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

Genetic evaluation of survival and productivity traits in Arman crossbred sheep

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.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.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

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

Abstract 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

Genetic evaluation of survival and productivity traits in Arman crossbred sheep

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

Study of Genetic Diversity of Sheep Breeds in Afghanistan Using SNP Markers

The objective of present study is analyzing genetic diversity among three Arab, Baloch and Gadic breeds using selected markers. Mutual comparisons of each two breeds were conducted to detect and accurately analyze differences between breeds. . 45 blood samples were collected from three districts of Herat province (Shindand, Gulran and Obe) of three Afghan sheep breeds (Arabi, Baloch and Gadic). 10 µL of blood was collected via the jugular vein in Venoject tubes with EDTA (Ethylene Diamine Tetraacetic Acid) for prevention of blood coagulation and immediately stored in a refrigerator at 4 °C. DNA was extracted from blood using the GenElute™ Blood Genomic DNA Kit. DNA concentration was determined using NanoDrop (Spectrophotometer ND-1000). In this research haplotypic blocks analysis in experimental regions, the way of their erosions and LD graphs are drawn using Haploview v4.2 software. Required information as inputs for this software consisted of genotypic information of markers in experimental regions similarly; the statistics that are used for LD calculation are the same correlational coefficients between r2 and surrounding SNPs. A total of 15 Arabi, 15 Baloch and 15 Gadic sheep breed were genotyped at 53862 SNP loci with the Ovine SNP chip50K Bead chip (http://www.illumina.com). usually those SNP that had been assigned to the 26 autosomes and X chromosome was measured) Then for each SNP, minor allele frequency (MAF) (over all animals) less than 2% were removed and percentage of calls rate ? 95% (how many sheep the marker worked for) was removed (Teo YY, Fry AE, Clark TG, Tai ES, Seielstad M: On the usage of HWE for identifying genotyping errors. Annals of Human Genetics 2007, 71:701-703). Biodiversity is usually described in terms of three intimately connected levels, namely Species diversity, Genetic diversity, Ecosystem diversity. Considering excess of heterozygosity within studied breeds, one can conclude that these breeds are not threatening in terms of heterozygosity decline and can be considered as an appropriate genetic reserve for different husbandry and eugenic purposes in Afghanistan. Furthermore high heterozygosity in studied chromosomes in Arab, Baloch and Gadic breeds suggest high diversity within population in spite of carrying out eugenic activities on livestock due to managerial plans which has managed to reduce the consistency level and keep the diversity in acceptable level