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El estudio analizó, en dos años, los efectos de raza [Brahman (BHM; n= 65); Suizo Europeo (SE; n= 56)], suplementación con Zilpaterol® (ZIL; tratadas o testigo), estación de nacimiento (primavera u otoño) y sus interacciones, sobre superficie corporal (SC), edad (EPB), peso corporal (PPB), condición corporal (CC), profundidad del músculo largo dorsal (MD), grosor de grasa dorsal (GD) y concentración sérica de leptina (LEP) a la pubertad (PB) de 121 vaquillas. A la PB, las BHM fueron más pesadas y tuvieron más edad que las SE (376.8 ± 7.4 vs 302.0 ± 6.6 kg; 588.1 ± 14.7 vs 445.5 ± 12.5 días). ZIL aumentó EPB, PPB, CC y MD, pero no afectó GD y LEP. Las BHM tuvieron 18 % más SC que las SE. Sin embargo, la diferencia en PPB/SC fue sólo de 6.4 %. Cuando se usó peso metabólico (PM) como proporción de la SC (PM/SC) en lugar de PPB, la diferencia entre BHM y SE desapareció (P>0.05). El GD fue 63.7 % mayor en BHM que en SE. Las nacidas en primavera iniciaron la PB con 24.4 % menos GD que las nacidas en otoño. La mayoría de las vaquillas BHM (73.8 %) inició la PB en los meses en que las horas luz iban en aumento (P

Objective: The aim was to characterize the genetic diversity evolution of the registered Mexican Charolais cattle population by pedigree analysis. Methods: Data consisted of 331,390 pedigree records of animals born from 1934 to 2018. Average complete generation equivalent, generation interval, effective population size (Ne), and effective numbers of founders (fe), ancestors (fa), and founder genomes (Ng) were calculated for seven five-year periods. The inbreeding coefficient was calculated per year of birth, from 1984 to 2018, whereas the gene contribution of the most influential ancestors was calculated for the latter period. Results: Average complete generation equivalent consistently increased across periods, from 4.76, for the first period (1984 through 1988), to 7.86, for the last period (2014 through 2018). The inbreeding coefficient showed a relative steadiness across the last seventeen years, oscillating from 0.0110 to 0.0145. During the last period, the average generation interval for the father-offspring pathways was nearly 1 yr. longer than that of the mother-offspring pathways. The effective population size increased steadily since 1984 (105.0) and until 2013 (237.1), but showed a minor decline from 2013 to 2018 (233.2). The population displayed an increase in the fa since 1984 and until 2008; however, showed a small decrease during the last decade. The effective number of founder genomes increased from 1984 to 2003, but revealed loss of genetic variability during the last fifteen years (from 136.4 to 127.7). The fa:fe ratio suggests that the genetic diversity loss was partially caused by formation of genetic bottlenecks in the pedigree; in addition, the Ng:fa ratio indicates loss of founder alleles due to genetic drift. The most influential ancestor explained 1.8% of the total genetic variability in the progeny born from 2014 to 2018. Conclusion: Inbreeding, Ne, fa, and Ng are rather beyond critical levels; therefore, the current genetic status of the population is not at risk.

El objetivo de este trabajo fue estimar la respuesta a la selección a través de diferentes índices de selección entre producción de metano y producción y componentes de la leche en los sistemas de lechería tropical especializada, doble propósito y lechería familiar. El muestreo de las emisiones de metano se realizó durante la ordeña mediante el equipo Guardian-NG. Se tomaron muestras de leche de manera individual durante el muestreo de metano. La extracción de ADN se realizó de folículos pilosos de todos los animales incluidos en el estudio. La estimación de los componentes de varianza y covarianza se realizó mediante la metodología de modelos mixtos. Se utilizaron los marcadores moleculares para construir la matriz de relaciones genómicas (Matriz G), debido a que no se contaba con información genealógica completa. La heredabilidad estimada para las emisiones de metano durante la ordeña fue de 0.18 y 0.32 para los análisis univariados y bivariados, respectivamente. Los resultados de las correlaciones genéticas entre porcentaje de grasa y proteína en leche con las emisiones de metano durante la ordeña fueron negativas, -0.09 y -0.18 respectivamente. La respuesta a la selección estimada mediante los índices de selección demostró que es factible obtener reducciones de hasta 0.021 mg/l de emisiones de metano durante la ordeña en cinco generaciones; lo anterior sin detrimento en los componentes de la leche.

