Genomic Prediction for Abortion in Lactating Holstein Dairy Cows.

Abortion in dairy cattle causes great economic losses due to reduced animal health, increase in culling rates, reduction in calf production, and milk yield, among others. Although the etiology of abortions can be of various origins, previous research has shown a genetic component. The objectives of this study were to (1) describe the development of the genomic prediction for cow abortions in lactating Holstein dairy cattle based on producer-recorded data and ssGBLUP methodology and (2) evaluate the efficacy of genomic predictions for cow abortions in commercial herds of US Holstein cows using data from herds that do not contribute phenotypic information to the evaluation. We hypothesized that cows with greater genomic predictions for cow abortions (Z_Abort STA) would have a reduced incidence of abortion. Phenotypic data on abortions, pedigree, and genotypes were collected directly from commercial dairy producers upon obtaining their permission. Abortion was defined as the loss of a confirmed pregnancy after 42 and prior to 260 days of gestation, treated as a binary outcome (0, 1), and analyzed using a threshold model. Data from a different subset of animals were used to test the efficacy of the prediction. The additive genetic variance for the cow abortion trait (Z_Abort) was 0.1235 and heritability was 0.0773. For all animals with genotypes (n = 1,662,251), mean reliability was 42%, and genomic predicted transmitting abilities (gPTAs) ranged from −8.8 to 12.4. Z_Abort had a positive correlation with cow and calf health traits and reproductive traits, and a negative correlation with production traits. Z_Abort effectively identified cows with a greater or lesser risk of abortion (16.6% vs. 11.0% for the worst and best genomics groups, respectively; p < 0.0001). The inclusion of cow abortion genomic predictions in a multi-trait selection index would allow dairy producers and consultants to reduce the incidence of abortion and to select high-producing, healthier, and more profitable cows.

Genomic Prediction for Twin Pregnancies.

Twinning is a multifactorial trait influenced by both genetic and environmental factors that can negatively impact animal welfare and economic sustainability on commercial dairy operations. To date, using genetic selection as a tool for reducing twinning rates on commercial dairies has been proposed, but not yet implemented. In response to this market need, Zoetis (Kalamazoo, MI, USA) has developed a genomic prediction for twin pregnancies, and included it in a comprehensive multitrait selection index. The objectives of this study were to (1) describe a genetic evaluation for twinning in Holstein cattle, (2) demonstrate the efficacy of the predictions, (3) propose strategies to reduce twin pregnancies using this information. Data were retrieved from commercial dairies and provided directly by producers upon obtaining their permission. The twin pregnancies trait (TWIN) was defined as a pregnancy resulting in birth or abortion of twin calves, classified as a binary (0,1) event, and analysed using a threshold animal model. Predictions for a subset of cows were compared to their on-farm twin records. The heritability for twin pregnancies was 0.088, and genomic predicted transmitting abilities ((g)PTAs) ranged from -7.45-20.79. Genetic correlations between TWIN and other traits were low, meaning that improvement for TWIN will not negatively impact improvement for other traits. TWIN was effectively demonstrated to identify cows most and least likely to experience a twin pregnancy in a given lactation, regardless of reproductive protocol used. Effective inclusion of the prediction in a multitrait selection index offers producers a comprehensive tool to inform selection and management decisions. When combined with sound management practices, this presents a compelling opportunity for dairy producers to proactively reduce the incidence of twin pregnancies on commercial dairy operations.

Non-invasive nuclear magnetic resonance analysis of male and female embryo metabolites during in vitro embryo culture.

INTRODUCTION: In the past 20+ years, several studies of bovine embryo production showed how the ratio of male to female embryos changes if embryos are made in vivo or in vitro. It is known that in in vitro systems, the sex ratio is in favor of males when there are high levels of glucose, and favors females when the principal energetic substrate is one other than glucose, like citrate. OBJECTIVES: The aim of this study was to evaluate the embryo metabolism during three important periods of in vitro development: the early development (from day 1 until day 3), the middle of culture (day 3 until day 5), and later development (day 5 until day 7). METHODS: To obtain this information we evaluated the spent medium from each time period by 1H NMR. RESULTS: Our results confirm that embryo metabolism is different between sexes. The new information obtained by identifies markers that we can use to predict the embryo sex. CONCLUSION: These results open a new, non-invasive method to evaluate sex of the embryos before the transfer. In the first period of embryo culture, valine concentration is good indicator (66.7% accurate), while in the last phase of culture, pyruvate depletion is the best marker (64% accurate) to evaluate the sex of the embryo.

