Predicted Transmitting Ability Research Articles

Associations of bovine beta-casein and kappa-casein genotypes with genomic merit in Holstein Friesian cattle

Abstract. The relationship between the index values used to evaluate the genomic value and essential markers such as casein genes provides important information at the herd level. Therefore, this study aimed to determine the association between casein gene genotypes and the indices of genetic merit in Holstein Friesian cattle. A total of 805 cows were genotyped using the Affymetrix® Axiom® array system. We used data composed of the total performance index (TPI) and net merit (NM) values as well as the predicted transmitting abilities (PTAs) indices, including milk, fat, fat percentage, protein, protein percentage, combined fat and protein (CFP), productive life (PL), somatic cell score (SCS), daughter pregnancy rate (DPR), livability (LV), udder composite (UDC), and feet–legs composite (FLC) of each animal. The statistical analysis consisted of a one-way analysis of variance (ANOVA) test followed by Tukey's test. The A2A2 and the AB genotypes were predominant in the CSN2 and CSN3 genes, respectively. The A2A2 animals were found to have higher TPI and NM values. Moreover, they exhibited higher PTA values for proteins, CFP, and PL. On the other hand, the A1A1 genotype was significantly associated with the highest UDC. Concerning the CSN3 haplotypes, the BB animals had higher protein percentage and PL than alternative haplotypes. The AA and AB haplotypes were found to be significantly associated with the highest SCS and DPR values, respectively. In addition, the BE haplotype had the highest NM. Selection procedures focusing on casein genes in dairy cattle are becoming increasingly common worldwide, especially for A2 milk. However, herd-based dynamics are also fundamental to providing a desired genetic merit for the animals. This study may be valuable for further analyses regarding selection decisions using the breeding values of candidate animals in commercial dairy herds.

Genetic analysis of lactation consistency in U.S. Holsteins using temporal variation in daily milk weights

The ability of a dairy cow to perform reliably over time is an interesting trait to include in dairy cattle breeding programs aimed at improving dairy cow resilience. Consistency, defined as the quality of performing as expected each day of the lactation, could be highly associated with resilience, defined as animal's ability to maintain health and performance in the presence of environmental challenges, including pathogens, heat waves, and nutritional changes. A total of 51,415,022 daily milk weights collected from 2018 to 2023 were provided for 255,191 multiparous Holstein cows milked 3 times daily in conventional parlor systems on farms in 32 states. The temporal variance (TempVar) of milk yield from 5 to 305 d postpartum was computed as the log-transformed variance of daily deviations between observed and expected individual milk weights. Lower values of TempVar imply smaller day-to-day deviations from expectations, indicating consistent performance, whereas larger values indicate inconsistent performance. Expected daily milk weights were computed using 3 nonparametric and parametric regression models: 1) LOESS regression with a 0.75 span; 2) polynomial quantile regression using the median (0.5 quantile), and 3) polynomial quantile regression using a 0.7 quantile. The univariate statistical model included age at first calving and herd-year-season as fixed effects and cow as a random effect. Heritability estimates (standard errors) of TempVar phenotypes calculated over the entire lactation ranged between 0.227 (0.011) and 0.237 (0.011), demonstrating that cows are genetically predisposed to display consistent or inconsistent performance. Estimated genetic correlations calculated using a multiple trait model between TempVar traits and between lactations were high (>0.95), indicating TempVar is repeatable across lactations and robust to the model used to compute expected daily milk yield. Higher TempVar phenotypes reflect more variation in performance, hence greater inconsistency, which is undesirable. Therefore, correlations between predicted transmitting abilities (PTAs) for TempVar and milk yield of 0.57 indicate that high-producing cows exhibit more day-to-day variation in performance. Correlations with productive life and livability were -0.38 and -0.48, respectively. Correlations between PTAs for TempVar and those of postpartum health traits were also negative, ranging from -0.41 to -0.08. Given that health traits are derived from disease resistance measurements, and higher health trait PTAs are preferred, our results indicate that more consistent cows tend to have fewer health problems and greater longevity. Overall, our findings suggest that temporal variation in daily milk weights can be used to identify consistent animals that maintain expected performance throughout the lactation, which will enable selection for greater resilience to management and environmental perturbations.

