Digital scoring of welfare traits in Atlantic salmon (Salmo salar L.) - a proof of concept study quantifying dorsal fin haemorrhaging via hyperspectral imaging

IntroductionMorphological injuries are well-established Operational Welfare Indicators (OWIs) for farmed animals including fish. They are often scored manually by human observers and this process can be laborious and prone to subjectivity and error. In this study we evaluated the use of a hyperspectral imaging system to quantify the presence and severity of external haemorrhaging in Atlantic salmon focusing on dorsal fins as a proof of concept OWI.MethodsTwo inexperienced observers manually audited dorsal fin injuries on 234 post-smolt Atlantic salmon following a standardized protocol that scored fin erosion on a 0-3 scale and also classified the injury as active/healed. The same fish were then imaged with a hyperspectral camera system and the manually scored visual assessments were compared with hyperspectral images of the same fin. Hyperspectral images were processed to segment out the dorsal fin of each fish and the presence of blood in the tissue was quantified by analysing the spectral information, yielding a fin haemorrhaging index.ResultsThe hyperspectral imaging platform was robust at detecting blood in fins and could help classify active injuries more accurately than human observers. The agreement between human scorers and the image analysis tool for classifying active bleeding vs healed/undamaged fins was good with a Cohen’s kappa of 0.81 and 0.90. Accuracy between the fin haemorrhaging index and the human observers was moderate (0.61 and 0.57) and on par with the agreement between the two human observers (0.68), demonstrating the difficulty in classifying injuries that result in a reduction in fin size but may or may not result in fin haemorrhaging.DiscussionThese results demonstrate the potential power of hyperspectral imaging to improve welfare audits in aquaculture, especially where manual injury classification schemes have potentially mixed traits that involve haemorrhaging. The data also suggests that the hyperspectral camera can detect bleeding that is not readily visible to the human eye. There is a need for further testing and validation to integrate these tools into existing welfare auditing programs, but the potential advantages of the automated approach include increased sensitivity, accuracy and throughput, while producing quantitative data for researchers or management

Genetic parameters of fillet fatty acids and fat deposition in gilthead seabream (Sparus aurata) using the novel 30 k Medfish SNP array

Lipid-related traits are important candidates for a breeding goal for gilthead seabream, because they affect both fish and human health, as well as production efficiency. However, to date there have been very few estimates of genetic parameters for these traits, and the genetic relationship between fatty acids and other important traits have never been reported for gilthead seabream. Therefore, the aim of this study was to estimate genomic heritability and genetic relationships of fat deposition traits and individual muscle fatty acids in a commercial population of gilthead seabream using the novel ~30 k MedFish SNP array. In total 967 gilthead seabream fed with a commercial feed were genotyped with the MedFish SNP chip which included ~30 K informative markers for this species. On average, the fish weighed 372 g. The mean content of eicosapentaenoic acid (EPA) + docosahexaenoic acid (DHA) was 822 mg per 100 g fillet. The heritability of muscle fat, viscera weight and percentage viscera were in the range of 0.34–0.46. The genetic correlation of body weight with muscle fat was 0.12, indicating that genetic variation in muscle fat is largely independent of the weight of the fish. The heritability of the product of endogenous fatty acid synthesis (n = 240), palmitoleic acid (16:1n-7), was high (0.43). The estimated heritability of EPA (%) and DHA (%) was 0.39 and 0.33, respectively. Both EPA and DHA had low, non-significant genetic correlations with body weight, and DHA had a negative genetic correlation with muscle fat (−0.53). It is possible to increase EPA and DHA content in gilthead seabream fillets by selective breeding. The high heritability of 16:1n-7, a marker of de novo lipogenesis, suggests that there is a strong genetic component to this metabolic pathway in gilthead seabream. Muscle fat deposition and body weight seem to be independent traits, and selective breeding for faster growth is not likely to influence the proportional content of EPA and DHA

Interchangeability between methane measurements in dairy cows assessed by comparing precision and agreement of two non-invasive infrared methods

In this study we assess the interchangeability and statistical agreement of two prevalent instruments from the non-invasive "sniffer" method and compare their precision. Furthermore, we develop and validate an effective algorithm for aligning time series data from multiple instruments to remove the effects of variable and fixed time shifts from the instrument comparison. The CH4 and CO2 gas concentrations for both instruments were found to differ for population means (P < 0.05) and intra-cow variation (precision) (P < 0.05) and for inter-cow variation (P < 0.05). The CH4 and CO2 gas concentrations from both instruments can be used interchangeably to increase statistical power for example, in genetic evaluations, provided sources of disagreement are corrected through calibration and standardisation. Additionally, averaging readings of cows over a longer period of time (one week) is an effective noise reduction technique which provides phenotypes with considerable inter-cow variation

Can greenhouse gases in breath be used to genetically improve feed efficiency of dairy cows?