Genome-Wide Association Study for Identifying Loci that Affect Fillet Yield, Carcass, and Body Weight Traits in Rainbow Trout (Oncorhynchus mykiss).

Fillet yield (FY, %) is an economically-important trait in rainbow trout aquaculture that affects production efficiency. Despite that, FY has received little attention in breeding programs because it is difficult to measure on a large number of fish and cannot be directly measured on breeding candidates. The recent development of a high-density SNP array for rainbow trout has provided the needed tool for studying the underlying genetic architecture of this trait. A genome-wide association study (GWAS) was conducted for FY, body weight at 10 (BW10) and 13 (BW13) months post-hatching, head-off carcass weight (CAR), and fillet weight (FW) in a pedigreed rainbow trout population selectively bred for improved growth performance. The GWAS analysis was performed using the weighted single-step GBLUP method (wssGWAS). Phenotypic records of 1447 fish (1.5 kg at harvest) from 299 full-sib families in three successive generations, of which 875 fish from 196 full-sib families were genotyped, were used in the GWAS analysis. A total of 38,107 polymorphic SNPs were analyzed in a univariate model with hatch year and harvest group as fixed effects, harvest weight as a continuous covariate, and animal and common environment as random effects. A new linkage map was developed to create windows of 20 adjacent SNPs for use in the GWAS. The two windows with largest effect for FY and FW were located on chromosome Omy9 and explained only 1.0-1.5% of genetic variance, thus suggesting a polygenic architecture affected by multiple loci with small effects in this population. One window on Omy5 explained 1.4 and 1.0% of the genetic variance for BW10 and BW13, respectively. Three windows located on Omy27, Omy17, and Omy9 (same window detected for FY) explained 1.7, 1.7, and 1.0%, respectively, of genetic variance for CAR. Among the detected 100 SNPs, 55% were located directly in genes (intron and exons). Nucleotide sequences of intragenic SNPs were blasted to the Mus musculus genome to create a putative gene network. The network suggests that differences in the ability to maintain a proliferative and renewable population of myogenic precursor cells may affect variation in growth and fillet yield in rainbow trout.

Differential Transcriptome Networks between IDO1-Knockout and Wild-Type Mice in Brain Microglia and Macrophages.

Microglia in the brain and macrophages in peripheral organs are cell types responsible for immune response to challenges. Indoleamine 2,3-dioxygenase 1 (IDO1) is an immunomodulatory enzyme of the tryptophan pathway that is expressed in the brain. The higher activity of IDO1 in response to immune challenge has been implicated in behavioral disorders. The impact of IDO1 depletion on the microglia transcriptome has not been studied. An investigation of the transcript networks in the brain microglia from IDO1-knockout (IDO1-KO) mice was undertaken, relative to peripheral macrophages and to wild-type (WT) mice under unchallenged conditions. Over 105 transcript isoforms were differentially expressed between WT and IDO1-KO within cell type. Within microglia, Saa3 and Irg1 were over-expressed in IDO1-KO relative to WT. Within macrophages, Csf3 and Sele were over-expressed in IDO1-KO relative to WT. Among the genes differentially expressed between strains, enriched biological processes included ion homeostasis and ensheathment of neurons within microglia, and cytokine and chemokine expression within macrophages. Over 11,110 transcript isoforms were differentially expressed between microglia and macrophages and of these, over 10,800 transcripts overlapped between strains. Enriched biological processes among the genes over- and under-expressed in microglia relative to macrophages included cell adhesion and apoptosis, respectively. Detected only in microglia or macrophages were 421 and 43 transcript isoforms, respectively. Alternative splicing between cell types based on differential transcript isoform abundance was detected in 210 genes including Phf11d, H2afy, and Abr. Across strains, networks depicted a predominance of genes under-expressed in microglia relative to macrophages that may be a precursor for the different response of both cell types to challenges. The detected transcriptome differences enhance the understanding of the role of IDO1 in the microglia transcriptome under unchallenged conditions.

Microglia Transcriptome Changes in a Model of Depressive Behavior after Immune Challenge.