El objetivo del presente estudio fue evaluar el impacto de la inclusión de información extranjera de sementales de la raza Holstein, sobre su evaluación genética para las características de producción de leche (PL), grasa (PG) y proteína (PP) en kilogramos. Lo anterior, se logró mediante la comparación de valores genéticos (VG) y confiabilidades (CF), agrupación de sementales por número de hijas, ordenamiento de los sementales y la superioridad genética esperada por año ((∆I_s)⁄ys), con diferentes escenarios determinados por la intensidad de selección (〖ip〗_s) de sementales usados en la evaluación genética nacional (EG-MEX), los incorporados a la evaluación genética internacional con hijas en México (EG-I) y la evaluación genética internacional con o sin hijas en México (EG-MACE). En total, se analizó la información de 5,825 sementales en la para PL y 3,914 para PG y PP. El impacto de la información extranjera en la EG-MEX es positivo, debido a que mejora la CF de los VG de los sementales usados en México. También, permitió observar diferencias importantes de los VG y CF entre las evaluaciones, generando una oportunidad de mejoramiento en la población Holstein mexicana; por lo que, es recomendable continuar con la participación en el programa de Interbull, y considerar el uso de la información validada de manera internacional en los procesos de selección de animales productores de leche y sus componentes. Estas acciones pueden contribuir de manera importante en el incremento del progreso genético productivo a nivel nacional.

Desde su llegada a México, las cabras han experimentado un largo proceso de adaptación y selección, dando como resultado animales locales de elevada rusticidad. Sin embargo, la importación de razas mejoradas y el intento de sustituir a los genotipos criollos por éstas, ha llevado a gran parte de este ganado al borde de la extinción. Un ejemplo es la cabra criolla negra (CCN), reconocida por su rusticidad y la calidad de su leche. El objetivo del presente trabajo fue caracterizar genéticamente una población de CCN. Se utilizaron 30 microsatélites, obteniendo; el número de alelos por marcador (NA), el número medio de alelos (MNA), número efectivo de alelos (Ae), la heterocigosidad observada (Ho) y esperada (He), el contenido de información polimórfica (PIC), el índice de fijación calculado con el estadístico FIS y el equilibrio de Hardy Weinberg (HWE). La población fue comparada con 13 razas caprinas del proyecto BioGoat. Los resultados mostraron que existe una elevada diversidad genética en este ganado. Se obtuvieron 243 alelos con un MNA de 8.1 alelos por locus. Los marcadores resultaron muy informativos con un PIC de 0.6. La He promedio de 0.71 y Ho de 0.62 puede indicar que existe un ligero desequilibrio en la población. La distancia de Reynolds mostró que la CCN se encuentra más distanciada genéticamente de la población Anglonubia y más cercana a la Murciano-Granadina. Los resultados aquí presentados sugieren que la población CCN representa una estructura racial bien diferenciada de las poblaciones incluidas en el estudio.

Mexican Creole Cattle (MCC) derived from cattle of the Iberian Peninsula, mainly from Andalucia and Extremadura, and were introduced in central America the 16th century. Copy Number Variants (CNVs) are structural variants contributing to the genetic diversity among populations and related to variation in phenotypic expression. More than half of the identified CNVs regions in human and livestock include protein-coding genes involved in essential function, as cellular functionality, metabolic pathways and disease susceptibility. The aim of this study is to investigate the CNVs genomic variation in the MCC population. A total of 48 unrelated individuals (5 males and 43 females) were genotyped with the BovineHD Genotyping BeadChip Illumina, containing 7,77,962 polymorphic SNPs. A total of 2170 CNVs were detected in 40 individuals, summarized into 733 CNV regions, covering 32.1 Mb of the bovine autosome genome. Functional analysis of the CNVRs identified 131 genes mainly involved in immune response and inflammation, and 923 overlapping QTL classified in six difference QTL-term categories. Cluster and PCA analyses showed a samples distribution in concordance with the geographical origins of the sub-populations, highlighting both a sharing genetic background together with a diversification of populations as a response to adaptation to different and adverse environments.

The Pelibuey sheep has adaptability to climatic variations, resistance to parasites, and good maternal ability, whereas some ewes present multiple births, which increases the litter size in farm sheep. The litter size in some wool sheep breeds is associated with the presence of mutations, mainly in the family of the transforming growth factor &beta, (TGF-&beta, ) genes. To explore genetic mechanisms underlying the variation in litter size, we conducted a genome-wide association study in two groups of Pelibuey sheep (multiparous sheep with two lambs per birth vs. uniparous sheep with a single lamb at birth) using the OvineSNP50 BeadChip. We identified a total of 57 putative SNPs markers (p &lt, 3.0 &times, 10&minus, 3, Bonferroni correction). The candidate genes that may be associated with litter size in Pelibuey sheep are CLSTN2, MTMR2, DLG1, CGA, ABCG5, TRPM6, and HTR1E. Genomic regions were also identified that contain three quantitative trait loci (QTLs) for aseasonal reproduction (ASREP), milk yield (MY), and body weight (BW). These results allowed us to identify SNPs associated with genes that could be involved in the reproductive process related to prolificacy.

