Genetic analysis of carcass traits of steers adjusted to age, weight, or fat thickness slaughter endpoints

Carcass measurements from 1,664 steers from the Germ Plasm Utilization project at U.S. Meat Animal Research Center were used to estimate heritabilities (h2) of, and genetic correlations (rg) among, 14 carcass traits adjusted to different endpoints (age, carcass weight, and fat thickness): HCW (kg), dressing percent (DP), adjusted fat thickness (AFT, cm), LM area (LMA, cm2), KPH (%), marbling score (MS), yield grade (YG), predicted percentage of retail product (PRP), retail product weight (RPW, kg), fat weight (FW, kg), bone weight (BNW, kg), actual percentage retail product (RPP), fat percent (FP), and bone percent. Fixed effects in the model included breed group, feed energy level, dam age, birth year, significant (P \u3c 0.05) interactions, covariate for days on feed, and the appropriate covariate for endpoint nested (except age) within breed group. Random effects in the model were additive genetic effect of animal and total maternal effect of dam. Parameters were estimated by REML. For some traits, estimates of h2 and phenotypic variance changed with different endpoints. Estimates of h2 for HCW,DP, RPW, and BNW at constant age, weight, or fat thickness were 0.27, —, and 0.41; 0.19, 0.26, and 0.18; 0.42, 0.32, and 0.50; and 0.43, 0.32, and 0.48, respectively. Magnitude and/or sign of rg also changed across endpoints for 54 of the 91 trait pairs. Estimates for HCW-LMA, AFTRPW, LMA-YG, LMA-PRP, LMA-FW, LMA-RPP, and LMA-FP at constant age, weight, or fat thickness were 0.32, —, and 0.51; −0.26, −0.77, and —; −0.71, −0.89, and −0.66; 0.68, 0.85, and 0.63; −0.16, −0.51, and 0.22; 0.47, 0.57, and 0.27; and −0.44, −0.43, and −0.18, respectively. Fat thickness was highly correlated with YG (0.86 and 0.85 for common age and weight) and PRP (−0.85 and −0.82 for common age and weight), indicating that selection for decreased fat thickness would improve YG and PRP. Carcass quality, however, would be affected negatively because of moderate rg (0.34 and 0.35 for common age and weight) between MS and AFT. Estimates of h2 and phenotypic variance indicate that enough genetic variation exists to change measures of carcass merit by direct selection. For some carcass traits, however, magnitude of change would depend on effect of endpoint on h2 and phenotypic variance. Correlated responses to selection would differ depending on endpoint

Copy number variation mapping and genomic variation of autochthonous and commercial turkey populations

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\u2019Italia, 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\uae. 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\u2014189 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

Biotecnologías reproductivas en el ganado bovino: cinco décadas de investigación en México

The main bovine reproductive biotechnologies are recapitulated herein in five sections, and their historical development and current status are analyzed, including the results generated in Mexico. In the 1970s, estrus synchronization and ovulation induction began; thus, the reproductive cycle started to be controlled with the resources available at that time, based on the knowledge of bovine reproductive physiology. Over the years, hormone therapy evolved as new compounds were discovered, refining methods to standardize the effect and generating new methods for the release of hormones. The most widely used biotechnology in the world, artificial insemination, owes its expansion to advances in semen processing, among which the development of diluents, cryopreservation, semen sexing, and computer-assisted sperm analysis stand out. The embryonic era began with the development of multi-ovulation and methods for collecting, evaluating, transferring, and cryopreserving embryos. The second embryonic era came with the fully in vitro production of embryos from immature eggs and frozen sperm, known as in vitro embryo production. Great research and material resources have been invested in this procedure, rendering it a pillar of genetic improvement and productivity, in combination with two other tools: sexed semen and genomic evaluations. A golden age of in vitro embryo production is on the horizon, with the possibility to produce accurate modifications in the embryo genome, thanks to gene editing technology.A lo largo de cinco secciones, se recapitulan las principales biotecnologías reproductivas en el bovino, se analiza su desarrollo histórico, estado actual, y se incluyen resultados generados en México. En la década de 1970, se inició la sincronización estral e inducción de la ovulación donde, basados en el conocimiento de la fisiología reproductiva bovina, se empezó a controlar el ciclo reproductivo con recursos disponibles en aquel entonces. Con los años, la terapia hormonal evolucionó conforme se descubrieron nuevos compuestos, refinando métodos para estandarizar el efecto y generar nuevos métodos de liberación de las hormonas. La biotecnología más usada en el mundo, la inseminación artificial, debe su expansión a los avances en el procesamiento del semen, donde destaca el desarrollo de diluyentes, la criopreservación, el sexado del semen y el análisis espermático asistido por computadora. La era embrionaria inició con el desarrollo de la multiovulación y los métodos para colectar, evaluar, transferir y criopreservar los embriones. La segunda era embrionaria llegó con la producción de embriones completamente in vitro, partiendo de óvulos inmaduros y semen congelado, en lo que se denominó la producción in vitro de embriones. En ésta, se han invertido grandes recursos de investigación, y materiales, para hacerla un pilar del mejoramiento genético y la productividad, en combinación con otras dos herramientas, el semen sexado y las evaluaciones genómicas. Se vislumbra una época de oro de la producción in vitro de embriones con la posibilidad de modificar el genoma de embriones con precisión, gracias a la tecnología de edición de genes

