Identification of selection signatures in Capra hircus and Capra aegagrus in Iran.

Identification of selection signatures may provide a better understanding of domestication process and candidate genes contributing to this process. In this study, two populations of domestic and wild goats from Iran were analyzed to identify selection signatures. RSB, iHS, and XP-EHH statistics were used in order to identify robust selection signatures in the goat genome. Genotype data of domestic and wild goats from the NextGen project was used. The data was related to 18 Capra aegagrus (wild goat) and 20 Capra hircus (domestic goat) from Iran. The iHS method indicated 675 and 441 selection signatures in C. aegagrus and C. hircus, respectively. RSB and XP-EHH methods showed about 370 and 447 selection signatures in C. aegagrus and C. hircus, respectively. These selection signatures were mainly associated with milk production, fleece trait, mammary epithelial cells, reproduction, and immune system.

Differential Expression of RNAseq Imprinted Genes from Bovine Females Before and After Puberty.

The productivity of beef cows depends on early reproduction traits such as puberty and has an economic impact on the efficiency of production system. Imprinted genes modulate many important endocrine processes such as growth, the onset of puberty and maternal reproductive and behavior. The role of imprinted genes in puberty is a challenging subject since they show the reciprocal role of maternal and paternal genomes in progeny. Although, there are evidences of the involvement of imprint genes in puberty in human, the role of this type of genes in the onset of puberty in cattle has not been studied yet. Here we examined the expression of 27 imprinted genes in pre and post puberty in a bovine model to find differentially expressed imprinted genes in maternal-paternal purebreds and reciprocal crosses across eight tissues and discussed the task of these genes in this crucial process of development and in onset of puberty. DLK1 and MKRN3 that previously described as cause of the central precocious puberty (CPP) in human were differentially expressed in this study. Functional annotation analysis of differentially imprinted genes in different tissues showed significant biological processes of cellular response to growth factor stimulus, response to growth factor, response to parathyroid hormone, developmental growth and the importance of alternative splicing. The results of this study have implications in understanding the role of imprinted genes in the onset of puberty in cattle.

Characterization of bovine (Bos taurus) imprinted genes from genomic to amino acid attributes by data mining approaches.

Genomic imprinting results in monoallelic expression of genes in mammals and flowering plants. Understanding the function of imprinted genes improves our knowledge of the regulatory processes in the genome. In this study, we have employed classification and clustering algorithms with attribute weighting to specify the unique attributes of both imprinted (monoallelic) and biallelic expressed genes. We have obtained characteristics of 22 known monoallelically expressed (imprinted) and 8 biallelic expressed genes that have been experimentally validated alongside 208 randomly selected genes in bovine (Bos taurus). Attribute weighting methods and various supervised and unsupervised algorithms in machine learning were applied. Unique characteristics were discovered and used to distinguish mono and biallelic expressed genes from each other in bovine. To obtain the accuracy of classification, 10-fold cross-validation with concerning each combination of attribute weighting (feature selection) and machine learning algorithms, was used. Our approach was able to accurately predict mono and biallelic genes using the genomics and proteomics attributes.

Using quantile regression for fitting lactation curve in dairy cows.

The main objective of this study was to compare the performance of different 'nonlinear quantile regression' models evaluated at the τth quantile (0·25, 0·50, and 0·75) of milk production traits and somatic cell score (SCS) in Iranian Holstein dairy cows. Data were collected by the Animal Breeding Center of Iran from 1991 to 2011, comprising 101 051 monthly milk production traits and SCS records of 13 977 cows in 183 herds. Incomplete gamma (Wood), exponential (Wilmink), Dijkstra and polynomial (Ali & Schaeffer) functions were implemented in the quantile regression. Residual mean square, Akaike information criterion and log-likelihood from different models and quantiles indicated that in the same quantile, the best models were Wilmink for milk yield, Dijkstra for fat percentage and Ali & Schaeffer for protein percentage. Over all models the best model fit occurred at quantile 0·50 for milk yield, fat and protein percentage, whereas, for SCS the 0·25th quantile was best. The best model to describe SCS was Dijkstra at quantiles 0·25 and 0·50, and Ali & Schaeffer at quantile 0·75. Wood function had the worst performance amongst all traits. Quantile regression is specifically appropriate for SCS which has a mixed multimodal distribution.

