Opportunities and challenges from the use of genomic selection for beef cattle breeding in Latin America

In 2009, Latin American countries had approximately 401 million cattle (29% of the world’s total cattle population) and produced 8.2 million tonnes of beef, equivalent to 29% of the world’s total production (FAO, 2011). Beef in Latin American countries is produced under widely differing climates (ranging from tropical to temperate), resources available (vegetation, food), types of markets, and genetic backgrounds of the animals. The main production systems are classified as beef and dual-purpose cattle. The genetic backgrounds of animals vary from purebred European (Bos taurus taurus) or Zebu (Bos taurus indicus) to crossbreeds (Figures 1 and 2). Beef production systems may also be characterized by their management intensification levels as grazing only, grazing with food supplementation, and feedlot production. The main beef-producing countries are Brazil (51.6% of the total Latin American beef production), Argentina (18.5%), Mexico (9.4%), and Colombia (5.1%). Other countries contributing more than 1% of the total regional production are Uruguay, Venezuela, Paraguay, Bolivia, Ecuador, and Chile (Table 1). Latin America is a region of the world that can significantly increase its production in response to beef demand. Brazil has a mature beef cattle industry based on grass-fed cattle, in which feeding B. taurus indicus cattle, especially the Nellore breed, is a common practice. Over the last 8 years, beef production in Brazil has become one of the most important activities for employment and wealth creation. Foot-and-mouth disease issues are still a factor limiting the increase in Latin American beef exports (Ferraz and de Felício, 2010; Domingues Millen et al., 2011). Only a few Latin American countries, including Chile and Mexico, have the status of being free of this disease without vaccination. In most countries, the disease is controlled using a combination of free areas without vaccination and areas with vaccination. Other countries with a strong B. taurus indicus background in their beef cattle populations are those with large tropical areas dedicated to beef cattle production, such as Colombia, Venezuela, and Paraguay. Beef production in Argentina, Chile, Uruguay, and some portions of Brazil and Mexico is based mainly around the production of B. taurus taurus cattle (Peel et al., 2010; Arelovich et al., 2011; Domingues Millen et al., 2011). The Mexican beef cattle industry consists of 2 nearly separate market components. Beef producers in the northern part of Mexico have largely focused on the production of calves for export to the United States (Galyean et al., 2011). European beef genetics have been widely used in the region, beginning with importations of Hereford cattle and continuing with today’s popularity of Angus and Brangus along with several continental breeds, such as Charolais and Simmental. The central and southern regions of Mexico have historically produced grass-fed beef for the national market as well as dual-purpose dairy-Zebu crossbred cattle to produce milk and beef (Peel et al., 2010). Currently, breeding programs for the genetic evaluation of beef cattle in Latin America are based on statistical analyses in which performance and pedigree information are integrated. These analyses are based on a mixed model methodology, in particular the animal model statistical approach using best linear unbiased prediction methods to obtain estimated breeding values (EBV) for economically important traits. This methodology for obtaining EBV has been set up in Argentina, Brazil, Colombia, Mexico, Uruguay, Venezuela, and other countries. It has been established for specific purebred populations and also for some crossbred populations, such as multibreed populations with a dual purpose (beef and milk) in the Latin American humid tropics, which involve animals crossbred between B. taurus taurus and B. taurus indicus and composite breeds. Most programs focus on evaluating growth and reproductive traits, although a few have included longevity (stayability), heifer pregnancy, conformation, and carcass and meat quality traits

Relationships between seasonality, body characteristics and leptin at the beginning of puberty in Bos taurus taurus and Bos taurus indicus heifers in the Mexican tropics

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 (P0.05). The DF was 63.7 % higher in BHM than in BR. Those born in spring started PB with 24.4 % less DF than those born in autumn. Most of the BHM heifers (73.8 %) started PB in the months when light hours were increasing (P<0.05), while in BRs, the beginning of PB was uniformly distributed throughout the year, regardless of the length of light hours; this effect was present in the two years of study. It is concluded that the establishment of puberty is a multifactorial phenomenon; seasonality affects BHM and BR differently and, apparently, BS is an important factor, probably associated with efficiency in energy use. This paper reiterates the importance of dorsal fat and documents, for the first time, MW/BS and its association with the establishment of puberty

Impacto de la inclusión de información extranjera sobre la evaluación genética mexicana de sementales Holstein

