Relationship between dairy cow genetic merit and profit on commercial spring calving dairy farms

Because not all animal factors influencing profitability can be included in total merit breeding indices for profitability, the association between animal total merit index and true profitability, taking cognisance of all factors associated with costs and revenues, is generally not known. One method to estimate such associations is at the herd level, associating herd average genetic merit with herd profitability. The objective of this study was to primarily relate herd average genetic merit for a range of traits, including the Irish total merit index, with indicators of performance, including profitability, using correlation and multiple regression analyses. Physical, genetic and financial performance data from 1131 Irish seasonal calving pasture-based dairy farms were available following edits; data on some herds were available for more than 1 year of the 3-year study period (2007 to 2009). Herd average economic breeding index (EBI) was associated with reduced herd average phenotypic milk yield but with greater milk composition, resulting in higher milk prices. Moderate positive correlations (0.26 to 0.61) existed between genetic merit for an individual trait and average herd performance for that trait (e.g. genetic merit for milk yield and average per cow milk yield). Following adjustment for year, stocking rate, herd size and quantity of purchased feed in the multiple regression analysis, average herd EBI was positively and linearly associated with net margin per cow and per litre as well as gross revenue output per cow and per litre. The change in net margin per cow per unit change in the total merit index was €1.94 (s.e. = 0.42), which was not different from the expectation of €2. This study, based on a large data set of commercial herds with accurate information on profitability and genetic merit, confirms that, after accounting for confounding factors, the change in herd profitability per unit change in herd genetic merit for the total merit index is within expectations.     

Aligning health and welfare principles and practice in organic dairy systems: a review

This review provides an assessment of research findings into the current practices and standards and the principles and aspirations for organic dairy production, with respect to the health and welfare of the dairy cow. The relationships between the four main factors: management, environment, genetics and nutrition and their impact on the health and welfare status of organic dairy cows are considered. The concept that good animal health and welfare is more than merely the absence of disease, with behavioural aspects of health and welfare such as physiological and psychological needs, is also discussed. These factors are inter-related and important in all dairy systems, irrespective of whether the system is organic, low-input or intensive. Incidences of individual clinical and sub-clinical diseases that are recorded in conventional dairy systems also occur in organic dairy systems, with infertility, lameness and mastitis being the major problems. However, the magnitude of the incidence of many of these diseases may be either lower or higher in organic systems due to different management practices and the standards defined for organic milk production that, for example, prohibit the routine use of conventional medicines and require the feeding of high-forage diets. In relation to different systems, it is important to note that contrary to a common assumption, good welfare does not necessarily occur with more extensive systems. The type of organic system (self-sufficient, purchased-feed) also has the potential to have a major influence on the incidence of health problems and the reproductive status of organic dairy herds. Health status is also influenced by environmental and welfare factors, including the method of rearing replacement animals, type of housing and the geographical and climatic conditions of individual farms. Overall, this review identifies where conflicts arise between current practice and the organic principles and standards, and aims to provide suggestions to bring about further improvement in organic dairy health and welfare.     

Genetic association between body energy measured throughout lactation and fertility in dairy cattle

The objective of this study was to quantify the genetic association of body energy assessed throughout lactation with a cow's fertility. Nine direct and indirect body energy traits were defined at different stages of lactation. Four were daily records of energy balance, energy content, cumulative effective energy (CEE) and body condition score (BCS) calculated between lactation days 4 and 311. The other five traits included duration of negative energy balance (DNEB), rate of recovery during DNEB (RNEB), sum of negative energy balance (SNEB), nadir of energy content (NEC) and number of days from calving to NEC. Of these traits, energy balance, DNEB, RNEB and SNEB were primarily based on individual cow feed intake and milk yield, and considered direct measures of body energy. The other traits were calculated from body lipid and protein changes, predicted from BCS and live weight profiles, and were considered indirect measures of body energy. Fertility was defined by number of days between calving and commencement of luteal activity (DLA), first observed oestrus (DH) and conception (DC), and number of services per conception. A total of 957 cows in their first four lactations were considered in the study. Genetic models fitted cubic splines to define longitudinal traits (energy balance, energy content, CEE and BCS) and calculate heritability and genetic correlation with fertility. Daily heritability estimate ranges were 0.10 to 0.34, 0.35 to 0.61, 0.32 to 0.53 and 0.24 to 0.56 for energy balance, energy content, CEE and BCS, respectively, and, in most cases, tended to increase towards the middle of lactation and remain relatively stable thereafter. Of the other body energy traits, heritability of NEC (0.44) was the most notable. Statistically significant (P < 0.05) genetic correlations of DH with daily energy balance, energy content, CEE and BCS ranged from -0.16 to -0.28, -0.35 to -0.48, -0.16 to -0.26 and -0.37 to -0.44, respectively. For DC, respective estimates were -0.28 to -0.64, -0.37 to -0.60, -0.30 to -0.48 and -0.29 to -0.53. For DLA, they ranged from -0.47 to -0.56 with energy content and from -0.50 to -0.74 with BCS. Of special interest was the genetic correlation of NEC with DH (-0.54) and DC (-0.48). Results suggest that indirect measures of body energy have the strongest genetic association with cow fertility. NEC and early lactation (circa day 50) BCS and energy content are the most useful traits for selection in terms of the correlated improvement in a cow's capacity to resume her reproductive activity post partum.     