Genomic evaluation of late-term abortion in cows recorded through Dairy Herd Improvement test plans

Late-term abortions cause significant economic loss and are of great concern for dairy herds. Late-term abortions >152 d and <251 d of gestation that terminate a lactation or initiate a new lactation have long been recorded by Dairy Herd Improvement (DHI). For 24.8 million DHI lactations, the average recorded incidence of late-term abortions across all years (2001–2018) was 1.2%. However, the 1.3% incidence of abortions reported in 2012 has declined to <1.0% incidence since 2015. Small adjustments were applied to the 82 million daughter pregnancy rate (DPR), 29 million cow conception rate (CCR), and 9 million heifer conception rate (HCR) records to account for late-term abortions more accurately. Fertility credits for CCR and HCR were changed to treat the last breeding as a failure instead of success if the next calving was coded as a late-term abortion. Similarly, when computing DPR, days open is now set to the maximum value of 250 instead of the reported days open if the next reported calving is an abortion. The test of these changes showed very small changes in standard deviation and high correlations (0.997) of adjusted predicted transmitting abilities (PTA) with official PTA from about 20,000 Holstein bulls born since 2000 with >50% reliability. For late-term abortion as a trait, estimated heritability was only 0.001 and PTA had a standard deviation of only 0.1% for recent sires with high reliability (>75%). Young animal genomic PTA have near 50% reliability but range only from −0.5 to +0.4 because of the low incidence and heritability. Genetic trend was slightly favorable and late-term abortion PTA were correlated favorably by 0.27 with net merit, 0.49 with productive life, 0.33 with livability, 0.23 with CCR, 0.20 with HCR, 0.26 with DPR, −0.31 with somatic cell score, −0.24 with daughter stillbirth, and −0.26 with daughter dystocia. Thus, PTA for late-term abortions should not be needed as a separate fertility trait and instead these minor edit changes should suffice. The PTA for late-term abortions would add little value because national evaluations for current fertility traits already account for those economic losses.

The association between insemination eligibility and reproductive performance of nulliparous heifers on subsequent body weight and milk production of primiparous Holstein cows

The objective of this retrospective cohort study was to determine the association between insemination eligibility and reproductive performance of nulliparous heifers with subsequent body weight (BW) at 30 d in milk (DIM) and milk production at wk 4, 8, and 12 of lactation of primiparous cows. The final data set included 1,849 primiparous Holstein cows from a commercial dairy herd. Data extracted from a commercial dairy herd management software program included parent average predicted transmitting abilities (PTA), bovine respiratory disease (BRD) incidence, pregnancies per artificial insemination (P/AI) at first insemination as nulliparous heifers, BW at 30 DIM, percent mature body weight (%MBW), and mean weekly milk production at wk 4, 8, and 12 of lactation. Heifers were eligible for first insemination at 380 d of age and were detected in estrus and artificially inseminated with sexed semen. Quartiles based on BW at 30 DIM and %MBW were created in ascending order as follows: Q1 (lightest; n = 462), Q2 (light-moderate; n = 456), Q3 (moderate; n = 472), and Q4 (heaviest; n = 459). Only Q3 and Q4 cows achieved ≥85% MBW postcalving based on the herd MBW of 686.2 kg. The incidence of BRD during heifer development was greatest for Q1 cows, and Q1 cows had fewer days on feed as heifers than Q4 cows, resulting in a shorter growth period to achieve ≥85% MBW postcalving. Overall, Q1 cows had a greater PTA for daughter pregnancy rate and heifer conception rate than Q4 cows, which was associated with approximately 26 percentage points more P/AI at first insemination as heifers for Q1 than for Q4 cows. Finally, Q1 cows yielded approximately 5 kg per cow/d less milk than Q4 cows. Thus, insemination eligibility and reproductive performance of heifers, calfhood BRD incidence, and genetic potential for reproductive performance were associated with BW at 30 DIM and milk production at wk 4, 8, and 12 of lactation of primiparous cows.

Effect of supplement crude protein concentration on milk production over the main grazing season and on nitrogen excretion in late-lactation grazing dairy cows

The objectives of this study are to evaluate the effects of (1) a potential interaction between supplement crude protein (CP) concentration and differing cow genotypes on milk production, (2) differing cow genotypes on milk production, and (3) decreasing the supplement CP concentration on milk production and N excretion during the main grazing season within a spring-calving herd. A 2 × 2 factorial arrangement experiment, with 2 feeding strategies [14%; n = 30 (lower CP; LCP) and 18%; n = 28 (higher CP; HCP) CP concentrate supplements] offered at varying levels according to pasture availability and days in milk (DIM) was conducted over the main grazing season from April 3 to September 3, 2019, at University College Dublin Lyons Farm. Cows were also grouped into 2 genotype groups: lower milk genotype; n = 30 [LM; milk kg predicted transmitting ability (PTA): 45 ± 68.6 (mean ± SD); fat kg PTA: 10 ± 4.9; and protein kg PTA: 7 ± 2.3] and higher milk genotype; n = 28 [HM; milk kg PTA: 203 ± 55.0; fat kg PTA: 13 ± 3.8; and protein kg PTA: 10 ± 2.4]. A total of 46 multiparous and 12 primiparous (total; 58) Holstein Friesian dairy cows were blocked on parity and balanced on DIM, body condition score, and Economic Breeding Index. Cows were offered a basal diet of grazed perennial ryegrass pasture. The N partitioning study took place from August 25 to 30, 2019 (187 ± 15.2 DIM). No interactions were observed for any milk production or milk composition parameter. No effect of supplement CP concentration was observed for any total accumulated milk production, daily milk production, or milk composition parameter measured. The HM cows had increased daily milk yield (+1.9 kg), fat and protein (+0.15 kg), and energy-corrected milk (+1.7 kg), compared with the LM cows. Furthermore, HM cows had decreased milk protein concentration (-0.1%) compared with LM cows. For the N partitioning study, cows offered LCP had increased pasture dry matter intake (PDMI; +0.9 kg/d), dietary N intake (+0.022 kg/d), feces N excretion (+0.016 kg/d), and decreased N partitioning to milk (-2%), and N utilization efficiency (-2.3%). In conclusion, offering cows LCP had no negative influence on milk production or milk composition over the main grazing season where high pasture quality was maintained. However, any potential negative effects of offering LCP on milk production may have been offset by the increased PDMI. Furthermore, offering cows LCP decreased N utilization efficiency due to the higher PDMI and feed N intake associated with cows on this treatment in our study.