This study aimed to evaluate the impact of including foreign information of Holstein sires on their genetic evaluation for the following traits: milk, fat, and protein production in kilograms. This was achieved by comparing breeding values (BV) and reliabilities (R), grouping of sires by number of daughters, ordering of sires, and the genetic superiority expected per year ( ), with different scenarios determined by the selection intensity ( ) of sires used in the national genetic evaluation (MEX-GE), those incorporated into the international genetic evaluation with daughters in Mexico (I-GE), and the international genetic evaluation with or without daughters in Mexico (MACE-GE). In total, was analyzed the information of 5,825 sires for MP and 3,914 for FP and PP. The foreign information has a positive impact in the MEX-GE as it improves R and the BV of the sires used in Mexico. It also allowed to observe important differences in the BV and R between evaluations, generating an opportunity to improve the Mexican Holstein population. Therefore, it is recommended continuing participating in the Interbull program and consider using the internationally validated information in the selection process of dairy cattle and their components. These actions can significantly contribute to the increase of the productive genetic progress in Mexico.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

Morfometría del cerdo de traspatio en áreas rurales de México

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<0.05) for BW, BL, CG, HW, RW, TU, TM, PI, BI and RWI. Coefficients of variation (VC) showed the minor and major values for BW (18.8 %) and CG (27.8 %). VC were 13.0, 14.6 and 45.8 % for PI, BI and RWI. Least squares means for MH, CU and UD were: 48.06±6.17a, 35.93±3.04b and 61.11±7.42a kg (BW); 77.81±3.65ab, 69.56±2.02ª and 88.52±4.93b  cm (BL); 80.55±3.98ab, 71.72±2.20a and 93.23±5.37b cm (CG); 56.88±2.45ab, 51.26±1.36a and 60.32±3.31b cm (HW); 57±4a, 71±19b and 62±34a % (HD); 68±31ab, 70±14a and 61±27b% (TU); 65±30a, 56±12b and 62±3a% (TM). The MH and UD populations were similar in morphometry and different from the CU population. The CU population showed lower weight, smaller size and calmer temperament. The characterization of these populations is important for designing strategies for their conservation and efficient use.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<0.05) for BW, BL, CG, HW, RW, TU, TM, PI, BI and RWI. Coefficients of variation (VC) showed the minor and major values for BW (18.8 %) and CG (27.8 %). VC were 13.0, 14.6 and 45.8 % for PI, BI and RWI. Least squares means for MH, CU and UD were: 48.06±6.17a, 35.93±3.04b and 61.11±7.42a kg (BW); 77.81±3.65ab, 69.56±2.02ª and 88.52±4.93b  cm (BL); 80.55±3.98ab, 71.72±2.20a and 93.23±5.37b cm (CG); 56.88±2.45ab, 51.26±1.36a and 60.32±3.31b cm (HW); 57±4a, 71±19b and 62±34a % (HD); 68±31ab, 70±14a and 61±27b% (TU); 65±30a, 56±12b and 62±3a% (TM). The MH and UD populations were similar in morphometry and different from the CU population. The CU population showed lower weight, smaller size and calmer temperament. The characterization of these populations is important for designing strategies for their conservation and efficient use.  Para caracterizar a las poblaciones del cerdo Pelón Mexicano (PPM), cerdo Cuino (PCU) y cerdos                   cruzados (PCI) se analizó información de 241 entrevistas realizadas durante 2013. Las variables analizadas fueron: peso corporal (Peco), longitud de cabeza (Loca), longitud del cuerpo (Locu), circunferencia del pecho (Circu), altura a la cruz         (Acruz), ancho de pelvis (Anpe), número de pezones (Nupe), pelo denso o escaso (Cape), presencia o ausencia de colmillos (Colm), hocico corto o largo (Hoc), orejas erguidas o no erguidas (Posio), temperamento tranquilo o inquieto (Tem),  índice de proporcionalidad (IP), índice corporal (IC) e índice de peso relativo (IPR). Los datos se analizaron con GLM y GENMOD del SAS. Los modelos estadísticos incluyeron Estado y Población. Población influyó (P<0.05) Peco, Locu, Circu, Acruz, Cape, Colm, Tem IP, IC e IPR. Los coeficientes de variación (CV) mostraron a Peco y Anpe como las características con menor y mayor variación (18.8 y 27.8 %). Para IP, IC e IPR los CV fueron 13.0, 14.6 y 45.8 %.Las medias de cuadrados mínimos para PPM, PCU y PCI fueron 48.06±6.17a, 35.93±3.04b y 61.11±7.42a kg (Peco); 77.81±3.65ab, 69.56±2.02a y 88.52±4.93b cm (Locu); 80.55±3.98ab, 71.72±2.20a y 93.23±5.37b cm (Circu); 56.88±2.45ab, 51.26±1.36a y 60.32±3.31b cm (Acruz); 57±4a, 71±19b y 62±34a% (Cape); 68±31ab, 70±14a y 61±27b% (Colm); 65±30a, 56±12b y 62±3a% (Tem). PPM y PCI fueron similares en morfometría pero diferentes de PCU. La población PCU mostró menor peso, menor talla y temperamento más inquieto. Caracterizar a estas poblaciones es importante para diseñar estrategias para su conservación y uso eficiente