Genomic and genetic variation among six Italian chicken native breeds (Livornese, Mericanel della Brianza, Milanino, Bionda Piemontese, Bianca di Saluzzo and Siciliana) were studied using single nucleotide polymorphism (SNP) and copy number variants (CNV) as markers. A total of 94 DNA samples genotyped with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix) were used in the analyses. The results showed the genetic and genomic variability occurring among the six Italian chicken breeds. The genetic relationship among animals was established with a principal component analysis. The genetic diversity within breeds was calculated using heterozygosity values (expected and observed) and with Wright’s F-statistics. The individual-based CNV calling, based on log R ratio and B-allele frequency values, was done by the Hidden–Markov Model (HMM) of PennCNV software on autosomes. A hierarchical agglomerative clustering was applied in each population according to the absence or presence of definite CNV regions (CNV were grouped by overlapping of at least 1 bp). The CNV map was built on a total of 1003 CNV found in individual samples, after grouping by overlaps, resulting in 564 unique CNV regions (344 gains, 213 losses and 7 complex), for a total of 9.43 Mb of sequence and 1.03% of the chicken assembly autosome. All the approaches using SNP data showed that the Siciliana breed clearly differentiate from other populations, the Livornese breed separates into two distinct groups according to the feather colour (i.e. white and black) and the Bionda Piemontese and Bianca di Saluzzo breeds are closely related. The genetic variability found using SNP is comparable with that found by other authors in the same breeds using microsatellite markers. The CNV markers analysis clearly confirmed the SNP results.

This study aims at investigating genomic diversity of several turkey populations using Copy Number Variants (CNVs). A total of 115 individuals from six Italian breeds (Colle Euganei, Bronzato Comune Italiano, Parma e Piacenza, Brianzolo, Nero d’Italia, and Ermellinato di Rovigo), seven Narragansett, 38 commercial hybrids, and 30 Mexican turkeys, were genotyped with the Affymetrix 600K single nucleotide polymorphism (SNP) turkey array. The CNV calling was performed with the Hidden Markov Model of PennCNV software and with the Copy Number Analysis Module of SVS 8.4 by Golden Helix®. CNV were summarized into CNV regions (CNVRs) at population level using BEDTools. Variability among populations has been addressed by hierarchical clustering (pvclust R package) and by principal component analysis (PCA). A total of 2,987 CNVs were identified covering 4.65% of the autosomes of the Turkey_5.0/melGal5 assembly. The CNVRs identified in at least two individuals were 362—189 gains, 116 losses, and 57 complexes. Among these regions the 51% contain annotated genes. This study is the first CNV mapping of turkey population using 600K chip. CNVs clustered the individuals according to population and their geographical origin. CNVs are known to be indicators also of adaptation, as some researches in different species are suggesting.

Simple Summary Bovine tuberculosis is an infectious disease of cattle caused by Mycobacterium bovis characterized by the formation of tubercles in any organ or tissue. Bovine tuberculosis represents a significant veterinary and public health problem in many parts of the world. It is zoonotic, transmitted to humans through consumption of infected milk and other cattle products. Although many factors influence infection and progression of the disease, there must be an important host genetic component that explains why some animals get sick and others remain healty. We present evidence of genetic variants associated with resistance to tuberculosis in Mexican Holstein dairy cattle using a case-control approach with a selective DNA pooling. Here, we identified novel quantitative trait loci regions harboring genes involved in Mycobacterium spp. immune response. This is a first screening about resistance to tuberculosis infection on Mexican Holstein cattle based on a dense single nucleotide polymorphism chip. The identified genes belong to both, the already known, and the undisclosed quantitative trait loci regions. Abstract Bovine tuberculosis (bTB) is a disease of cattle that represents a risk to public health and causes severe economic losses to the livestock industry. Recently, genetic studies, like genome-wide association studies (GWAS) have greatly improved the investigation of complex diseases identifying thousands of disease-associated genomic variants. Here, we present evidence of genetic variants associated with resistance to TB in Mexican dairy cattle using a case-control approach with a selective DNA pooling experimental design. A total of 154 QTLRs (quantitative trait loci regions) at 10% PFP (proportion of false positives), 42 at 5% PFP and 5 at 1% PFP have been identified, which harbored 172 annotated genes. On BTA13, five new QTLRs were identified in the MACROD2 and KIF16B genes, supporting their involvement in resistance to bTB. Six QTLRs harbor seven annotated genes that have been previously reported as involved in immune response against Mycobacterium spp: BTA (Bos taurus autosome) 1 (CD80), BTA3 (CTSS), BTA 3 (FCGR1A), BTA 23 (HFE), BTA 25 (IL21R), and BTA 29 (ANO9 and SIGIRR). We identified novel QTLRs harboring genes involved in Mycobacterium spp. immune response. This is a first screening for resistance to TB infection on Mexican dairy cattle based on a dense SNP (Single Nucleotide Polymorphism) chip.