Late-gestation heat stress abatement in dairy heifers promotes thermoregulation and improves productivity

Multiparous, nonlactating pregnant cows are negatively affected by heat stress, but the effect of heat stress on more thermotolerant pregnant heifers has received less attention. Our objective was to characterize the effect of late-gestation heat abatement on thermoregulatory responses and subsequent milk production of nulliparous Holstein heifers. Pregnant heifers, blocked by body condition score (BCS) and predicted transmitting ability (PTA) for milk, were enrolled in either heat stress (HT, shade of freestall barn; n = 16) or cooling (CL, shade of freestall barn, water soakers, and fans; n = 15) environments during the last 60 d of pregnancy (~8 weeks). Rectal temperature (RT; thermometer), respiration rate (RR; breaths/min), sweating rate (SR; VapoMeter, Delfin Technologies, Kuopio, Finland), and skin temperature (ST; infrared thermometer) were measured thrice weekly from enrollment to calving. Vaginal temperature (VT; i-button intravaginal device) was measured every 10 min for 7 consecutive days at wk -8, -6, -4, and -2 relative to calving and averaged hourly. Daily thermoregulatory patterns assessed by SR and ST, were measured every 4 h over a 36-h time interval at wk -6, -4, and -2 relative to calving. Upon calving, milk, protein, and fat yields were recorded twice daily for 15 wk. The average temperature-humidity index (Hobo Pro temperature probe, Onset Computer Corporation, Pocasset, MA) in the barn during the precalving period was 77 (minimum of 72, maximum of 82). Only heifers that gave birth to a female calf (CL = 12, HT = 14) were included in the statistical analysis. In the precalving period, CL heifers had lower RR (44.3 vs. 60.0 ± 1.6 breaths/min), RT (38.7 vs. 38.8 ± 0.04°C), unshaved ST (34.7 vs. 35.3 ± 0.17°C), and unshaved SR (19.0 vs. 35.2 ± 1.9 g/m2h), relative to HT heifers. Additionally, VT was lower in CL heifers during wk -4, and -2, specifically during early morning and early afternoon hours. When measured over a 36-h time interval, ST and SR were lower in CL heifers, when compared with HT heifers for all weeks. Notably, ST was reduced overnight and SR was reduced during the daytime. Cooled heifers had higher milk yield (35.8 vs. 31.9 ± 1.4 kg/d), when compared with HT heifers. Similar to multiparous cows, our data indicate that actively cooling heifers in late pregnancy is effective in promoting thermoregulation and results in elevated milk production postcalving.

Major quantitative trait loci influencing milk production and conformation traits in Guernsey dairy cattle detected on Bos taurus autosome 19

The goal of this study was to identify potential quantitative trait loci (QTL) for 27 production, fitness, and conformation traits of Guernsey cattle through genome-wide association (GWA) analyses, with extra emphasis on BTA19, where major QTL were observed for several traits. Animals' de-regressed predicted transmitting abilities (PTA) from the December 2018 traditional US evaluation were used as phenotypes. All of the Guernsey cattle included in the QTL analyses were predictor animals in the reference population, ranging from 1,077 to 1,685 animals for different traits. Single-trait GWA analyses were carried out by a mixed-model approach for all 27 traits using imputed high-density genotypes. A major QTL was detected on BTA19, influencing several milk production traits, conformation traits, and livability of Guernsey cattle, and the most significant SNP lie in the region of 26.2 to 28.3 Mb. The myosin heavy chain 10 (MYH10) gene residing within this region was found to be highly associated with milk production and body conformation traits of dairy cattle. After the initial GWA analyses, which suggested that many significant SNP are in linkage with one another, conditional analyses were used for fine mapping. The top significant SNP on BTA19 were fixed as covariables in the model, one at a time, until no more significant SNP were detected on BTA19. After this fine-mapping approach was applied, only 1 significant SNP was detected on BTA19 for most traits, but multiple, independent significant SNP were found for protein yield, dairy form, and stature. In addition, the haplotype that hosts the major QTL on BTA19 was traced to a US Guernsey born in 1954. The haplotype is common in the breed, indicating a long-term influence of this QTL on the US Guernsey population.