Genetics of milking characteristics in dairy cows

Genetic selection for milking speed is feasible. The existence of a correlation structure between milking speed and milk yield, however, necessitates a selection strategy to increase milking speed with no repercussion on genetic merit for milk yield. Residual milking duration (RMD) and residual milking duration including somatic cell score (RMDS), defined as the residuals from a regression model of milking duration on milk yield or milk yield plus somatic cell score (SCS) have been advocated. The objective of this study was to undertake a first ever genetic analysis of these novel traits. Data on electronically recorded milking duration and other milking characteristics from 235 005 test-day records on 74 608 cows in 1075 Irish dairy herds were available. Variance components for the milking characteristic traits were estimated using animal linear mixed models and covariances with other performance traits, including udder-related type traits, were estimated using sire models. The heritability of milking duration, RMD and RMDS was 0.20, 0.22 and 0.18, respectively. There were little differences in the heritability of RMD or RMDS when defined using genetic regression. The genetic standard deviation of RMDS defined on the phenotypic or genetic level was 36.8 s and 37.6 s, respectively, clearly indicating considerable exploitable genetic variation in milking duration independent of both milk yield and SCS. The genetic correlation between phenotypically derived RMDS and milk yield was favourable (−0.43), but RMDS was unfavourably genetically correlated with SCS (−0.30); the genetic correlations with both traits when RMDS was defined at a genetic level were zero. RMDS defined at the phenotypic level was negatively (i.e. unfavourable) genetically correlated (−0.35; s.e. = 0.15) with mastitis; however, when defined using genetic regression, shorter RMDS was not associated with greater expected incidence of mastitis. RMDS, defined at the genetic level, is a useful heritable trait with ample genetic variation for inclusion in a national breeding strategy without influencing genetic gain in either milk yield or udder health.     

Factors affecting reproductive performance in Ontario dairy herds

Data were collected on reproductive, health and production events in 45 dairy herds in southwestern and eastern Ontario, Canada, from July 1990 to July 1993. Mean and median days in milk at first estrus, at first service, and at conception were 85.1 and 83.9, 94.0 and 88.9, and 126.3 and 115.5 d, respectively. The mean estrus detection rate was 48.3%, with a minimum of 28.4% and a maximum of 64.2%. The mean overall conception rate was 46.7%, with a minimum of 29.8% and a maximum of 70.7%. The most commonly used used therapeutic agents were GnRH (11.5% lactational incidence risk) and PG (13.1% lactational incidence risk). Estrus management accounted for the largest portion of PG use in the herds studied (69.4%). Results of a two sample t-test indicated no significant difference in reproductive performance among herds housed in free-stall compared with those housed in tie-stall barns. Multivariate linear regression models of 3 reproductive performance measures indicated that cows with ovarian cysts and/or increased peak milk production had significantly longer calving-to-first estrus and calving-to-conception intervals as well as lower conception rates than average producing cows without cysts. Cows with metritis were found to have significantly shorter calving-to-conception intervals but no detectable difference in conception rate or calving-to-first estrus interval than their herdmates. As lactation number increased reproductive performance improved. Cows that were observed in estrus earlier conceived earlier. Animals receiving uterine infusions had significantly longer calving-to-conception intervals and lower conception rates than their herdmates. There was no detectable difference in reproductive performance for cows treated with GnRH or PG compared with the nontreated cows. An increased estrus detection rate was associated with shorter calving-to-conception intervals and lower conception rates. Based on the range of performance in the study herds, the factors with the greatest potential influence on calving-to-conception interval in the average herd were the estrus detection rate and conception rate.     

