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Danish Pig Research Centre: Annual Report 2010: Breeding & Genetics

by 5m Editor
1 September 2011, at 12:00am

Progress in genetics, sales of breeding stock and R&D in genetics in Denmark are outlined in the latest annual report from the Danish Pig Research Centre.


Genetic Progress and Sale of Breeding Stock

Genetic progress

The female breeds Landrace and Large White still show great progress in the trait 'live pigs on day 5'.

Progress in longevity averages approximately 0.02, which means that the likelihood of a sow being used in her second parity has increased by two percentage points.

Progress in FCR remains stable at approximately 0.028 for finishers, which is primarily attributed to progress for Duroc. An outline of all traits is provided in table 1.

Production level

This last year, 5,036 boars were performance- tested at Bøgildgård – of these 2,249 Duroc boars. More than 40,000 boars and 51,000 female pigs have been tested in the nucleus herds. Tables 2 and 3 show the average production levels.

As shown in table 5, Large White has 13.3 live pigs on day 5, and Landrace 11.8. The figures are based on the average of purebred litters used for breeding.


Table 1. Genetic progress for 2007-2010 for each trait and breed and an average of a D(LY) finisher



Table 2. Nucleus herds – average production results for boars, 2009/10.
* Note that daily gain (30-100 kg) is calculated on the basis of weighing of live animals, ie. differences in killing out % between the breeds are not included.



Table 3. Nucleus herds –- average production results for young sows, 2009/10.
* Note that daily gain (30-100 kg) is calculated on the basis of weighing of live animals, ie. differences in killing out % between the breeds are not included.



Table 4. Average production results from performance test station Bøgildgård, 2009/10.



Table 5. Nucleus herds – litter size of purebred litters, 2009/10 (litters with code 100).

AI boars

Landrace and Large White boars at the AI stations are in production on average 5.6 months and 5.2 months, respectively, whereas Duroc boars are in production an average of 10.8 months. Time in production for Duroc boars has thus increased by one month since last year. Despite a longer time in production for Duroc, the average index for active Duroc boars has also increased slightly (see table 6).


Table 6. Index and time in production of AI boars.

Sale of semen

A total of 4,558,000 Duroc semen doses were sold in Denmark, which is a slight increase compared with last year. It is now also possible to sell Duroc semen to other countries and, as a result, 411,000 doses were sold abroad. The sale of Landrace and Large White semen in Denmark stagnated around 135,000 doses whereas the sale abroad doubled since last year.

Sale of breeding stock

The sale of purebred animals is generally dropping in Denmark but increasing in foreign countries. In Denmark, the sale of purebred female animals has dropped from about 11,000 to about 6,000. However, the export of purebred females has increased, as shown in table 7.

This is also the case for hybrids where the sale of gilts in Denmark dropped slightly from 284,555 last year to 279,950. However, in that same period the export of hybrid gilts increased from 134,435 to 154,344. Consequently, the export of hybrid gilts constitutes one third of the total sale of hybrid gilts (see figure 1).

The total income from fees on genetic material currently amounts to DKK59 million a year. These fees cover a large part of the trial activities of Pig Research Centre.


Table 7. Sale totalled 446,393 animals in 2009/10 of which 33% were exported.
In 2009/10, sale amounted to 458,625 animals of which 37% were exported. Besides the animals sold from Danish farms, 20,900 hybrid gilts were sold from DanBred Multiplication in foreign countries



Figure 1. Sale of hybrids from Danish multiplication herds (July-year).

Genetic Research and Development

Genomic selection

With genomic selection, it is possible to increase progress in breeding for all traits and at the same time reduce inbreeding. In practice, genomic selection means that the breeding value of an animal is determined through DNA testing, which is a great deal more accurate than previous methods.

The aim of the project 'Genomic selection' is to obtain sufficient knowledge to be able to use genomic selection in pig breeding. The project is made in cooperation with the Faculty of Agricultural Sciences at Foulum, and is financially supported by the Innovation Act.

It was expected that genomic selection would be implemented in the genetic work with Durocs in October 2010.

Genomic selection in practice
A breeding system with genomic selection is not much different from a conventional breeding system.

Breeding stock will still need performance testing, and a conventional breeding value must be calculated. The breeding value is used for deciding which animals to DNA test since it is not financially possible to DNA test all animals. DNA testing also makes it possible to calculate a more accurate breeding value – a genomic breeding value – to be used for deciding if an animal will be used for breeding.

Breeding system with genomic selection
  1. Testing of animals
  2. Calculation of conventional breeding value
  3. DNA testing
  4. Calculation of genomic breeding value
  5. Final decision in breeding

Only points 3 and 4 in the box above differ from a conventional breeding system, and researchers are therefore concentrating on the genomic breeding value and on selecting the right animals for DNA testing.

Genomic breeding value

The first analyses show that with genomic selection it is possible to calculate genomic breeding values that increase the accuracy of the breeding value at the time of selection. This paves the way for more accurate selection of breeding stock in the future.

Figure 2 demonstrates how the current breeding values for lean meat percentage in young animals can be predicted with genomic breeding values. The correlation must be evaluated in relation to the average of the parents' breeding values, which is the expected breeding value used for young animals today. With genomic breeding values, it will be possible to separate litter mates on the basis of a DNA test alone.