The relationships among sire’s predicted transmitting ability for daughter pregnancy rate and cow conception rate and daughter’s reproductive performance in Canadian Holstein cows

The objectives of this study were to (1) characterize the variability for sire’s predicted transmitting ability (PTA) for daughter’s pregnancy rate (DPR) and cow conception rate (CCR), (2) determine the relationships among sire’s PTA for DPR, sire’s PTA for CCR, daughter’s parity, and daughter’s 305-d mature-equivalent (ME) milk production, and (3) evaluate the associations among sire’s PTA for DPR and CCR and daughter’s reproductive performance [pregnancy to first artificial insemination (P/AI), pregnancy by 150 d in milk (PR150) and pregnancy loss (PL) after first AI] in Canadian Holstein cows. The data were obtained from 822 lactating Holstein cows from 10 commercial dairy herds located in Alberta. Overall mean (range) for sire’s PTA for DPR and CCR was −0.09 (−9.6 to 8.2) and −0.05 (−9.9 to 7.4), respectively. Sire’s PTA for DPR was strongly and positively associated with sire’s PTA for CCR (r = 0.89; P < 0.01). Sire’s PTA for DPR and CCR were weakly and negatively associated with parity (r = −0.15 and −0.17, respectively; P < 0.01); however, the amount of phenotypic variation in sire’s PTA for DPR and CCR explainable by parity was small (coefficient of determination; R2 = 0.02). The daughter’s 305-d ME milk production tended to be weakly but positively associated with sire’s PTA for DPR (r = 0.06; P = 0.07) and CCR (r = 0.06; P = 0.10); however, the amount of phenotypic variation in daughter’s 305-d ME milk production explainable by changes in sire’s PTA for DPR or CCR was small (R2 = 0.004 and 0.003, respectively). Overall P/AI, PR150 and PL were 38, 65 and 12%, respectively. Sire’s PTA for DPR tended to be associated with P/AI (P = 0.08) but was significantly associated with PR150 (P = 0.03). For every unit increase in sire’s PTA for DPR, the estimated probabilities for P/AI and PR150 increased by 6.2 and 7.5%, respectively. Sire’s PTA for CCR was not associated with P/AI or PR150. Neither sire’s PTA for DPR nor CCR were associated with PL. In summary, sire’s PTA for DPR and CCR were highly variable and positively correlated. Sire’s PTA for DPR was associated with daughter’s P/AI and PR150, but sire’s PTA for CCR was not associated with any of the measured reproductive outcomes. Therefore, selecting sires with high PTA for DPR has the potential to improve the reproductive efficiency of Canadian dairy herds.

Relationship between sire predicted transmitting ability for daughter pregnancy rate and daughter's reproductive performance and milk production in Japanese dairy herds.

Modern genetic improvement in dairy cattle is directed towards improvement of fertility; however, reproduction traits generally exhibit a genetic antagonism with milk yield. Herein, we aimed to clarify the effects of sire predicted transmitting ability (PTA) for daughter pregnancy rate (DPR) on the reproductive performance and milk yield of daughters in Japanese dairy herds. We conducted a retrospective cohort study on four dairy herds in eastern Hokkaido, Japan, using 1,612 records from 1,018 cows with first, second, or third calvings between March 2015 and September 2018. First, we classified sires into three groups based on the tertile value of their DPR estimate: ≤ −2.2 (low), −2.1 to −0.4 (intermediate), and ≥ −0.3 (high). Subsequently, we compared the sire PTA estimates, reproductive performance, and milk production among DPR groups for each parity of the daughters. In the first and second parity, the hazard of pregnancy by 200 days postpartum was highest in cows from the high-DPR group (P < 0.05); in the third parity, it was unaffected by DPR group. Although sire PTA for milk production in cows from the low-DPR group was highest, actual milk production was unaffected by DPR group regardless of parity. Our findings demonstrate that using sires with PTA for high fertility can enable farmers to improve reproductive performance without decreasing milk yield in Japanese dairy herds. However, it should be noted that sires with PTA for high fertility are at risk for reducing the genetic merit for milk production.

Choice of artificial insemination beef bulls used to mate with female dairy cattle