Attribute selection and model evaluation for the maternal and paternal imprinted genes in bovine (Bos Taurus) using supervised machine learning algorithms.

Imprinted genes display biased expression of paternal and maternal alleles in mammals. They are marked through epigenetic process during gametogenesis. Characterization of imprinted genes has expanded our understanding of the regulation and function of genes. In the current study, 22 experimentally validated imprinted genes in bovine (Bos Taurus) were analysed. Several supervised machine learning algorithms and attribute weighting methods were used to find characteristics of different types of imprinted genes and suggest a classification method for finding maternally and paternally expressed genes in bovine. For assessing the best model and comparing attributes in other organisms, we have also conducted a comparative analysis for human and sheep imprinted genes. According to the results of the present study, GC contents 10 and 100 kb upstream, Gly and Gln amino acids, Ile/ATC codon usage, LINE and SINE in 100kbup and length of first intron were significantly different between the maternal and paternal genes in cattle. Considering all species together, we found that GC content 100 kb up, LINE 100 kb up and the frequency of amino acids like Gly, Gln and Met were the most important attributes for identifying the paternal and maternal imprinted genes. These findings could imply conservation pattern in the attributes among these species.

Genetic evaluation of survival and productivity traits in Arman crossbred sheep / Evaluación genética de las características de supervivencia y productividad en ovinos cruzados Arman / Avaliação genética de características de sobrevivência e produtividade em ovinos mestiços Arman

Abstract Background: Arman sheep breed was synthesized by crossing several breeds, including Baluchi, Ghezel, Chios, and Suffolk. Objective: To estimate the (co)variance components and genetic parameters using the restricted maximum likelihood via twelve animal models for lamb survival and four animal models for ewe productivity traits. Methods: Data and pedigree information were collected at Abbasabad Sheep Breeding Station, Khorasan Razavi province, north-east of Iran, from 1999 to 2011. The traits studied were lamb survival rate (LSR), litter size at birth (LSB), litter size at weaning (LSW), litter mean weight per lambing (LMWL), litter mean weight per lamb weaned (LMWLW), total litter weight at birth (TLWB), and total litter weight at weaning (TLWW). Moreover, multivariate analyses were performed to estimate covariance between the traits. Results: Direct heritability estimates (h2a) for LSR was 0.081 and increased to 0.253 after correcting. Maternal genetic effects (h2m) and common litter effects (l2) accounted for 4 and 11.3% of the phenotypic variance for LSR, respectively. The estimations of h2a were 0.131, 0.080, 0.111, 0.190, 0.118, and 0.150 for LSB, LSW, LMWL, LMWLW, TLWB, and TLWW, respectively. The estimated fractions of variance -attributed to permanent environmental effects on ewe, (pe2) were 0.038, 0.050, 0.071, 0.060, and 0.050 for LSB, LSW, LMWL, TLWB, and TLWW, respectively. Service sire effects (S2) were significant for LSW, LMWL, and TLWB, being 0.038, 0.030, and 0.049, respectively. Direct genetic correlations showed a vast range from 0.13 for LSB-LMWL to 0.91 for LMWL-TLWW. Conclusion: Results indicate that genetic change not only depends on the heritability of traits, but also on the observed phenotypic variation; therefore, improvement of non-genetic factors should be included in the breeding programs.