In order to evaluate the morphostructural variability of the Black Creole goat (BCG), the present study was carried out in a population of 226 animals from eight localities and 14 morphometric variables were taken. Descriptive statistics for the variables were obtained and 10 of these presented variation coefficients of less than 10%. The degree of harmony in the morphology of the population was determined by the number of positive correlations with significant differences (p &lt, 0.05), including a correlation test using Spearman&rsquo, s method. In order to reduce the matrix of variables, a principal components analysis was performed, and it was evaluated based on Kaiser&rsquo, s criteria (eigenvalue &gt, 1). Finally, a hierarchical analysis of conglomerates using Ward&rsquo, s method was performed using the Euclidean distance to evaluate the distances among localities. Morphometric variables were also included to visualize the relationship among the localities and their average per variable. The results showed that the animals evaluated presented a certain degree of homogeneity and maintained a highly harmonic model. The BCG population showed a high aptitude for milk production, which confirmed the zootechnical purpose of the breed. The BCG populations evaluated maintain similar morphostructural profiles specific to them that can distinguish this population from other animal breeds.

The aim of this study was to evaluate the effect of including calving age (CA) on genetic evaluation models for Holstein cattle. The evaluated models included the permanent environment, the sire-herd interactions, and the animals and residual effects as random. The fixed effects included the average production of milk, fat, and protein and the herd-year-season effect. The analyzed data included 603,521 records of milk production (in kg) corresponding to 438,098 animals from 527 herds. Additionally, there were 179,122 records of fat and protein components, corresponding to 148,930 animals from 137 herds. The records were classified by first lactation only (FL) and all available lactations (AL) for validation test (VT). The FL records corresponded to 275,487 milk production records with a mean of 10,874.1 ± 2773.9 kg at a mean CA of 25.6 ± 4.2 months. For FL, the milk components consisted of 78,955 records with a mean fat production of 392.86 ± 89.9 kg, a mean protein production of 362.8 ± 74.9 kg and a mean CA of 25.2 ± 4.1 months. For AL, the number of records was 603,521 for milk production with a mean of 10,802.8 ± 2905.9 kg and a mean CA of 35.6 ± 11.5 months. For the milk components, there were 179,122 records with a mean of 36.1 ± 9.5 months for CA and 388.3 ± 98.4 kg and 356.7 ± 82.6 kg for fat and protein, respectively. Three models were compared: the base model (M0) described above, and two alternative models that included CA in a linear and quadratic form (M1 and M2, respectively). Estimations of the variance components (VC) and breeding value (BV) were obtained using a repeatability animal model, with the same phenotypic and pedigree information used for all models. To select the best fit model for the data, a likelihood ratio test (LRtest) was used. A validation test (VT) was also applied to each model to evaluate the consistency of the genetic trends for females with information on AL and FL. The inclusion of CA in its linear form (M1) was the model that achieved the best results in the LRtest and an acceptable value for the VT. These results show that CA improves the model fit for BV prediction and reliability.

Records from Charolais, Charbray and Charolais-Zebu crosses provided by Charolais–Charbray Herd Book de Mexico, were used to estimate heritabilities and genetic correlations between scrotal circumference (SC, n = 18,972), heifer fertility (HF, n = 91,250), and stayability (STAY, n = 17,696). Measurements of SC were adjusted to 365 days limiting the age range from 320 to 410 days of age. The trait HF was coded as 1 if the heifer calved before 1,281 d of age and 0 otherwise. The trait STAY was defined as the probability of whether or not a cow calved a second calf before the six years of age given that, at least, the cow had calved a calf at three years of age or before. A three trait animal model and a Bayesian linear-threshold-threshold analysis were used to estimate (co)variance components. Heritability estimates were 0.18 ± 0.02, 0.11 ± 0.01, and 0.26 ± 0.03 for SC, HF and STAY, respectively. Strong genetic correlations were detected between SC and STAY (0.76 ± 0.04), and between HF and STAY (0.57 ± 0.07), suggesting that selection of sires based on SC, and HF could lead to an improvement of STAY of cows in the Charolais–Charbray population of Mexico. A weak genetic correlation was found between SC and HF (−0.08 ± 0.10). Overall, the heritabilities and genetic correlations estimated for the three traits evaluated in this study support the feasibility of improving by selection the reproductive performance of the Charolais–Charbray population of Mexico.