Understanding the preferences of dairy cattle producers when selecting beef bulls for mating can help inform beef breeding programs as well as provide default parameters in mating advice systems. The objective of the present study was to characterize the genetic merit of beef artificial insemination (AI) bulls used in dairy herds, with particular reference to traits associated with both calving performance and carcass merit. The characteristics of the beef AI bulls used were compared with those of the dairy AI bulls used on the same farms. A total of 2,733,524 AI records from 928,437 females in 5,967 Irish dairy herds were used. Sire predicted transmitting ability (PTA) values and associated reliability values for calving performance and carcass traits based on national genetic evaluations from prior to the insemination were used. Fixed effects models were used to relate both genetic merit and the associated reliability of the dairy and beef bulls used on the farm with herd size, the extent of Holstein-Friesian × Jersey crossbreeding adopted by the herd, whether the herd used a technician insemination service or do-it-yourself, and the parity of the female mated. The mean direct calving difficulty PTA of the beef bulls used was 1.85 units higher than that of the dairy bulls but with over 3 times greater variability in the beef bulls. This 1.85 units equates biologically to an expectation of 1.85 more dystocia events per 100 dairy cows mated in the beef × dairy matings. The mean calving difficulty PTA of the dairy AI bulls used reduced with increasing herd size, whereas the mean calving difficulty PTA of the beef AI bulls used increased as herd size increased from 75 cows or fewer to 155 cows; the largest herds (>155 cows) used notably easier-calving beef bulls, albeit the calving difficulty PTA of the beef bulls was 3.33 units versus 1.67 units for the dairy bulls used in these herds. Although we found a general tendency for larger herds to use dairy AI bulls with lower reliability, this trend was not obvious in the beef AI bulls used. Irrespective of whether dairy or beef AI bulls were considered, herds that operated more extensive Holstein-Friesian × Jersey crossbreeding (i.e., more than 50% crossbred cows) used, on average, easier calving, shorter gestation-length bulls with lighter expected progeny carcasses of poorer conformation. Mean calving difficulty PTA of dairy bulls used increased from 1.39 in heifers to 1.79 in first-parity cows and to 1.82 in second-parity cows, remaining relatively constant thereafter. In contrast, the mean calving difficulty PTA of the beef bulls used increased consistently with cow parity. Results from the present study demonstrate a clear difference in the mean acceptable genetic merit of beef AI bulls relative to dairy AI bulls but also indicates that these acceptable limits vary by herd characteristics.

Genetic evaluation of milking buffaloes (Bubalus bubalis): bull ranking

ABSTRACT The objective of this study was to evaluate genetic aspects related to production and reproductive efficiency of Murrah and Mediterranean buffaloes and their crosses. A ranking of bulls from Embrapa Eastern Amazonia was also composed to guide assisted mating. Birth records of 2,322 Murrah, Mediterranean, and crossbred buffaloes from the Embrapa Eastern Amazon herd, from 1953 to 2013, as well as information on production and reproductive traits were used. Genetic analyzes were performed in the WOMBAT software using the animal model with two-trait analysis. While heritability (h2) for total milk production (TMP) and fat milk percentage (F) were generally high, for reproductive traits h2 tended to be low. Genetic correlations for TMP with the other traits were low and negative, except for TMP with calving interval (CI) and service period (SP) in the Mediterranean breed and with age at first calving (AFC) and SP in crossbred, which were positive and high. Bull 1001 had high predicted transmitting ability (PTA) for TMP, so it should transmit a greater volume of milk to his offspring, although it had a lower PTA for F. There was sufficient variability within the herd to work with genetic management for both production and reproductive efficiency.

Resultados evaluación genética para producción de leche hasta el día 270 en búfalas en Colombia, 2018

La sexta evaluación genética, para producción de leche hasta el día 270 en búfalas en Colombia, se realizó en colaboración entre la Universidad CES y la Asociación Colombiana de Criadores de Búfalos (ACB). Se usó la información genealógica de 77.602 búfalos y productiva de 34.195 lactancias de 9.969 búfalas provenientes de 15 bufaleras. Para estimar la heredabilidad y la habilidad predicha de transmisión (PTA) de los animales se usó un modelo animal en el que se incluyó como efectos aleatorios: el genético aditivo, el ambiente permanente y el efecto residual; y como efectos fijos: número de parto y grupo contemporáneo. El promedio de producción de leche fue de 989,2 kg. La heredabilidad estimada fue de 0,31, este valor sugiere que la selección puede ser usada como estrategia para aumentar la producción de leche en el rebaño bufalino de Colombia. En los archivos anexos se presentan los listados de los animales (reproductores y jóvenes) con los mejores PTA.

Linkage between predictive transmitting ability of a genetic index, potential milk production, and a dynamic model

With the increased use of information and communication technology-based tools and devices across traditional desktop computers and smartphones, models and decision-support systems are becoming more accessible for farmers to improve the decision-making process at the farm level. However, despite the focus of research and industry providers to develop tools that are easy to adopt by the end user, milk-production prediction models require substantial parameterization information for accurate milk production simulations. For these models to be useful at an individual animal level, they require the potential milk yield of the individual animals (and possibly potential fat and protein yields) to be captured and parameterized within the model to allow accurate simulations of the interaction of the animal with the system. The focus of this study was to link 3 predicted transmitting ability (PTA) traits from the Economic Breeding Index (PTA for milk yield, fat, and protein) with potential index parameters for milk, fat, and protein required as inputs to a herd-based dynamic milk model. We compiled a data set of 1,904 lactations that included different experiments conducted at 2 closed sites during a 14-yr period (2003-2016). The treatments implied different stocking rates, concentrate supplementation levels, calving dates, and genetic potential. The first step, using 75% of the data randomly selected, was to link the milk, fat, and protein yields achieved within each lactation to their respective PTA value, stocking rate, parity, and concentrate supplementation level. The equations generated were transformed to correspond to inputs to the pasture-based herd dynamic milk model. The equations created were used in conjunction with the model to predict milk, fat, and protein production. Then, using the remaining 25% data of the data set, the simulations were compared against the actual milk produced during the experiments. When the model was tested, it was capable of predicting the lactation milk, fat, and protein yield with a relative prediction error of <10% at the herd level and <13% at the individual animal level.

