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The objective of this study was to predict genomic breeding values for milk yield of crossbred dairy cattle under different scenarios using single-step genomic BLUP (ssGBLUP). The data set included 13,880,217 milk yield measurements on 6,830,415 cows. Genotypes of 89,558 Holstein, 40,769 Jersey, and 22,373 Holstein-Jersey crossbred animals were used, of which all Holstein, 9,313 Jersey, and 1,667 crossbred animals had phenotypic records. Genotypes were imputed to 45K SNP markers. The SNP effects were estimated from single-breed evaluations for Jersey (JE), Holstein (HO) and crossbreds (CROSS), and multibreed evaluations including all Jersey and Holstein (JE_HO) or approximately equal proportions of Jersey, Holstein, and crossbred animals (MIX). Indirect predictions (IP) of the validation animals (358 crossbred animals with phenotypes excluded from evaluations) were calculated using the resulting SNP effects. Additionally, breed proportions (BP) of crossbred animals were applied as a weight when IP were estimated based on each pure breed. The predictive ability of IP was calculated as the Pearson correlation between IP and phenotypes of the validation animals adjusted for fixed effects in the model. Regression of adjusted phenotypes on IP was used to assess the inflation of IP. The predictive ability of IP for CROSS, JE, HO, JE_HO, and MIX scenario was 0.50, 0.50, 0.47, 0.50, and 0.46, respectively. Using BP was the least successful, with a predictive ability of 0.32. The inflation of the IP for crossbred animals using CROSS, JE, HO, JE_HO, MIX, and BP scenarios were 1.17, 0.65, 0.55, 0.78, 1.00, and 0.85, respectively. The IP of crossbred animals can be predicted using single-step GBLUP under a scenario that includes purebred genotypes.

The number of Jersey cows in the United States has been steadily increasing in recent years according to Council on Dairy Cattle Breeding statistics. To help producers reduce the risk of health disorders in their Jersey animals, Zoetis has developed genomic predictions for wellness traits in Jersey cattle using producer-recorded data. The traits included mastitis (MAST), metritis, retained placenta, displaced abomasum (DA), ketosis, lameness, and milk fever in cows and respiratory disease, scours, and calf livability (DEAD) in calves. Phenotypic data on health events, pedigree, and genotypes were collected directly from producers upon obtaining their permission. Each trait was defined as a binary event, having a value of 1 if an animal has been recorded with a disorder and 0 otherwise. The number of phenotypic records ranged from 216,166 for DA to 628,958 for MAST for cow traits and from 186,505 for scours to 380,429 for DEAD for calf traits. The number of genotyped animals was 41,271. All traits were analyzed using a univariate threshold animal model. The model for cow wellness traits included the fixed effect of parity and random effects of herd × year × season of calving, animal, and permanent environment. The model for calf wellness traits included the fixed effect of year of birth × calving season × region and random effects of herd × year of birth and animal. A total of 45,163 SNP were used in genomic analyses. Animals genotyped with low-density chips were imputed to the required number of markers. All analyses were based on the single-step genomic BLUP. Heritabilities ranged from 0.061 for DA to 0.120 for lameness. Predicted transmitting abilities were expressed in percentage points as deviations from the average estimated probability of a disorder in the base population. Reliabilities of genomic predicted transmitting abilities had average values between 32% (DA) and 51% (MAST and DEAD). The results indicate that a direct evaluation of cow and calf wellness traits under a genomic threshold model is feasible and offers predictions with average reliabilities comparable with other lowly heritable traits for Jersey cattle.

