Danish Pig Research Centre Annual Report 2012: Genetic Research and Development02 May 2013
Progress in breeding objectives through the use of genomic selection are described in the latest annual report from the Danish Pig Research Centre, with a focus on boar taint, feed conversion and behaviour traits.
The most recent revision of the breeding objective for Duroc, Landrace and Large White took place in March 2011,when the traits included in the objective and the weighting of them were revised The traits currently included in the breeding objective are shown in Figures 2 and 3.
Genomic selection enables an increase in genetic progress for all traits and, at the same time. reduces inbreeding. In practice, Genomic selection enables - through information from DNA testing - a more accurate estimate of an animal's breeding index than previously.
Genomic selection has undergone a dramatic development in the past few years. In 2010, genomic selection was introduced for Duroc and the Research Centre was the first in the world to apply genomic selection in pig breeding. In 2011, Landrace and Large White were included, and a new calculation method developed by Research Centre Foulum at Aarhus University was implemented.
The Centre will continue to improve genomic selection, in particular working on DNA testing as many candidates as financially possible while at the same time selecting the right candidates.
Effect of Genomic Selection
As with all kinds of projections, it is difficult to evaluate the effect of genomic selection on genetic progress. The most recent simulations indicate that the greatest effects concern Landrace and Large White, where an increase in progress of 20 to 25 per cent compared with the traditional breeding methods is expected. For Duroc, a 10 to 15 per cent increase is expected. For all breeds, inbreeding will drop as a consequence of genetic selection.
The increase in progress is attributed to improvement of most traits. For Landrace and Large White particularly, LP5 and daily gain have improved through genomic selection, and for Duroc especially, daily gain and FCR have improved.
The full potential of genomic selection is not yet achieved as that would require DNA testing of minimum 40 per cent of the breeding candidates compared to 10 per cent today. However, several activities are aimed at bringing us closer to the full potential, among which is a new project that will deliver more DNA tests at the same costs.
Genomic selection in DanAvi is based on a chip that examines 60,000 points on the DNA strand However. it is now being investigated whether it is possible to use a smaller and cheaper chip that only examines 7,000 points on the DNA strand and subsequently use these points to analyse what is stored on the missing points. This would make it possible to DNA test more pigs largely without compromising the accuracy of the breeding values.
Genomic selection improves the possibilities for breeding for traits that traditionally are highly difficult to breed for, such as improved sow longevity and maternal traits. However, to include these traits in selection, they must be measurable either in nucleus breeding herds or in commercial herds.
In order to improve sow traits, PRC is currently analysing data from large commercial herds with LY sows. Throughout winter 2012/13, they expect to evaluate the value of using data from commercial herds. Overall, incredible progress has been made with genomic selection and in just a few years, the results will be reflected in Danish pig herds. However, they are still working on optimising the work and producing even better breeding candidates.
Breeding Against Boar Taint
In the EU, a voluntary agreement has been made to abandon castration in 2018 in order to improve pig welfare. It is therefore currently being investigated how to reduce the prevalence of boar taint in Danish pig breeds through breeding and genetics.
Boar taint is primarily attributed to the chemical compounds, androstenone and skatole, while indole is less important. Research has documented that part of the Danish pig population carries genes that cause boar taint in meat from slaughtered male pigs. Several studies have confirmed that heritability of skatole in Danish populations varies from 0.19 to 0.33 across the breeds. Two Danish studies demonstrated that heritability of androstenone for Danish Landrace varied from 0.54 to 0.59. It is essential to stress that breeding is the only way to generally reduce androstenone levels and thereby reduce boar taint.
In a three-year project, genetic correlations between traits for boar taint and the economically most important traits included in the current breeding objective are being mapped. Preliminary results for Landrace indicate faint or slightly favourable genetic correlations between boar taint and production traits, which is confirmed by foreign studies. If a decision is made to breed against boar taint, it is crucial to be particularly aware of boar fertility, which is why data from all Danish AI stations is now systematically being compiled for further analysis.
Genomic selection is also a cornerstone in this project. The future breeding index for boar taint will be determined on the basis of genomic information with this method, which is already incorporated in DanAvl’s evaluation of breeding values. One of the advantages of this method is that phenotypic data from genotyped and non-genotyped animals can be handled in the same analysis. The project is also aimed at detection of rare gene variants. Researchers expect that these genes, or SNPs, that heavily affect boar taint will improve the prediction of a boar’s genetic value through a greater accuracy across breeds.
The PRC leads the way to sustainability and improved animal welfare in pig production as it is possible to quit surgical castration in the long term provided the genetic correlations to fertility traits are not predominantly negative. Overall, the aim of the project is to enable pig producers to produce meat from entire male pigs that is free of boar taint whereby Danish consumers will be able to enjoy an odour- free meatball.
