Abstract The objective of this study was to identify in Angus and Brangus breed animals with extreme temperament, measured as exit velocity, genomic regions and candidate genes associated with bovine temperament. The population was genotyped with the Genomic Profiler HD 150K chip and after the genome-wide association analysis, the SNPs rs133956611 (P=2.65 E-06) and rs81144933 (P=9.58 E-06) were associated with temperament. The mapping analysis of the regions close to the SNP rs81144933 identified the SNCA (alpha-synuclein) and MMRN1 (multimerin-1) genes at 222.8 and 435.9 Kb downstream respectively, while for the rs133956611 loci the gene GPRIN3 (GPRIN family-member-3) was identified at 245.7 Kb upstream, all three genes are located on the BTA6 chromosome. The analysis of SNCA protein-protein interactions allowed the identification of the genes APP (β-amyloid precursor protein), PARK7 (parkinsonism-associated-deglycase), UCHL1 (ubiquitin-C-terminal-hydrolase-L1), PARK2 (parkin-RBR- E3-ubiquitin-protein-ligase), and genes of the SLC family as candidates to be associated with bovine temperament. All these candidate genes and their interacting were resequenced, which allowed the discovery of new SNPs in the SNCA and APP genes. Of these, the SNPs located in introns 5, 8 and 11 of the APP gene affect splicing site motifs. These results indicate that SNCA and its interacting genes are candidates to be related to bovine temperament.

Resumen El objetivo de este estudio fue identificar en animales de raza Angus y Brangus con temperamento extremo, medido como velocidad de salida, regiones genómicas y genes candidatos asociados con el temperamento bovino. La población fue genotipada con el chip Genomic Profiler HD 150K y después del análisis de asociación del genoma completo, los SNP rs133956611 (P= 2.65 E-06) y rs81144933 (P= 9.58 E-06) se asociaron con el temperamento. El análisis de mapeo de las regiones cercanas al SNP rs81144933 identificó los genes SNCA (alfa-sinucleína) y MMRN1 (multimerin-1) a 222.8 y 435.9 Kb corriente abajo, respectivamente, mientras que para los loci rs133956611 se identificó el gen GPRIN3 (familia GPRIN- miembro 3) a 245.7 Kb corriente arriba, los tres genes se encuentran en el cromosoma BTA6. El análisis de las interacciones proteína-proteína de SNCA permitió la identificación de los genes APP (proteína precursora de β-amiloide), PARK7 (deglicasa asociada al parkinsonismo), UCHL1 (ubiquitina C-terminal hidrolasa L1), PARK2 (parkina-RBR-E3-ubiquitina-proteína-ligasa), y genes de la familia SLC como candidatos a estar asociados con el temperamento bovino. Todos estos genes candidatos y su interacción fueron resecuenciados, lo que permitió el descubrimiento de nuevos SNP en los genes SNCA y APP. De estos, los SNP localizados en los intrones 5, 8 y 11 del gen APP afectan a los motivos del sitio de empalme. Estos resultados indican que el SNCA y sus genes interactuantes son candidatos para estar relacionados con el temperamento bovino.

ABSTRACT The objective of this study was to evaluate the effect of intronic single nucleotide polymorphisms (SNP) on temperament traits in a Brahman cattle population. The SNP located in CACNG4, EXOC4, NRXN3, and SLC9A4 candidate genes were genotyped in 250 animals with temperament records of exit velocity, pen score, and temperament score. Rs3423464051:G>A in the CACNG4 gene was associated with exit velocity and temperament score. An in silico analysis of the five intronic SNP showed that alternative alleles of CACNG4-rs3423464051, EXOC4-rs109393235, and SLC9A4-rs109722627 SNP could alter branch point sites during splicing, while a protein–protein interaction network analysis demonstrated a GRIA2 gene-mediated interaction between CACNG4 and NRXN3. The present results support previously reported evidence regarding bovine temperament-related candidate genes, particularly CACNG4, which is a confirmed candidate gene in need of more detailed analyses to reveal its role in temperament-related traits.