Resumen Antecedentes: Las ovejas Arman fueron sintetizadas a través del cruzamiento de varias razas, incluyendo Baluchi, Ghezel, Chios y Suffolk. Objetivo: Estimar los componentes de (co)varianza y parámetros genéticos por máxima verosimilitud restringida a través de doce modelos animales para la sobrevivencia de los corderos y cuatro modelos para características de productividad. Métodos: Los datos y la información de pedigrí se recogieron en la Estación de Cría Abbasabad, provincia de Khorasan Razavi, noreste de Irán, entre 1999 y 2011. Las características estudiadas fueron la tasa de supervivencia de los corderos (LSR), tamaño de la camada al nacimiento (LSB), tamaño de la camada al destete (LSW), peso promedio de la camada por parto (LMWL), peso promedio de la camada por cordero destetado (LMWLW), peso total de la camada al nacer (TLWB), y peso total de la camada al destete (TLWW). Además, se realizaron análisis multivariados para estimar la covarianza entre los rasgos. Resultados: La estimacion de heredabilidad directa (h2 ) para LSR2a fue 0,081 y aumentó a 0,253 después de la corrección. Los efectos genéticos maternos (h m) y los efectos comunes de la camada (l2) representaron el 4 y el 11,3% de la varianza fenotípica para LSR, respectuvamente. Las estimaciones de h2 fueron 0,131, 0,080, 0,111, 0,190, 0,118 y 0,150 para LSB, LSW, LMWL, LMWLW, TLWB y TLWW, respectivamente. Las fracciones estimadas de varianza -atribuidas a los efectos ambientales permanentes en las ovejas, (pe2) fueron 0,038, 0,050, 0,071, 0,060 y 0,050 para LSB, LSW, LMWL, TLWB y TLWW, respectivamente. Los efectos del servicio de carneros (S2) fueron significativos para LSW, LMWL y TLWB, siendo 0,038, 0,030 y 0,049, respectivamente. Las correlaciones genéticas directas mostraron un amplio rango de 0,13 para LSB-LMWL a 0,91 para LMWL-TLWW. Conclusión: Los resultados indicaron que el cambio genético no sólo depende de la heredabilidad de los caracteres, sino también de la variación fenotípica observada; por lo tanto, el mejoramiento de los factores no genéticos debe ser incluido en las programas de mejora.

Resumo Antecedentes: Arman ovelhas foi sintetizado pelo cruzamento de quatro raças incluindo Balúchi, Ghezel, Chios e Suffolk. Objetivo: Estimar os componentes de (co)variância e parâmetros genéticos por máxima verossimilhança restrita através de doze modelos animais para a sobrevivência dos cordeiros e quatro modelos animais para características de produtividade. Métodos: Os dados e as informações de pedigree foram coletadas no Abbāsābād Estação de Criação, província de Khorasan Razavi, nordeste do Irã desde 1999 a 2011. As características estudadas foram a taxa de sobrevivência de cordeiro (LSR), tamanho de leitegada ao nascimento (LSB), tamanho de leitegada ao desmame (LSW), peso médio da leitegada por entrega (LMWL), peso médio da leitegada por cordeiro desmamado (LMWLW), o peso total da leitegada ao nascimento (TLWB) e peso total da leitegada ao desmame (TLWW). Além disso, as análises multivariadas foram realizadas para estimar a covariância entre as características. Resultados: As estimativas de herdabilidade direta (h2 ) para 2a LSR foi 0,081 e aumentada até 0,253 após correcção. Os efeitos genéticos maternos (h m) e os efeitos comuns de leitegada (l2) representaram 4 e 11,3% da variância fenotípica de LSR, respectivamente. Estimativas de 2 foram 0,131, 0,080, 0,111, 0,190, 0,118 e 0,150 para a LSB, LSW, LMWL, LMWLW, TLWB e TLWW, a2 respectivamente. As fracções de variância -atribuídos aos efeitos ambientais permanentes em ovelhas, (pe ) foram 0,038, 0,050, 0,071, 0,060 e 0,050 para a LSB, LSW, LMWL, TLWB e TLWW. Os efeitos de serviço de carneiros (s2) foram significativos para LSW, LMWL e TLWB sendo 0,038, 0,030 e 0,049, respectivamente. As correlações genéticas diretas mostrou uma gama de 0,13-0,91 LSB-LMWL para LMWL-TLWW. Conclusão: Os resultados indicaram que a modificação genética não só depende da hereditariedade de traços, mas também da variação fenotípica observada; portanto, a melhoria dos fatores não-genéticos devem ser incluídos em nos programas de melhoramento.

Preparation of fish waste silage and its effect on the growth performance and meat quality of broiler chickens.

