Genomic analyses and biological validation of candidate genes for rectal temperature as an indicator of heat stress in Holstein cattle

Heat stress is a major cause of welfare issues and economic losses to the worldwide dairy cattle industry. Genetic selection for heat tolerance has a great potential to positively affect the dairy industry, as the gains are permanent and cumulative over generations. Rectal temperature (RT) is hypothesized to be a good indicator trait of heat tolerance. Therefore, this study investigated the genetic architecture of RT by estimating genetic parameters, performing genome-wide association studies, and biologically validating potential candidate genes identified to be related to RT in Holstein cattle. A total of 33,013 RT records from 7,598 cows were used in this study. In addition, 1,114 cows were genotyped using the Illumina 150K Bovine BeadChip (Illumina, San Diego, CA). Rectal temperature measurements taken in the morning (AMRT) and in the afternoon (PMRT) are moderately heritable traits, with estimates of 0.09 ± 0.02 and 0.04 ± 0.01, respectively. These 2 traits are also highly genetically correlated (r = 0.90 ± 0.08). A total of 10 SNPs (located on BTA3, BTA4, BTA8, BTA13, BTA14, and BTA29) were found to be significantly associated with AMRT and PMRT. Subsequently, gene expression analyses were performed to validate the key functional genes identified (SPAG17, FAM107B, TSNARE1, RALYL, and PHRF1). This was done through in vitro exposure of peripheral blood mononuclear cells (PBMC) to different temperatures (37°C, 39°C, and 42°C). The relative mRNA expression of 2 genes, FAM107B and PHRF1, significantly changed between the control and heat stressed PBMC. In summary, RT is heritable, and enough genetic variability exists to enable genetic improvement of heat tolerance in Holstein cattle. Important genomic regions were identified and biologically validated; FAM107B and PHRF1 are the main candidate genes identified to influence heat stress response in dairy cattle.     

Performance of Holstein and Swedish-Red × Jersey/Holstein crossbred dairy cows within low- and medium-concentrate grassland-based systems

This 2 × 2 factorial design experiment was conducted to compare the performance of spring-calving Holstein dairy cows (HOL, n = 34) with Swedish Red × Jersey/Holstein crossbred (SR × J/HOL, n = 34) dairy cows within low and medium concentrate input grassland-based dairy systems. The experiment commenced when cows calved and encompassed 1 full lactation. Cows were offered diets containing grass silage and concentrates [70:30 dry matter (DM) ratio, and 40:60 DM ratio, for low and medium, respectively] until turnout, grazed grass plus either 1.0 or 4.0 kg of concentrate/d during the grazing period (low and medium, respectively), and grass silage and concentrates (85:15 DM ratio, and 70:30 DM ratio, for low and medium, respectively) from rehousing and until drying off. No significant genotype × system interactions were present for any of the feed intake or full-lactation milk production data examined. Full-lactation concentrate DM intakes were 769 and 1,902 kg/cow for the low and medium systems, respectively, whereas HOL cows had a higher total DM intake than SR × J/HOL cows in early lactation, but not in late lactation. Although HOL cows had a higher lactation milk yield than SR × J/HOL cows, the latter produced milk with a higher fat and protein content, and thus fat plus protein yield was unaffected by genotype. Milk produced by the SR × J/HOL cows had a higher degree of saturation of fatty acids than milk produced by the HOL cows, and the somatic cell score of milk produced by the former was also higher. Throughout the lactation, HOL cows were on average 30 kg heavier than SR × J/HOL cows, whereas the SR × J/HOL cows had a higher body condition score than the HOL cows. Holstein cows had a higher incidence of mastitis and ovarian dysfunction that SR × J/HOL cows.     

