Flexible feeding: Dairy cow personality affects changes in feeding behavior and milk production under feed competition conditions.

The objective of this study was to determine the effect of individual cow personality traits on feeding behavior and production under low levels of feeding competition, and to determine whether personality traits influence how feeding behavior changes in response to greater feeding competition. Forty-two Holstein cows were assigned to 1 automated feed bin per cow (low competition condition) from 15 to 28 d in milk (DIM; period 1, P1), and 2 feed bins per 3 cows (higher competition condition) from 63 to 76 DIM (period 2, P2). A total mixed ration (TMR) was fed into the automated feed bins which recorded each feed bin visit time, duration, and intake. Cow personality traits were assessed at 21 DIM during P1 and at 70 DIM during P2 using a combined arena test, measuring behavioral responses to a novel environment, novel object, and novel human. Principal components analysis of behaviors observed during the P1 combined arena test revealed 1 factor (interpreted as active-explorative) from the novel environment test explaining 51% of the variance, and 3 factors (interpreted as fearfulness, active-explorative, and sociability toward conspecifics) from each of the novel object (76% cumulative variance) and human (75% cumulative variance) tests. The principal components analysis of behaviors observed during the P2 combined arena test revealed 2 factors jointly from the environment, object, and human tests (interpreted as fearfulness and active-explorative) that together explained 68% of the variance. Fearfulness and active-explorative trait scores were correlated across P1 and P2, indicating stability of personality over a challenging period and advancing DIM. In P2 when competition for feed was increased at greater stage of lactation, the more active-explorative cows appeared to make few alterations to their feeding behavior, yet still maintained their milk yield, compared with lower competition in P1. In contrast, cows who were more fearful increased their feed bin visits from P1 to P2, and less fearful cows increased their eating rate, without increased milk production, despite advanced lactation. Overall, the results indicate that cows of different personalities adopt different feeding strategies in response to a change in their environment, and may benefit from tailored management during challenging periods.

Effects of concentrate allowance and individual dairy cow personality traits on behavior and production of dairy cows milked in a free-traffic automated milking system.

The primary objective of this study was to determine whether the level of concentrate allowance in an automated milking system (AMS) affects the feed intake, eating behavior, milking activity, and performance of lactating dairy cows. The secondary objective of this study was to describe how the response to concentrate allocation, specifically in feeding and milking behavior, varies with cow personality traits. Fifteen Holstein cows were used in a crossover design with two 28-d periods, each including 14 d of adaptation and 14 d of data collection. The cows were housed in a freestall pen with free-traffic access to the AMS. Treatments consisted of a basal partial mixed ration (PMR) common to both treatment groups, with a concentrate allowance (on dry matter basis) of (1) 3.0 kg/d in the AMS (L-AMS) or (2) 6.0 kg/d in the AMS (H-AMS). Between the 2 treatment periods, each cow was assessed for personality traits using a combined arena test consisting of exposure to a novel environment, novel object, and novel human. Principal component analysis of behaviors observed during the novel environment and object tests revealed 3 factors (interpreted as active, social, and alert-curious) that together explained 76% of the variance, whereas principal component analysis of the novel human test revealed 2 factors (interpreted as active-vocal and fearful of novel humans) that together explained 77% of the variance. When on the H-AMS treatment, PMR dry matter intake (DMI) was less (24.5 vs. 26.0 kg/d) and AMS concentrate delivery was greater (5.9 vs. 3.1 kg/d), as per design. Consequently, total DMI was greater on the H-AMS treatment (30.4 vs. 29.1 kg/d). When on the H-AMS treatment, cows who were more alert-curious consumed more PMR, whereas cows who were more fearful of the novel human were less likely to receive the maximum amount of AMS concentrate available, limiting their total DMI and increasing the day-to-day variability of that intake. Although this was a preliminary study, these data suggest an association between dairy cow personality traits and how cows respond to increased AMS concentrate allowance.

Endotoxin-induced cytokine, chemokine and white blood cell profiles of variable stress-responding sheep.

Individual variation of the hypothalamic-pituitary-adrenal (HPA) axis response to stress could contribute to variable stress resiliency of livestock. During stress events, the innate immune system can also become activated and work in concert with the neuroendocrine system to restore homeostasis, while minimizing tissue damage. The purpose of this study was to assess immune function in variable stress-responding sheep in response to bacterial lipopolysaccharide (LPS) endotoxin immune-challenge. High (HSR, n = 12), middle (MSR, n = 12), and low-stress responders (LSR, n = 12) were selected from a population of 112 female lambs and classified based on serum cortisol concentration after receiving an intravenous bolus of LPS (400 ng/kg). Blood was collected from the jugular vein at 0 and 4 hrs post-LPS challenge to monitor changes in serum pro- and anti-inflammatory cytokines and chemokines, and white blood cell populations. Rectal temperature was recorded hourly to monitor fever. HSR had the greatest increase in rectal temperature and strongest pro-inflammatory IL-6 and IFN-γ cytokine responses compared to MSR and LSR. HSR and MSR had stronger anti-inflammatory IL-10 cytokine and CCL2 chemokine responses than LSR. White blood cell counts changed between 0 and 4 h; however, no differences were detected among the variable stress response groups. The distinct inflammatory response in variable stress responding sheep could contribute to individual differences in stress resiliency and this warrants investigation in the context of other types of stress.