BACKGROUND: This experiment was conducted to evaluate the effects of replacing soybean meal with fish-waste silage (FWS) in diets on growth performance and meat quality in broiler chickens. Fish waste (FW) was fermented with molasses and Lactobacillus plantarum and Aspergillus oryzae for 15 days. A total of 240 day-old male Cobb 500 broiler chickens were used in a 42-day experiment in which the birds were randomly allotted to one of five dietary treatments (containing 0, 30, 60, 90, and 120 g kg-1 FWS) in a completely randomized design. RESULTS: Results indicated that the fermentation process significantly reduced pH and ether extract, but it increased crude protein content and lactic acid bacteria count in FW. The use of FWS significantly improved daily weight gain and feed conversion ratio of broilers. The amount of thiobarbiturate-reducing substances and lipid content in chicken's meat fed diet containing FWS was significantly lower than in the group fed a control diet. CONCLUSION: In conclusion, the microbial fermentation process is effective in improving nutritive values of FW. Feeding up to 120 g kg-1 FWS also improves the performance and meat quality of birds and can be used as a suitable protein source in broiler chickens' diet. © 2018 Society of Chemical Industry.

Fermented rapeseed meal is effective in controlling Salmonella enterica serovar Typhimurium infection and improving growth performance in broiler chicks.

The aim of present experiment was to assess the effects of fermented rapeseed meal (FRSM) on Salmonella enterica serovar Typhimurium (S. Typhimurium) colonization and growth performance in broiler chicks. Two hundred forty day-old male Cobb 500 broiler chicks were divided into six experimental treatments with four replicates and 10 birds per each. The treatments were including two positive and negative controls which birds received a basal corn-soybean diet as well as four others which birds received the diets that rapeseed meal (RSM) or FRSM was replaced with soybean meal at 50 and 100% levels. All chicks except the negative control birds were challenged orally with 105 CFU of S. Typhimurium at 3days of age. Results showed that birds were fed FRSM had significantly greater lactic acid bacteria populations and lesser S. Typhimurium colonization in ileal and cecal sections compared to others (P<0.05). The less percentage of liver and bursa of fabricius was belonged to negative control group. At 10day, feeding chicks with diet containing FRSM, but not RSM, significantly decreased the organ invasion by S. Typhimurium (P<0.05). Heterophil to lymphocyte ratio was significantly lesser in chicks were fed FRSM compared to those fed RSM or positive control (P<0.05). Birds were fed FRSM had significantly higher weight gain and better feed conversion ratio compared to those birds were fed RSM (P<0.05). The findings of present experiment concerning positive effects of feeding FRSM on reducing S. Typhimurium and improving growth performance show that this processed protein source can be considered as a nutritional effective strategy to control Salmonella contamination in broiler chicks.

Comparison of three boosting methods in parent-offspring trios for genotype imputation using simulation study.

BACKGROUND: Genotype imputation is an important process of predicting unknown genotypes, which uses reference population with dense genotypes to predict missing genotypes for both human and animal genetic variations at a low cost. Machine learning methods specially boosting methods have been used in genetic studies to explore the underlying genetic profile of disease and build models capable of predicting missing values of a marker. METHODS: In this study strategies and factors affecting the imputation accuracy of parent-offspring trios compared from lower-density SNP panels (5 K) to high density (10 K) SNP panel using three different Boosting methods namely TotalBoost (TB), LogitBoost (LB) and AdaBoost (AB). The methods employed using simulated data to impute the un-typed SNPs in parent-offspring trios. Four different datasets of G1 (100 trios with 5 k SNPs), G2 (100 trios with 10 k SNPs), G3 (500 trios with 5 k SNPs), and G4 (500 trio with 10 k SNPs) were simulated. In four datasets all parents were genotyped completely, and offspring genotyped with a lower density panel. RESULTS: Comparison of the three methods for imputation showed that the LB outperformed AB and TB for imputation accuracy. The time of computation were different between methods. The AB was the fastest algorithm. The higher SNP densities resulted the increase of the accuracy of imputation. Larger trios (i.e. 500) was better for performance of LB and TB. CONCLUSIONS: The conclusion is that the three methods do well in terms of imputation accuracy also the dense chip is recommended for imputation of parent-offspring trios.