Short communication: Heritability estimates for susceptibility to Mycobacterium avium ssp. paratuberculosis infection in Chinese Holstein cattle

Paratuberculosis in ruminants, which is caused by Mycobacterium avium ssp. paratuberculosis (MAP), is a contagious, chronic enteric disease associated with economic losses, animal welfare, and health implications in dairy cattle production. In this study, we estimated the variance components and heritability of susceptibility to MAP infection in Chinese Holstein cattle. We collected 4,937 serum samples from cows in 7 dairy herds in the Beijing region of China and used the ELISA test to detect antibodies to MAP. Three statistical models were implemented to estimate heritabilities: (1) a linear model (ELISA sample-to-positive ratios as a continuous trait); (2) a binary threshold model (positive/negative from ELISA results); and (3) an ordered threshold model (ELISA results as an ordered categorical model with categories 1 to 5 corresponding to negative, uncertain, mildly positive, intermediate positive, and strongly positive). The heritability estimates ranged from 0.0389 to 0.1069, indicating that genetic factors affect MAP infection susceptibility in Chinese Holstein cattle.     

Validation of genomic predictions for wellness traits in US Holstein cows

The objective of this study was to evaluate the efficacy of wellness trait genetic predictions in commercial herds of US Holstein cows from herds that do not contribute phenotypic information to the evaluation. Tissue samples for DNA extraction were collected from more than 3,400 randomly selected pregnant Holstein females in 11 herds and 2 age groups (69% nulliparous, 31% primiparous) approximately 30 to 60 d before their expected calving date. Lactation records from cows that calved between September 1, 2015, and December 31, 2015, were included in the analysis. Genomically enhanced predicted transmitting abilities for the wellness traits of retained placenta, metritis, ketosis, displaced abomasum, mastitis, and lameness were estimated by the Zoetis genetic evaluation and converted into standardized transmitting abilities. Mean reliabilities of the animals in the study ranged between 45 and 47% for each of the 6 traits. Animals were ranked by their standardized transmitting abilities within herd and age group then assigned to 1 of 4 groups of percentile-based genetic groups of equal size. Adverse health events, including retained placenta, metritis, ketosis, displaced abomasum, mastitis, and lameness, were collected from on-farm herd management software, and animal phenotype was coded as either healthy (0), diseased (1), or excluded for each of the 6 outcomes of interest. Statistical analysis was performed using a generalized linear mixed model with genetic group, age group, and lactation as fixed effects, whereas herd and animal nested within herd were set as random effects. Results of the analysis indicated that the wellness trait predictions were associated with differences in phenotypic disease incidence between the worst and best genetic groups. The difference between the worst and best genetic groups in recorded disease incidence was 2.9% for retained placenta, 10.8% for metritis, 1.1% for displaced abomasum, 1.7% for ketosis, 7.4% for mastitis, and 3.9% for lameness. Odds ratio estimates between the highest and lowest genetic groups ranged from 1.6 (lameness) to 17.1 (displaced abomasum) for the 6 traits analyzed. These results indicate that wellness trait information of young calves and heifers can be used to effectively predict meaningful differences in future health performance. Improving wellness traits through direct genetic selection presents a compelling opportunity for dairy producers to help reduce disease incidence and improve profitability when coupled with sound management practices.     

Effects of dietary physically effective neutral detergent fiber content on the feeding behavior,digestibility, and growth of 8- to 10-month-old Holstein replacement heifers

The objective of this study was to evaluate the effects of dietary physically effective neutral detergent fiber (peNDF) content on the feeding behavior, digestion, ruminal fermentation parameters, and growth of 8- to 10-mo-old dairy heifers and to predict the adequacy of dietary fiber in growing dairy heifers. Twenty-four Holstein dairy heifers (245 ± 10.8 d of age, 305.6 ± 8.5 kg initial live weight) were randomly divided into 4 treatments with 6 replicates as a completely randomized design. During the 60-d period with a 10-d adaptation, heifers were offered 1 of 4 diets, which were chemically identical but included different peNDF_8.0 (particle size is >8 mm and <19 mm) content (% DM): 10.8, 13.5, 18.0, or 19.8%, which was achieved by chopping forage into different lengths (fine = 1 cm, short = 3 cm, medium = 5 cm, and long = 7 cm). The concentrate and silage were mixed and fed restrictedly and exclusive of forage (Chinese ryegrass hay) were offered ad libitum. The body weight and frame size of the heifers were measured every 15 d during the experimental period. Samples of the rumen content (2 h after the morning feeding) were taken for pH, ammonia, and volatile fatty acid determination. The dry matter intake and average daily gain of the heifers were not significantly affected by peNDF_8.0 content. The body frame size (including withers height, body length, and heart girth) of the heifers was not increased significantly by enhanced peNDF_8.0 content. Ruminal pH and ammonia concentration were both increased with increasing dietary peNDF_8.0 content. The ruminal total volatile fatty acid concentration and percentage of acetate and butyrate profiles were not significantly affected by dietary peNDF_8.0 content. However, the enhanced peNDF_8.0 content led to a decrease in the propionate percentage. The ratio of acetate to propionate in the 13.5% treatment was highest among the treatments. Increasing the particle size and dietary peNDF_8.0 content resulted in increased eating and chewing time but had no effect on rumination time. Heifer total eating and chewing time and eating and chewing time per kilogram of dry matter intake were increased with increasing dietary peNDF_8.0 content. The apparent digestibility of acid detergent fiber and crude protein was improved with an increasing content of dietary peNDF_8.0. The results suggest that an optimal or advisable dietary particle size and peNDF_8.0 content improves chewing activity, rumen fluid pH, and ruminal fermentation. The data based on feeding behavioral and growth responses of heifers as well as rumen fermentation and digestion by improving total eating and chewing time indicate that 18.0% dietary peNDF_8.0 content is the most suitable for 8- to 10-mo-old Holstein heifers.     