LAY SUMMARYAcute inflammation was studied in sheep stress-phenotyped using bacterial lipopolysaccharide. Sheep selected based on stress responsiveness (i.e. serum cortisol concentration) have different immune responses to bacterial stress. Specifically, high-stress responders have a more pronounced inflammatory response than low-stress responders.

Marker genes as predictors of shared genomic function.

BACKGROUND: Although high-throughput marker gene studies provide valuable insight into the diversity and relative abundance of taxa in microbial communities, they do not provide direct measures of their functional capacity. Recently, scientists have shown a general desire to predict functional profiles of microbial communities based on phylogenetic identification inferred from marker genes, and recent tools have been developed to link the two. However, to date, no large-scale examination has quantified the correlation between the marker gene based taxonomic identity and protein coding gene conservation. Here we utilize 4872 representative prokaryotic genomes from NCBI to investigate the relationship between marker gene identity and shared protein coding gene content. RESULTS: Even at 99-100% marker gene identity, genomes share on average less than 75% of their protein coding gene content. This occurs regardless of the marker gene(s) used: V4 region of the 16S rRNA, complete 16S rRNA, or single copy orthologs through a multi-locus sequence analysis. An important aspect related to this observation is the intra-organism variation of 16S copies from a single genome. Although the majority of 16S copies were found to have high sequence similarity (> 99%), several genomes contained copies that were highly diverged (< 97% identity). CONCLUSIONS: This is the largest comparison between marker gene similarity and shared protein coding gene content to date. The study highlights the limitations of inferring a microbial community's functions based on marker gene phylogeny. The data presented expands upon the results of previous studies that examined one or few bacterial species and supports the hypothesis that 16S rRNA and other marker genes cannot be directly used to fully predict the functional potential of a bacterial community.

PALADIN: protein alignment for functional profiling whole metagenome shotgun data.

MOTIVATION: Whole metagenome shotgun sequencing is a powerful approach for assaying the functional potential of microbial communities. We currently lack tools that efficiently and accurately align DNA reads against protein references, the technique necessary for constructing a functional profile. Here, we present PALADIN-a novel modification of the Burrows-Wheeler Aligner that provides accurate alignment, robust reporting capabilities and orders-of-magnitude improved efficiency by directly mapping in protein space. RESULTS: We compared the accuracy and efficiency of PALADIN against existing tools that employ nucleotide or protein alignment algorithms. Using simulated reads, PALADIN consistently outperformed the popular DNA read mappers BWA and NovoAlign in detected proteins, percentage of reads mapped and ontological similarity. We also compared PALADIN against four existing protein alignment tools: BLASTX, RAPSearch2, DIAMOND and Lambda, using empirically obtained reads. PALADIN yielded results seven times faster than the best performing alternative, DIAMOND and nearly 8000 times faster than BLASTX. PALADIN's accuracy was comparable to all tested solutions. AVAILABILITY AND IMPLEMENTATION: PALADIN was implemented in C, and its source code and documentation are available at https://github.com/twestbrookunh/paladin. CONTACT: anthonyw@wildcats.unh.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Effects of alternative deep bedding options on dairy cow preference, lying behavior, cleanliness, and teat end contamination.

Cows spend more time lying down when stalls are soft and dry, and bedding plays a key role in the comfort of the lying surface. The first objective of this study (experiment 1) was to compare cow preference for 2 types of alternative deep-bedding materials, switchgrass and switchgrass-lime, using wheat straw on a rubber mat as a control. Nine Holstein lactating cows were submitted in trios to a 3-choice preference test over 14 d (2 d of adaptation, 3 d of restriction to each stall, and 3 d of free access to all 3 stalls). Cows were housed individually in pens containing 3 stalls with different lying surfaces: (1) rubber mat with chopped wheat straw (WS); (2) deep-bedded switchgrass (SG); and (3) deep-bedded switchgrass, water, and lime mixture (SGL). The second objective (experiment 2) was to test, in freestall housing, the effects of these 3 types of bedding on lying behavior, cow cleanliness, and teat end bacterial contamination. Bedding treatments were compared in a 3 × 3 Latin square design using 24 cows split into groups of 8, with bedding materials being switched every 4 wk. Lying behavior was measured with data loggers in both studies. During experiment 1, cows chose to spend more time lying and had more frequent lying bouts on SG (9.4 h/d; 8.2 bouts/d) than on SGL (1.0 h/d; 0.9 bouts/d). They also spent more time standing and stood more frequently in stalls with SG (2.0 h/d; 10.1 bouts/d) than in those with SGL (0.6 h/d; 2.6 bouts/d), and stood longer in stalls with SG than with WS (0.6 h/d). In experiment 2, the total lying time, frequency of lying bouts, and mean lying bout duration were, on average, 9.7 ± 1.03 h/d, 8.2 ± 0.93 bouts/d, and 1.2 ± 0.06 h/bout, respectively, and did not differ between treatments. No treatment effects were found for cow cleanliness scores. Bedding dry matter was highest for SG (74.1%), lowest for SGL (63.5%), and intermediate for WS (68.6%) [standard error of the mean (SEM) = 1.57%]. This may explain the higher teat end count of coliforms for cows on SGL (0.92 log10 cfu/g) compared with WS (0.13 log10 cfu/g) (SEM = 0.144 log10 cfu/g). In conclusion, cows preferred the deep-bedded switchgrass surface over the other 2 surfaces, and deep-bedded switchgrass appears to be a suitable bedding alternative for dairy cows.