Abstract Reproduction is a key element in cattle production systems. Systems biology approaches, including those involving gene networks, have been applied to genetic dissection complex phenotypes in cattle. A set of 385 genes associated with reproductive traits in cattle were included in a protein-protein network analysis to identify and prioritize candidate genes related to phenotypic differences in cattle reproduction. Genes belonging to the ubiquitin family - Ubiquitin C (Ubc, Gene ID: 444874) and Ubiquitin B (Ubb, Gene ID: 281370) -had the highest probability of being associated with these traits in cattle. Both proteins were identified as important hubs in a protein-protein interaction network, each having 3,775 interactions of 3,856 possible. Resequencing of the Ubb gene coding region to evaluate the presence of SNPs in a discovery population identified the G/T (rs110366695) transversion. This causes emergence of a stop codon and a protein truncated by 287 aa. The allelic frequency distributions found in two beef cattle breeds highlight the promise of further research into the effects of protein truncation and the potential of these proteins as molecular markers for semen quality.

Resumen La reproducción es un elemento clave en los sistemas de producción de ganado bovino. Se han aplicado los enfoques de biología de sistemas, incluidos los que involucran las redes de genes, a la disección genética de fenotipos complejos de ganado. Se hizo un análisis de la red proteína-proteína, incluyendo un conjunto de 385 genes asociados con rasgos reproductivos en el ganado, para identificar y priorizar genes candidatos relacionados con las diferencias fenotípicas en la reproducción del ganado. Los genes que pertenecen a la familia de la ubiquitina - Ubiquitina C (Ubc, ID del gen: 444874) y Ubiquitina B (Ubb, ID del gen: 281370) - presentaron la mayor probabilidad de estar asociados con estos rasgos en el ganado. Se identificaron ambas proteínas como centros muy importantes en una red de interacción proteína-proteína ya que cada una tienen 3,775 interacciones de 3,856 posibles. Al resecuenciar la región de codificación del gen Ubb para evaluar la presencia de SNP en una población de descubrimiento, se identificó la transversión G/T (rs110366695), que provoca la aparición de un codón de terminación y una proteína truncada en 287 aa. Las distribuciones de frecuencia alélicas descubiertos en dos razas de ganado vacuno podrían justificar investigaciones adicionales enfocados en explorar tanto los efectos del truncamiento de proteínas como el potencial de estas proteínas como marcadores moleculares para la calidad del semen.

Abstract A full understanding of how specific genes affect live weight variables is required for their incorporation into genetic improvement programs. An analysis was done of the allelic frequencies of 28 single nucleotide polymorphisms (SNP) located in candidate genes for growth in cattle to identify their effect on live weight traits in Charolais and Simmental herds in the state of Tamaulipas, Mexico. Hair samples were collected from 313 animals and genotyped using the Sequenom MassARRAY system. Genotype analysis showed that all the markers were polymorphic in the evaluated populations and their allelic frequencies were significantly different between the two breeds (P<0.05). An association analysis found that in the Charolais population the marker PRL + 2723 had a significant effect (P= 0.0350) on birth weight and the marker GHR-6.1 affected weaning weight (P= 0.0226). In the Simmental population GHR-6.1 was associated with yearling weight and the marker LEP-3100 (P=0.0249) had a significant effect on weaning weight. The tested 28 SNP panel is polymorphic in both breeds and three of the markers had a significant effect on the evaluated live weight parameters. They can therefore be potentially validated for use as tools in the selection and breeding of beef cattle in Tamaulipas.