Cloning and Expression of Iranian Turkmen-thoroughbred Horse Follicle Stimulating Hormone in Pichia pastoris.

BACKGROUND: Follicle stimulating hormone (FSH) plays an essential role in reproductive physiology and follicular development. OBJECTIVE: A new variant of the equine fsh (efsh) gene was cloned, sequenced, and expressed in Pichia pastoris (P. pastoris) GS115 yeast expression system. MATERIALS AND METHODS: The full-length cDNAs of the efshα and efshß chains were amplified by reverse transcription polymerase chain reaction (RT-PCR) using the total RNA isolated from an Iranian Turkmen-thoroughbred horse's anterior pituitary gland. The amplified efsh chains were cloned into the pPIC9 vector and transferred into P. pastoris. The secretion of recombined eFSH using P. pastoris expression system was confirmed by Western blotting and immunoprecipitation (IP) methods. RESULTS: The DNA sequence of the efshß chain accession number JX861871, predicted two putative differential nucleotide arrays, both of which are located in the 3'UTR. Western blotting showed a molecular mass of 13 and 18 kDa for eFSHα and eFSHß subunits, respectively. The expression of desired protein was confirmed by protein G immunoprecipitation kit. CONCLUSIONS: eFSH successfully expressed in P. pastoris. These findings lay a foundation to improve ovulation and embryo recovery rates as well as the efficiency of total embryo-transfer process in mares.

Effects of monensin and increasing crude protein in early lactation on performance of dairy cows.

Twenty-four Holstein dairy cows were used to evaluate the singular and combined effects of different level of crude protein and monensin treatments during the early lactation on digestion and milk yield of dairy cows. The experiment was designed as completely randomized with a 3x2 factorial arrangement of treatments. The factors were three Concentrations of CP supplement (19.5, 21.4 and 23.4% of dry matter) and two levels of monensin (0 and 350 mg per cow per day). This experiment consist of three periods and each period was 3 week in length. Monensin did not affect DMI, milk yield, lactose and SNF but it reduced milk fat and protein percentage. Monensin premix significantly decreased rumen ammonia but rumen pH and microbial protein synthesis was not affected by monensin treatment. Although, Monensin treatment increased apparent digestibility of DM, NDF, ADF, CP, but they were not significantly. Increasing dietary CP, improved milk and protein production, but did not alter the other components of milk. Digestibility of NDF, ADF, CP were improved by increasing dietary CP. Increasing diet CP from 19.5 to 21.4% did not significantly increase ruminal ammonia, but increasing to 23.4% have significant effect on it. There was a linear relationship between level of crud protein in the diet and urine volume excretion. Microbial protein synthesis was affected by increasing CP level; on this way maximum protein synthesis was achieved in 21.4% CP.

Effects of niacin on milk production and blood parameters in early lactation of dairy cows.

To investigate the effects of niacin supplementation in the diet of high producing cows at early lactation, 21 holstein dairy cows were used in this experiment. Animal were assigned in to three groups based on their milk yield and calving date soon after parturition. They were received a basal diet and 0 (group 1), 6 (group 2), 12 (group 3) g of supplementation niacin per day over a 10 weeks experimental period. Milk volume was recorded and milk samples were collected for each cow at two weeks interval for analysis of fat, protein, lactose and SNF (Solid-None Fat). Blood samples were also taken for the measurement of glucose, triglyceride, Beta-hydroxy butyrate and total protein at two weeks intervals. No significant difference were observed between milk yield, milk fat, protein, lactose and SNF content in cows received niacin compared to the control group (p > 0.05). Plasma glucose in groups 2 and 3 compared to the control were higher and this difference were statistically significant (p < 0.05). Blood triglycerides were not significantly affected by niacin supplementation. BHBA were lower in cows received niacin and this difference were significant (p < 0.05). The trend of changes in the amount of blood total protein were identical in all three groups whole the level of this factor was always higher in control group compared to the others groups. Niacin has showed an increase in the level of plasma glucose and a notable decrease in the amount of blood triglyceride, beta-hydroxy butyrate and total protein, which may be due to the effect of this vitamin on the energy metabolism in cows.