A method of outdoor housing dairy calves in pairs using individual calf hutches.

Interest in housing dairy calves in groups is currently growing. Group housing using individual calf hutches, a resource already available in most dairy farms in North America, could provide a novel housing method that can be a simple way to implement group housing on farm. The main objective of this study was to determine whether pair housing dairy calves in hutches outdoors would result in similar weight gain and milk intake compared with individual housing in hutches. The study was designed to avoid competition for resources (including milk and solid feed, teat, bucket, outdoor space, and hutch) to test a setup that has the potential to maximize performance and calf growth. Secondary objectives were to document how calves in both treatments use their environment in terms of time spent and behaviors performed in each area, how paired calves interact, and the time they spend together. Single calves (n = 6/season) were housed in 1 hutch with an attached outdoor environment; paired calves (n = 6 pairs/season) were given twice the resources. Calves were fed up to 16 L/d of milk replacer. Daily milk intake and weekly weight gains were recorded. Behavioral observations were recorded live once per week for 5 (summer) or 4 (winter) nonconsecutive periods. Paired and single calves had similar weight gain (averaging from 1.1 to 1.3 kg/d across trials) and milk intake (averaging from 11.1 to 13.7 kg/d across trials), showing no difference in performance between treatments. Low occurrences of cross sucking (averaging from 0.1 to 0.4 bouts/h of observation per pen across trials) and displacements at the teat (0.8 to 1.4 bouts/h of observation per pen across trials) were found. All calves altered their behavior in some way to accommodate companions; paired calves were seen interacting and spending time together (i.e., lying in the same hutch), and in the summer trial single calves spent less time lying inside the hutch than paired calves, presumably to have visual access to other calves. The solution of mixed indoor and outdoor housing environments tested as part of this study showed that calves make use of all spaces provided to them in winter and in summer conditions while maintaining good performance. Housing calves in pairs using individual hutches can be a suitable alternative to housing calves individually in hutches outdoors.

Technical note: Assessing lameness in tie-stalls using live stall lameness scoring.

Video stall lameness scoring (SLS) has been shown to be comparable to video locomotion scoring for evaluating lameness in dairy cows housed in tie-stalls and may be a more practical and easier method to measure lameness in a herd. We compared live SLS to video SLS and to live locomotion scoring. A total of 685 lactating cows subsampled from 27 commercial dairy herds were examined for lameness through live and video SLS. Cows scored with the live or video SLS system were scored for 4 behavioral indicators while still in their stall: weight shifting (shift), standing on the edge of the stall (edge), uneven weight bearing while standing (rest), and uneven weight bearing while moving from side to side (uneven). Two observers live scored and video scored for SLS. Lameness prevalence from video SLS and live SLS were similar (31 vs. 30%, respectively). Prevalence of the behavioral indicators varied from 0.59 to 58.2%. Sensitivity and specificity of live SLS was calculated using video SLS as the gold standard for lameness detection in tie-stalls. Sensitivity of live SLS was 0.83 and specificity was 0.94. False positives and false negatives for lameness were 14.4 and 16.8%, respectively. When comparing the prevalence of lameness measured through video or live SLS at the herd level, live SLS for lameness was correlated to video SLS (r = 0.91) with a Cohen's kappa coefficient of 0.79 (95% confidence limit = 0.73-0.84). Average exact agreement in the behavior indicators observed ranged from 80 to 100%. A subsample of 250 cows from 5 herds were scored for live SLS and live locomotion by a third observer. Intra- and interobserver reliability for live SLS and live locomotion scoring were found to have a kappa coefficient of 0.53 (95% confidence limit = 0.43-0.64) when determining a cow as lame through SLS or locomotion scoring. Live SLS was correlated with live locomotion scoring (r = 0.92). However, lameness prevalence was lower when using live SLS (28.4%) compared with locomotion scoring (38%). In summary, live SLS may be an acceptable method to replace video SLS to identify lame cows and rank tie-stall herds in terms of lameness prevalence without having to remove the cows from their stalls or view videos to score; however, it may underestimate lameness prevalence compared with locomotion scoring methods.

Effect of feed type and method of presentation on feeding behavior, intake, and growth of dairy calves fed a high level of milk.