Depression symptoms following immune response to a challenge have been reported after the recovery from sickness. A RNA-Seq study of the dysregulation of the microglia transcriptome in a model of inflammation-associated depressive behavior was undertaken. The transcriptome of microglia from mice at day 7 after Bacille Calmette Guérin (BCG) challenge was compared to that from unchallenged Control mice and to the transcriptome from peripheral macrophages from the same mice. Among the 562 and 3,851 genes differentially expressed between BCG-challenged and Control mice in microglia and macrophages respectively, 353 genes overlapped between these cells types. Among the most differentially expressed genes in the microglia, serum amyloid A3 (Saa3) and cell adhesion molecule 3 (Cadm3) were over-expressed and coiled-coil domain containing 162 (Ccdc162) and titin-cap (Tcap) were under-expressed in BCG-challenged relative to Control. Many of the differentially expressed genes between BCG-challenged and Control mice were associated with neurological disorders encompassing depression symptoms. Across cell types, S100 calcium binding protein A9 (S100A9), interleukin 1 beta (Il1b) and kynurenine 3-monooxygenase (Kmo) were differentially expressed between challenged and control mice. Immune response, chemotaxis, and chemokine activity were among the functional categories enriched by the differentially expressed genes. Functional categories enriched among the 9,117 genes differentially expressed between cell types included leukocyte regulation and activation, chemokine and cytokine activities, MAP kinase activity, and apoptosis. More than 200 genes exhibited alternative splicing events between cell types including WNK lysine deficient protein kinase 1 (Wnk1) and microtubule-actin crosslinking factor 1(Macf1). Network visualization revealed the capability of microglia to exhibit transcriptome dysregulation in response to immune challenge still after resolution of sickness symptoms, albeit lower than that observed in macrophages. The persistent transcriptome dysregulation in the microglia shared patterns with neurological disorders indicating that the associated persistent depressive symptoms share a common transcriptome basis.

Genetic parameters of days open in Charolais cattle of Cuba / Parámetros genéticos de los días abiertos en ganado Charolais de Cuba / Parâmetros genéticos dos dias vazios no gado Charolês de Cuba

Background: there is little information in Cuba regarding the genetic components of the postpartum period in beef cattle. Objective: to compare estimates of genetic parameters of days open (DO) obtained with three models in Charolais cattle of Cuba. Methods: data from individual reproductive control of Charolais cattle from 17 herds in two Cuban companies were analyzed. The sample consisted of 16,891 calvings from 4,593 cows, daughters of 190 sires and 2,770 dams. Up to 10 parities per female between years 1981 and 2005 were considered. The WOMBAT program was used to estimate variance components. Three models were applied; an univariate model (UM) for each separate parity until the sixth calving; a repeatability model (RM) with all parities; and a random regression model (ARM) taking the number of calving as an independent variable. Results: the overall average for DO was 171 ± 93 days. The trend of the average value for DO in each calving was decreasing from the first to the tenth parity, with a seasonal performance around 155 days between the fourth and eighth calving. DO heritability estimated by UM was variable, with values of 0.03 for the first calving and 0.06 for the sixth. These variations cannot be observed with RM that estimated a heritability of 0.06. Values of 0.05 in the first calving until 0.07 in the tenth were estimated with ARM. Genetic correlations among DO for different parities were close to unity. Conclusions: changes of the estimated heritability for DO through the productive life of a female can be observed with ARM. The heritability estimates were low and did not differ from the results reported in other beef cattle breeds.