Estimation of regional genetic parameters for mortality and 305-d milk yield of US Holsteins in the first 3 parities

Several research reports have indicated increasing dairy cow mortality in recent years. The objectives of this research were to characterize the phenotypic differences in mortality in the first 3 parities across 3 regions of the United States to estimate the heritability of mortality of Holstein cows across regions and parities, and to estimate genetic and environmental correlations between milk yield and mortality across parities and regions. Dairy Herd Information (DHI) milk yield and mortality data were obtained from 3 different US regions: the Southeast (SE), Southwest (SW), and Northeast (NE). A total of 3,522,824 records for the first 3 parities were used: 732,009 (SE), 656,768 (SW), and 2,134,047 (NE) from 1999 to 2008. Cows that received a termination code of 6—“Cow died on the dairy; downer cows that were euthanized should be included here”—were given a mortality score of 2 (dead), whereas all other codes were assigned a mortality score of 1 (alive). Average annual mortalities in the first 3 parities across regions ranged from 2.2 to 7.2%, with mortality frequency increasing with increasing parity across all regions and with the SE having the highest mortality frequency. For genetic analysis, a 2-trait (305-d milk yield and mortality) linear-threshold animal model that fitted fixed effects of herd-year (for 305-d milk yield), cow age, days in milk (in month classes), month-of-termination, and random effects of herd-year (for mortality), animal, and residual was implemented. The model was used to estimate variance components separately for each region and parity. Heritability estimates for mortality were similar for all regions and parities, ranging from 0.04 to 0.07. Genetic correlations between mortality and 305-d milk yield across the first 3 parities were 0.14, 0.20, and 0.29 in SE; −0.01, 0.01, and 0.31 in SW; and 0.28, 0.33, and 0.19 in NE. We detected an adverse genetic relationship between milk production and mortality; however, the moderate magnitudes of the genetic correlations suggest that indices that include both milk yield and mortality could be effective in identifying sires that would provide opportunities for minimizing death loss even when selecting for increased milk yield.     

Effects of blade tenderization,aging method and aging time on meat quality characteristics of Longissimus lumborum steaks from cull Holstein cows

The effects of blade tenderization (BT), two aging methods (dry (D) and wet (W)), and aging time (2 and 23 d) on tenderness, color, and sensory properties of Longissimus lumborum muscles from 12 cull Holstein cows were evaluated. Dry-aged loins had higher combined trim and aging losses than control (C) for both D- and W-aging, mostly because of excess trim losses. BT steaks had WBSF of 33.13 N while C steaks had WBSF of 41.46 N (P = 0.09). Aging decreased WBSF. Blade tenderized steaks had higher cook loss than C steaks. Aging, W-aging, and BT × W-aging improved myofibrillar (sensory) tenderness scores. Aging and/or BT improves sensory panel tenderness cull cow Longissimus lumborum steaks. Aging and blade tenderization combined can increase tenderness and value of Longissimus steaks from cull Holstein cows.     

