Multibreed genomic prediction using summary statistics and a breed-origin-of-alleles approach

Because of an increasing interest in crossbreeding between dairy breeds in dairy cattle herds, farmers are requesting breeding values for crossbred animals. However, genomically enhanced breeding values are difficult to predict in crossbred populations because the genetic make-up of crossbred individuals is unlikely to follow the same pattern as for purebreds. Furthermore, sharing genotype and phenotype information between breed populations are not always possible, which means that genetic merit (GM) for crossbred animals may be predicted without the information needed from some pure breeds, resulting in low prediction accuracy. This simulation study investigated the consequences of using summary statistics from single-breed genomic predictions for some or all pure breeds in two- and three-breed rotational crosses, rather than their raw data. A genomic prediction model taking into account the breed-origin of alleles (BOA) was considered. Because of a high genomic correlation between the breeds simulated (0.62-0.87), the prediction accuracies using the BOA approach were similar to a joint model, assuming homogeneous SNP effects for these breeds. Having a reference population with summary statistics available from all pure breeds and full phenotype and genotype information from crossbreds yielded almost as high prediction accuracies (0.720-0.768) as having a reference population with full information from all pure breeds and crossbreds (0.753-0.789). Lacking information from the pure breeds yielded much lower prediction accuracies (0.590-0.676). Furthermore, including crossbred animals in a combined reference population also benefitted prediction accuracies in the purebred animals, especially for the smallest breed population

Association between selected antimicrobial resistance genes and antimicrobial exposure in Danish pig farms

Abstract Bacterial antimicrobial resistance (AMR) in pigs is an important public health concern due to its possible transfer to humans. We aimed at quantifying the relationship between the lifetime exposure of antimicrobials and seven antimicrobial resistance genes in Danish slaughter pig farms. AMR gene levels were quantified by qPCR of total-community DNA in faecal samples obtained from 681 batches of slaughter pigs. The lifetime exposure to antimicrobials was estimated at batch level for the piglet, weaner, and finisher periods individually for the sampled batches. We showed that the effect of antimicrobial exposure on the levels of AMR genes was complex and unique for each individual gene. Several antimicrobial classes had both negative and positive correlations with the AMR genes. From 10–42% of the variation in AMR gene levels could be explained in the final regression models, indicating that antimicrobial exposure is not the only important determinant of the AMR gene levels

Conservation of a native dairy cattle breed through terminal crossbreeding with commercial dairy breeds

Farmers play a key role in conserving native livestock breeds, but without economic support, farms with native breeds may not be viable. We hypothesized that terminal crossbreeding can improve herd economy and decrease the economic support needed from society. Three scenarios were simulated using SimHerd Crossbred: a herd of purebred Swedish Polled Cattle, a herd of purebred Swedish Red, and a herd of 75% Swedish Polled Cattle and 25% F1 crossbreds. The results showed annual contribution margin per cow in the herd can be increased by euro181 by crossbreeding compared with pure-breeding with the native breed, giving a 13.6% growth in contribution margin. However, the needed cost in subsidies paid by the government will remain unchanged if the population size of the native breed is to be maintained. Combining a crossbreeding strategy with the marketing of niche products may facilitate the conservation of native cattle

Dairy cattle farmers' preferences for different breeding tools

Breeding technologies play a significant role in improving dairy cattle production. Scientifically proven tools for improved management and genetic gain in dairy herds, such as sexed semen, beef semen, genomic testing, dairy crossbreeding, and multiple ovulation embryo transfer (MOET), are readily available to dairy farmers. However, despite good accessibility, decreasing costs, and continuous development of these tools, their use in Sweden is limited. This study investigated Swedish dairy farmers' preferences for breeding tools through a survey including a discrete choice experiment. The survey was distributed online to 1 521 Swedish farmers and by an open link published through a farming magazine. In total, the study included 204 completed responses. The discrete choice experiment consisted of 10 questions with two alternative combinations, which gave 48 combinations in total. Utility values and part-worth values were computed using a conditional logit model based on the responses in the discrete choice experiment for nine groups of respondents: one group with all respondents, two groups based on respondents using dairy crossbreeding or not within the past 12 months, two based on herd size, two based on respondent age, and two based on whether respondents had used breeding advisory services or not. The strongest preferences in all groups were for using sexed semen and beef semen. Genomic testing was also significantly preferred by all groups of respondents. Except in large herds, MOET on own animals was significantly and relatively strongly disfavoured by all groups. Buying embryos had no significant utility value to any group. Dairy crossbreeding had low and insignificant utility values in the group of all respondents, but it was strongly favoured by the group that had used dairy crossbreeding within the past 12 months, and it was disfavoured by the group that had not. Part-worth values of combined breeding tools showed that combinations of sexed and beef semen, alone or with genomic testing without dairy crossbreeding, were the most preferred tools. Compared with the most common combinations of breeding tools used in the past 12 months, the part-worth values indicated that Swedish dairy farmers may prefer to use breeding tools more than they do today. Statements on the different breeding tools indicated that the respondents agreed with the benefits attributed to the breeding tools, but these benefits may not be worth the cost of genomic testing and the time consumption of MOET. These valuable insights can be used for further development of breeding tools

