Analysis of nonsynonymous SNPs in candidate genes that influence bovine temperament and evaluation of their effect in Brahman cattle.

BACKGROUND: Temperament is an important production trait in cattle and multiple strategies had been developed to generate molecular markers to assist animal selection. As nonsynonymous single nucleotide polymorphisms are markers with the potential to affect gene functions, they could be useful to predict phenotypic effects. Genetic selection of less stress-responsive, temperamental animals is desirable from an economic and welfare point of view. METHODS AND RESULTS: Two nonsynonymous single nucleotide polymorphisms identified in HTR1B and SLC18A2 candidate genes for temperament were analyzed in silico to determine their effects on protein structure. Those nsSNPs allowing changes in proteins were selected for a temperament association analysis in a Brahman population. Transversion effects on protein structure were evaluated in silico for each amino acid change model, revealing structural changes in the proteins of the HTR1B and SLC18A2 genes. The selected nsSNPs were genotyped in a Brahman population (n = 138), and their genotypic effects on three temperament traits were analyzed: exit velocity, pen score, and temperament score. Only the SNP rs209984404-HTR1B (C/A) showed a significant association (P = 0.0144) with pen score. The heterozygous genotype showed a pen score value 1.17 points lower than that of the homozygous CC genotype. CONCLUSION: The results showed that in silico analysis could direct the selection of nsSNPs with the potential to change the protein. Non-synonymous single nucleotide polymorphisms causing structural changes and reduced protein stability were identified. Only rs209984404-HTR1B shows that the allele affecting protein stability was associated with the genotype linked to docility in cattle.

Genetic Variants and Their Putative Effects on microRNA-Seed Sites: Characterization of the 3' Untranslated Region of Genes Associated with Temperament.

The 3' untranslated region has an important role in gene regulation through microRNAs, and it has been estimated that microRNAs regulate up to 50% of coding genes in mammals. With the aim of allelic variant identification of 3' untranslated region microRNA seed sites, the 3' untranslated region was searched for seed sites of four temperament-associated genes (CACNG4, EXOC4, NRXN3, and SLC9A4). The microRNA seed sites were predicted in the four genes, and the CACNG4 gene had the greatest number with 12 predictions. To search for variants affecting the predicted microRNA seed sites, the four 3' untranslated regions were re-sequenced in a Brahman cattle population. Eleven single nucleotide polymorphisms were identified in the CACNG4, and eleven in the SLC9A4. Rs522648682:T>G of the CACNG4 gene was located at the predicted seed site for bta-miR-191. Rs522648682:T>G evidenced an association with both exit velocity (p = 0.0054) and temperament score (p = 0.0097). The genotype TT had a lower mean exit velocity (2.93 ± 0.4 m/s) compared with the TG and GG genotypes (3.91 ± 0.46 m/s and 3.67 ± 0.46 m/s, respectively). The allele associated with the temperamental phenotype antagonizes the seed site, disrupting the bta-miR-191 recognition. The G allele of CACNG4-rs522648682 has the potential to influence bovine temperament through a mechanism associated with unspecific recognition of bta-miR-191.

Novel genes involved in the genetic architecture of temperament in Brahman cattle.

Cattle temperament is a complex and economically relevant trait. The objective of this study was to identify genomic regions and genes associated with cattle temperament. From a Brahman cattle population of 1,370 animals evaluated for temperament traits (Exit velocity-EV, Pen Score-PS, Temperament Score-TS), two groups of temperament-contrasting animals were identified based on their EV-average values ±1/2 standard deviation (SD). To be considered in the calm group, the EV of females ranged between 0.16-1.82 m/s (n = 50) and the EV of males ranged between 0.4-1.56 m/s (n = 48). Females were classified as temperamental if their EV ranged between 3.13-7.66 m/s (n = 46) and males were classified as temperamental if their EV ranged between 3.05-10.83 m/s (n = 45). Selected animals were genotyped using a total of 139,376 SNPs (GGP-HD-150K), evaluated for their association with EV. The Genome-Wide Association analysis (GWAS) identified fourteen SNPs: rs135340276, rs134895560, rs110190635, rs42949831, rs135982573, rs109393235, rs109531929, rs135087545, rs41839733, rs42486577, rs136661522, rs110882543, rs110864071, rs109722627, (P<8.1E-05), nine of them were located on intergenic regions, harboring seventeen genes, of which only ACER3, VRK2, FANCL and SLCO3A1 were considered candidate associated with bovine temperament due to their reported biological functions. Five SNPs were located at introns of the NRXN3, EXOC4, CACNG4 and SLC9A4 genes. The indicated candidate genes are implicated in a wide range of behavioural phenotypes and complex cognitive functions. The association of the fourteen SNPs on bovine temperament traits (EV, PS and TS) was evaluated; all these SNPs were significant for EV; only some were associated with PS and TS. Fourteen SNPs were associated with EV which allowed the identification of twenty-one candidate genes for Brahman temperament. From a functional point of view, the five intronic SNPs identified in this study, are candidates to address control of bovine temperament, further investigation will probe their role in expression of this trait.