Polymorphisms in the bovine lactoferrin promoter are associated with reproductive performance and somatic cell count

Lactoferrin plays an important role in the innate immune system, with well-characterized antibacterial, antiviral, and immune modulatory properties. The objective of this study was to determine the allele and haplotype frequency of polymorphisms at positions −586, −190, and −28 of the bovine lactoferrin promoter in Holstein-Friesians and to quantify their association with performance using phenotypic data on progeny from 848 sires. Associations between genotypes and performance were quantified using weighted mixed models with genotyped individuals included as a random effect, and average expected relationships among individuals accounted for through a numerator relationship matrix. The dependent variables were daughter yield deviation for production traits and deregressed predicted transmitting ability for calving interval and functional survival. The C to T polymorphism at −586, which distorts a putative activating protein 2 (AP-2) binding site, was associated with a shorter calving interval and higher somatic cell score. The G to A polymorphism at −190, located in a putative selective promoter factor 1 (SP-1) binding site, was associated with a longer calving interval and decreased functional survival. A third polymorphism (A to C) at position −28, found within the noncanonical TATA box, had a tendency to associate with functional survival. On the basis of the data we proposed a haplotype combination that was associated with improved reproductive performance in the Holstein-Friesian breed. We hypothesized that the observable phenotypic associations with lactoferrin promoter polymorphisms can potentially be explained by allele-specific differences in constitutive or inducible levels of gene expression. The lack of a pleiotropic effect of the single nucleotide polymorphisms studied on both fertility and milk production traits strengthens the importance of these polymorphisms, or at least the lactoferrin promoter, in selection for improved fertility.     

Effect of lying behavior on uterine blood flow in cows during the third trimester of gestation

Seven Holstein cows (BW = 639.4 +/- 28.8 kg, age = 62.6 +/- 6.9 mo, parity = 3.1 +/- 0.4 yr) (mean +/- SE) were used to measure uterine blood flow using a transit time ultrasonic flow meter. Ultrasonic flow probes were implanted (d 218 +/- 4 of gestation) around both uterine arteries (n = 3) or the gravid uterine artery (n = 4) to measure variations in uterine blood flow through this vessel in response to postural change (standing and lying). Implantation of the ultrasonic blood flow probe was successful in all 7 cows. Uterine blood flow was measured for 22.9, 23.1, and 21.4 h/d on d 226, 248, and 269 of gestation, respectively. Cows exhibited normal durations of gestation (272.8 +/- 1.6 d), gave birth to normal healthy calves (birth weight = 41.5 +/- 3.0 kg), and did not retain their placenta. Uterine blood flow to the gravid horn during lying was greater than during standing on d 226 (standing vs. lying, 8.04 vs. 8.79 L/min, respectively), d 248 (9.87 vs. 11.06 L/min), and d 269 (8.15 vs. 9.74 L/min) of gestation. Cows spent nearly 50% of their time lying during our observations at all gestational ages. Greater blood supply to the gravid uterus was observed during lying than during standing in this study.     

Effect of lameness on ovarian activity in postpartum holstein cows

A longitudinal study was conducted to examine the relationship between lameness and delayed ovarian cyclicity during the first 60 d postpartum and days to first luteal activity during the first 300 d postpartum in Holstein cows. Two hundred thirty-eight cows from a 600-cow dairy that calved during a 12-mo period were used. Cows were classified into 1 of 6 categories of lameness during the first 35 d postpartum using a locomotion scoring system. Cows were blood-sampled weekly for detection of plasma progesterone concentrations during the first 300 d postpartum. Cows with delayed resumption of ovarian cyclicity were defined as those with progesterone concentrations consistently <1 ng/mL during the first 60 d postpartum. The null hypothesis that risk of delayed cyclicity is the same in cows classified as nonlame, moderately lame, or lame (after adjusting for potential modifying or confounding effects of loss of body condition and other variables related with delayed cyclicity) was tested using logistic regression. Analysis of results of the study reported here support the hypothesis that lameness is associated with delayed ovarian activity in Holstein cows during the early postpartum period. Cows classified as lame had 3.5 times greater odds of delayed cyclicity, compared with cows classified as nonlame. Attributable proportion analysis indicated that delayed ovarian cyclicity in lame cows would be reduced by 71%, if lameness had been prevented.