Análisis de variables morfológicas de pavos de traspatio mexicanos (Meleagris gallopavo gallopavo)

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<0.01) en machos y 113 g en hembras (P<0.01) por cada centímetro que aumentó la circunferencia de la pechuga. Los colores predominantes en el plumaje, la piel y el tarso fueron negro, blanco y café, respectivamente. El pavo de traspatio mexicano presentó dimorfismo sexual significativo y alta correlación fenotípica entre circunferencia de la pechuga y peso corporal

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Efectos de cruzamiento para producción de leche y características de crecimiento en bovinos de doble propósito en el trópico húmedo

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) ysus 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<0.10) de PG/HS, PG/SP y HT/SM sobre PL y PG/SP, PG/SM, HT/SM y RC/HS sobre PN. PG/HS y PG/SPpresentaron efecto (P<0.10) sobre P205, P365 y P540 y PG/SM sólo sobre P205. Para P205, P365 y P540 hubo efecto (P<0.10) de HT y RC en todas las cruzas. Los resultados aquí presentados permitirán establecer algunas estrategias de aprovechamiento de los efectos genéticos aditivos y no aditivos presentes en las poblaciones cruzadas de bovinos de doble propósito en el trópico húmedo

Genetic diversity assessment of the Mexican Simmental population through pedigree analysis

ABSTRACT The purpose of this study was to examine the genetic variability of the Mexican Simmental. Inbreeding was calculated by year for animals born from 1985 to 2014. Proportion of ancestors known, average equivalent complete generations, generation interval, and effective size, as well as the effective numbers of founders, ancestors, and founder genomes were calculated for animals born in six periods (1985-1989, 1990-1994, 1995-1999, 2000-2004, 2005-2009, and 2010-2014). The year 1985 was selected as the initial year to form the subpopulations since the registration of the first Simmental cattle born in Mexico began in this year. Gene contributions of ancestors with the highest genetic influence were also calculated, using data of animals born in the latter period. Coefficients of inbreeding were low, ranging from 0.0068 to 0.0165. The average number of equivalent complete generations increased from 3.71, for the 1985-1989 subpopulation, to 5.83, for the 2010-2014 subpopulation. The population showed an effective population size of 186.6 animals in the last period. The numbers of founders, ancestors, and founder genomes increased from 1985 to 2004, but decreased from 2005 to 2014. The ratio of effective number of ancestors to effective number of founders and the ratio of effective number of founder genomes to effective number of ancestors were 0.31 and 0.66 and 0.27 and 0.63 for animals born in the 2005-2009 and 2010-2014 periods, respectively, revealing loss of diversity due to bottlenecks and genetic drift in the last decade. One ancestor explained 3.4% of the total genetic variability of the progeny born from 2010 to 2014, whereas the first fifteen ancestors explained 20% of such variability. The pedigree analysis showed Mexican Simmental cattle are not currently endangered

Genome-Wide Association Study Reveals Candidate Genes for Litter Size Traits in Pelibuey Sheep

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

Efecto de la selección genética en contra de las emisiones de metano sobre los componentes de la leche

This study aimed to estimate the response to selection through different selection indices between methane production and milk production and its components in specialized tropical, dual-purpose, and family dairy systems. Methane emissions were sampled during milking using the Guardian-NG gas monitor; milk samples were collected individually during methane sampling. DNA was extracted from the hair follicles of all the animals included in this study. The variance and covariance components were estimated using the mixed model methodology. Due to the incomplete genealogical information, molecular markers were used to build the genomic relationship matrix (Matrix G). The estimated heritability for methane emissions during milking was 0.18 and 0.32 for the univariate and bivariate analysis, respectively. The genetic correlation between the milk fat and protein percentages and methane emissions during milking was negative, -0.09 and -0.18, respectively. The response to selection, estimated through selection indices, demonstrated that it is feasible to reduce methane emissions up to 0.021 mg/L during milking in five generations without detriment to milk components.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