The objective of this study was to assess the effect of different feed types and method of feed presentation in the first 12 wk of life on the feeding behavior, intake, and growth of calves fed a high milk level. Forty-eight neonatal Holstein calves were individually housed and randomly assigned to 1 of 4 treatments and fed solid feed ad libitum: silage-based total mixed ration (TMR), concentrate (CON), and chopped hay and concentrate presented in 2 manners: mixed (MIX) or separate (SEP). All calves were offered 12 L/d of acidified milk replacer (1.8 kg of dry matter) until d 38 at which time step-down weaning by 1 L/d began. At d 50 calves no longer received milk, and all calves on SEP and CON treatments were offered the MIX diet until the end of the trial, whereas TMR and MIX calves did not change feeds. Feed intakes were recorded daily, and calves were weighed twice per week. Rumination time was observed on the last 3 d of alternate weeks (wk 3, 5, 7, 9, and 11) for 1h beginning at 1500 h. Time spent feeding was determined for the last 2 d of alternate weeks. In the preweaning stage (d 1-37) average daily gain was similar for all calves (1.1 kg/d). The TMR calves had lower average daily gain than calves on the other 3 treatments during both the weaning (d 38-49; 0.2 vs. 0.7 kg/d) and postweaning (d 50-84; 0.5 vs. 1.2 kg/d) stages. This result is related to the lower dry matter intake of calves fed TMR in comparison with MIX, SEP, and CON calves in the weaning (0.2 vs. 0.5 kg/d) and postweaning (1.8 vs. 2.8 kg/d) stages. Given dry matter content of the feeds (TMR=52%, other diets=89%), the as-fed intake of the calves was similar across treatments in all 3 stages. Calves offered hay in addition to concentrate showed no difference in concentrate intake in the first 7 wk of life. Interestingly, TMR calves spent more time feeding during the postweaning stage than MIX, SEP, and CON calves (308 vs. 194 min/d) and exhibited a slower feeding rate postweaning (5.9 vs. 14.4 g of dry matter per minute). It appears that during weaning, and postweaning, calves fed TMR were attempting to maximize their nutrient intake but were unable to match that of calves in other treatments because of the high moisture content of their feed, and thus were unable to achieve similar average daily gain. Additionally, growth and total intake throughout the preweaning and weaning stages were similar for calves fed chopped hay along with concentrate and those not offered hay, suggesting no detrimental effect of feeding forage.

Investigation of dairy cattle ease of movement on new methyl methacrylate resin aggregate floorings.

Freestall dairy farms commonly present issues with cattle slips and falls caused by smooth flooring and manure slurry. This study examined the effect of 4 new methyl methacrylate (MMA) resin aggregate flooring types (1-4) compared with rubber (positive) and concrete (negative control) on dairy cow (n=18) ease of movement when walking on straight and right-angled corridors. Our hypothesis was that cow ease of movement when walking on the MMA surfaces would be better than when walking on traction milled concrete, and at least as good as when walking on rubber. Cattle ease of movement was measured using kinematics, accelerometers, and visual observation of gait and associated behaviors. Stride length, swing time, stance time, and hoof height were obtained from kinematic evaluation. Acceleration and asymmetry of variance were measured with accelerometers. Locomotion score and behaviors associated with lameness, such as arch back, head bob, tracking up, step asymmetry, and reluctance to bear weight were visually observed. Stride length, swing time, stance time, and the number of steps taken were the only variables affected by flooring type. Differences between flooring types for these variables were tested using a generalized linear mixed model with cow as a random effect, week as a random block factor, and flooring type as a fixed effect. Multiple comparisons with a Scheffé adjustment were done to analyze differences among flooring types. Stride length was 0.14 m longer (better) on rubber when compared with concrete, and 0.11 and 0.17 m shorter on MMA 1 and 2 compared with rubber. On MMA 3 and 4, stride length did not differ from either rubber or concrete. Swing time was 0.04 s shorter (worse) on MMA 1 than on rubber, but did not differ from any other flooring. Stance time was 0.18 s longer (worse) on MMA 2 when compared with rubber, but it did not differ from any other treatment. The number of steps was higher on MMA 4 compared with rubber (4.57 vs. 3.95 steps), but did not differ from any other treatment. Of all the MMA floors tested, MMA 3 was the only one that was consistently as good as rubber (positive control). All 4 MMA floors never differed from concrete (negative control) in any of the ease of movement variables measured. These results suggest that MMA 3 may improve cow ease of movement, compared with the other MMA floors, but more research is required to confirm these findings.

Incidence rate of pathogen-specific clinical mastitis on conventional and organic Canadian dairy farms.