Responses in mammary and splanchnic metabolism to altered lysine supply in dairy cows

Lysine is usually taken up in excess by the mammary gland (MG) relative to milk protein output, allowing for mammary synthesis of non-essential (NE) amino acids (AA) from Lys-N. It is unclear whether this NEAA synthesis from Lys is obligate or whether more efficient use of Lys can be made under limiting conditions. Six multi-catheterized dairy cows received a basal diet low in protein plus an abomasal infusion of AA (560 g/day) with or without Lys (50.3 g/day), in a crossover design with 7-day periods. On day 7, all cows received a 7.5-h jugular infusion of [2-15N]lysine. Six blood samples were collected from arterial, portal, hepatic and mammary vessels at 45 min intervals. In addition, cows were milked at 6 and 7 h with the milk casein plus arterial and mammary plasma collected at 7 h analyzed for AA enrichment. Milk protein concentration and casein yield tended (P < 0.10) to decrease with Lys deletion, while Lys secretion in milk protein was lowered (P < 0.05). The addition of Lys in the AA mixture increased the net portal absorption of Lys by the amount infused, suggesting limited oxidation of this extra supply by the gut. Net liver flux of Lys was unaltered by treatment and, therefore, net splanchnic release of Lys reflected closely the amounts absorbed. For both treatments, however, post-liver supply was greater than mammary uptake, which exceeded milk output. Nonetheless, while Lys deletion decreased mammary uptake by 10.1 mmol/h, Lys in milk protein secretion was reduced by only 3.9 mmol/h. On a net basis, there was no evidence of the additional uptake of any other measured AA during the Lys deletion. The mammary uptake to output ratio of Lys decreased from 1.37 to 1.12, but still showed an excess with Lys deletion. The total amount of 15N in milk protein did not change with treatment but the distribution into AA was altered. In conditions that simulated normal feeding (Lys infused), 83% of the 15N was present as Lys, with Glx, Asx, Ser and Ala harvesting, respectively, 6.8%, 2.4%, 2.1% and 1.0%. With Lys depletion, N-transfers from Lys to other AA within the MG were still present, but rates were considerably lower. This would suggest that part, at least, of Lys catabolism in the MG is either needed or cannot be prevented completely, even at low supply of Lys. Such catabolism will provide N to support the synthesis of NEAA.     

Microencapsulated sodium selenite supplementation in dairy cows: effects on selenium status

The objective of this study was to compare the efficiency of transfer of selenium (Se) to plasma and milk from inorganic sodium selenite, either free or microencapsulated, and from selenized yeast in dairy cows. The study consisted of an in situ-nylon bags incubation, and in an in vivo experiment to compare the Se status of cows supplemented with either sodium selenite, microencapsulated sodium selenite, or Se yeast. Thirty dairy cows, divided in five groups, were fed the following diets: the control group (CTR) received a total mixed ration supplemented with sodium selenite in order to have 0.3 mg/kg DM of total Se; 0.3M and 0.5M groups received the same control diet supplemented with lipid microencapsulated sodium selenite to provide 0.3 and 0.5 mg/kg DM of total Se, respectively; 0.3Y and 0.5Y groups received selenized yeast to provide 0.3 and 0.5 mg/kg of total Se, respectively. Cows were fed the supplements for 56 days during which milk, blood, and fecal samples were collected weekly to conduct analysis of Se and glutathione peroxidase (GSH-px) activity. Se concentration in the nylon bags was assessed to 72%, 64%, and 40% of the initial value (time 0) after 4, 8, and 24 h of incubation, respectively. In vivo, cows supplemented with 0.3 mg/kg of microencapsulated Se had higher milk Se concentration compared to CTR. The increment was more pronounced at the highest inclusion rate (0.5 mg/kg, 0.5M group). GSH-px activity was not significantly affected by treatments. The results indicate that lipid microencapsulation has the potential to protect nutrients from complete rumen reduction and that Se from microencapsulated selenite is incorporated in milk more efficiently than the free form. Microencapsulated sodium selenite was shown to be comparable to Se-yeast in terms of availability and incorporation in milk when fed at 0.3 mg/kg DM, whereas the inclusion in the diet at 0.5 mg/kg DM resulted in higher plasma and milk concentrations than selenized yeast.     