Reducing calf morbidity and mortality is important for attaining financial sustainability and improving animal welfare on commercial dairy operations. Zoetis (Kalamazoo, MI) has developed genomic predictions for calf wellness traits in Holsteins that include calf respiratory disease (RESP; recorded between 0 and 365 d of age), calf scours (DIAR; recorded between 2 and 50 d of age), and calf livability (DEAD; recorded between 2 and 365 d of age). Phenotype and pedigree data were from commercial dairies and provided directly by producers upon obtaining their permission. The number of records ranged from 741,484 for DIAR to 1,926,261 for DEAD. The number of genotyped animals was 325,025. All traits were analyzed using a univariate threshold animal model including fixed effect of year of birth × calving season × region, and random effects of herd × year of birth and animal. A total of 45,425 SNP were used in genomic analyses. Animals genotyped with low-density chips were imputed to the required number of SNP. All analyses were conducted using single-step genomic BLUP implementing the "algorithm for proven and young" (APY) animals designed to accommodate very large numbers of genotypes. Estimated heritabilities were 0.042, 0.045, and 0.060 for RESP, DIAR, and DEAD, respectively. The genomic predicted transmitting abilities ranged between -8.0 and 24.0, -11.5 and 28.5, and -6.5 to 22.8 for RESP, DIAR, and DEAD, respectively. Reliabilities of breeding values were obtained by approximation based on partitioning of a function of reliability into contributions from records, pedigree, and genotypes, where the genotype contribution was approximated using the diagonal value of the genomic relationship matrix. The average reliabilities for the genotyped animals were 41.9, 42.6, and 47.3% for RESP, DIAR, and DEAD, respectively. Estimated genomic predicted transmitting abilities and reliabilities were approximately normally distributed for all analyzed traits. Approximated genetic correlations of calf wellness with Zoetis dairy wellness traits and traits included in the US national genetic evaluation were low to moderate. The results indicate that direct evaluation of calf wellness traits under a genomic threshold model is feasible and offers predictions with average reliabilities comparable to other lowly heritable traits. Genetic selection for calf wellness traits presents a compelling opportunity for dairy producers to help manage herd replacement costs and improve overall profitability.

Simple Summary Twinning in dairy cattle is caused by many different factors, both genetic (i.e., inherited) and non-genetic (i.e., animal management). In dairy operations, twinning is an undesirable trait associated with other reproductive and metabolic diseases, higher operational costs, and higher rates of culling on farm. The animal welfare and economic impacts have resulted in the development of a genomic prediction for twinning (i.e., TWIN) by Zoetis such that producers can make informed breeding decisions for breeding Holstein females that are less likely to become pregnant with twins in a given lactation. This prediction is included in a holistic breeding tool (i.e., selection index) for producers so that they can improve multiple health, fertility, and production traits in parallel with reducing twinning when making breeding decisions for future generations. The objectives of the present study were (1) to describe how the twinning prediction was developed (and included in a selection index), (2) show that the prediction works effectively using real life farm data, and (3) propose how this genetic tool can be used in collaboration with management practices to proactively reduce twin pregnancies on farm. The results of this study provide evidence that twinning can be proactively managed on dairy farms using genetically powered tools. Abstract 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.

A pedigreed rainbow trout population (~ 100 families per generation) was selected for five generations to improve growth performance to the standard ~ 500-gram US market weight and beyond (> 1 kg). Body weights (BW) were recorded each generation at 5, 8, 10, and 13 months post-hatch. Selection was applied to a two-trait index of estimated breeding values for 10-month body weight (i.e., approximate market weight) and thermal growth coefficient between 10 and 13 months, and both traits were given equal weighting in the index. Objectives of this study were to estimate direct selection responses for BW traits and thermal growth coefficient, and correlated response for condition factor traits. Heritability estimates were 0.28 ± 0.08 to 0.43 ± 0.14 for BW between 5 and 13 months post-hatch, 0.12 ± 0.03 for thermal growth coefficient, and 0.40 ± 0.04 and 0.36 ± 0.04 for condition factor at 10 and 13 months post-hatch, respectively. Genetic correlations among the four BW measures were highest between adjacent BW measures (0.54 ± 0.19 to 0.82 ± 0.05) and decreased as time between measures increased. Genetic correlation between thermal growth coefficient and 10-month BW was low (0.18 ± 0.13), and genetic correlations between condition factor and BW measured at the same age were moderate (0.39 ± 0.09 to 0.45 ± 0.08). Compared to randomly-mated control lines, selection response in the selected line averaged 10.6% (5-month BW), 9.8% (8-month BW), 12.7% (10-month BW), 11.9% (13-month BW), 2.1% (thermal growth coefficient), 3.4% (10-month condition factor), and 3.3% (13-month condition factor) per generation. The rate of inbreeding averaged 0.86% per generation in the selection line, with a cumulative inbreeding estimate of 4.5% in the last generation. The low heritability of thermal growth coefficient, and low genetic correlation with 10-month BW, resulted in only modest selection response for thermal growth coefficient. Larger heritabilities of BW measured at fixed ages, and large genetic correlations between serial BW measures, suggest that direct selection on BW will be more favorable than selection on TGC. This study demonstrates the large and sustained potential for genetic improvement of growth performance in domesticated rainbow trout with only modest accumulation of inbreeding, and provides empirical selection response estimates that have direct inference to commercial breeding programs aiming to select for growth to larger market BW. Statement of relevance Quantitative genetics data from this relatively long-term and large-scale selective breeding program have direct inference to commercial breeding programs selecting for improved growth, but for which maintenance of control lines is not practical.