Características das ondas de desenvolvimento folicular em novilhas Bos taurus indicus pré-púberes de dois tamanhos diferentes

The purpose of this study was to evaluate in a period of 42 days prior to the onset of puberty (PB), the effects of size (small size and large size) of prepubertal Brahman heifers (BHM) on; age, characteristics of follicular dynamics, and body composition parameters. In addition, the frame score (body structure) was calculated as an additional estimator of height. We defined PB as the first ovulation preceded by the observation of estrus and followed by the formation of a corpus luteum (CL) of normal duration. Prepubertal BHM (10) heifers were used. The feeding was individual with corn silage and commercial concentrate to obtain similar weight gains. Measurements of weight and body condition score (BCS) were performed every 14 d. Ovulation and the formation of the CL were confirmed according to the monitoring of the ovarian structures by ultrasonography. Statistically, correlation analysis and analysis of variance were performed with the GLM procedure of SAS. A significant effect of size on the total number of follicles at PB was found, where small-sized heifers had 16 follicles, while those of large size had 12 follicles at PB (P < 0.0001). The frame score of the undersized animals was 10 % higher than that of the oversized heifers (P < 0.0001). Likewise, the frame score had a significant effect (P < 0.0001) on the total number of follicles in the PB. In conclusion, the effect of height in prepubertal animals is a complex characteristic, associated with body composition parameters, which affects some of the characteristics of follicular dynamics, and is worth further study in Zebu cattle.En un periodo de 42 días previos al inicio de la pubertad (PB), se estudiaron los efectos de la talla (talla chica y talla grande) de vaquillas prepúberes de la raza Brahman (BHM) sobre; la edad, características de la dinámica folicular y parámetros de composición corporal. Además, se calculó el frame score (estructura corporal) como estimador adicional de la talla. La PB fue definida como la primera ovulación precedida por la observación del estro y seguida por la formación de un cuerpo lúteo de duración normal. Se utilizaron 10 vaquillas BHM. La alimentación fue individual con ensilado de maíz y concentrado comercial para obtención de ganancias de peso similares. Se realizaron pesajes y se midió la condición corporal (CC) cada 14 d. De acuerdo al monitoreo ultrasonográfico de las estructuras ováricas se confirmó la ovulación y la formación del cuerpo lúteo (CL). Estadísticamente se realizó un análisis de correlación y análisis de varianza con el procedimiento GLM del SAS. Se encontró efecto significativo de la talla sobre el número total de folículos a la PB, en donde las vaquillas de talla chica registraron 16 folículos, mientras que las de talla grande tuvieron 12 folículos a la PB (P < 0.0001). El frame score de los animales de talla chica fue 10 % mayor que la de las vaquillas de talla grande (P < 0.0001). Así mismo, se observó que el frame score tuvo un efecto significativo (P < 0.0001) sobre el número total de folículos a la PB. Se concluye que el efecto de la talla en animales prepúberes una característica compleja, que está asociada con los parámetros de composición corporal y que afecta algunas de las características de la dinámica folicular y que además vale la pena seguir estudiando en el ganado Cebú.Em um período de 42 dias antes do início da puberdade (PB), os efeitos do tamanho (pequeno e grande porte) de novilhas Brahman pré-púberes (BHM) sobre; idade, características da dinâmica folicular e parâmetros de composição corporal. Além disso, a pontuação do quadro (estrutura corporal) foi calculada como um estimador adicional de altura. BP foi definido como a primeira ovulação precedida pela observação do estro e seguida pela formação de um corpo lúteo de duração normal. Foram utilizadas 10 novilhas BHM. A alimentação foi individual com silagem de milho e concentrado comercial para obtenção de ganhos de peso semelhantes. Pesagens foram realizadas e a condição corporal (CC) foi medida a cada 14 dias. De acordo com o acompanhamento ultrassonográfico das estruturas ovarianas, foi confirmada a ovulação e a formação do corpo lúteo (CL). Estatisticamente, uma análise de correlação e análise de variância foram realizadas com o procedimento GLM do SAS. Um efeito significativo do tamanho sobre o número total de folículos no BP foi encontrado, onde novilhas de pequeno porte tiveram 16 folículos, enquanto as de grande porte tiveram 12 folículos no BP (P < 0,0001). O escore estrutural dos animais subdimensionados foi 10% maior do que o das novilhas superdimensionadas (P < 0,0001). Da mesma forma, observou-se que o frame score teve efeito significativo (P < 0,0001) sobre o número total de folículos no PB. Conclui-se que o efeito da altura em animais pré-púberes é uma característica complexa, que está associada a parâmetros de composição corporal e que afeta algumas das características da dinâmica folicular, e que também merece um estudo mais aprofundado em zebuínos

Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef

BACKGROUND: Africa is home to numerous cattle breeds whose diversity has been shaped by subtle combinations of human and natural selection. African Sanga cattle are an intermediate type of cattle resulting from interbreeding between Bos taurus and Bos indicus subspecies. Recently, research has asserted the potential of Sanga breeds for commercial beef production with better meat quality as compared to Bos indicus breeds. Here, we identified meat quality related gene regions that are positively selected in Ankole (Sanga) cattle breeds as compared to indicus (Boran, Ogaden, and Kenana) breeds using cross-population (XP-EHH and XP-CLR) statistical methods. RESULTS: We identified 238 (XP-EHH) and 213 (XP-CLR) positively selected genes, of which 97 were detected from both statistics. Among the genes obtained, we primarily reported those involved in different biological process and pathways associated with meat quality traits. Genes (CAPZB, COL9A2, PDGFRA, MAP3K5, ZNF410, and PKM2) involved in muscle structure and metabolism affect meat tenderness. Genes (PLA2G2A, PARK2, ZNF410, MAP2K3, PLCD3, PLCD1, and ROCK1) related to intramuscular fat (IMF) are involved in adipose metabolism and adipogenesis. MB and SLC48A1 affect meat color. In addition, we identified genes (TIMP2, PKM2, PRKG1, MAP3K5, and ATP8A1) related to feeding efficiency. Among the enriched Gene Ontology Biological Process (GO BP) terms, actin cytoskeleton organization, actin filament-based process, and protein ubiquitination are associated with meat tenderness whereas cellular component organization, negative regulation of actin filament depolymerization and negative regulation of protein complex disassembly are involved in adipocyte regulation. The MAPK pathway is responsible for cell proliferation and plays an important role in hyperplastic growth, which has a positive effect on meat tenderness. CONCLUSION: Results revealed several candidate genes positively selected in Ankole cattle in relation to meat quality characteristics. The genes identified are involved in muscle structure and metabolism, and adipose metabolism and adipogenesis. These genes help in the understanding of the biological mechanisms controlling beef quality characteristics in African Ankole cattle. These results provide a basis for further research on the genomic characteristics of Ankole and other Sanga cattle breeds for quality beef. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-016-0467-1) contains supplementary material, which is available to authorized users

Effects of age, weight and fatness slaughter end points on estimates of genetic parameters for carcass traits