Mycobacterium bovis infection in cattle persists in Mexico, posing a threat to human health. Control of bovine tuberculosis, through the National Program Against Bovine Tuberculosis, has led to the decrease of disease prevalence in most of the country, except for high dairy production regions. Genotyping of M. bovis has been performed mainly by spoligotyping and variable number tandem repeats (VNTR), but higher resolution power can be useful for a finer definition of the spread of the disease. Whole genome sequencing and spoligotyping was performed for a set of 322 M. bovis isolates from different sources in Mexico: Baja California, Coahuila, Estado de Mexico, Guanajuato, Hidalgo, Jalisco, Queretaro and Veracruz, from dairy and beef cattle, as well as humans. Twelve main genetic clades were obtained through WGS and genetic diversity analysis. A clear differentiation of the Baja California isolates was seen as they clustered together exclusively. However, isolates from the central states showed no specific clustering whatsoever. Although WGS proves to have higher resolving power than spoligotyping, and since there was concordance between WGS and spoligotyping results, we consider that the latter is still an efficient and practical method for monitoring bovine tuberculosis in developing countries, where resources for higher technology are scarce.

Mitochondrial DNA (mtDNA) insertions have been detected in the nuclear genome of many eukaryotes. These sequences are pseudogenes originated by horizontal transfer of mtDNA fragments into the nuclear genome, producing nuclear DNA sequences of mitochondrial origin (numt). In this study we determined the frequency and distribution of mtDNA-originated pseudogenes in the turkey (Meleagris gallopavo) nuclear genome. The turkey reference genome (Turkey_2.01) was aligned with the reference linearized mtDNA sequence using last. A total of 32 numt sequences (corresponding to 18 numt regions derived by unique insertional events) were identified in the turkey nuclear genome (size ranging from 66 to 1415 bp; identity against the modern turkey mtDNA corresponding region ranging from 62% to 100%). Numts were distributed in nine chromosomes and in one scaffold. They derived from parts of 10 mtDNA protein-coding genes, ribosomal genes, the control region and 10 tRNA genes. Seven numt regions reported in the turkey genome were identified in orthologues positions in the Gallus gallus genome and therefore were present in the ancestral genome that in the Cretaceous originated the lineages of the modern crown Galliformes. Five recently integrated turkey numts were validated by PCR in 168 turkeys of six different domestic populations. None of the analysed numts were polymorphic (i.e. absence of the inserted sequence, as reported in numts of recent integration in other species), suggesting that the reticulate speciation model is not useful for explaining the origin of the domesticated turkey lineage.

Genetic variation enables both adaptive evolutionary changes and artificial selection. Genetic makeup of populations is the result of a long-term process of selection and adaptation to specific environments and ecosystems. The aim of this study was to characterize the genetic variability of México's chicken population to reveal any underlying population structure. A total of 213 chickens were sampled in different rural production units located in 25 states of México. Genotypes were obtained using the Affymetrix Axiom ® 600 K Chicken Genotyping Array. The Identity by Descent (IBD) and the principal components analysis (PCA) were performed by SVS software on pruned single nucleotide polymorphisms (SNPs). ADMIXTURE analyses identified 3 ancestors and the proportion of the genetic contribution of each of them has been determined in each individual. The results of the Neighbor-Joining (NJ) analysis resulted consistent with those obtained by the PCA. All methods utilized in this study did not allow a classification of Mexican chicken in distinct clusters or groups. A total of 3,059 run of homozygosity (ROH) were identified and, being mainly short in length (

Background Copy number variations are genome polymorphism that influence phenotypic variation and are an important source of genetic variation in populations. The aim of this study was to investigate genetic variability in the Mexican Creole chicken population using CNVs. Results The Hidden Markov Model of the PennCNV software detected a total of 1924 CNVs in the genome of the 256 samples processed with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix). The mapped CNVs comprised 1538 gains and 386 losses, resulting at population level in 1216 CNV regions (CNVRs), of which 959 gains, 226 losses and 31 complex (i.e. containing both losses and gains). The CNVRs covered a total of 47 Mb of the whole genome sequence length, corresponding to 5.12% of the chicken galGal4 autosome assembly. Conclusions This study allowed a deep insight into the structural variation in the genome of unselected Mexican chicken population, which up to now has not been genetically characterized. The genomic study disclosed that the population, even if presenting extreme morphological variation, cannot be organized in differentiated genetic subpopulations. Finally this study provides a chicken CNV map based on the 600 K SNP chip array jointly with a genome-wide gene copy number estimates in a native unselected for more than 500 years chicken population. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0524-4) contains supplementary material, which is available to authorized users.