Differing genetic trend estimates from traditional and genomic evaluations of genotyped animals as evidence of preselection bias in US Holsteins

The objective of this study was to compare genetic trends from single-step genomic BLUP (ssGBLUP) and traditional BLUP models for milk production traits of US Holsteins. Phenotypes were 305-d milk, fat, and protein yields from 21,527,040 cows recorded between January 1990 and August 2015. The pedigree file included 29,651,623 animals and was limited to 3 generations back from recorded or genotyped animals. Genotypes for 764,029 animals were used, and analyses were by a 3-trait repeatability model as used in the US official genetic evaluation. Unknown-parent groups were incorporated into the inverse of a relationship matrix (H-1 in ssGBLUP and A-1 in BLUP) with the QP transformation. For ssGBLUP, 18,359 genotyped animals were randomly chosen as core animals to calculate the inverse of the genomic relationship matrix with the APY algorithm. Computations took 6.5 h and 1.4 GB of memory for BLUP, and 13 h and 115 GB of memory for ssGBLUP. For genotyped sires with at least 10 daughters, the average genetic levels for predicted transmitting ability (PTA) and genomic PTA were similar up to 2008, with a higher level for ssGBLUP later (approximately by 36 kg for milk, 2.1 kg for fat, and 1.1 kg for protein for bulls born in 2010). For genotyped cows, the average genetic levels were similar up to 2006, with a higher level for ssGBLUP (approximately by 91 kg for milk, 3.6 kg for fat, and 2.7 kg for protein for cows born in 2012). For all cows, the average levels were slightly higher for ssGBLUP, with much smaller differences than for genotyped cows. Trends for BLUP indicate bias due to genomic preselection for genotyped sires and cows. For official evaluations released in December 2016, traditional PTA had the same trend as multiple-step genomic PTA for both genotyped bulls and cows except for the youngest bulls, who had traditional PTA slightly lower than genomic PTA. For genotyped bulls born in recent years, genetic gain for official traditional and genomic evaluations was similar in contrast to ssGBLUP and BLUP differences. Official PTA for cows were adjusted so that the Mendelian sampling variance was comparable with that for bulls, and those adjustments likely removed bias due to genomic preselection from traditional PTA, especially for genotyped cows. The ssGBLUP method seems to account partially for that bias and is computationally suitable for national evaluations.

A comparison of 4 predictive models of calving assistance and difficulty in dairy heifers and cows

The aim of this study was to build and compare predictive models of calving difficulty in dairy heifers and cows for the purpose of decision support and simulation modeling. Models to predict 3 levels of calving difficulty (unassisted, slight assistance, and considerable or veterinary assistance) were created using 4 machine learning techniques: multinomial regression, decision trees, random forests, and neural networks. The data used were sourced from 2,076 calving records in 10 Irish dairy herds. In total, 19.9 and 5.9% of calving events required slight assistance and considerable or veterinary assistance, respectively. Variables related to parity, genetics, BCS, breed, previous calving, and reproductive events and the calf were included in the analysis. Based on a stepwise regression modeling process, the variables included in the models were the dam's direct and maternal calving difficulty predicted transmitting abilities (PTA), BCS at calving, parity; calving assistance or difficulty at the previous calving; proportion of Holstein breed; sire breed; sire direct calving difficulty PTA; twinning; and 2-way interactions between calving BCS and previous calving difficulty and the direct calving difficulty PTA of dam and sire. The models were built using bootstrapping procedures on 70% of the data set. The held-back 30% of the data was used to evaluate the predictive performance of the models in terms of discrimination and calibration. The decision tree and random forest models omitted the effect of twinning and included only subsets of sire breeds. Only multinomial regression and neural networks explicitly included the modeled interactions. Calving BCS, calving difficulty PTA, and previous calving assistance ranked as highly important variables for all 4 models. The area under the receiver operating characteristic curve (ranging from 0.64 to 0.79) indicates that all of the models had good overall discriminatory power. The neural network and multinomial regression models performed best, correctly classifying 75% of calving cases and showing superior calibration, with an average error in predicted probability of 3.7 and 4.5%, respectively. The neural network and multinomial regression models developed are both suitable for use in decision-support and simulation modeling.

Genetic parameters of calving ease using sire-maternal grandsire model in Korean Holsteins.