Mastitis is a common and costly production disease on dairy farms. In Canada, the incidence rate of clinical mastitis (IRCM) has been determined for conventionally managed dairy farms; however, no studies to date have assessed rates in organically managed systems. The objectives of this observational study were (1) to determine the producer-reported IRCM and predominant pathogen types on conventional and organic dairy farms in Southern Ontario, Canada, and (2) to evaluate the association of both mean overall IRCM and pathogen-specific IRCM with management system, housing type, and pasture access. Data from 59 dairy farms in Southern Ontario, Canada, distributed across conventional (n=41) and organic management (n=18) systems, were collected from April 2011 to May 2012. In addition to management system, farms were categorized by housing method (loose or tie-stall) and pasture access for lactating cows. Participating producers identified and collected samples from 936 cases of clinical mastitis. The most frequently isolated mastitis pathogens were coagulase-negative staphylococci, Bacillus spp., Streptococcus spp., Staphylococcus aureus, and Escherichia coli. The IRCM was higher on conventional farms than organic (23.7 vs. 13.2 cases per 100 cow-years) and was not associated with housing type (loose or tie-stall), pasture access, or herd-average milk yield. Bulk tank somatic cell count tended to be lower on conventional farms than organic (222,000 vs. 272,000 cells/mL). Pathogen-specific IRCM attributed to Staph. aureus, Bacillus spp., and E. coli was greater on conventional than organic farms, but was not associated with housing or any other factors. In conclusion, organic management was associated with reduced overall and pathogen-specific IRCM.

The effects of providing portable shade at pasture on dairy cow behavior and physiology.

Access to pasture has advantages for cows such as reduced lameness and improved udder health, but also may expose cows to stressors such as extreme heat. The objective of this study was to understand how portable shade affected physiological and behavioral responses of pastured dairy cows in a Canadian summer. Over 8wk, a total of 24 lactating Holstein cows were separated into 2 treatments, one with access to shade and a control without access to shade. The cows were pastured in groups of 4, with 3 field sections per treatment. Instantaneous scan sampling of behaviors (drinking, lying, grazing, other) performed in the shade or not were recorded every 5min for 3h/d during the hottest part of the day (peak hours: 1130-1530h) 3d/wk. Ambient temperature, humidity, and vaginal temperature were recorded at 10-min intervals. Daily milk production was also recorded. Differences between treatments by week were analyzed using the generalized linear mixed model with group as random effect and treatment as fixed effect. Cows with shade access were observed at the water trough up to 6.42 times less and lying down up to 1.75 times more. Cows with shade access grazed up to 1.5 times more but only when the temperature-humidity index was above their comfort threshold (≥72) during the hottest part of the day (wk 2). Cows sought shade when it was made available, but spent less than half of their time observed (%) in the shade (40.8±4.67) with the exception of wk 2 when most of the time was spent under the shade (74.3±4.77). Daily lying time was highest during peak hours for cows with shade access. However, no overall difference in total lying time between the 2 treatments was observed. No differences were found in vaginal temperature or milk production between treatments with the exception of wk 1 for daily milk production, which was higher for cows in the control treatment. In conclusion, cows sought shade when it was provided at pasture, whereas cows without access to shade seemed to alter their behavior to cope with heat stress, as seen from the lack of physiological differences between treatments. The results indicate that providing cows with access to pasture under a temperate climate does not seem to have any detrimental physiological or production effects and providing them with shade can potentially decrease production costs and help with water conservation strategies as fewer cows were observed at the water when shade was provided.

Feeding preferences and voluntary feed intake of dairy cows: Effect of conservation and harvest time of birdsfoot trefoil and chicory.

Bioactive forages contain compounds, such as tannins, that are active against pathogens. They have been successfully used in ruminants to control parasite infections. Because cattle may find bioactive forages unpalatable, it is of interest to know if an afternoon harvest time, which has been shown to increase the percentage of nonstructural carbohydrates (NSC), hence palatability, may mitigate this. The objectives of this study were to quantify voluntary intake and preference of dairy cows for 2 bioactive forages, harvested in the morning and evening, in addition to determining their time spent grazing on each forage species. The forage species evaluated were fresh chicory harvested at 0700 h (FCAM) and 1800 h (FCPM), fresh birdsfoot trefoil harvested at 0700 h (FBAM) and 1800 h (FBPM), birdsfoot trefoil baleage harvested the previous summer at 0700 h (BBAM) and at 1800 h (BBPM), and third-cut alfalfa baleage harvested the previous summer and used as control (CON). Single forages were offered ad libitum in 30-min tests to 14 dairy cows to determine intake in a 7 × 7 Latin square (experiment 1). Every possible pair of forages (21 pairs) was then presented for a 30-min test to 8 different dairy cows, and feed intake was measured (experiment 2). Finally, time spent grazing on chicory and birdsfoot trefoil was measured on 12 dairy cows (experiment 3). The tests consisted of 2 d of restriction on 1 of the 2 fields for 1h, and 2 d of free-choice sessions (1h) between the 2 fields adjacent to each other. Grazing time and location of the animals on the field was assessed through 2-min scan sampling. In experiment 1, the highest voluntary intakes were for CON, BBPM, and BBAM. In experiment 2, BBPM was preferentially consumed over all other forages followed by CON and BBAM. Multidimensional scaling showed that preference for BBPM, CON, and BBAM in dimension 1 was positively associated with dry matter and nitrogen content, and negatively associated with hemicellulose and soluble N/total N. No relationships between dimension coordinates and any of the measured chemical composition variables could be found for the other 2 dimensions. In experiment 3, cows spent 71% of their time grazing in the birdsfoot trefoil field and 23% in the chicory field during the free-choice sessions. In conclusion, cows in the present experiments showed an overall preference toward baled forages compared with fresh forages, most notably toward birdsfoot trefoil baleage. Cow preference did not appear to be linked to harvest time (a.m. vs. p.m.).