Antecedentes: en Cuba existe poca información relacionada con los componentes genéticos del periodo posparto en bovinos para carne. Objetivo: comparar los estimados de parámetros genéticos de los días abiertos (DO) obtenidos con tres modelos en ganado Charolais de Cuba. Métodos: los datos del control reproductivo individual de vacas Charolais de 17 hatos en dos empresas de Cuba fueron analizados. La muestra estuvo conformada por 16.891 partos de 4.593 vacas, hijas de 190 padres y 2.770 madres. Fueron considerados hasta 10 partos por hembras que ocurrieron entre 1981 y 2005. Se utilizó el programa WOMBAT para la estimación de componentes de varianza. Se aplicaron tres modelos; un modelo univariado (UM) para cada parto independiente hasta el sexto parto; un modelo de repetibilidad (RM) con todos los partos; y un modelo de regresión aleatoria (ARM) tomando el número del parto como variable independiente. Resultados: la media general de DO fue de 171 ± 93 días. La tendencia del valor promedio para DO en cada parto fue decreciente desde el primero al décimo, con un comportamiento estacional alrededor de 155 días entre el cuarto y el octavo parto. La heredabilidad de DO estimada por UM fue variable con valores de 0,03 en el primer parto y 0,06 en el sexto. Estas variaciones no pueden ser observadas con el RM que estimó una heredabilidad de 0,06. Valores de 0,05 en el primer parto hasta 0,07 en el décimo fueron estimados con el ARM. Las correlaciones genéticas entre DO para los diferentes partos fueron cercanos a la unidad. Conclusiones: los cambios de la heredabilidad estimada para DO a través de la vida productiva de una hembra pueden ser observados con los ARM. Los estimados de heredabilidad fueron bajos y no difiere de los resultados reportados en otras razas de ganado bovino para carne.

Antecedentes: em Cuba há pouca informação sobre os componentes genéticos do período pós-parto em bovinos de corte. Objetivo: comparar as estimativas de parâmetros genéticos de dias vazios (DO) obtidos com os três modelos em bovinos Charolês de Cuba. Métodos: os dados de controle reprodutivo individual de bovinos Charolês de 17 rebanhos em duas empresas de Cuba foram analisados. A amostra consistiu de 16.891 partos de 4.593 vacas, filhas de 190 touros e 2.770 matrizes. Até 10 partos foram considerados por fêmea que ocorreram entre 1981 e 2005. O programa WOMBAT foi utilizado para estimar os componentes da variância. Três modelos foram aplicados; um modelo univariado (UM) para cada paridade separado até o sexto parto; um modelo de repetibilidade (RM) com todas as parições; e um modelo de regressão aleatória (ARM), tendo o número de partos como uma variável independente. Resultados: a média geral foi de 171 ± 93 dias. A tendência do valor médio para o DO em cada parto foi diminuindo desde o primeiro até o décimo parto com um desempenho sazonal em torno de 155 dias entre o quarto e oitavo parto. A herdabilidade estimada para DO pela UM foi variável com valores de 0,03 no primeiro parto e 0,06 no sexto. Essas variações não podem ser observadas com RM que estimou uma herdabilidade de 0,06. Os valores de 0,05 no primeiro parto até 0,07 no décimo foram estimados com ARM. As correlações genéticas entre DO para diferentes partos foram próximas da unidade. Conclusões: alterações da herdabilidade estimada para DO durante a vida produtiva de uma fêmea pode ser observado com ARM. As estimativas de herdabilidade foram baixas e não diferiram entre os resultados apresentados em outras raças de gado de corte.

Contribution of semen trait selection, artificial insemination technique, and semen dose to the profitability of pig production systems: A simulation study.

The economic impact of selection for semen traits on pig production systems and potential interaction with artificial insemination (AI) technique and semen dose remains partially understood. The objectives of this study were to compare the financial indicators (gross return, net profit, cost) in a three-tier pig production system under one of two selection strategies: a traditional strategy including nine paternal and maternal traits (S9) and an advanced strategy that adds four semen traits (S13). Maternal traits included the number of pigs born alive, litter birth weight, adjusted 21-day litter weight, and the number of pigs at 21 days, and paternal traits included days to 113.5 kg, back fat, average daily gain, feed efficiency, and carcass lean percentage. The four semen traits included volume, concentration, progressive motility of spermatozoa, and abnormal spermatozoa. Simultaneously, the impact of two AI techniques and a range of fresh refrigerated semen doses including cervical AI with 3 × 10(9) (CAI3) and 2 × 10(9) (CAI2) sperm cells/dose, and intrauterine AI with 1.5 × 10(9) (IUI1.5), 0.75 × 10(9) (IUI0.75), and 0.5 × 10(9) (IUI0.5) sperm cells/dose were evaluated. These factors were also evaluated using a range of farrowing rates (60%-90%), litter sizes (8-14 live-born pigs), and a selected semen collection frequency. The financial impact of the factors was assessed through simulation of a three-way crossbreeding system (maternal nucleus lines A and B and paternal nucleus line C) using ZPLAN. The highest return on investment (profit/cost) of boars was observed at 2.33 collections/wk (three periods of 24 hours between collections). Under this schedule, a significant (P < 0.0001) interaction between the selection strategy and the AI technique-dose combination was identified for the gross return; meanwhile, significant (P < 0.0001) additive effects of the selection strategy and AI technique-dose combination were observed for the net profit. The highest gross return was obtained under S13 with IUI0.75 and IUI0.5. The net profit of S13 was 34.37% higher than the traditional S9 (P < 0.0001). The net profit favored IUI0.5 with relative differences of 4.13%, 2.41%, 1.72%, and 0.43% compared to CAI3, CAI2, IUI1.5, and IUI0.75, respectively. The advanced selection strategy proposed including four semen traits is recommended on the basis of the higher profitability relative to the traditional strategy.