El objetivo fue estudiar y modelar las curvas de lactancia individuales en vacas Siboney, comparando cuatro modelos matemáticos. En total, 31,631 registros de producción de leche del día de control (PDC) de 3,697 lactancias (1 a 5) provenientes de 2,632 vacas Siboney de Cuba (5/8 Holstein 3/8 Cebú Cubano) registrados mensualmente entre 1994 y 2003 se ajustaron mediante las funciones de Wood, Wilmink, Ali-Schaeffer y Polinomios de Legendre. Los parámetros se estimaron usando regresiones no lineales y la bondad de ajuste se midió mediante el coeficiente de determinación ajustado (R2A). Se obtuvieron valores de R2A > 0.75 en 23, 24, 28 y 36 % de las lactancias para los modelos de Wood, Wilmink, Ali-Schaeffer y Polinomios de Legendre, respectivamente. Los modelos de Wood y Wilmink describieron cuatro tipos de curvas; y los modelos de Ali-Schaeffer y los Polinomios de Legendre 17 y 20, de los 32 grupos teóricos posibles. Las correlaciones entre los parámetros para la función de Ali-Schaeffer fueron superiores a las estimadas para los polinomios de Legendre. Las funciones propuestas representaron las diferentes formas entre curvas de lactancia y en especial, los modelos de cinco parámetros detectaron mayor diversidad que el resto de las funciones.Esto apunta que, aunque formas adicionales pueden considerarse como derivaciones de los dos grupos clásicos de curvas típicas o atípicas, esta práctica podría comprometer la variabilidad entre curvas de lactancia en un hato, por lo que serán necesarios más estudios.

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. 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). To obtain this information we evaluated the spent medium from each time period by 1H NMR. 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. 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.

Objectives were to determine the interaction of prepartum supplement level and age at weaning on cow BW, BCS, milk production, reproduction, and calf performance up to weaning in a fall-calving system over 2 yr. Mature, multiparous, Angus × Simmental cows (yr 1: 326 cows, 9 pastures, BW = 632 ± 67 kg, and BCS = 5.7 ± 0.58; yr 2: 383 cows, 9 pastures, BW = 606 ± 70 kg, and BCS = 5.8 ± 0.74) were used in a split-plot design that included 3 supplement levels-no supplement (NS), low supplement (LS; 2.16 kg∙cow∙d), or high supplement (HS; 8.61 kg∙cow∙d)-and 2 ages at weaning-78 ± 11 d of age (early weaned; EW) or 186 ± 11 d of age (normal weaned; NW). Cows grazed endophyte-infected tall fescue/red clover pastures and were bunk fed supplement (70% dried distillers' grains with solubles and 30% soybean hulls) 103 ± 11 d prepartum to 2 ± 11 d postpartum. Cow BW was greater ( < 0.01) for cows fed HS at precalving (49 ± 11 d prepartum), postcalving (26 ± 11 d postpartum), and postbreeding (81 d after AI) compared with cows fed NS and LS. Prepartum supplementation did not affect ( ≥ 0.62) calf birth BW, percent of calves dead at birth, or percent of cows calving unassisted. Prepartum supplementation tended ( = 0.10) to improve AI conception. Early weaning increased ( ≤ 0.05) AI conception and postbreeding cow BW and BCS compared with cows with NW calves. Neither prepartum supplementation nor age at weaning affected ( ≥ 0.28) overall pregnancy rate. At time of early weaning, BW was increased ( = 0.05) for steers from cows fed LS compared with steers from cows fed NS. Steer BW at time of normal weaning and ADG between early and normal weaning was greater ( < 0.01) for EW steers compared with NW steers. A year × age at weaning interaction occurred ( < 0.01) for ultrasound marbling score at time of normal weaning. In yr 1, marbling was decreased ( = 0.04) for EW steers compared with NW steers; however, in yr 2, marbling was increased ( < 0.01) for EW steers compared with NW steers. In conclusion, there was no interaction between level of supplement during late gestation and age at weaning on cow BW, BCS, milk production, AI conception, and overall pregnancy rate in mature beef cows nor in their steer progeny's BW or ultrasound marbling. Both prepartum supplementation and early weaning improved cow BW, BCS, and reproduction. Minimal effects of dam prepartum supplement level on calf performance up to weaning were observed. Early weaning improved calf growth but had inconsistent effects on ultrasound marbling across years.