An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits.

BACKGROUND: Although Daphnia is increasingly recognized as a model for ecological genomics and biomedical research, there is, as of yet, no high-resolution genetic map for the genus. Such a map would provide an important tool for mapping phenotypes and assembling the genome. Here we estimate the genome size of Daphnia magna and describe the construction of an SNP array based linkage map. We then test the suitability of the map for life history and behavioural trait mapping. The two parent genotypes used to produce the map derived from D. magna populations with and without fish predation, respectively and are therefore expected to show divergent behaviour and life-histories. RESULTS: Using flow cytometry we estimated the genome size of D. magna to be about 238 mb. We developed an SNP array tailored to type SNPs in a D. magna F2 panel and used it to construct a D. magna linkage map, which included 1,324 informative markers. The map produced ten linkage groups ranging from 108.9 to 203.6 cM, with an average distance between markers of 1.13 cM and a total map length of 1,483.6 cM (Kosambi corrected). The physical length per cM is estimated to be 160 kb. Mapping infertility genes, life history traits and behavioural traits on this map revealed several significant QTL peaks and showed a complex pattern of underlying genetics, with different traits showing strongly different genetic architectures. CONCLUSIONS: The new linkage map of D. magna constructed here allowed us to characterize genetic differences among parent genotypes from populations with ecological differences. The QTL effect plots are partially consistent with our expectation of local adaptation under contrasting predation regimes. Furthermore, the new genetic map will be an important tool for the Daphnia research community and will contribute to the physical map of the D. magna genome project and the further mapping of phenotypic traits. The clones used to produce the linkage map are maintained in a stock collection and can be used for mapping QTLs of traits that show variance among the F2 clones.

Loss of ovarian estrogens causes only mild deterioration of glucose homeostasis in female ZDF rats preventable by voluntary running exercise.

Studies on normoglycemic ovariectomized Sprague-Dawley rats have provided insights about the effects of estrogen deficiency on insulin resistance in lean individuals. It is not completely clear if subjects with pre-established obesity and insulin resistance are at greater risk of developing type 2 diabetes when ovarian estrogens are no longer secreted, and if physical activity can protect against this susceptibility. Contrasting with their male counterparts, obese and insulin resistant female ZDF (Zucker diabetic fatty) rats do not become hyperglycemic when fed a standard diet. The aim of the study was to evaluate the hypothesis that withdrawal of ovarian estrogens in insulin resistant female ZDF rats would trigger overt hyperglycemia, provided they remain physically inactive. Female ZDF rats underwent either an ovariectomy (OVX) or a simulated surgery (SHAM). Thereafter, OVX rats engaged either in voluntary wheel cage running (OVX-Active), or like the Sham rats, remained sedentary (OVX-Sed) for 6 weeks. Fasting glycemia, insulinemia, and glucose tolerance were not altered in OVX-Sed as compared to SHAM-Sed rats. However, OVX-Sed rats showed altered liver triglyceride and glycogen contents, increased pancreatic insulin content and reduced insulin-stimulated muscle pAKT as compared to SHAM-Sed rats. Physical activity in OVX rats lowered fasting glucose and insulin levels, improved glucose tolerance and insulin-stimulated skeletal muscle glucose uptake as compared to OVX-Sed rats. OVX-induced alterations in pancreatic insulin content and liver glycogen and triglyceride contents were significantly improved by physical activity. Loss of ovarian estrogens did not cause overt hyperglycemia in insulin-resistant female ZDF rats. Physical activity improved glucose homeostasis despite estrogen deficiency.

Competition during the milk-feeding stage influences the development of feeding behavior of pair-housed dairy calves.