Whole genome (re)sequencing provides new opportunities to discover Copy Number Variation (CNV) on the genome. Due to the continuous reduction in sequencing costs, it has become as the principal methodology to detect CNV in livestock. One parameter that increases the genotyping cost is the depth of the coverage during sequencing. The main aim of this note was to assess the variation on CNV identification with different depth coverage and readlength on genome sequencing. The results point out that sequences coming from short read-length require less depth coverage than those obtained with long read-length. In addition, small CNV require deeper coverage to be detected. These results can reduce the discovering and genotyping costs since sequencing technologies with short read-lengths are often less costly. Finally, a general formula was derived to optimize the sequencing costs.

║*Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autonoma de Mexico, Ciudad Universitaria, Distrito Federal, Mexico, 04510; †National Animal Disease Center, Agricultural Research Service, US Department of Agriculture (USDA), 1920 Dayton Ave., Ames, IA 50010; ‡Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de Sao Paulo (USP), Rua Duque de Caxias Norte, 225–Campus da USP, Piras-sununga, Sao Paulo, Brazil 13635-900; §Centro de Investigacion Regional Golfo-Centro, Instituto Nacional de Investigaciones Forestales Agricolas y Pecuarias (INIFAP), Medellin de Bravo, Veracruz, Mexico 94277; #Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare, Universita degli Studi di Milano, Via Celoria 10, Milano, Italia 20133; and ║Campo Experimental Valles Centrales–Centro de Investigacion Regional Pacifi co Sur, INIFAP, Melchor Ocampo 7, Etla, Oaxaca, Mexico 68200

The overall goal of this study was to investigate milk flow traits in Italian Holstein-Friesian cows and, in particular, the bimodality of milk flow, defined as delayed milk ejection at the start of milking. Using a milkometer, 2,886 records were collected from 133 herds in northern Italy from 2001 to 2007. All records included 5 time-period measurements for milk flow, somatic cell score (SCS), milk yield, 8 udder type traits, and the presence or absence of bimodality in milk flow. Genetic parameters were estimated using linear animal models for continuous traits such as milk flow, udder type, SCS, and milk production, whereas bimodality was analyzed as a categorical trait. With the exception of decreasing time (which had a very small heritability value of 0.06), heritability values for milk flow traits were moderate, ranging from 0.10 (ascending time) to 0.41 (maximum milk flow). In addition, moderate to high genetic correlations were estimated between total milking time and other time measures (from 0.78 to 0.87), and among time flow traits (from 0.62 to 0.91). The decreasing time was the trait most genetically correlated with udder type traits, with correlation values of 0.92 with rear udder height, 0.85 with rear udder width, and 0.73 with teat placement. Large udders with strong attachments were also associated with greater milk production. Heritability estimated for bimodality was 0.43, and its genetic correlation with milk flow traits and SCS indicated a sizable genetic component underlying this trait. Bimodality was negatively associated with milk production; shorter milking times and greater peak milk levels were genetically correlated with more frequent bimodal flows, indicating that faster milk release would result in an increase in bimodal patterns. The negative genetic correlation of bimodality with SCS (-0.30) and the genetic correlation between milk flow traits and SCS suggest that the relationship between milkability and SCS is probably nonlinear and that intermediate flow rates are optimal with respect to mastitis susceptibility. Quicker milk flow over a shorter period would increase the frequency of bimodal curves in milking, whereas the correlation between bimodality and both ascending and descending time was less clear.

The primary objective was to compare various mathematical models to describe scrotal circumference (SC) and paired testis volume development in Blackbelly ram lambs. The study was conducted in the state of Queretaro, Mexico (20° 43' N, 100° 15' W). Spring-born Blackbelly ram lambs (n = 41) were housed outdoors and fed alfalfa hay and concentrate. Body weight, SC, and testis length, diameter, and volume were recorded every 2 wk from 24 to 172 d of age (June 18 to November 3). The following mathematical functions were used to model SC-age and testis volume-age relationship: Von Bertalanffy, Brody, Gompertz, Logistic, and Richards. The suitability of the models was evaluated based on parameter values and standard errors, residual mean square, the coefficient of determination (R 2 ), and the average prediction error (APE). All models, except for Brody's, had good fit to SC (R 2 > 0.98) and testis volume (R 2 > 0.95), and produced similar growth curves in the range of ages studied. The logistic model predicted SC at maturity quite well, 33.6 ± 0.6 cm as compared with 33.9 ± 0.5 cm observed in adult animals; all models had APE's smaller than ±7% between 56 and 168 d of age. The Bertalanffy model predicted testis volume at maturity quite well, 513 ± 22 cm 3 as compared with 488 ± 20 cm 3 calculated for adult animals. The logistic model had a good fit to testis volume during the period of study, but underestimated the volume at maturity by 28%. All models, except for Brody's, had APE's smaller than ±14% between 98 and 168 d of age. The logistic and Bertalanffy models predicted the inflection point for SC at 83 and 59 d of age, and testis volume at 116 and 109 d of age, respectively. In conclusion, all models, except for Brody's, had good fit to actual SC and testis volume data in the range of age evaluated, whereas the logistic and Bertalanffy's models made the best predictions for adult SC and testis volume, respectively.