Resumen El objetivo del estudio fue analizar las frecuencias alélicas de 28 Polimorfismos de un solo nucleótido (SNP) localizados en genes candidatos para crecimiento en bovinos, así como determinar su efecto sobre rasgos de peso vivo en hatos de las razas Charolais y Simmental. Se tomaron muestras de pelo de 313 animales provenientes de cinco hatos ubicados en cuatro municipios de Tamaulipas y se genotipificaron con la tecnología de Sequenom Mass Array. Todos los marcadores resultaron ser polimórficos en las poblaciones evaluadas y sus frecuencias alélicas fueron significativamente diferentes entre razas (P<0.05). El análisis de asociación determinó que en los animales de la raza Charolais, el marcador PRL+2723 tiene un efecto significativo (P=0.0350) sobre el peso al nacimiento y el marcador localizado en el gen GHR (GHR-6.1), sobre peso al destete (P=0.0226). El GHR-6.1 también se asoció con el peso al año en los animales de la raza Simmental. El marcador LEP-3100 (P=0.0249) también tuvo un efecto significativo sobre el peso al destete en los animales Simmental. El panel probado es polimórfico en las dos razas evaluadas y tres de los marcadores tuvieron efecto significativo en los parámetros de peso vivo evaluados, por lo que tienen el potencial de validarse y usarse como una herramienta adicional en la selección y mejoramiento genético del ganado de carne en Tamaulipas.

ABSTRACT. The aim of the present work was to perform a genetic verification of Herichthys species and assess their phylogenetic relationship by Cytochrome B gene resequencing in two sampling sites from Tamaulipas. Samples from Panal river in Playa Tepehuajes, Soto la Marina and samples from Carrizal river in Aldama were included. The complete sequences were analyzed with bioinformatics tools and the genetic similarity showed that Aldama samples resembled Herichthys carpintis species (> 99%) and Tepehuajes samples were confirmed as Herichthys cyanoguttatus. The assessed phylogenetic trees for genetic distance comparison among current samples and other cichlids species support the previously found results. This study suggest that cytochrome B gene is useful for genetic identification of cichlid species, such as from Tamaulipas.

RESUMEN. El objetivo del presente estudio fue verificar genéticamente la identidad de especies del genero Herichthys y estudiar su relación fiolgenética utilizando secuencias de citocromo B mitocondrial. Se incluyeron muestras de dos sitios de Tamaulipas de dicha especie: en el río Panal ubicado en Playa Tepehuajes, Soto la Marina y en el río Carrizal ubicado en Aldama. Se analizaron las secuencias completas del gen mitocondrial citocromo B con herramientas bioinformáticas, los resultados de similitud genética indican que las muestras de Aldama tienen mayor similitud (> 99%) con la especie Herichthys carpintis. Mientras que las muestras de Tepehuajes, confirmaron la identidad supuesta con Herichthys cyanoguttatus. Los árboles filogenéticos analizados con la finalidad de comparar la distancia genética de las muestras con diferentes especies de cíclidos, confirmaron la similitud encontrada previamente. Los resultados sugieren que el citocromo B es un marcador útil en la identificación de especies de cíclidos de Tamaulipas.

Abstract We investigated whether a panel of molecular markers previously associated with temperament has an effect on live growth traits. Phenotypic data from 412 Charolais cows categorized according to their age in adult and young cows were used to determine Pearson's correlations between birth (BW), weaning (WW), and yearling live (YW) weight and temperament traits (measured as exit velocity [EV] and temperament score [TS]). For association analysis, selective genotyping of a group of 80 cows identified as the most docile and temperamental were genotyped with a 151-SNP (single-nucleotide polymorphisms) panel of molecular markers previously associated with temperament. Significant Pearson's correlations between birth weight and weaning weight and the two temperament measurements (EV and TS) were observed only in the young cow group. Significant effects of ten SNP on BW and WW were observed. Four markers located on candidate genes for temperament traits also had an effect on birth weight and weaning weight in Charolais cows, which indicates that both traits could be influenced by the same genes.

ABSTRACT The effect of three localized genetic markers in growth hormone (GH), Insulin-like growth factor 1 (IGF-1) and leptin (LEP) genes on feed efficiency indicators was evaluated using records from 136 young bulls of the Charolais, Angus and Brangus breeds during a productive behavior test. The analysis of association between the genotypes obtained and the productive traits evaluated showed a significant effect of the GH-Alu marker on CRA (p = 0.032) in the Angus breed, and in the Charolais one; this result shows that its inclusion in the initial efforts for the determination of efficiency phenotypes in Mexico and its consequent application in selection and breeding strategies are possible.