Analytical workflow profiling gene expression in murine macrophages.

Comprehensive and simultaneous analysis of all genes in a biological sample is a capability of RNA-Seq technology. Analysis of the entire transcriptome benefits from summarization of genes at the functional level. As a cellular response of interest not previously explored with RNA-Seq, peritoneal macrophages from mice under two conditions (control and immunologically challenged) were analyzed for gene expression differences. Quantification of individual transcripts modeled RNA-Seq read distribution and uncertainty (using a Beta Negative Binomial distribution), then tested for differential transcript expression (False Discovery Rate-adjusted p-value < 0.05). Enrichment of functional categories utilized the list of differentially expressed genes. A total of 2079 differentially expressed transcripts representing 1884 genes were detected. Enrichment of 92 categories from Gene Ontology Biological Processes and Molecular Functions, and KEGG pathways were grouped into 6 clusters. Clusters included defense and inflammatory response (Enrichment Score = 11.24) and ribosomal activity (Enrichment Score = 17.89). Our work provides a context to the fine detail of individual gene expression differences in murine peritoneal macrophages during immunological challenge with high throughput RNA-Seq.

Bivariate genome-wide association analysis of the growth and intake components of feed efficiency.

Single nucleotide polymorphisms (SNPs) associated with average daily gain (ADG) and dry matter intake (DMI), two major components of feed efficiency in cattle, were identified in a genome-wide association study (GWAS). Uni- and multi-SNP models were used to describe feed efficiency in a training data set and the results were confirmed in a validation data set. Results from the univariate and bivariate analyses of ADG and DMI, adjusted by the feedlot beef steer maintenance requirements, were compared. The bivariate uni-SNP analysis identified (P-value <0.0001) 11 SNPs, meanwhile the univariate analyses of ADG and DMI identified 8 and 9 SNPs, respectively. Among the six SNPs confirmed in the validation data set, five SNPs were mapped to KDELC2, PHOX2A, and TMEM40. Findings from the uni-SNP models were used to develop highly accurate predictive multi-SNP models in the training data set. Despite the substantially smaller size of the validation data set, the training multi-SNP models had slightly lower predictive ability when applied to the validation data set. Six Gene Ontology molecular functions related to ion transport activity were enriched (P-value <0.001) among the genes associated with the detected SNPs. The findings from this study demonstrate the complementary value of the uni- and multi-SNP models, and univariate and bivariate GWAS analyses. The identified SNPs can be used for genome-enabled improvement of feed efficiency in feedlot beef cattle, and can aid in the design of empirical studies to further confirm the associations.

Single nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattle.