This study investigated how the feeding behavior of pair-housed calves develops in response to reduced teat and feed place availability. Twenty Holstein bull calves were pair housed and provided with milk replacer (MR) and grain concentrate ad libitum via either (1) 1 teat and feed bucket/pen, such that calves could not feed simultaneously [competitive feeding (CF)] or (2) 2 teats and feed buckets/pen [noncompetitive feeding (NCF)]. The calves were weaned during wk 7 of life by incrementally diluting the MR. Postweaning, all pens were managed identically and offered a complete pelleted diet ad libitum via 2 feed buckets/pen (NCF) in period 1 (wk 8 and 9) and period 3 (wk 12 and 13) and exposed to a competitive challenge with CF in period 2 (wk 10 and 11). Feeding times and competitive interactions were recorded from video for 3 d/wk in wk 2, 4, and 6 and 2 d/wk in wk 8 to 13. Meal criteria were used to calculate daily meal frequency, meal time, and synchronized meal time (the percentage of meal time when calves within the pen were engaged in simultaneous meals). Milk replacer intake was subject to a treatment × week interaction, with calves in CF pens having lower MR intake (wk 2: 8.3 vs. 10.0 L/calf per day for CF vs. NCF), but compensating by increasing intake to a greater extent over time (wk 4-5: 13.3 vs. 11.7 L/d for CF vs. NCF). Corresponding to MR intake, meal frequencies and feeding times evolved differently over this period, increasing in CF pens and decreasing in NCF pens (wk 2: 5.8 vs. 11.1 and wk 4-6: 6.2 vs. 5.1 meals/d for CF vs. NCF). Calves in CF pens also spent less time engaged in synchronized meals (28 vs. 51% of meal time; standard error=7.1) and displaced each other 5 times more frequently during synchronized eating. Postweaning, calves in previously CF pens maintained 5 times greater displacement frequencies and had fewer overlapping meals than calves in previously NCF pens (34.5 vs. 40.7% of meals, respectively). Postweaning, when calves were all fed noncompetitively (2 buckets/pen in periods 1 and 3), calves previously fed CF had greater intakes in period 3 (4.87 vs. 4.44 kg/d) and a tendency for greater intake in period 1 (2.80 vs. 2.63 kg/d), greater rates of intake in period 3 (87.8 vs. 72.0 g/min) and a tendency for greater rates of intake in period 1 (44.3 vs. 38.9 g/min), and greater meal frequencies in both periods (11.1 vs. 9.9 meals/d). In the competitive challenge period (1 bucket/pen in period 2), intake, rates of intake, and meal frequencies were subject to treatment × week interactions: calves in NCF pens had lower intake and meal frequencies, but increased meal frequency, intake, and rate of intake over time to a greater extent than calves previously in CF pens. These results indicate that calves are able to adapt to moderate competition by increasing meal frequency and that behavioral responses to competition persist postweaning.

Ovariectomy stimulates hepatic fat and cholesterol accumulation in high-fat diet-fed rats.

This study was designed to determine how estrogens withdrawal during a high-fat (HF) diet regimen affects liver triacylglycerol (TAG) and cholesterol accumulation. Female Sprague-Dawley rats were submitted to a HF (42% energy as fat) or a standard (SD) diet for 6 weeks before being either ovariectomized (Ovx) or sham operated (Sham). Thereafter, Ovx and Sham rats were kept on the same diet for another 6 weeks leading to euthanasia. Liver TAG content was increased (p<0.01) in Ovx rats but not by the HF diet alone. However, the combination of HF diet and Ovx resulted in a greater liver TAG accumulation (p<0.06) than that observed in Ovx-SD/SD. Measurement of molecular markers of liver lipid metabolism revealed an increase in transcripts of markers of lipid oxidation (CPT-1 and PGC1; p<0.05) in rats fed the HF diet. This increase was, however, substantially less if HF fed rats were Ovx. Liver total cholesterol levels were increased (p<0.01) only in the Ovx-HF/HF rats while plasma cholesterol levels were increased in Ovx-SD/SD and in SHAM-HF/HF and Ovx-HF/HF rats. Transcripts of molecular markers of cholesterol metabolism suggest that biliary acids synthesis (CYP7a-1) was reduced in Ovx-SD/SD and Sham-HF/HF rats and even more so in Ovx-HF/HF rats. It is concluded that the effects of a HF diet on liver TAG accumulation are especially observed in Ovx rats possibly through a reduction in hepatic lipid oxidation. The combination of Ovx and HF diet also acts synergistically to favor liver cholesterol accumulation.

Associations of housing, management, milking activity, and standing and lying behavior of dairy cows milked in automatic systems.

The objective of this cross-sectional study was to describe the housing, feeding management, and characteristics (parity and stage of lactation) of cows on commercial automatic milking system (AMS) dairies and their associations with the standing and lying behavior patterns and milking activity (frequency and yield) of lactating dairy cows. Thirteen AMS herds were enrolled in the study, with an average herd size of 71±30 (mean ± SD; range: 34 to 131) lactating cows. All of the herds used freestall barns, each set up for free cow traffic to the AMS. On-farm measurements were taken to determine stocking density at the freestalls (0.9±0.1 cows/stall; mean ± SD), feed bunk (0.66±0.17 m of feed bunk space/cow; mean ± SD), and AMS units (55±11 cows/AMS; mean ± SD). A random sample of 30 cows/herd was selected to monitor standing and lying behavior for 4d using electronic data loggers. Times of feed delivery and feed push-up were recorded daily by the herd managers. Milking times, frequency, and yield were automatically recorded by the AMS units. Data were analyzed in a multivariable mixed regression model to determine which herd-level (housing and feeding management) and cow-level (parity, DIM, and milk yield) factors were associated with behavior and milking activity measures. Lying bout lengths were found to be negatively associated with milk yield and tended to be positively associated with more space at the feed bunk. Increased lying duration was associated with cows of lower milk production, increased space at the feed bunk, and increased frequency of feed push-up. Longer postmilking standing durations were associated with cows of higher parity. An association existed between cows milking less frequently when they were further in lactation, were of higher parity, and as stocking density at the AMS (cows/AMS) increased. Milk yield was positively associated with increased space at the feed bunk and higher parity and negatively associated with DIM. From this study, it can be concluded that increased milking frequency may be achieved in AMS herds by reducing stocking density at the AMS unit. Further, in AMS systems, greater milk yield and lying duration may be achieved by ensuring that cows have ample feed bunk space and have their feed readily available to them in the bunk.