There is considerable interest in improving feed utilization of dairy cattle while limiting losses to the environment (i.e., greenhouse gases, GHG). To breed for feed-efficient or climate-friendly cattle, it is first necessary to obtain accurate estimates of genetic parameters and correlations of feed intake, greenhouse gases, and production traits. Reducing dry matter take (DMI) requirements while maintaining production has high economic value to farmers, but DMI is costly to record and thus limited to small research or nucleus herds. Conversely, enteric methane (CH4) currently has no economic value, is also costly to record, and is limited to small experimental trials. However, breath gas concentrations of methane (CH4c) and carbon dioxide (CO2c) are relatively cheap to measure at high throughput under commercial conditions by installing sniffers in automated milking stations. The objective of this study was to assess the genetic correlations between DMI, body weight (BW), fat- and protein-corrected milk yield (FPCM), and GHG-related traits: CH4c and CO2c from Denmark (DNK) and the Netherlands (NLD). A second objective was to assess the genetic potential for improving feed efficiency and the added benefits of using CH4c and CO2c as indicators. Feed intake data were available on 703 primiparous cows in DNK and 524 in NLD; CH4c and CO2c records were available on 434 primiparous cows in DNK and 656 in NLD. The GHG-related traits were heritable (e.g., CH4c h2: DNK = 0.26, NLD = 0.15) but were differentially genetically correlated with DMI and feed efficiency in both magnitude and sign, depending on the population and the definition of feed efficiency. Across feed efficiency traits and DMI, having bulls with 100 daughters with FPCM, BW, and GHG traits resulted in sufficiently high accuracy to almost negate the need for DMI records. Despite differences in genetic correlation structure, the relatively cheap GHG-related traits showed considerable potential for improving the accuracy of breeding values of highly valuable feed intake and feed efficiency traits.</p

Review: Selecting for improved feed efficiency and reduced methane emissions in dairy cattle

It may be possible for dairy farms to improve profitability and reduce environmental impacts by selecting for higher feed efficiency and lower methane (CH4) emission traits. It remains to be clarified how CH4 emission and feed efficiency traits are related to each other, which will require direct and accurate measurements of both of these traits in large numbers of animals under the conditions in which they are expected to perform. The ranking of animals for feed efficiency and CH4 emission traits can differ depending upon the type and duration of measurement used, the trait definitions and calculations used, the period in lactation examined and the production system, as well as interactions among these factors. Because the correlation values obtained between feed efficiency and CH4 emission data are likely to be biased when either or both are expressed as ratios, therefore researchers would be well advised to maintain weighted components of the ratios in the selection index. Nutrition studies indicate that selecting low emitting animals may result in reduced efficiency of cell wall digestion, that is NDF, a key ruminant characteristic in human food production. Moreover, many interacting biological factors that are not measured directly, including digestion rate, passage rate, the rumen microbiome and rumen fermentation, may influence feed efficiency and CH4 emission. Elucidating these mechanisms may improve dairy farmers ability to select for feed efficiency and reduced CH4 emission.</p

Ranking cows’ methane emissions under commercial conditions with sniffers versus respiration chambers

This study assessed the ranking of dairy cows using individual-level correlations for methane (CH 4 ) emission on-farm using sniffers and in respiration chambers. In total 20 lactating dairy cows, ten Holstein and ten Jerseys were recorded using sniffers installed in milking robots for three weeks of lactation and subsequently in respiration chambers (RC) where they were each recorded on three occasions within the RC. Bivariate linear mixed models were used to determine the individual-level correlations (r I ) between sniffer and RC phenotypes as proxies for genetic correlations. Despite differences in feeding and management, the predicted CH 4 production from sniffers correlated highly with RC CH 4 production r I = 0.77 ± 0.18 and CH 4 breath concentration correlated nearly as well with RC CH 4 production r I = 0.75 ± 0.20. These correlations between sniffers on-farm and RC demonstrate the potential of sniffers measurements as large-scale indicator traits for CH 4 emissions in dairy cattle. </p