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.

Comparative In silico Study of Sex-Determining Region Y (SRY) Protein Sequences Involved in Sex-Determining.

BACKGROUND: The SRY gene (SRY) provides instructions for making a transcription factor called the sex-determining region Y protein. The sex-determining region Y protein causes a fetus to develop as a male. In this study, SRY of 15 spices included of human, chimpanzee, dog, pig, rat, cattle, buffalo, goat, sheep, horse, zebra, frog, urial, dolphin and killer whale were used for determine of bioinformatic differences. METHODS: Nucleotide sequences of SRY were retrieved from the NCBI databank. Bioinformatic analysis of SRY is done by CLC Main Workbench version 5.5 and ClustalW (http:/www.ebi.ac.uk/clustalw/) and MEGA6 softwares. RESULTS: The multiple sequence alignment results indicated that SRY protein sequences from Orcinus orca (killer whale) and Tursiopsaduncus (dolphin) have least genetic distance of 0.33 in these 15 species and are 99.67% identical at the amino acid level. Homosapiens and Pantroglodytes (chimpanzee) have the next lowest genetic distance of 1.35 and are 98.65% identical at the amino acid level. CONCLUSION: These findings indicate that the SRY proteins are conserved in the 15 species, and their evolutionary relationships are similar.