Quantitative trait loci mapping in dairy cattle: review and meta-analysis

From an extensive review of public domain information on dairy cattle quantitative trait loci (QTL), we have prepared a draft online QTL map for dairy production traits. Most publications (45 out of 55 reviewed) reported QTL for the major milk production traits (milk, fat and protein yield, and fat and protein concentration (%)) and somatic cell score. Relatively few QTL studies have been reported for more complex traits such as mastitis, fertility and health. The collated QTL map shows some chromosomal regions with a high density of QTL, as well as a substantial number of QTL at single chromosomal locations. To extract the most information from these published records, a meta-analysis was conducted to obtain consensus on QTL location and allelic substitution effect of these QTL. This required modification and development of statistical methodologies. The meta-analysis indicated a number of consensus regions, the most striking being two distinct regions affecting milk yield on chromosome 6 at 49 cM and 87 cM explaining 4.2 and 3.6 percent of the genetic variance of milk yield, respectively. The first of these regions (near marker BM143) affects five separate milk production traits (protein yield, protein percent, fat yield, fat percent, as well as milk yield).     

Impacts of intensive dairy production on smallholder farm women in coastal Kenya

Welfare impacts of an intensive dairy technology package on women and their families are investigated on 32 smallholder crop-livestock farms in the sub-humid zone off Kilifi District, Coast Province, Kenya. Farms were stratified according to male or female extension contact. A female enumerator interviewed the wife or female head of household on each farm regarding her present and past household responsibilities and the affects of the intensive dairy enterprise on these duties and upon the welfare of the household. On three-quarters of the male contact farms, dairy operators were women. Across all farms, women performed half of all dairy-related activities, but only on female contact farms did income from the dairy enterprise accrue to women in proportion to their labor input. The equitable return of benefits to labor corresponded with better dairy unit performance on female contact farms, where women also indicated greater access to and autonomy over household resources and decision-making. Irrespective of extension contact, there was broad consensus among the women interviewed that intensive dairying has led to improved household welfare, primarily through increased household income and milk consumption. There was also wide agreement, however, that these gains have been achieved at the expense of more work for women. Women on female contact farms were observed spending dairy income on food for the household and childrens' schooling more often than their counterparts on male contact farms. Based on these and other findings, the study concludes that gender of the extension contact, dairy operator and farm owner were determinants of the intra-household impacts of intensive dairying on the smallholder farms in this study. Recommendations for design and delivery of livestock technologies for crop-based farming systems, with special emphasis on how to minimize negative impact on vulnerable household members, are inferred from study findings.Formerly International Livestock Research Institute, P.O. Box 30709, Nairobi, Kenya.     

New phenotypes for new breeding goals in dairy cattle

Cattle production faces new challenges regarding sustainability with its three pillars - economic, societal and environmental. The following three main factors will drive dairy cattle selection in the future: (1) During a long period, intensive selection for enhanced productivity has deteriorated most functional traits, some reaching a critical point and needing to be restored. This is especially the case for the Holstein breed and for female fertility, mastitis resistance, longevity and metabolic diseases. (2) Genomic selection offers two new opportunities: as the potential genetic gain can be almost doubled, more traits can be efficiently selected; phenotype recording can be decoupled from selection and limited to several thousand animals. (3) Additional information from other traits can be used, either from existing traditional recording systems at the farm level or from the recent and rapid development of new technologies and precision farming. Milk composition (i.e. mainly fatty acids) should be adapted to better meet human nutritional requirements. Fatty acids can be measured through a new interpretation of the usual medium infrared spectra. Milk composition can also provide additional information about reproduction and health. Modern milk recorders also provide new information, that is, on milking speed or on the shape of milking curves. Electronic devices measuring physiological or activity parameters can predict physiological status like estrus or diseases, and can record behavioral traits. Slaughterhouse data may permit effective selection on carcass traits. Efficient observatories should be set up for early detection of new emerging genetic defects. In the near future, social acceptance of cattle production could depend on its capacity to decrease its ecological footprint. The first solution consists in increasing survival and longevity to reduce replacement needs and the number of nonproductive animals. At the individual level, selection on rumen activity may lead to decreased methane production and concomitantly to improved feed efficiency. A major effort should be dedicated to this new field of research and particularly to rumen flora metagenomics. Low input in cattle production is very important and tomorrow's cow will need to adapt to a less intensive production environment, particularly lower feed quality and limited care. Finally, global climate change will increase pathogen pressure, thus more accurate predictors for disease resistance will be required.     