El objetivo del estudio fue ana lizar el impacto de factores ambientales, así como estimar componentes de (co)varianza de caracteres reproductivos en el bovino Chacuba. Para ello se utilizaron 4,957 registros de vacas, hijas de 893 madres y 110 sementales. Se probaron modelos que consideraron el número de parto, el sexo del becerr o y los grupos de contemporáneas (hato-año-época de parto) como efectos fijos. La época de parto se incluyó como bi mestre, trimestre, cuatrimestre o semestre. Los caracteres intervalo parto concepción (IPC), intervalo entre partos (IP) y servicios por concepción (SC) se analizaron con un modelo univariado y multivariado utilizando el pr ograma ASReml. El número de parto ( P 0.05) no fue un efecto significativo. Las heredabilidades para los rasgos analizados fueron bajas con valores de 0.14±0.02, 0.15±0.02 y 0.04±0.01 para IPC, IP y SC, r espectivamente. Las correlaciones genéticas fueron altas entre IPC e IP (0.99±0.43) pero bajas entre IPC y SC (0.10± 0.14) y entre IP y SC (0.09±0.11). Los modelos de estimación de parámetros genéticos para IPC, IP y SC en vacas Ch acuba deben considerar el número de parto y los grupos de contemporáneas que incluyan hato-año-bimestre. La sele cción indirecta para el intervalo entre partos a partir del intervalo parto-concepción puede ser implementada, dada la correlación genética entre estos caracteres.

Artificial insemination technique and semen preparation impact boar utilization efficiency, genetic dissemination, and biosecurity. Intrauterine (IUI) and deep intrauterine (DUI) AI techniques require lower number of spermatozoa per dose compared to conven- tional (CON) AI. Frozen semen (FRO) has been associ- ated with lower reproductive performance compared to fresh semen (FRE) preparation. The combined effects of 3 AI techniques (CON, IUI, and DUI) and 2 semen prepa- rations (FRE and FRO) on the financial indicators of a pig crossbreeding system were studied. A 3-tier system was simulated in ZPLAN and the genetic improvement in a representative scenario was characterized. The cross of nucleus lines B and A generated 200,000 BA sows at the multiplier level. The BA sows were inseminated (CON, IUI, or DUI) with FRE or FRO from line C boars at the commercial level. Semen preparation and AI technique were represented by distinct sow:boar ratios in the C × BA cross. A range of farrowing rates (60 to 90%) and litter sizes (8 to 14 liveborn pigs) were tested. Genetic improve- ment per year for number born alive, adjusted 21-d litter weight, days to 113.5 kg, backfat, and ADG were 0.01 pigs per litter, 0.06 kg, -0.09 d, -0.29 mm, and 0.88 g, respectively. On average, the net profit for FRE (FRO) increased (P-value < 0.0001) from CON to IUI and DUI by 2.2 (3.2%) and 2.6% (4%), respectively. The differenc- es in profit between techniques were driven by differences in costs. Differences in fixed costs between IUI and DUI relative to CON were -2.4 (-5.2%) and -3.4% (-7.4%), respectively. The differences in total costs between FRE and FRO were lower than -5%. The difference in variable costs between FRE and FRO ranged from -5.3 (CON) to -24.7% (DUI). Overall, insemination technique and semen preparation had a nonlinear effect on profit. The average relative difference in profit between FRE and FRO was less than 3% for the scenarios studied.