ObjectiveCalving ease (CE) is a complex reproductive trait of economic importance in dairy cattle. This study was aimed to investigate the genetic merits of CE for Holsteins in Korea.MethodsA total of 297,614 field records of CE, from 2000 to 2015, from first parity Holstein heifers were recorded initially. After necessary data pruning such as age at first calving (18 to 42 mo), gestation length, and presence of sire information, final datasets for CE consisted of 147,526 and 132,080 records for service sire calving ease (SCE) and daughter calving ease (DCE) evaluations, respectively. The CE categories were ordered and scores ranged from CE1 to CE5 (CE1, easy; CE2, slight assistance; CE3, moderate assistance; CE4, difficult calving; CE5, extreme difficulty calving). A linear transformation of CE score was obtained on each category using Snell procedure, and a scaling factor was applied to attain the spread between 0 (CE5) and 100% (CE1). A sire-maternal grandsire model analysis was performed using ASREML 3.0 software package.ResultsThe estimated direct heritability (h2) from SCE and DCE evaluations were 0.11±0.01 and 0.08±0.01, respectively. Maternal h2 estimates were 0.05±0.02 and 0.04±0.01 from SCE and DCE approaches, respectively. Estimates of genetic correlations between direct and maternal genetic components were −0.68±0.09 (SCE) and −0.71±0.09 (DCE). The average direct genetic effect increased over time, whereas average maternal effect was low and consistent. The estimated direct predicted transmitting ability (PTA) was desirable and increasing over time, but the maternal PTA was undesirable and decreasing.ConclusionThe evidence on sufficient genetic variances in this study could reflect a possible selection improvement over time regarding ease of calving. It is expected that the estimated genetic parameters could be a valuable resource to formulate sire selection and breeding plans which would be directed towards the reduction of calving difficulty in Korean Holsteins.

Association of single nucleotide polymorphisms in candidate genes previously related to genetic variation in fertility with phenotypic measurements of reproductive function in Holstein cows

Many genetic markers related to health or production traits are not evaluated in populations independent of the discovery population or related to phenotype. Here we evaluated 68 single nucleotide polymorphisms (SNP) in candidate genes previously associated with genetic merit for fertility and production traits for association with phenotypic measurements of fertility in a population of Holstein cows that was selected based on predicted transmitting ability (PTA) for daughter pregnancy rate (DPR; high, ≥1, n = 989; low, ≤ -1.0, n = 1,285). Cows with a high PTA for DPR had higher pregnancy rate at first service, fewer services per conception, and fewer days open than cows with a low PTA for DPR. Of the 68 SNP, 11 were associated with pregnancy rate at first service, 16 with services per conception, and 19 with days open. Single nucleotide polymorphisms in 12 genes (BDH2, BSP3, CAST, CD2, CD14, FUT1, FYB, GCNT3, HSD17B7, IBSP, OCLN, and PCCB) had significant associations with 2 fertility traits, and SNP in 4 genes (CSPP1, FCER1G, PMM2, and TBC1D24) had significant associations with each of the 3 traits. Results from this experiment were compared with results from 2 earlier studies in which the SNP were associated with genetic estimates of fertility. One study involved the same animals as used here, and the other study was of an independent population of bulls. A total of 13 SNP associated with 1 or more phenotypic estimates of fertility were directionally associated with genetic estimates of fertility in the same cow population. Moreover, 14 SNP associated with reproductive phenotype were directionally associated with genetic estimates of fertility in the bull population. Nine SNP (located in BCAS, BSP3, CAST, FUT1, HSD17B7, OCLN, PCCB, PMM2, and TBC1D24) had a directional association with fertility in all 3 studies. Examination of the function of the genes with SNP associated with reproduction in more than one study indicates the importance of steroid hormones and immune function as determinants of reproductive function. All but 1 of the 68 evaluated SNP were variable in 11 breeds besides Holstein, indicating the potential effects of these SNP on reproductive function across breeds of cattle.

Use of single nucleotide polymorphisms in candidate genes associated with daughter pregnancy rate for prediction of genetic merit for reproduction in Holstein cows.

We evaluated 69 SNPs in genes previously related to fertility and production traits for their relationship to daughter pregnancy rate (DPR), cow conception rate (CCR) and heifer conception rate (HCR) in a separate population of Holstein cows grouped according to their predicted transmitting ability (PTA) [≤-1 (n=1287) and ≥1.5 (n=1036)] for DPR. Genotyping was performed using Sequenom MassARRAY(®) . There were a total of 39 SNPs associated with the three fertility traits. The SNPs that explained the greater proportion of the genetic variation for DPR were COQ9 (3.2%), EPAS1 (1.0%), CAST (1.0%), C7H19orf60 (1.0%) and MRPL48 (1.0%); for CCR were GOLGA4 (2.4%), COQ9 (1.8%), EPAS1 (1.1%) and MRPL48 (0.8%); and for HCR were HSD17B7 (1.0%), AP3B1 (0.8%), HSD17B12 (0.7%) and CACNA1D (0.6%). Inclusion of 39 SNPs previously associated with DPR in the genetic evaluation system increased the reliability of PTA for DPR by 0.20%. Many of the genes represented by SNPs associated with fertility are involved in steroidogenesis or are regulated by steroids. A large proportion of SNPs previously associated with genetic merit for fertility in Holstein bulls maintained their association in a separate population of cows. The inclusion of these genes in genetic evaluation can improve reliabilities of genomic estimates for fertility.

