Search

Con el objetivo de definir el panel de polimorfismos de nucleótido simple (SNP) para pruebas de paternidad en bovinos, se analizaron los genotipos en tres razas (número de SNP evaluados e individuos muestreados): Hereford (HER; 202; 1317), Brangus (BRA; 217; 3431) y Limousin (LIM; 151; 8205). Dentro de raza, se descartó los SNP con porcentaje de individuos genotipados (PIG) menor a 90 %, con desequilibrio Hardy Weinberg (HW; P

The insulin-like growth factor-1 (IGF-1), a key hormone in muscle development was investigated for single-nucleotide polymorphisms (SNPs) upstream of the IGF-1 gene and their effects upon its cogna...

Raramuri Criollo cattle from the Chihuahuan desert in northern Mexico have been described as an ecological ecotype due to their enormous advantage in land grass utilization and their capacity to diversify their diet with cacti, forbs and woody plants. This diversification in diet utilization, could reflect upon their microbiome composition. The aim of this study was to characterize the rumen microbiome of Raramuri criollo cattle and to compare it to other lineages that graze in the same area. A total of 28 cows representing three linages [Criollo (n = 13), European (n = 9) and Criollo x European Crossbred (n = 6)] were grazed without supplementation for 45 days. DNA was extracted from ruminal samples and the V4 region of the 16S rRNA gene was sequenced on an Illumina platform. Data were analyzed with the QIIME2 software package and DADA2 plugin and the amplicon sequence variants were taxonomically classified with naïve Bayesian using the SILVA 16S rRNA gene reference database (version 132). Statistical analysis was performed by ANOVA and PERMANOVA for alpha and beta diversity indexes, respectively, and the non-strict version of linear discriminant analysis effect size (LEfSe) was used to determine significantly different taxa among lineages. Differences in beta diversity indexes (P < 0.05) were found in ruminal microbiome composition between Criollo and European groups, whereas the Crossbred showed intermediate values when compared to the pure breeds (Table 1). LEfSe analysis identified a total of 20 bacterial groups that explained differences between lineages, including one for Crossbreed, ten for European and nine for Criollo. These results show ruminal microbiome differences between Raramuri criollo cattle and the mainstream European breeds used in the northern Mexico Chihuahuan desert and reflect that those differences could be a consequence of dissimilar grazing behavior.

A genome-wide association study (GWAS) was performed to elucidate genetic architecture of growth traits in Braunvieh cattle. Methods: The study included 300 genotyped animals by the GeneSeek® Genomic Profiler Bovine LDv.4 panel, after quality control, 22,734 SNP and 276 animals were maintained in the analysis. The examined phenotypic data considered birth (BW), weaning (WW), and yearling weights. The association analysis was performed using the principal components method via the egscore function of the GenABEL version 1.8-0 package in the R environment. The marker rs133262280 located in BTA 22 was associated with BW, and two SNPs were associated with WW, rs43668789 (BTA 11) and rs136155567 (BTA 27). New QTL associated with these liveweight traits and four positional and functional candidate genes potentially involved in variations of the analyzed traits were identified. The most important genes in these genomic regions were MCM2 (minichromosome maintenance complex component 2), TPRA1 (transmembrane protein adipocyte associated 1), GALM (galactose mutarotase), and NRG1 (neuregulin 1), related to embryonic cleavage, bone and tissue growth, cell adhesion, and organic development. This study is the first to present a GWAS conducted in Braunvieh cattle in Mexico providing evidence for genetic architecture of assessed growth traits. Further specific analysis of found associated genes and regions will clarify its contribution to the genetic basis of growth-related traits.

A genome-wide association study (GWAS) for liveweight traits of Braunvieh cattle was performed. The study included 300 genotyped animals by the GeneSeek® Genomic Profiler Bovine LDv.4 panel; after quality control, 22,734 SNP and 276 animals were maintained in the analysis. The examined phenotypic data considered birth, weaning, and yearling weights. The association analysis was performed using the principal components method via the egscore function of the GenABEL version 1.8-0 package in the R environment. The marker rs133262280 located in BTA 22 was associated with birth weight, and two SNPs were associated with weaning weight, rs43668789 (BTA 11) and rs136155567 (BTA 27). New QTL associated with these liveweight traits and four positional and functional candidate genes potentially involved in variations of the analyzed traits were identified. The most important genes in these genomic regions were MCM2 (minichromosome maintenance complex component 2), TPRA1 (transmembrane protein adipocyte associated 1), GALM (galactose mutarotase), and NRG1 (neuregulin 1), with relationships with embryonic cleavage, bone and tissue growth, cell adhesion, and organic development. This study is the first to present a GWAS conducted in Braunvieh cattle in Mexico and represents a basis for future research. Further analyses of found associated regions will clarify its contribution to the genetic basis of growth-related traits.

Charolais cattle are one of the most important breeds for meat production worldwide; in Mexico, 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.