Korsning med mjölkkor – effekter på besättningsdynamik och ekonomiskt resultat

I denna simuleringsstudie jämförs besättningsstruktur samt produktionsresultat och ekonomiskt resultat för besättningar med renrasiga kor och besättningar med korsningskor. Vi har använt medeltal från Kokontrollen som ingångsvärden till simuleringsprogrammet SimHerd Crossbred. Holsteinkor (SH), röda kor (SRB) och korsningskor från systematisk slutkorsning (enkelkorsning, terminal cross) ingick i studien. Fyra olika typer av besättningar studerades: bara renrasiga SRBkor, en kärna av renrasiga SRB-kor och SHxSRB-korsningskor, bara renrasiga SH-kor, samt en kärna av renrasiga SH-kor och SRBxSH-korsningskor. Resultaten presenteras både för konventionell och ekologisk produktion, eftersom medeltal för kornas resultat och kostnader och intäkter skiljer sig mellan dessa produktionssystem. Simuleringen visar att det ekonomiska resultatet för mjölkproducenter förbättras när man går från en renrasig besättning till en besättning med korsning och det gäller för såväl konventionell som ekologisk produktion. För besättningar med SRB-kärna blev förbättringen av det ekonomiska resultatet vid övergång till korsning större för ekologisk produktion än för konventionell produktion. Det är kopplat till ett högre avräkningspris för mjölk i ekologisk produktion. Besättningsstrukturen i en besättning med korsning påverkas av djurens reproduktion och funktionella egenskaper. Det medför att utrymmet för korsningskor är större i besättningar med SRB-kärna än i besättningar med SHkärna

Screening mammography beliefs and recommendations: a web-based survey of primary care physicians

<p>Abstract</p> <p>Background</p> <p>The appropriateness and cost-effectiveness of screening mammography (SM) for women younger than 50 and older than 74 years is debated in the clinical research community, among health care providers, and by the American public. This study explored primary care physicians' (PCPs) perceptions of the influence of clinical practice guidelines for SM; the recommendations for SM in response to hypothetical case scenarios; and the factors associated with perceived SM effectiveness and recommendations in the US from June to December 2009 before the United States Preventive Services Task Force (USPSTF) recently revised guidelines.</p> <p>Methods</p> <p>A nationally representative sample of 11,922 PCPs was surveyed using a web-based questionnaire. The response rate was 5.7% (684); (41%) 271 family physicians (FP), (36%) 232 general internal medicine physicians (IM), (23%) 150 obstetrician-gynaecologists (OBG), and (0.2%) 31 others. Cross-sectional analysis examined PCPs perceived effectiveness of SM, and recommendation for SM in response to hypothetical case scenarios. PCPs responses were measured using 4-5 point adjectival scales. Differences in perceived effectiveness and recommendations for SM were examined after adjusting for PCPs specialty, race/ethnicity, and the US region.</p> <p>Results</p> <p>Compared to IM and FP, OBG considered SM more effective in reducing breast cancer mortality among women aged 40-49 years (<it>p </it>= 0.003). Physicians consistently recommended mammography to women aged 50-69 years with no differences by specialty (<it>p </it>= 0.11). However, 94% of OBG "always recommended" SM to younger and 86% of older women compared to 81% and 67% for IM and 84% and 59% for FP respectively (<it>p = </it>< .001). In ordinal regression analysis, OBG specialty was a significant predictor for perceived higher SM effectiveness and recommendations for younger and older women. In evaluating hypothetical scenarios, overall PCPs would recommend SM for the 80 year woman with CHF with a significant variation by specialty (38% of OBG, 18% of FP, 17% of IM; <it>p </it>= < .001).</p> <p>Conclusions</p> <p>A majority of physicians, especially OBG, favour aggressive breast cancer screening for women from 40 through 79 years of age, including women with short life expectancy. Policy interventions should focus on educating providers to provide tailored recommendations for mammography based on individualized cancer risk, health status, and preferences.</p

Improving human and environmental health in urban informal settlements: the Revitalising Informal Settlements and their Environments (RISE) programme

Daniel Reidpath - ORCID: 0000-0002-8796-0420 https://orcid.org/0000-0002-8796-0420https://doi.org/10.1016/S2542-5196(18)30114-12pubpubSuppl