Genetic progress is inextricably linked with inbreeding. However, failure to reduce inbreeding will, in the long term, reduce genetic progress and increase the risk of genetic diseases and defects. All breeding companies therefore apply methods for limiting inbreeding.
In 2012, DanAvl implemented a new tool called EVA for Duroc, which aims at minimising the increase in inbreeding. With EVA, it is now possible to achieve the same level of genetic progress, while at the same time minimising the increase in inbreeding. When inbreeding drops, genetic progress will increase. EVA could therefore be seen as an insurance that guarantees continued genetic progress for many years to come.
The challenge to implementing EVA is to match theory and practice. Together with researchers at Research Centre Foulum of Aarhus University, PRC has analysed how to adapt EVA to the real world, while still gaining full benefit of EVA. Results demonstrated that we can make a range of adjustments of EVA without compromising the ability to reduce inbreeding.
EVA was implemented on a trial basis for Duroc in 2012 and will be implemented for Landrace and Large White in 2013 after a thorough evaluation.
Breeding Improves FCR
The outcome of a recent study shows that breeding does improve FCR Feed costs drop by DKK3.10 per finisher annually and the environmental impact is reduced.
FCR was always an important trait in Danish pig breeding and the sub index for FCR therefore carries great weight in the overall breeding index The aim is to reduce FCR by reducing the total average amount of feed eaten by a finisher. This will reduce the financial costs and environmental consequences of finisher production.
Breeding for FCR
FCR is measured individually on all purebred boars that are performance tested at test station Bøgildgård. There, feed intake is monitored with feeding machines that record individual feed intake of each pig in a pen.
FCR is not recorded in the on-farm performance testing that takes place in Danish nucleus breeding herds. On-farm testing includes recording of daily gain, lean meat percentage and the exterior of the pigs only. However, we know the correlation between FCR, daily gain and lean meat percentage from data obtained at Bøgildgård and with this information, it is possible to determine the expected FCR of pigs in on farm testing Therefore, both data from Bøgildgård included in the calculation of the breeding index. This way, we achieve a greater genetic reduction in FCR than not including data from the on-farm testing to the index calculation.
For years, annual genetic progress in the breeding system has averaged approximately 0.03 FUgp per kg gain.
The aim was to establish whether genetic progress for reduced FCR could also be found in a herd where feed consumption is recorded at group level in pens accommodating 20 boars each.
Over a two-year trial period, average FCR dropped by 02 FUgp per kg for 20 boars in a double pen from an average of 2.5 to 2.3 FUgp per kg. This reduction was attributed to a combination of management genetics and randomness. The genetic component of the total reduction was determined on the basis of the genetic reduction in sub index for FCR of related animals in the breeding system.
Results demonstrated that 93 per cent of the genetic progress for FCR was found in the herd. Thus, the impact on FCR is determined at 0.93, which is not significantly different from 1.0, representing the full impact of the genetic gain of FCR. Pens housing pigs with a low average sub-index for FCR had a lower FCR than pens housing pigs with a high average sub-index for FCR. If the difference in average sub-indices between two pens each holding 20 pigs is 0.1 sub-index point, the difference in FCR will be 0.093 FUgp per kg gain.
In conclusion, the sub index for FCR that is based on recordings for individual pigs at Bøgildgård can be documented in FCR recordings at pen level in a commercial herd.
An entirely new method of selection will make it possible to breed for more ‘sociable’ pigs, i.e. pigs that affect their pen mates positively - or at least not negatively - by virtue of, for instance, their behaviour or disease resistance traits. These may be pigs that do not compete for feed or do not carry infections. With this method, it will be possible to achieve further progress in production traits.
In 2011, PRC initiated a new project to establish whether this method can be applied on DanAvI breeding stock. It will be investigated whether genetic progress for- for instance, daily gain - can be improved and perhaps, as a spin off, make the pigs less aggressive and less prone to tail-biting.
The method may potentially be revolutionary as it does not require routine recordings of additional traits such as behaviour and disease resistance. Instead, through statistics and recordings of which pigs are housed in which pen it is possible to utilise the fact that the daily gain of the pigs in a group does not simply express the genetic potential for daily gain. It is also an expression of the ‘social’ abilities of the pen mates. A pig with a low daily gain may, for instance, have aggressive pen-mates or pen-mates carrying disease, which causes the pig to eat less or to become sick, slowing its growth rate.
As a minimum, the project will run until 2015 and in 2014, PRC hopes to demonstrate both the expected genetic progress in daily gain and the welfare-related spin-offs.