Review: welfare of dairy cows in continuously housed and pasture-based production systems

There is increasing interest in the use of continuous housing systems for dairy cows, with various reasons put forward to advocate such systems. However, the welfare of dairy cows is typically perceived to be better within pasture-based systems, although such judgements are often not scientifically based. The aim of this review was to interrogate the existing scientific literature to compare the welfare, including health, of dairy cows in continuously housed and pasture-based systems. Although summarising existing work, knowledge gaps and directions for future research are also identified. The scope of the review is broad, examining relevant topics under three main headings; health, behaviour and physiology. Regarding health, cows on pasture-based systems had lower levels of lameness, hoof pathologies, hock lesions, mastitis, uterine disease and mortality compared with cows on continuously housed systems. Pasture access also had benefits for dairy cow behaviour, in terms of grazing, improved lying/resting times and lower levels of aggression. Moreover, when given the choice between pasture and indoor housing, cows showed an overall preference for pasture, particularly at night. However, the review highlighted the need for a deeper understanding of cow preference and behaviour. Potential areas for concern within pasture-based systems included physiological indicators of more severe negative energy balance, and in some situations, the potential for compromised welfare with exposure to unpredictable weather conditions. In summary, the results from this review highlight that there remain considerable animal welfare benefits from incorporating pasture access into dairy production systems.     

Prevalence and antimicrobial resistance of Campylobacter in US dairy cattle

AIMS: To obtain an overview of the prevalence and antimicrobial resistance of Campylobacter in faeces of US dairy cows in 2002. METHODS AND RESULTS: Faeces from 1435 cows, representing 96 dairy operations in 21 US states, were collected for the culture of Campylobacter. A total of 735 Campylobacter strains were isolated (51.2% positive samples) with 94 operations positive (97.9%) for Campylobacter. From this collection, 532 isolates (473 Campylobacter jejuni and 59 Campylobacter coli) were randomly selected for susceptibility testing to eight antimicrobials: azithromycin, chloramphenicol, ciprofloxacin, clindamycin, erythromycin, gentamicin, nalidixic acid and tetracycline. The C. jejuni isolates exhibited resistance to tetracycline (47.4%), nalidixic acid (4.0%) and ciprofloxacin (2.5%), while the C. coli strains exhibited some resistance to all antimicrobials except chloramphenicol and ciprofloxacin. Only 3.6% of the C. jejuni isolates were resistant to two or more antimicrobials but 20.3% of the C. coli strains were multiresistant. CONCLUSIONS: On most operations, at least one cow was positive for Campylobacter and more than half of the cows sampled were shedding Campylobacter. The C. coli isolates had significantly higher levels of resistance to macrolides and to tetracycline compared with the C. jejuni strains, but were susceptible to ciprofloxacin. SIGNIFICANCE AND IMPACT OF THE STUDY: This study demonstrated a high prevalence of Campylobacter on US dairy operations; however, US dairy cattle have not been recognized as a major source of human infection compared with poultry. Campylobacter coli appears to develop antimicrobial resistance more readily than C. jejuni from the same environment.     