Effect of milk feeding level on development of feeding behavior in dairy calves.

Evidence exists that early life experiences may influence development of characteristic feeding patterns in dairy cattle. The objective of this study was to determine the effect of milk feeding level on performance and development of feeding patterns in dairy calves. Twenty Holstein bull calves were assigned at birth to a milk replacer feeding level, fed via a teat: (1) ad libitum (ADL) or (2) restricted feeding at 5 L/d (0.75 kg of milk replacer) in 2 feedings/d (RES). All calves were offered concentrate ad libitum during the milk feeding stage. Calves were weaned gradually during wk 7 and then fed a pelleted diet ad libitum for 7 wk. Calves were weighed 2 times/wk. Feed and milk intakes were recorded daily. Feeding behavior was recorded from video for 5 d in each of wk 3, 6, 8, 11, and 14. Calves fed ADL consumed 2.6 times more milk, had greater weight gain (1.2 vs. 0.6 kg/d), and consumed less solid feed (45.2 vs. 98.0 g/d) during the milk feeding period than did calves fed RES. As expected, providing milk ADL resulted in more frequent meals (in wk 6, 7.1 vs. 2.0) and more evenly distributed diurnal patterns of feeding activity compared with the RES milk level. When considering all sucking bouts (milk feeding and nonnutritive sucking), no difference was observed between treatments in daily bout frequency or sucking time/bout. Postweaning, calves fed RES had initially greater rate of intake (24.9 vs. 17.8 g/min) and meal size (160.8 vs. 117.2 g/meal). Diurnal feeding patterns also differed in the first week after weaning, with ADL calves feeding less continuously at the time of feed delivery. Meal characteristics and diurnal patterns of feeding activity were similar between calves by the end of the trial. However, milk feeding level had a longer-term effect on variability in feeding behavior, with calves fed RES having greater day-to-day variability in feeding time and meal size. Variability of meal characteristics also decreased over time across treatments. These results suggest that milk feeding level may have a short-term influence on postweaning feeding behavior. However, differences in early feeding patterns due to milk feeding level do not appear to affect longer-term development of feeding patterns.

Effect of early exposure to different feed presentations on feed sorting of dairy calves.

This study examined how early exposure to different feed presentations affects development of feed sorting in dairy calves. Twenty Holstein bull calves were exposed for the first 8 wk of life to 1 of 2 feed presentation treatments: concentrate and chopped grass hay (<2.5cm) offered ad libitum at a ratio of 7:3 as a mixture (MIX), or as separate components (COM). Calves received 8L/d of milk replacer (1.2kg of dry matter), with the amount progressively reduced after 5 wk to facilitate weaning by the end of wk 7. All calves received the MIX diet in wk 9 to 11 and, subsequently, a novel total mixed ration (TMR; containing 40.5% corn silage, 22.0% haylage, 21.5% high-moisture corn, and 16.0% protein supplement) in wk 12 to 13. Intake was recorded daily and calves were weighed twice a week. Fresh feed and orts were sampled on d 1 to 4 of wk 6, 8, 9, 11, 12, and 13 for analysis of feed sorting, which was assessed through nutrient analysis for the MIX diet and particle size analysis for the TMR. The particle separator had 3 screens (19, 8, and 1.18mm) producing long, medium, short, and fine particle fractions. Sorting of nutrients or particle fractions was calculated as the actual intake as a percentage of predicted intake; values >100% indicate sorting for, whereas values <100% indicate sorting against. Feed presentation did not affect dry matter intake or growth. Prior to weaning, all calves selected in favor of hay; MIX calves consumed more neutral detergent fiber (NDF) than predicted (103.6%) and less nonfiber carbohydrates (NFC) than predicted (92.6%), and COM calves consumed, as a percentage of dry matter intake, 40.3% hay (vs. 30% offered rate). In wk 8, calves fed COM consumed more NFC than calves fed MIX (1.0 vs. 0.95kg/d) and less NDF (0.43 vs. 0.54kg/d), indicating greater selection in favor of concentrate. However, when provided the MIX diet, calves previously fed COM did not sort, whereas calves previously fed MIX consumed more NFC intake than predicted (103.2%) and less NDF intake than predicted (97.6%). Calves previously fed MIX maintained increased sorting after transition to the novel TMR, sorting against long particles (86.5%) and for short (101.8%) and fine (101.2%) particles. These results indicate that initially providing dairy calves with solid feeds as separate components, compared with as a mixed ration, reduces the extent of feed sorting in the weeks after transition to a common ration.