Signatures of selection in Charolais beef cattle identified by genome-wide analysis.

Charolais cattle are one of the most important breeds for meat production worldwide; in México, its selection is mainly made by live weight traits. One strategy for mapping important genomic regions that might influence productive traits is the identification of signatures of selection. This type of genomic features contains loci with extended linkage disequilibrium (LD) and homozygosity patterns that are commonly associated with sites of quantitative trait locus (QTL). Therefore, the objective of this study was to identify the signatures of selection in Charolais cattle genotyped with the GeneSeek Genomic Profiler Bovine HD panel consisting of 77 K single nucleotide polymorphisms (SNPs). A total 61,311 SNPs and 819 samples were used for the analysis. Identification of signatures of selection was carried out using the integrated haplotype score (iHS) methodology implemented in the rehh R package. The top ten SNPs with the highest piHS values were located on BTA 4, 5, 6 and 14. By identifying markers in LD with top ten SNPs, the candidate regions defined were mapped to 52.8-59.3 Mb on BTA 4; 67.5-69.3 on BTA 5; 39.5-41.0 Mb on BTA 6; and 26.4-29.6 Mb on BTA 14. The comparison of these candidate regions with the bovine QTLdb effectively confirmed the association (p < 0.05) with QTL related to growth traits and other important productive traits. The genomic regions identified in this study indicated selection for growth traits on the Charolais population via the conservation of haplotypes on various chromosomes. These genomic regions and their associated genes could serve as the basis for haplotype association studies and for the identification of causal genes related to growth traits.

Signatures of Selection From Candidate Gene Polymorphisms Panel in Five Zebu Breeds

ABSTRACT The signals of selection using candidate genes polymorphism were studied in five zebu breeds of Mexico. Three loci from GHRH and complementarily Steroyl Co Desaturase F762, Dopamine Beta Hydroxilase 17299, and LEP3272 were identified under selection. Findings depict Zebu selection pressure mainly on Brahman breed resulting in a divergent structure pattern.

Associations of SNPs located at candidate genes to bovine growth traits, prioritized with an interaction networks construction approach.

BACKGROUND: For most domestic animal species, including bovines, it is difficult to identify causative genetic variants involved in economically relevant traits. The candidate gene approach is efficient because it investigates genes that are expected to be associated with the expression of a trait and defines whether the genetic variation present in a population is associated with phenotypic diversity. A potential limitation of this approach is the identification of candidates. This study used a bioinformatics approach to identify candidate genes via a search guided by a functional interaction network. RESULTS: A functional interaction network tool, BosNet, was constructed for Bos taurus. Predictions for candidate genes were performed using the guilt-by-association principle in BosNet. Association analyses identified five novel markers within BosNet-prioritized genes that had significant effects on different growth traits in Charolais and Brahman cattle. CONCLUSIONS: BosNet is an excellent tool for the identification of single nucleotide polymorphisms that are potentially associated with complex traits.

Single and composite influence of growth-related candidate gene polymorphisms on additive genetic variation of birth weight in Charolais beef cattle.

The objective of the present experiment work was to evaluate the effect of the inclusion of genomic information on the additive genetic variance of birth weight (BW) of Charolais cattle in Mexico. Variance components and heritability were estimated using four linear models. The first model was the base model (BM) from which single and composite effects of selected single-nucleotide polymorphism (SNP) markers were evaluated (BM1, BM2, and a composite BM3). Genetic markers were included in a regression model and analyzed by stepwise regression against adjusted BW from a panel of growth-related traits candidate gene markers. After two regression rounds, two SNPs (R (2) > 0.02) were chosen to include into the animal models as fixed effects. Growth hormone receptor gene GHR 4.2 and GHR 6.1 SNPs were selected from a panel of 39 SNPs. GHR 4.2 had a negligible effect on BW, whilst GHR6.1, interestingly, explained ∼9 % of genetic variance (p = 0.0877) with an αG>A = 0.509. The inclusion of markers in M2 and M3 reduced 19 and 15 % of the additive genetic variance, respectively. Both adjusted significantly better the linear model (LRT = p < 0.01). Results obtained suggest that the previous selection of markers in a candidate gene approach and subsequent inclusion of selected SNPs into animal model might provide a better fit, avoiding the overestimation of genetic variance components and breeding values for BW.

Genetic diversity of tyrosine hydroxylase (TH) and dopamine ß-hydroxylase (DBH) genes in cattle breeds.

DNA from four cattle breeds was used to re-sequence all of the exons and 56% of the introns of the bovine tyrosine hydroxylase (TH) gene and 97% and 13% of the bovine dopamine ß-hydroxylase (DBH) coding and non-coding sequences, respectively. Two novel single nucleotide polymorphisms (SNPs) and a microsatellite motif were found in the TH sequences. The DBH sequences contained 62 nucleotide changes, including eight non-synonymous SNPs (nsSNPs) that are of particular interest because they may alter protein function and therefore affect the phenotype. These DBH nsSNPs resulted in amino acid substitutions that were predicted to destabilize the protein structure. Six SNPs (one from TH and five from DBH non-synonymous SNPs) were genotyped in 140 animals; all of them were polymorphic and had a minor allele frequency of > 9%. There were significant differences in the intra- and inter-population haplotype distributions. The haplotype differences between Brahman cattle and the three B. t. taurus breeds (Charolais, Holstein and Lidia) were interesting from a behavioural point of view because of the differences in temperament between these breeds.