Genetic approaches to identify genomic regions associated with decreased susceptibility to bovine respiratory disease complex

One approach to reducing losses from BRDC is the implementation of selection of cattle that are less likely to be affected by disease by the use of dairy predicted transmitting ability (PTA) or beef expected progeny differences (EPD) for susceptibility to BRDC. The PTAs or EPDs would be based on genotypes associated with animals less susceptible to disease and incorporated into commercial genotyping platforms for industry use. The discovery of quantitative trait loci (QTL) associated with BRDC susceptibility is the first step in implementing the selection of cattle for enhanced resistance to BRDC. Feedlot crossbred Bos taurus (n=408) heifers from Washington were used to illustrate how genetic approaches identify BRDC susceptibility QTL that will form the basis for selection of cattle with increased resistance to the disease. The crossbred cattle consisted of 234 cases and 174 controls as defined by the McGuirk Health scoring system. Cases and controls remained in the same pens together throughout the study. The incidence of BRDC in the feedlot was 2.5% over a 15-month period. The distinction between cases and controls was based on the McGuirk health scoring system with possible integer scores ranging between 0 and 12; calves with scores &lt;4 were identified as controls and those with a score &gt;5 were identified as a case. Of the 174 controls, 4 (1.7%) subsequently became ill with BRDC and were reclassified as a case. The mean health score was 9.44 ± 1.19 for cases and 2.36 ± 0.61 for controls. Deeppharyngeal and mid-nasal swabs were taken for bacteriology and virology diagnostics. Histophilus somni had the greatest difference in prevalence between cases and controls (odds ratio = 1.65, 95% confidence interval 1.05 - 2.58, p &lt; 0.05) among the detected pathogens. A genome-wide association analysis (GWAA) and genomic heritability estimate was computed using Illumina BovineHD BeadChip genotypes. Heritability of susceptibility to BRDC was estimated at 37%. After correction for population stratification using 30 principal components, the genomic inflation factor was 1.02. Single nucleotide polymorphisms (SNPs) were filtered for low call rate (&lt;90%), Hardy-Weinberg disequilibrium (p &lt; 1x10-50) and low minor allele frequency (&lt;1%) which left 669,933 SNPs for the GWAA. Animals were also filtered for low genotyping call rate (&lt;90%) leaving 220 cases and 164 controls. The GWAA identified 43 QTL (p &lt; 5x10-5) on 15 chromosomes. The identification of QTL associated with BRDC susceptibility is the first step towards implementing selection of cattle that are less likely to be affected by BRDC through the use of genomic PTAs or EPDs.

The impact of 3 strategies for incorporating polled genetics into a dairy cattle breeding program on the overall herd genetic merit

Dehorning in cattle has been associated with behavioral, physiological, and neuroendocrine responses indicative of pain. Unaddressed, the pain associated with a routine production procedure could contribute to a negative public perception of livestock production practices. Alternative considerations of dehorning include the selection of polled cattle within herds, thereby avoiding pain and production loss. As polledness results from an autosomal dominant pattern of inheritance, genetic selection for polled cattle could reduce the prevalence of the horned trait. Herein we discuss 3 strategies to incorporate polled genetics into a cow herd and the estimated impact on the overall genetic merit of the herd. Furthermore, the availability and genetic merit of polled artificial insemination bulls in the United States is summarized. Both Holstein and Jersey dairy bulls registered with the National Association of Animal Breeders from December 2010 through April 2013 were queried. Polled bulls were identified as either being homozygous (PP) or heterozygous (Pp) and the average net merit (NM) predicted transmitting ability (PTA) of each sire group was calculated. The percentage of polled calves born each year over a 10-yr period was calculated for the following 3 scenarios: (A) various percentages of horned cows were randomly mated to Pp bulls, (B) various percentages of horned cows were preferentially mated to Pp bulls, and (C) horned cows were selectively mated to PP bulls, heterozygous cows to Pp bulls, and homozygous polled cows to horned bulls. Additionally, the change in NM PTA of the cow herd was calculated over the same period. The highest percentage of polled animals (87%) was achieved in scenario C. An evaluation of the herd NM PTA highlights the trade-offs associated with increasing polled genetics. Given the current genetic merit of horned and polled bulls, increasing the percentage of polled calves will decrease the NM PTA in Holstein, but may have minimal impact in Jersey herds. Decisions regarding selective breeding to increase polled genetics will need to be evaluated in the context of production objectives, cost of dehorning, and impact on overall genetic merit.