikevirus'. Here, we show that four additional ViI-like phages and three new environmentally isolated viunalikeviruses, all infecting plant and human pathogens, are very efficient generalised transducers capable of transducing chromosomal markers at frequencies of up to 10(-4) transductants per plaque-forming unit. We also demonstrate the interstrain transduction of plasmids and chromosomal markers, including genes involved in anabolism, genes for virulence and genes encoding secondary metabolites involved in biocontrol. We propose that all viunalikeviruses are likely to perform efficient horizontal gene transfer. Viunalikeviruses therefore represent useful agents for functional genomics and bacterial engineering, and for chemical and synthetic biology studies, but could be viewed as inappropriate choices for phage therapy.This research was supported by the EU Marie-Curie Intra-European Fellowship for Career Development (FP7- PEOPLE-2011-IEF) grant number 298003.This is the version of record of the article "Viunalikeviruses are environmentally common agents of horizontal gene transfer in pathogens and biocontrol bacteria" published in ISME Journal on August 2104 under the NPG Open Access option. The published version of record is available on the journal website at http://dx.doi.org/10.1038/ismej.2014.15

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

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

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

Sequence Analysis of Different Domains of Plasmodium Vivax Apical Membrane Antigen (PvAMA-1 Gene) Locus in Iran

Background: Plasmodium vivax is responsible for approximately 80 million malaria cases in the world. Apical membrane antigen1 (AMA-1) is a type I integral membrane protein present in all Plasmodium species. AMA-1 interferes in critical steps of invasion of human hepatocytes by sporozoites and red blood cells by merozoites and is one of the most immunodominant antigens for eliciting a protective immune response in human. It is considered as a promising antigen for inclusion in a vaccine against P. vivax. Since more knowledge is needed to lighten the scope of such antigen we compared genetic variation in P. vivax AMA-1from an Iranian isolate with those reported from some of the other malarious countries so far.Methods: P. vivax genomic DNA was extracted from the whole blood of an Iranian patient with patent P. vivax infection. The nucleotide sequence for 446 amino acid (AA) residues (42-488 of PvAMA-1) was amplified by PCR and cloned in pUC19 vector for sequencing.Results: Sequence analysis of the antigen showed a high degree of identity (99%) with strong homology to the PvAMA-1 gene of P. vivax S3 and SKO814 isolates from India and Korea (Asian isolates) respectively, and 96% similarity with P. vivax Sal-1 AMA-1 gene from El Salvador.Conclusions: We cloned and characterized three domains of PvAMA-1 gene from an Iranian patient. Predicted protein sequence of this gene showed some discrepancies in corresponding protein in comparing with similar genes reported from other malarious countries