Performance and financial consequences of stillbirth in Holstein dairy cattle

Stillbirth is an economically important trait on dairy farms. Knowledge of the consequences of, and the economic losses associated with stillbirth can help the producer when making management decisions. The objectives of this study were to determine the effects of stillbirth on productive and reproductive performance as well as financial losses due to stillbirth incidence in Iranian Holstein dairy farms. Economic and performance data were collected from nine Holstein dairy farms in Isfahan and Khorasan provinces of Iran from March 2008 to December 2013. The final data set included 160 410 calving records from 53 265 cows. A linear mixed model was developed to evaluate the effects of stillbirth on performance of primiparous and multiparous cows separately and overall. An economic model was used to estimate the economic losses due to stillbirth. The incidence of stillbirth cases per cow per year was 4.2% on average (3.4% to 6.8% at herd level). The least square means results showed that a case of stillbirth significantly (P<0.05) reduced 305-day milk production in multiparous cows and overall, but had no significant effects on primiparous cows production performance (P>0.05). Overall, a case of stillbirth reduced 305-day milk yield by 544.0±76.5 kg/cow per lactation. Stillbirth had no significant effects on 305-day fat and protein percentages in either primiparous or multiparous cows. Overall, cows that gave birth to stillborn calves had significantly increased days open by 14.6±2.6 days and the number of inseminations per conception by 0.2 compared with cows that gave birth to live calves (P<0.01). In general, the negative productive and reproductive effects associated with stillbirth were smaller and non-significant for primiparous cows compared with multiparous cows. The financial losses associated with stillbirth incidence averaged US$ 938 per case (range from $US 767 to $US 1189 in the nine investigated farms). The loss of a calf was not the only cost associated with stillbirth, as it accounted for 71.0% of the total cost. The costs of dystocia (7.6%) and culling and replacement expenses (6.3%) were the next most important costs associated with stillbirth. These results can be used to assess the potential return from management strategies to reduce the occurrence of stillbirths.     

Measures to improve dairy cow foot health: consequences for farmer income and dairy cow welfare

Dairy farming in western countries with cubicle housing is an efficient way of dairy farming. Though, a disadvantage is the high prevalence and incidence of foot disorders (clinical and subclinical), which cause high economic losses and also seriously impair the welfare of dairy cattle. To point out the importance of reducing the amount and severity of foot disorders, advice to farmers should include information about the scale of the problem and the consequences in terms of economics and animal welfare. To provide support in making decisions on implementing intervention measures, insight into costs and benefits of different measures should be available. The objective of this study, therefore, is to provide more insight into the costs and benefits, for farmer and cow, of different intervention measures to improve dairy cow foot health. Intervention measures were modeled when they were applicable on a dairy farm with cubicle housing and when sufficient information was available in literature. Net costs were calculated as the difference between the costs of the measure and the economic benefits resulting from the measure. Welfare benefits were calculated as well. Cost-effective measures are: improving lying surface (mattress and bedding, €7 and €1/cow per year, respectively), reducing stocking density (break even) and performing additional foot trimming (€1/cow per year). Simultaneously, these measures have a relative high welfare benefit. Labor costs play an important role in the cost-effectiveness of labor-intensive measures. More insight into cost-effectiveness and welfare benefits of intervention measures can help to prioritize when choosing between intervention measures.     

Leptin promoter mutations affect leptin levels and performance traits in dairy cows

Leptin concentrations in body fluids and tissues undergo dynamic changes during the periparturient period. Polymorphisms in the leptin gene have been shown to be associated with differences in leptin concentration during late pregnancy but not during lactation. As the promoter of leptin regulates the expression of leptin, polymorphisms in this region could play an important role in the differences in leptin expression observed during the periparturient period. We sequenced the leptin promoter and discovered 20 SNP in a 1.6-kbp region of the bovine leptin promoter. Fourteen of these SNP were genotyped for all animals and these were found to be associated with leptin concentrations during late pregnancy but not during lactation. Three of these SNP are located in a 135-bp promoter region and together explained 14.3% of the variance in prepartum leptin concentrations which indicates that this region might be important for pregnancy-induced leptin synthesis. In the association study of the 14 SNP with dairy traits three were separately found to be associated with fertility, energy balance and protein yield. These might serve as markers for future breeding programmes for better fertility and energy balance without significantly influencing milk yield in dairy cattle.     