RESUMEN Se evaluó el efecto de tres marcadores genéticos localizados en los genes de hormona de crecimiento (GH), factor de crecimiento semejante a insulina-1 (IGF-1) y leptina (LEP) sobre indicadores de eficiencia alimenticia, utilizando registros de 136 toretes de las razas Charolais, Angus y Brangus durante una prueba de comportamiento productivo. El análisis de asociación entre los genotipos obtenidos y los rasgos productivos evaluados mostró un efecto significativo del marcador GH-Alu sobre CRA (p = 0.032) en la raza Angus, y sobre el peso final ajustado (p = 0.041), en la Charolais; este resultado muestra que es posible su inclusión en los esfuerzos iniciales para la determinación de fenotipos de eficiencia en México y su consecuente aplicación en las estrategias de selección y mejoramiento genético.

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.

Abstract: K-casein (CSN3) gene is of particular interest in goat production due to the effect of its polymorphisms on milk quality and composition. The objective of this study was to assess the genotypic and allelic frequencies in CSN3 gene in the Saanen goat breed and its effect on milk production and some of its compositional traits. Allelic discrimination assays were designed to determine the variants (A, B or C) using qPCR and allelic discrimination method. Allelic frequencies for A, B and C were 0.23, 0.64 and 0.13, respectively. Association analysis indicated that the CSN3 was significantly associated only with protein percentage (p = 0.006). Results indicated that animals with AC, BB and CC genotypes showed higher milk protein percentage than those with genotype AB. This evidence suggests that genotypes favorable to this associated trait could be included into Saanen goat breeding strategies.

Resumen: El gen de la к-caseína (CSN3) es de especial interés debido al efecto de sus polimorfismos sobre la calidad y composición de la leche. El objetivo de este estudio fue investigar las frecuencias genotípicas y alélicas del gen CSN3 en la raza caprina Saanen y su efecto sobre la producción de leche y algunas de sus características de composición. Se diseñaron diferentes ensayos de discriminación alélica para determinar las variantes (A, B y C) mediante qPCR. Las frecuencias alélicas para las variantes A, B y C fueron de 0.23, 0.64 y 0.13, respectivamente. El análisis de asociación indicó que el gen CSN3 esta asociado solamente al porcentaje de proteína en leche (p = 0.006). Los resultados mostraron que los animales con los genotipos AC, BB y CC producen leche con mayor porcentaje de proteína que aquellos con el genotipo AB. Esta evidencia sugiere que los genotipos favorables para la característica asociada podrían incluirse en estrategias de selección asistida por marcadores en cabras de la raza Saanen.

ABSTRACT The objective of the present work was to identify and validate single nucleotide variations located in candidate genes to growth traits in tilapia (Oreochromis niloticus). Two transitions were identified in the promoter region of the growth hormone gene (GH); eight nucleotide changes were identified in introns and promoter region of the IGF-I gene; and a transition (T/C) was identified in the Myogenin gene (MyoG). The highest genotypic frequency (0.8) for GHpA1 and MyoG was found in the GG and TT homozygous individuals, while the highest frequency (0.9) for GHpB1 was observed in the CT heterozygous fish. There was no genotypic frequency in the CC homozygous tilapia for the GHpB1 and MyoG markers. Based on their allelic frequencies, validation as novel single nucleotide polymorphisms (SNP) of those variations located at O. niloticus GH and MyoG genes was possible. These new markers will allow their association with growth traits in tilapia to be exploited in order to determine their potential use as assisted-selection markers.