El objetivo fue evaluar algunas características morfológicas de gallinas de traspatio (n= 255) provenientes de 65 unidades rurales de producción, localizadas en 52 municipios de 18 estados de la República Mexicana. El modelo estadístico incluyó los efectos de sexo, estado y municipio anidado en estado. El efecto de sexo fue importante para todas las variables analizadas (P

Bovine tuberculosis (bTB) is a chronic disease of cattle and other animal species caused by Mycobacterium bovis . The importance of bTB is that it represents a risk to public health, and causes economic losses to the livestock industry. Because of this, many countries have established control and eradication programs with partial success. Therefore, the search for new strategies to control this disease is relevant. In Mexico, the prevalence of bTB is estimated in 16 % in dairy cattle and in less than 1 % in beef cattle; however, field studies have proved that in spite of the high prevalence in some herds (25-35 %), and long periods of exposure (3 to 5 yr average), the prevalence never reaches 100 %; this suggests that some animals are naturally resistant to tuberculosis. Considering that clinical manifestation of bTB depends on the interaction of various factors, it is reasonable to think that genetic variations in the host can be associated to resistance to this disease. This review, presents the state of the art in this matter; it describes the results of studies performed in different animal species and humans with the purpose of detecting genetic variation associated with disease resistance. The main genes associated with resistance are described and discussed individually. The conclusion is that genetic variation in cattle is associated with resistance to tuberculosis, and that this variation can be identified, measured, and incorporated into the current process of animal selection in the livestock industry to obtain animals more resistant to infection.

Con el objetivo de estimar las varianzas y covarianzas genéticas entre producción total de leche por lactación y crecimiento corporal en una población multirracial de bovinos de doble propósito en el trópico de México, se estimaron las varianzas y covarianzas genéticas entre la producción total de leche durante la primera (PTL1L), la segunda (PTL2L) y la tercera lactaciones (PTL3L), y las varianzas y covarianzas genéticas entre PTL1L con peso al nacimiento (PN) y los pesos ajustados a los 205 (P205) y 365 (P365) días de edad. Se utilizaron 1,349 registros de lactaciones de hembras de cruzas de razas cebuinas (CE) con Holstein (HS) [558], con Suizo Pardo (SP) [444] y con Simmental (SM) [357]. Se presentan las heredabilidades estimadas en ambos análisis. Las correlaciones genéticas encontradas en el primer análisis fueron 0.77 (± 0.16) entre PTL1L y PTL2L, 0.47 (± 0.25) entre PTL1L y PTL3L, y 0.73 (± 0.21) entre PTL2L y PTL3L. Las correlaciones genéticas encontradas en el segundo análisis fueron 0.10 (± 0.35) entre PTL1L y PN, 0.20 (± 0.25) entre PTL1L y P205 y 0.21 (± 0.32) entre PTL1L y P365. Se concluye que las correlaciones genéticas son positivas entre las tres primeras lactaciones y se sugiere una correlación positiva entre la primera lactación y características de crecimiento corporal, lo cual hace factible el planteamiento de programas de mejoramiento genético que tomen en cuenta ambas características de manera simultánea.

"Con el objetivo de evaluar los efectos de cruzamiento en tres subpoblaciones de ganado bovino cruzados de doble propósito en el trópico húmedo se utilizaron 5,040 lactancias y pesajes corporales al nacimiento [4,429] y pesos ajustados a 205 [3.878], 365 [3,017] y 540 [2,276] días (PN, P205, P365 y P540, respectivamente) de Cebú (CE) y sus cruzas con Holstein (HS), Suizo Pardo (SP) y Simmental (SM). Los efectos aditivos directos de raza (PG), heterocigocidad (HT) y pérdidas por recombinación (RC) se estimaron mediante un análisis de regresión a través de modelos mixtos. Los efectos fijos fueron el hato y año de parto, época, número de lactancia y sexo de la cría para producción total de leche (PL), así como el hato, y año de nacimiento y época para crecimiento corporal. Los efectos aleatorios para PL fueron el efecto genético directo (animal) y el ambiente permanente. Para crecimiento corporal fueron los efectos genéticos directos y maternos, así como los efectos ambientales permanentes maternos. Se obtuvieron efecto (P