El objetivo fue comparar los efectos de una metodología para la clasificación de épocas climáticas, que tradicionalmente son utilizadas para establecer épocas de nacimiento (EN) en estudios y experimentos estadísticos. Esta metodología se basa en un índice de aridez (IA) para clasificar las EN utilizando información meteorológica histórica. Se trabajó una base de datos con un pedigrí de 7,460 animales, se ajustaron dos modelos para peso al nacimiento y peso al destete en bovinos Charolais manejados en pastoreo extensivo. Los modelos incluyeron el efecto fijo de grupo contemporáneo (GC= subclase de hato, sexo, año y EN) y edad de la madre. Los mismos modelos se compararon utilizando una clasificación tradicional de estaciones del año para clasificar las EN. Al estimar los componentes de varianza y valores genéticos (DEP) con sus exactitudes, los modelos fueron diferentes de acuerdo a la prueba de razón de verosimilitudes (P

The objective of this study was to perform a genomewide association study (GWAS) for growth traits in Charolais beef cattle and to identify SNP markers and genes associated with these traits. Our study included 855 animals genotyped using 76,883 SNP from the GeneSeek Genomic Profiler Bovine HD panel. The examined phenotypic data included birth, weaning, and yearling weights as well as pre- and postweaning ADG. After quality control, 68,337 SNP and 823 animals were retained in the analysis. The association analysis was performed using the principal components method via the egscore function of the GenABEL version 1.8-0 package in the R environment. Eighteen SNP located in 13 BTA were associated with growth traits ( < 5 × 10). The most important genes in these genomic regions were (), (), (), (), and ( [angiotensinase C]), due to their relationships with perinatal and postnatal survival, bone growth, cell adhesion, regulation of adipogenesis, and appetite. In conclusion, this study is the first to describe a GWAS conducted in beef cattle in Mexico and represents a basis for further and future research. This study detected new QTL associated with growth traits and identified 5 positional and functional candidate genes that are potentially involved in variations of the analyzed traits. Future analyses of these regions could help to identify useful markers for marker-assisted selection and will contribute to the knowledge of the genetic basis of growth in cattle and be a foundation for genomic predictions in Mexican Charolais cattle.

The insulin-like growth factor-1 (IGF-1) plays a key role in muscle development and has been described in several studies as a candidate marker gene for growth traits in farm animals. The aim of the study was to investigate IGF-1 single nucleotide polymorphisms (SNPs) at the 5’ flanking region and their association with gene expression levels and phenotypic characteristics in lambs. The experiment was executed in two phases. First, a 265 bp-long region of gDNA localized up-stream of the IGF-1 gene was scanned for SNPs by sequencing. Sequence analysis revealed that animals with low IGF-1 plasm concentration had nucleotide changes from Guanine (G) to Cytosine (C) at position 85 (85G >C), and from G to Adenine (A) at position 87 (87G >A). A PCR-RFLP protocol was set up to accomplish allelic discrimination in 22 lambs sired by Dorper rams. The frequency of the variant-carrier lambs was 50 %. The statistical analysis showed differences (P < 0.05) between carrier and non-carrier female lambs for IGF-1 concentration at 13 d (168.76 ± 15.01 vs 229.95 ± 16.78), 41 d (191.02 ± 38.28 vs 324.50 ± 42.80) and 69 d (209.18 ± 30.63 vs 375.87 ± 34.2) of the feeding trial. Statistical differences (P < 0.05) were also found for total weight gain (22.16 ± 1.07 vs 26.75 ± 1.2). In a second phase, 55 Dorper females were genotyped, then 2 homozygotes, 5 heterozygotes and 5 wild-type for the variant were randomly selected for IGF-1 qPCR gene expression analysis. Gene expression was higher (fold-change 2.6) in non-carrier animals (P < 0.05). Nevertheless, daily weight gain and weight at 150 d were not statistically significant. The variant for the IGF-1 gene here reported has lower levels of gene expression. However, additional experiments are needed to measure phenotypic characteristics such as carcass traits, diameter and density of muscle fibers.

This study aimed to edit the SNPs panel for sheep paternity testing in Mexico. The genotypes of 10,097 individuals distributed in ten breeds were analyzed: Blackbelly (459), Charollais (209), White Dorper (122), Dorper (2106), Dorset (534), Hampshire (1,298), Katahdin (3864), Pelibuey (821), Suffolk (596), and Texel (88). In all breeds the panel was comprised of 84 SNPs; the allele frequencies, the polymorphic information content (PIC), and the Hardy-Weinberg (HW) equilibrium were evaluated. Within breeds, the SNPs with HW disequilibrium (p

Context Genomic prediction is now routinely used in many livestock species to rank individuals based on genomic breeding values (GEBV). Aims This study reports the first assessment aimed to evaluate the accuracy of direct GEBV for birth (BW) and weaning (WW) weights of registered Charolais cattle in Mexico. Methods The population assessed included 823 animals genotyped with an array of 77000 single nucleotide polymorphisms. Genomic prediction used genomic best linear unbiased prediction (GBLUP), Bayes C (BC), and single-step Bayesian regression (SSBR) methods in comparison with a pedigree-based BLUP method. Key results Our results show that the genomic prediction methods provided low and similar accuracies to BLUP. The prediction accuracy of GBLUP and BC were identical at 0.31 for BW and 0.29 for WW, similar to BLUP. Prediction accuracies of SSBR for BW and WW were up to 4% higher than those by BLUP. Conclusions Genomic prediction is feasible under current conditions, and provides a slight improvement using SSBR. Implications Some limitations on reference population size and structure were identified and need to be addressed to obtain more accurate predictions in liveweight traits under the prevalent cattle breeding conditions of Mexico.