Abstract: Allelic and genotypic frequencies of eight markers previously associated to genetic disorders and meat quality and located in the calpain (CAPN1-4751 and CAPN1-316), calpastatin (CAST-T1), thyroglobulin (TG5), myostatin (MSTN, Q204X), argininosuccinate synthase (ASS), monophosphate synthase (UMPS) and myophosphorylase (PYGM) genes, were determined from 493 registered Charolais animals sampled from two herds located at Sonora (n= 157) and three at Nuevo León (n= 336), Mexico. No carriers of mutated alleles of ASS and UMPS genes were found, but carriers of the MSTN Q204X allele were identified at frequencies of ≤ 1 % in Sonora populations and 8.6 to 14.4 % in Nuevo Leon. In addition, carriers of PYGM marker were identified at frequencies of 6.49 and 1% in a herd from Sonora and other from Nuevo León, respectively. Analysis of gene differentiation among herds and with four loci showed that there are highly significant differences within Northwest populations (P<0.0001) and between them and the Northeast (P<0.001), differentiation is mainly explained by the loci CAPN-316 and TG5. According to the obtained results, the periodic monitoring of the PYGM marker gene and of the allele Q204X the MSTN gene is propose; also it is important to implement strategies to confirm the usefulness of those markers associated with quality and productivity as a tool to complement breeding programs.

Resumen: Se determinaron las frecuencias alélicas y genotípicas de ocho marcadores localizados en los genes calpaína (CAPN, 4751 y 316), calpastatina (CASTT1) y tiroglobulina (TG5), asociados a calidad de carne, y en los genes, miostatina (MSTN, Q204X), arginino succinato sintasa (ASS), monofosfato sintasa (UMPS) y miofosforilasa (PYGM), asociados a enfermedades genéticas de ganado bovino. Se muestrearon 493 animales Charolais de registro de dos hatos ubicados en Sonora (n=157) y tres en Nuevo León (n=336). No se encontraron portadores de los alelos T-ASS y T-UMPS, pero sí portadores del alelo Q204X del gen MSTN en frecuencias de ≤ 1 % en las poblaciones de Sonora y de 8.6 a 14.4 % en las de Nuevo León. Además, se identificaron portadores del marcador del gen PYGM, en frecuencias del 6.5 y de 1.0 % para un hato de Sonora y otro de Nuevo León, respectivamente. El análisis de diferenciación génica pareado entre las poblaciones y con los cuatro loci mostró que hay diferencias altamente significativas dentro de poblaciones del noroeste (P<0.0001) y entre éstas y las del noreste (P<0.001), la cual es explicada principalmente por los loci CAPN-316 y TG5. De acuerdo a los resultados obtenidos se recomienda el monitoreo del marcador del gen PYGM y del alelo Q204X del gen MSTN, así como también implementar estrategias para confirmar la utilidad de los marcadores asociados a calidad y productividad como herramienta para complementar los programas de mejoramiento genético.

Channel catfish (Ictalurus punctatus) is one of the endemic fishes of North America with the greatest potential for aquaculture. Despite this, data of its current distribution is scare and many aspects of its dynamic and productive performance remain unknown. In the present study, results are reported from a literature search and field analysis for describing the current status of channel catfish in Mexico regarding its historical and current geographical distribution as well as the problems faced by fish farmers and production systems. We were able to identify a lack of information and indicators to properly assess the extent of the species natural habitat and its productive potential. The quality and availability of water are among the main problems of the industry. Food costs represent the larger cost-loss for producers and there is great heterogeneity on the management of both breeding and production farms. Much of the production dynamics follows a pattern of trial and error. It became clear the need to optimize and standardize the processes on the channel catfish production system and to properly characterize domestic and wild populations to maximize their potential.

El bagre de canal (Ictalurus punctatus) es uno de los peces endémicos de Norte América con mayor potencial para la acuicultura. A pesar de esto, los datos sobre su distribución actual son escasos y se desconocen muchos aspectos de su dinámica y desempeño productivo. En el presente estudio se reportan los resultados de una búsqueda bibliográfica y análisis de campo que permiten describir la situación actual del bagre de canal con respecto a su distribución geográfica histórica y actual, así como de la problemática que enfrentan los sistemas productivos de esta especie en México. Se identificó la falta de información e indicadores que permitan conocer la extensión de su hábitat natural, movilización o potencial productivo. La calidad y disponibilidad del agua figuran entre las principales problemáticas de la industria; el alimento supone el mayor gasto para los productores y existe gran heterogeneidad de manejo tanto en granjas reproductoras como de engorde, gran parte de la dinámica productiva sigue un modelo de ensayo y error. Se requiere optimizar y homologar los procesos del sistema productivo de bagre de canal, así como caracterizar correctamente las poblaciones domésticas y silvestres para aprovechar al máximo su potencial.