Importancia de la verificación-asignación de progenitores en sistemas extensivos de pie de cría / Importance of parentage verification-assignment in extensive multiple-sired breeding herds

Se aplicó un panel de nueve marcadores microsatélites para estructurar la genealogía de un hato de ganado Braford manejado bajo empadre múltiple y destinado a pié de cría, para evaluar las repercusiones de la adecuada asignación de progenitores, así como las implicaciones en su mejoramiento genético. Se logró la asignación de paternidad en el 100% de la progenie, mientras que en los ensayos de verificación de maternidad se estimó un porcentaje de error de asignación de aproximadamente 90%. Los resultados encontrados apoyan el uso de la asignación de paternidad para verificar la estructura genealógica (paternidad y maternidad) de hatos cuya certeza en el pedigrí es crítica para el mejoramiento genético de su raza, y en donde el sistema de manejo extensivo y empadre múltiple limitan el registro adecuado de la progenie al momento del parto.

To assess the implications of parentage assignation on herds-genetic improvement nine microsatellite markers were used in order to structure the genealogy of a multisired Braford herd. All progeny (100%) had satisfactory paternity assignment, conversely the maternity verification analysis showed assignation errors up to 90%. Our results support the use of molecular tools to verify the pedigree structure in those herds with management systems that limit the proper registration of progeny at calving.

Assessment of genetic structure in Mexican charolais herds using microsatellite markers

Knowledge of livestock genetic diversity is an essential step to respond to commercial demands and reach production objectives in different environments and production systems. The evaluation of animal genetic diversity is achieved by using molecular markers. Microsatellites are the most used markers for studies of this type. Eleven microsatellites were used to evaluate the genetic variation from three populations of Charolais cattle located in northeast Mexico. The studied populations exhibited a high allelic variability with a mean heterozygosity of 0.5. A moderate genetic differentiation between the Charolais populations (F ST = 0.079; P < 0.001) was observed. This suggests subdivisions in Charolais breed established in Mexico, due to genetic material origin, reproductive and selective management and local isolation.

Microsatellite variability analysis in farmed catfish (Ictalurus punctatus) from Tamaulipas, Mexico

Analysis of cultured catfish from six farms in Tamaulipas, Mexico was achieved using a combination of microsatellite PCR analysis and semiautomatic fluoresce-based detection, in order to provide a first assessment of the genetic variability on cultured catfish in Mexico. Five microsatellites showed extensive polymorphism with allele numbers ranging from 10 and 20. Overall observed heterozygosity at each locus ranged between 0.76 and 0.91 and the average polymorphic information content (PIC) for the five loci was 0.811, indicating that these loci can be used for studies of paternity identification, linkage and population genetics. On the basis of the F ST values (F ST = 0.03829; p = 0.00000) it appears that there was a small amount of genetic differentiation between the channel catfish stocks. The high intrapopulation allelic diversity was the most remarkable parameter.

Caracterización morfométrica de cuatro subespecies de venado cola blanca (Odocoileus virginianus) en la zona noreste de México / Morphometric charaterization of four white-tailed deer subspecies (Odocoileus virginianus) in the northeas region of Mexico

Con el objetivo de contribuir en la definición de las subespecies de venado cola blanca de México, se determinó la variabilidad morfométrica de las subespecies (Odocoileus virginianus carminis, O.v. miquihuanensis, O.v. texanus y O.v. veraecrucis) que se distribuyen en el Noreste de México. Se analizó la información de 592 individuos (579 O. v. texanus, seis O.v. veraecrucis, cuatro O.v. miquihuanesis y tres O.v. carminis), y 49 cráneos de O.v. texanus. La comparación entre la morfometría histórica y la del presente estudio mostró un 98% de similitud para O.v carminis, O.v. miquihuanensis y O.v veraecrucis y un 96% para O.v. texanus. Los contrastes otorgonales mostraron diferencias morfométricas (P<0,05) entre las subespecies. En O.v. texanus, la longitud total tendió a ser de mayor tamaño que en las otras subespecies, mientras que O.v. veraecrucis mostró diferencias significativas respecto a O.v. carminis y O.v. miquihuanesis en todas las variables. La mayor similitud por Distancia Euclidiana se presentó entre los machos de O.v. carminis y O.v. miquihuanensis (5,1), mientras que la de menor similitud fue entre los machos de O.v. texanus y los de las otras tres subespecies (19,9). Los machos adultos de Tamaulipas se diferenciaron significativamente (P<0,05) de los de Coahuila y Nuevo León.