Invited review: Improving feed efficiency in dairy production: challenges and possibilities

Despite substantial advances in milk production efficiency of dairy cattle over the last 50 years, rising feed costs remain a significant threat to producer profitability. There also is a greater emphasis being placed on reducing the negative impacts of dairy production on the environment; thus means to lower greenhouse gas (GHG) emissions and nutrient losses to the environment associated with cattle production are being sought. Improving feed efficiency among dairy cattle herds offers an opportunity to address both of these issues for the dairy industry. However, the best means to assess feed efficiency and make genetic progress in efficiency-related traits among lactating cows without negatively impacting other economically important traits is not entirely obvious. In this review, multiple measurements of feed efficiency for lactating cows are described, as well as the heritability of the traits and their genetic and phenotypic correlations with other production traits. The measure of feed efficiency, residual feed intake is discussed in detail in terms of the benefits for its selection, how it could be assessed in large commercial populations, as well as biological mechanisms contributing to its variation among cows, as it has become a commonly used method to estimate efficiency in the recent scientific literature.     

Identifying risk factors for poor hind limb cleanliness in Danish loose-housed dairy cows

The objective of this study was to identify possible risk factors for poor cow hind limb cleanliness in Danish loose-housed, lactating dairy cows. The study was conducted as a cross-sectional study of 1315 cows in 42 commercial Danish dairy herds with primarily Danish Holstein cows. The effect of four cow-level factors (parity, days in milk, daily lying time and lameness) and eight herd-level factors (herd size, milk production, milking system, floor type, access to pasture grazing, floor scraping frequency, hoof bathing frequency and hoof washing frequency) on the risk of having dirtier hind limbs were analysed using ordinal logistic regression fitting a proportional odds model. Cow hind limb cleanliness was scored using an ordinal score from 1 to 4: 1 being clean and 4 being covered in dirt. The odds ratios (ORs) estimated from the proportional odds model depict the effect of a risk factor on the odds of having a higher rather than a lower cleanliness score. First parity cows had an increased risk of being dirtier compared with third parity or older cows (OR=1.70). Compared with late lactation, early and mid lactation were associated with an increased risk of being dirtier (OR=2.07 and 1.33, respectively). Decreasing the daily time lying by 30 min was associated with an increased risk of being dirtier (OR=1.05). Furthermore, an increased risk of being dirtier was found in herds with no pasture access (OR=3.75).     

Imputation of ungenotyped parental genotypes in dairy and beef cattle from progeny genotypes

The objective of this study was to quantify the accuracy of imputing the genotype of parents using information on the genotype of their progeny and a family-based and population-based imputation algorithm. Two separate data sets were used, one containing both dairy and beef animals (n=3122) with high-density genotypes (735 151 single nucleotide polymorphisms (SNPs)) and the other containing just dairy animals (n=5489) with medium-density genotypes (51 602 SNPs). Imputation accuracy of three different genotype density panels were evaluated representing low (i.e. 6501 SNPs), medium and high density. The full genotypes of sires with genotyped half-sib progeny were masked and subsequently imputed. Genotyped half-sib progeny group sizes were altered from 4 up to 12 and the impact on imputation accuracy was quantified. Up to 157 and 258 sires were used to test the accuracy of imputation in the dairy plus beef data set and the dairy-only data set, respectively. The efficiency and accuracy of imputation was quantified as the proportion of genotypes that could not be imputed, and as both the genotype concordance rate and allele concordance rate. The median proportion of genotypes per animal that could not be imputed in the imputation process decreased as the number of genotyped half-sib progeny increased; values for the medium-density panel ranged from a median of 0.015 with a half-sib progeny group size of 4 to a median of 0.0014 to 0.0015 with a half-sib progeny group size of 8. The accuracy of imputation across different paternal half-sib progeny group sizes was similar in both data sets. Concordance rates increased considerably as the number of genotyped half-sib progeny increased from four (mean animal allele concordance rate of 0.94 in both data sets for the medium-density genotype panel) to five (mean animal allele concordance rate of 0.96 in both data sets for the medium-density genotype panel) after which it was relatively stable up to a half-sib progeny group size of eight. In the data set with dairy-only animals, sufficient sires with paternal half-sib progeny groups up to 12 were available and the within-animal mean genotype concordance rates continued to increase up to this group size. The accuracy of imputation was worst for the low-density genotypes, especially with smaller half-sib progeny group sizes but the difference in imputation accuracy between density panels diminished as progeny group size increased; the difference between high and medium-density genotype panels was relatively small across all half-sib progeny group sizes. Where biological material or genotypes are not available on individual animals, at least five progeny can be genotyped (on either a medium or high-density genotyping platform) and the parental alleles imputed with, on average, ⩾96% accuracy.