Beef tenderness is an important trait in consumer satisfaction and has been considered as the main trait for palatability, for which reason it is important to evaluate its variability in different cattle breeds. An experiment was designed to evaluate the Warner Bratzler Shear Force (WBSF) of Red Brangus cattle rib eye steaks and consumer acceptance. The tenderness of beef rib eye steaks was evaluated by the WBSF. A consumer preference evaluation test was carried out to quantitatively estimate tenderness, juiciness, flavor, doneness and general acceptance of the evaluated steaks. Mean WBSF was 5.03 kg ± 0.93 kg, theoretically indicating a tough beef. The distribution of the samples showed 21 % and 11 % of moderately tender and tender beef cuts, respectively. Cattle condition (bulls and steers) was not significant for the WBSF (p > 0.5). All the traits evaluated in the hedonic evaluation had approximately 6 points of a total of 8 (8 was best). Tenderness, juiciness and flavor presented a high and significant correlation (p < 0.5). None of the subjective traits was correlated with total acceptance. Under theoretical criteria, tender Red Brangus beef cuts are infrequent; however the beef has a good acceptance. Characterization studies may be necessary and useful to create marketing niches specific for this and other cattle breeds.

La suavidad de la carne bovina es un rasgo importante para la satisfacción del consumidor y es la principal característica asociada a su palatabilidad, por lo que es importante evaluar su variabilidad en diferentes razas bovinas. Un experimento fue diseñado para evaluar la Fuerza de Corte de Warner-Bratzler (FCWB) de carne del ojo de la costilla de bovinos Brangus rojos y su aceptabilidad. La suavidad de la carne fue evaluada mediante la FCWB; además, se realizó una evaluación de preferencia de consumo para estimar cuantitativamente la suavidad, jugosidad, sabor, término y aceptación general de los cortes evaluados. La media de la FCWB fue 5.03 kg ± 0.93 kg, lo que teóricamente representa una carne dura. En la distribución de las muestras se registraron 21 % y 11 % de cortes, respectivamente, de carne moderadamente suave y suave. La condición de los animales (toros o novillos) no fue significativa para la FCWB (p > 0.5). Todas las características evaluadas en la evaluación hedónica tuvieron alrededor de 6 puntos de un total de 8 (8 era mejor). La suavidad, jugosidad y sabor mostraron una correlación alta y significativa (p < 0.5). Ninguna de las características subjetivas tuvo correlación con la aceptabilidad total. Bajo criterios teóricos, la frecuencia de carne suave en Brangus rojo es baja, aun así mostró buena aceptabilidad. Estudios de caracterización podrían ser necesarios y útiles para la creación de nichos de comercialización específicos para esta y otras razas bovinas.

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 b-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.

Background: Channel catfish are one of the most important aquaculture species raised for food purposes in Mexico. Two temporal samples were obtained from the largest channel catfish breeding hatchery in Mexico to identify changes in genetic diversity and inbreeding that are promoted by traditional hatchery management. Results: The genetic parameter analysis of 11 microsatellite loci showed no significant change in genetic diversity (p > 0.05). However, a significant heterozygosis deficiency was detected (p < 0.001), and genetic structure analysis indicated moderate differentiation between the temporally divided populations (F ST = 0.08). A moderate level of inbreeding and a slight increase of the inbreeding coefficient from 0.23 to 0.27 were the result of traditional hatchery practices. To achieve an effective population size, the temporal approach resulted in a limited number of breeders to maintain genetic variability. Conclusions: Although no significant change in genetic diversity parameters was found, the heterozygote deficiency and low effective number of breeders suggest that there is a risk for increased inbreeding. Thus, we propose the need for controlled reproductive management and the establishment of genetic programs in hatcheries. Molecular tools can provide valuable information to facilitate the achievement of these goals.