The aim of this study was to model individual lactation curves for milk production in Alpine goats by comparing four models based on their fit to typical or atypical lactation curves. Three thousand five hundred and eighty-one test-day records were analyzed for 535 first lactations of Alpine goats controlled monthly between 1994 and 2008 in the Genetics Enterprise “Los Naranjos”, in the province of La Havana, Cuba. The mathematical models used to describe the lactation curve were: Wood, Wilmink, Ali-Schaeffer and Legendre’s orthogonal polynomials. Parameters were estimated utilizing nonlinear regression and iterative procedures. The criterion used to verify the goodness of fit was the adjusted coefficient of determination (R2ADJ). Goodness of fit based on R2ADJ>0.75 was accomplished for 46.3, 47.4, 60.5 and 69.9% of lactations for Wood, Wilmink, Ali-Schaeffer and Legendre´s polynomials, respectively. The three parameter models detected four types of curves, meanwhile Ali-Schaeffer and Legendre’s polynomials models were able to recognize 9 and 14 types of curves, respectively, from the 32 possible theoretical groups that were determined by combinations of the signs of the parameters of each model. Correlations between parameter values estimated for Ali-Schaeffer were higher than those estimated for Legendre´s polynomials. The different curve shapes found in the 5-parameter models can be considered as modifications of the two main groups of curve shapes known in the literature: typical and atypical. Results of this study indicate that Ali-Schaeffer and Legendre’s orthogonal polynomials models were the best functions to model adequately individual lactation curves of Alpine goats. Furthermore, the appearance of several groups of individual curves suggests the need of more research on comparison of individual models within group.

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 1,447 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 to 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.

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.

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.

Con el objetivo de estimar los valores de heredabilidad y las correlaciones genéticas entre cinco medidas de persistencia usando un modelo de regresión aleatoria con polinomios de Legendre, se analizaron 17,034 registros de producción de leche del día del control de 2,086 vacas Siboney de Cuba (primera lactancia) que parieron entre 1995 y 2003 en 50 hatos. Los estimados de heredabilidad para la persistencia de la lactación variaron de 0.18±0.02 a 0.29±0.02. Las correlaciones genéticas entre las diferentes medidas de persistencia oscilaron de -0.71 a 0.95. Las correlaciones genéticas entre la producción de leche en los distintos días del control, así como la producción acumulada hasta los 305 días de lactación (PL305) y las distintas medidas de persistencia tomaron valores de -0.06 hasta 0.11. Basado en los niveles de heredabilidad y en las correlaciones genéticas de las medidas de persistencia con la PL305, se concluye que es factible efectuar la selección conjunta para la PL305 y persistencia de la lactación en el ganado Siboney utilizando la diferencia en el área bajo la curva entre el tercio final de la lactación (día 201 al 300) y el tercio inicial del día 1 al 100, (sumatoria de la contribución de cada día, en el periodo de los 61 a 280 días de lactación, como una desviación de la producción en el día 60) como medidas de persistencia.

Four semen traits: volume (VOL), concentration (CON), progressive motility of spermatozoa (MOT), and abnormal spermatozoa (ABN) provide complementary information on boar fertility. Assessment of the impact of selection for semen traits is hindered by limited information on economic parameters. Objectives of this study were to estimate economic values for semen traits and to evaluate the genetic gain when these traits are incorporated into traditional selection strategies in a 3-tier system of swine production. Three-way (maternal nucleus lines A and B and paternal nucleus line C) and 4-way (additional paternal nucleus line D) crossbreeding schemes were compared. A novel population structure that accommodated selection for semen traits was developed. Three selection strategies were simulated. Selection Strategy I (baseline) encompassed selection for maternal traits: number of pigs born alive (NBA), litter birth weight (LBW), adjusted 21-d litter weight (A21), and number of pigs at 21 d (N21); and paternal traits: number of days to 113.5 kg (D113), backfat (BF), ADG, feed efficiency (FE), and carcass lean % (LEAN). Selection Strategy II included Strategy I and the number of usable semen doses per collection (DOSES), a function of the 4 semen traits. Selection Strategy III included Strategy I and the 4 semen traits individually. The estimated economic values of VOL, CON, MOT, ABN, and DOSES for 7 to 1 collections/wk ranged from $0.21 to $1.44/mL, $0.12 to $0.83/10 spermatozoa/mm, $0.61 to $12.66/%, -$0.53 to -$10.88/%, and $2.01 to $41.43/%, respectively. The decrease in the relative economic values of semen traits and DOSES with higher number of collections per wk was sharper between 1 and 2.33 collections/wk than between 2.33 and 7 collections/wk. The higher economic value of MOT and ABN relative to VOL and CON could be linked to the genetic variances and covariances of these traits. Average genetic gains for the maternal traits were comparable across strategies. Genetic gains for paternal traits, excluding semen traits, were greater in selection Strategy I than Strategies III and II. Genetic gains for paternal and maternal traits were greater in the 4- and 3-way schemes, respectively. The selection strategy including the 4 semen traits is recommended because this approach enables genetic gains for these traits without compromising the genetic gains for maternal traits and with minimal losses in genetic gains for paternal traits.