BACKGROUND: General, breed- and diet-dependent associations between feed efficiency in beef cattle and single nucleotide polymorphisms (SNPs) or haplotypes were identified on a population of 1321 steers using a 50 K SNP panel. Genomic associations with traditional two-step indicators of feed efficiency - residual feed intake (RFI), residual average daily gain (RADG), and residual intake gain (RIG) - were compared to associations with two complementary one-step indicators of feed efficiency: efficiency of intake (EI) and efficiency of gain (EG). Associations uncovered in a training data set were evaluated on independent validation data set. A multi-SNP model was developed to predict feed efficiency. Functional analysis of genes harboring SNPs significantly associated with feed efficiency and network visualization aided in the interpretation of the results. RESULTS: For the five feed efficiency indicators, the numbers of general, breed-dependent, and diet-dependent associations with SNPs (P-value < 0.0001) were 31, 40, and 25, and with haplotypes were six, ten, and nine, respectively. Of these, 20 SNP and six haplotype associations overlapped between RFI and EI, and five SNP and one haplotype associations overlapped between RADG and EG. This result confirms the complementary value of the one and two-step indicators. The multi-SNP models included 89 SNPs and offered a precise prediction of the five feed efficiency indicators. The associations of 17 SNPs and 7 haplotypes with feed efficiency were confirmed on the validation data set. Nine clusters of Gene Ontology and KEGG pathway categories (mean P-value < 0.001) including, 9nucleotide binding; ion transport, phosphorous metabolic process, and the MAPK signaling pathway were overrepresented among the genes harboring the SNPs associated with feed efficiency. CONCLUSIONS: The general SNP associations suggest that a single panel of genomic variants can be used regardless of breed and diet. The breed- and diet-dependent associations between SNPs and feed efficiency suggest that further refinement of variant panels require the consideration of the breed and management practices. The unique genomic variants associated with the one- and two-step indicators suggest that both types of indicators offer complementary description of feed efficiency that can be exploited for genome-enabled selection purposes.

Parámetros genéticos del crecimiento y la reproducción en ganado cebú / Genetic parameters of growth and reproduction in zebu cattle

Con el propósito de conocer las correlaciones genéticas entre los rangos de crecimiento en toros y las características reproductivas en vacas cebú de Cuba, se utilizaron 9490 registros de toros que terminaron la prueba de comportamiento en pastoreo, a los cuales se les registró el peso final (PF) a los 18 meses de edad; así mismo se emplearon 13.517 registros de sus medio hermanas, a las que se les registró la edad a la primera inseminación (EPI), la edad al primer parto (EPP) y los servicios por gestación (SXG): Los datos fueron colectados en cinco centros genéticos entre 1988 y 2001. Todos los animales eran hijos de 267 toros. Los valores promedios encontrados fueron 343,3 kg, 26,5 meses, 37,7 meses Y 1,76 para PF, EPI,EPP y SXG, respectivamente. Los índices de herencia (H2) fueron 0,054, 0,091 y 0,021 para PF, EPI, EPP y SXG, respectivamente. Las correlaciones genéticas entre PF y los rasgos reproductivos oscilaron entre -0,216 y -0,340. Entre los caracteres reproductivos, las correlaciones genéticas fueron de 0,544 a 0,982. Se concluyó que los valores de H2 estimados para el ganado cebú en Cuba están dentro del rango publicado en la literatura internacional y que la selección continuada para el incremento del peso corporal a los 18 meses de edad en los toros no afectaría negativamente la eficiencia reproductiva en las vacas...

Estimación de componentes de (CO) varianza para la producción de leche del día del control en ganado siboney utilizando un modelo de regresión aleatoria / Estimation of (CO) variance components for the test-day milk yield in siboney cattle using a random regression model

Con el fin de estimar los componentes de (co)varianza para la producción de leche del día del control en ganado Siboney (5/8 Holstein 3/8 Cebú Cubano) se utilizó un modelo de regresión aleatoria y se analizó el comportamiento de los estimadores al tener en cuenta la heterogeneidad de varianza residual (or2). Se analizaron 17034 registros de producción de leche del día del control (PDC) de 2086 vacas Siboney de primer parto que parieron entre 1995 y 2003. Las vacas, provenientes de 50 hatos, fueron hijas de 153 padres y 1179 madres. El pedigrí estuvo conformado por 5471 individuos y se garantizó que las hembras tuvieran, como mínimo, los primeros cuatro controles de producción de leche. Se trabajó con modelos de regresión aleatoria probando diferentes órdenes de polinomios de Legendre, para luego seleccionar mediante el logaritmo de convergencia y el criterio de Akaike el modelo de orden 4 para la varianza aditiva y de orden 5 para el ambiente permanente (AG4PE5), al cual se le aplicó heterogeneidad de or2. Los estimados de heredabilidad oscilaron entre 0,21 y 0,31 con valor máximo a los 177 días de lactancia. Las correlaciones genéticas fueron elevadas y a la mitad de la lactancia tomaron valores >0,95. Los resultados destacan la importancia de modelar la heterogeneidad de or2, debido a que se obtiene un mejor ajuste en la estimación de los componentes de (co)varianza para la producción de leche del día del control.