Data from 241 interviews collected in 2013 was analyzed to characterize populations of pigs (Mexican Hairless Pig (MH), Cuino Pig (CU) and Crossbred Pig (UD)). Variables were body weight (BW), head length (HL), body length (BL), thoracic perimeter (CG), height at withers (HW), croup width (RW), number of nipples (TC), dense or sparse hair (HD), presence or absence of tusks (TU), short or long snout (ST), upright or floppy ears (ER), calm or restless temperament (TM), proportionality index (PI), body index (BI) and relative weight index (RWI). Analyses were carried out with GLM and GENMOD of SAS. Models included state and population. Population was significant (P

International audience; Background Genomic selection estimates genetic merit based on dense SNP (single nucleotide polymorphism) genotypes and phenotypes. This requires that SNPs explain a large fraction of the genetic variance. The objectives of this work were: (1) to estimate the fraction of genetic variance explained by dense genome-wide markers using 54 K SNP chip genotyping, and (2) to evaluate the effect of alternative marker-based relationship matrices and corrections for the base population on the fraction of the genetic variance explained by markers.MethodsTwo alternative marker-based relationship matrices were estimated using 35 706 SNPs on 1086 dairy bulls. Both pedigree- and marker-based relationship matrices were fitted simultaneously or separately in an animal model to estimate the fraction of variance not explained by the markers, i.e. the fraction explained by the pedigree. The phenotypes considered in the analysis were the deregressed estimated breeding values (dEBV) for milk, fat and protein yield and for somatic cell score (SCS).ResultsWhen dEBV were not sufficiently accurate (50 or 70%), the estimated fraction of the genetic variance explained by the markers was around 65% for yield traits and 45% for SCS. Scaling marker genotypes with locus-specific frequencies of heterozygotes slightly increased the variance explained by markers, compared with scaling with the average frequency of heterozygotes across loci. The estimated fraction of the genetic variance explained by the markers using separately both relationships matrices followed the same trends but the results were underestimated. With less accurate dEBV estimates, the fraction of the genetic variance explained by markers was underestimated, which is probably an artifact due to the dEBV being estimated by a pedigree-based animal model.ConclusionsWhen using only highly accurate dEBV, the proportion of the genetic variance explained by the Illumina 54 K SNP chip was approximately 80% for Brown Swiss cattle. These results depend on the SNP chip used and the family structure of the population, i.e. more dense SNPs and closer family relationships are expected to result in a higher fraction of the variance explained by the SNPs.

Background It is commonly assumed that prediction of genome-wide breeding values in genomic selection is achieved by capitalizing on linkage disequilibrium between markers and QTL but also on genetic relationships. Here, we investigated the reliability of predicting genome-wide breeding values based on population-wide linkage disequilibrium information, based on identity-by-descent relationships within the known pedigree, and to what extent linkage disequilibrium information improves predictions based on identity-by-descent genomic relationship information. Methods The study was performed on milk, fat, and protein yield, using genotype data on 35 706 SNP and deregressed proofs of 1086 Italian Brown Swiss bulls. Genome-wide breeding values were predicted using a genomic identity-by-state relationship matrix and a genomic identity-by-descent relationship matrix (averaged over all marker loci). The identity-by-descent matrix was calculated by linkage analysis using one to five generations of pedigree data. Results We showed that genome-wide breeding values prediction based only on identity-by-descent genomic relationships within the known pedigree was as or more reliable than that based on identity-by-state, which implicitly also accounts for genomic relationships that occurred before the known pedigree. Furthermore, combining the two matrices did not improve the prediction compared to using identity-by-descent alone. Including different numbers of generations in the pedigree showed that most of the information in genome-wide breeding values prediction comes from animals with known common ancestors less than four generations back in the pedigree. Conclusions Our results show that, in pedigreed breeding populations, the accuracy of genome-wide breeding values obtained by identity-by-descent relationships was not improved by identity-by-state information. Although, in principle, genomic selection based on identity-by-state does not require pedigree data, it does use the available pedigree structure. Our findings may explain why the prediction equations derived for one breed may not predict accurate genome-wide breeding values when applied to other breeds, since family structures differ among breeds.

El objetivo fue evaluar algunas características morfológicas de pavos de traspatio (n=248) provenientes de 126 unidades rurales de producción localizadas en 75 municipios de 24 estados de la República Mexicana. El modelo estadístico incluyó sexo, estado y municipio anidado en estado. Las tres variables explicativas afectaron a todas las variables de respuesta (P0.05). Los machos tuvieron mayor (P0.05). El peso corporal aumentó 143 g (P