The influence of slaughter end points of age, carcass weight and fat thickness (covariates) on estimates of phenotypic variances ([special characters omitted]), heritabilities (h2) for, and genetic correlations (rg) among, 14 carcass traits of purebred and composite steers from 12 breeds was studied. In addition, the effects of different levels of fat thickness and hot carcass weight as end points on estimates of breed effects and retained heterosis (individual and maternal combined) were also examined. Parameters were estimated by REML using animal models. In general, estimates of [special characters omitted] and h2 for carcass traits indicate that enough phenotypic and genetic variation exist to change measures of carcass merit by single-trait selection. For some carcass traits, however, the magnitude of change would depend on the effect of slaughter end point as estimates of [special characters omitted] and h2 were often different for different end points. The largest differences in estimates of h2 with different end points were for hot carcass weight and retail product weight. Among all parameters estimated, the greatest effects of end points were on estimates of r g for 54 of the 91 pairs of traits, which in some cases not only changed in magnitude (0.15 or more), but also in sign. Therefore, expected correlated responses to selection would also differ depending on end point. Ranking of breeds and expression of heterosis also varied for many carcass traits depending on slaughter end points. As an example, the estimate of retained heterosis for actual retail product as a percentage of hot carcass weight for the MARC III composite breed was significantly negative (-1.27%) at 0.7 cm, but was significantly positive (2.55%) at 1.5 cm of fat thickness. Furthermore, some estimates of heterosis also doubled in magnitude depending on levels of fat thickness end point. Age, weight and fatness end points influenced the sign and(or) the magnitude of estimates of genetic parameters for several carcass traits

Heritability estimates for carcass traits of cattle: a review

We present estimates of heritability for carcass traits of cattle published in the scientific literature. Seventy-two papers published form 1962 to 2004, which reported estimates of heritability for carcass traits, were reviewed. The unweighted means of estimates of heritability for 14 carcass traits by slaughter end point (age, weight, and fat depth) were calculated. Among the three end points, carcass weight, backfat thickness, longissimus muscle area, and marbling score were the carcass traits with the most estimates of heritability (56≤n≤66). The averages for these traits indicate that they are similarly and moderately heritable (0.40, 0.36, 0.40, and 0.37, respectively). However, heritability estimates for most traits varied greatly, which could be due to differences in breed groups, methods of estimation, and effects in the model, number of records, measurement errors, sex, and management. Few studies have compared heritability estimates for carcass traits adjusted to different end points. Results from such studies have been inconsistent, although some studies revealed that heritability estimates for several carcass traits are sensitive to the covariate included in the model for the end point, implying that direct response to selection would be different for some traits depending on slaughter end point. The effect of different end points on estimates of heritability for many carcass traits has not been studied

Genetic variation in wholesale carcass cuts predicted from digital images in cattle

peer-reviewedThe objective of this study was to quantify the genetic variation in carcass cuts predicted using digital image analysis in commercial cross-bred cattle. The data set comprised 38 404 steers and 14 318 heifers from commercial Irish herds. The traits investigated included the weights of lower value cuts (LVC), medium value cuts (MVC), high value cuts (HVC), very high value cuts (VHVC) and total meat weight. In addition, the weights of total fat and total bones were available on the steers. Heritability of carcass cut weights, within gender, was estimated using an animal linear model, whereas genetic and phenotypic correlations among cuts were estimated using a sire linear model. Carcass weight was included as a covariate in all models. In the steers, heritability ranged from 0.13 (s.e.50.02) for VHVC to 0.49 (s.e.50.03) for total bone weight, and in the heifers heritability ranged from 0.15 (s.e.50.04) for MVC to 0.72 (s.e.50.06) for total meat weight. The coefficient of genetic variation for the different cuts varied from 1.4% to 3.6%. Genetic correlations between the different cut weights were all positive and ranged from 0.45 (s.e.50.08) to 0.89 (s.e.50.03) in the steers, and from 0.47 (s.e.50.14) to 0.82 (s.e.50.06) in the heifers. Genetic correlations between the wholesale cut weights and carcass conformation ranged from 0.32 (s.e.50.06) to 0.45 (s.e.50.07) in the steers, and from 0.10 (s.e.50.12) to 0.38 (s.e.50.09) in the heifers. Genetic correlations between the same wholesale cut traits in steers and heifers ranged from 0.54 (s.e.50.14) for MVC to 0.79 (s.e.50.06) for total meat weight; genetic correlations between carcass weight and carcass classification for conformation and fat score in both genders varied from 0.80 to 0.87. The existence of genetic variation in carcass cut traits, coupled with the routine availability of predicted cut weights from digital image analysis, clearly shows the potential to genetically improve carcass value