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.

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 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.

El objetivo de este trabajo fue estimar componentes de (co)varianza de caracteres reproductivos y su relación genética con el peso al destete (PD) en el ganado Cebú de Cuba. Se utilizaron datos de 51,193 partos de 17,890 vacas paridas entre 1981 y 2000 en 48 hatos. El pedigrí incluyó 23,903 individuos. Para estimar las correlaciones genéticas entre el PD y los caracteres reproductivos se utilizaron 67,829 registros, 19,768 fueron para PD y 48,061 para rasgos reproductivos. Se aplicaron modelos univariados y bivariados con el procedimiento REML y utilizando el programa ASREML. La heredabilidad para las variables reproductivas fue baja (0.01 a 0.09). Las correlaciones genéticas entre días abiertos (DA) fueron altas entre los tres primeros partos (0.92 a 0.99) y menores entre estos y los posteriores (0.45 a 0.90). Las correlaciones genéticas entre los DA y el intervalo a la primera inseminación, intervalo entre partos y servicios por gestación fueron de 0.98, 0.99 y 0.39, respectivamente. Las correlaciones genéticas del PD con los rasgos reproductivos señalados variaron de 0.04 a 0.07. Se concluye que la heredabilidad estimada para los caracteres reproductivos fue baja, las correlaciones genéticas entre ellos por lo general fueron altas, y su correlación genética con el peso al destete fue baja.

Summary 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. Keywords: beef cattle, fertility, genetic correlations, heritability, post-partum interval. Resumen Antecedentes: en Cuba existe poca informacion relacionada con los componentes geneticos del periodo posparto en bovinos para carne. Objetivo: comparar los estimados de parametros geneticos de los dias abiertos (DO) obtenidos con tres modelos en ganado Charolais de Cuba. Metodos: 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 utilizo el programa WOMBAT para la estimacion 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 regresion aleatoria (ARM) tomando el numero del parto como variable independiente. Resultados: la media general de DO fue de 171 ± 93 dias. La tendencia del valor promedio para DO en cada parto fue decreciente desde el primero al decimo, con un comportamiento estacional alrededor de 155 dias 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 estimo una heredabilidad de 0,06. Valores de 0,05 en el primer parto hasta 0,07 en el decimo fueron estimados con el ARM. Las correlaciones geneticas entre DO para los diferentes partos fueron cercanos a la unidad. Conclusiones: los cambios de la heredabilidad estimada para DO a traves 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. Palabras clave: bovinos para carne, correlaciones geneticas, fertilidad, heredabilidad, intervalo post-parto. Resumo Antecedentes: em Cuba ha pouca informacao sobre os componentes geneticos do periodo pos-parto em bovinos de corte. Objetivo: comparar as estimativas de parâmetros geneticos de dias vazios (DO) obtidos com os tres modelos em bovinos Charoles de Cuba. Metodos: os dados de controle reprodutivo individual de bovinos Charoles 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. Ate 10 partos foram considerados por femea que ocorreram entre 1981 e 2005. O programa WOMBAT foi utilizado para estimar os componentes da variância. Tres modelos foram aplicados; um modelo univariado (UM) para cada paridade separado ate o sexto parto; um modelo de repetibilidade (RM) com todas as paricoes; e um modelo de regressao aleatoria (ARM), tendo o numero de partos como uma variavel independente. Resultados: a media geral foi de 171 ± 93 dias. A tendencia do valor medio para o DO em cada parto foi diminuindo desde o primeiro ate o decimo parto com um desempenho sazonal em torno de 155 dias entre o quarto e oitavo parto. A herdabilidade estimada para DO pela UM foi variavel com valores de 0,03 no primeiro parto e 0,06 no sexto. Essas variacoes nao podem ser observadas com RM que estimou uma herdabilidade de 0,06. Os valores de 0,05 no primeiro parto ate 0,07 no decimo foram estimados com ARM. As correlacoes geneticas entre DO para diferentes partos foram proximas da unidade. Conclusoes: alteracoes da herdabilidade estimada para DO durante a vida produtiva de uma femea pode ser observado com ARM. As estimativas de herdabilidade foram baixas e nao diferiram entre os resultados apresentados em outras racas de gado de corte. Palavras chave: bovino de corte, correlacao genetica, fertilidade, herdabilidade, intervalo pos-parto.