Genomic selection will affect all animals in the breeding system but the greatest changes will be seen in DNA-tested animals. The effect can be compared to the results obtained when testing for feed conversion at Bøgildgård. Just as an animal with good genetic traits will score the highest breeding value if tested at Bøgildgård, an animal with good genetic traits will also score the highest breeding value when DNA tested.

In 2009, Pig Research Centre (PRC) started using a newly developed chip for DNA typing of the 2,000 best Duroc breeding stock used in breeding the last ten years. These animals now make it possible for us to implement genomic selection for Duroc.


Figure 2. Correlation between breeding values and traditional breeding values of 170 young Landrace animals.

Animals for DNA testing

It is possible to make genomic selection more efficient by carefully selecting which breeding candidates to DNA test. When a small percentage of the breeding candidates are DNA tested, we will achieve a large part of the genetic progress that would be obtained if all animals are DNA tested.

Genomic selection requires that the breeding candidates be DNA-tested. The DNA tests are used for calculating accurate breeding values on these candidates. However, DNA testing is expensive (approximately DKK1,000 per test), and it is therefore not practically possible to test all breeding candidates – around 20,000 candidates per breed per year. Fortunately, it is not necessary to DNA test all candidates.

The results are based on the computer programme, ADAM, with which breeding strategies for pigs are evaluated through computerised simulation of our breeding system.

The potential genetic progress from genomic selection can be achieved by DNA testing a percentage of the breeding candidates (figure 3). When we implement genomic selection in the breeding system and pick breeding candidates for DNA testing on the basis of conventional breeding values, we will be able to achieve the full potential genetic progress by DNA testing only 40 per cent of the breeding candidates. It is thus not possible to increase this progress by DNA testing more than 40 per cent of the breeding candidates.

Approximately 80 per cent of the progress can be achieved by DNA testing 20 per cent of the breeding candidates, and 55 per cent progress can be achieved by DNA testing only 5 per cent of the candidates. It is therefore not necessary to DNA test more than 40 per cent of the breeding candidates, and more than 50 per cent of the progress can be achieved by DNA testing only five per cent of the candidates.

The greatest genetic progress is achieved by DNA testing both sows and boars (figure 2). Progress can be increased by seven to 15 per cent by DNA testing boars as well as sows instead of only one gender. It is thereby profitable to DNA test both boars and sows in our breeding system.

We will achieve more genetic progress for the DNA tests by introducing selection strategies instead of picking breeding candidates solely on the basis of conventional breeding values. Preliminary results demonstrate that if we DNA test a small percentage of the breeding candidates and we use certain selection strategies for picking animals for testing, we will achieve even more of the potential progress from genomic selection. There is something to be gained from implementing selection strategies in our breeding system.


Figure 3. Expected genetic progress in the Danish breeding system with genomic selection where 5, 10, 20 and 40% of the breeding candidates were DNA tested.
For each scenario, the DNA tests were separated according to gender. Genetic progress is presented in relation to the potential progress from genomic selection and progress from conventional breeding.

Perspectives

There is a great need for continued research as knowledge from other countries cannot be transferred directly to our breeds. With genomic selection, it will become easier to breed for traits that previously were difficult to breed for. Examples of this are breeding for increased pH in meat after slaughter; improved longevity in sows; and improved maternal traits. However, to be able to include these traits in breeding, they must be measurable – either in nucleus herds or in commercial herds.

Pig Research Centre is currently compiling data on a large German sow farm with Danish LY sows with the aim of improving sow traits. Data is collected for, for instance, live pigs on day 5 (LP5), sow longevity and 14G, which is the trait for a sow's ability rear pigs. With 14G, it is recorded how many piglets are weaned after placing 14 piglets with the sow within three days post-partum.

Genomic selection is expected to result in:

  • Increased progress for existing traits
  • Possibility for including new traits in the breeding objectives such as longevity and maternal traits – if these traits can be measured.

Project F4

Since 2003, pig breeding has centred on increasing the percentage of animals resistant to specific coli bacteria of the type F4 ab/ac. Selection for increased resistance to post-weaning diarrhoea runs parallel with the regular BLUP selection in Landrace, Large White and Duroc.

Boars that are relevant for breeding are F4 tested upon transfer to AI quarantine, i.e. their F4 status is known when they enter the AI station. Sows for breeding are not subjected to F4 testing in principle. However, there is an economic advantage in testing boar mothers as it will thereby be possible indirectly to determine the F4 genotype of many boars. The siblings of the boars will also obtain known genotype, and as these sows are indeed the best sows of the breed, we will indirectly obtain a fairly large gain as the daughters will also produce offspring of known genotype. Figure 4 shows the status for resistant performance-tested young animals.


Figure 4. Annual average frequency of F4 Coli-resistant performance-tested young animals in Duroc, Large White and Landrace nucleus populations.

Longevity of sows

The aim of the project on sow longevity is to develop new and more efficient methods for genetic evaluation of sows to improve their longevity, i,e. their productive life.

The project includes:

  • Improvement of the current methods for describing sow longevity through new statistical methods.
  • Adjustment and expansion of genetic models for modelling of the time passing until a certain event occurs so that these models can be used for modelling of longevity in sows.
  • Multivariate genetic models in which longevity is analysed in the same model as the other traits in the breeding objective to investigate how selection for improved longevity affects the other traits and vice versa.

Regardless of whether DNA based or traditional breeding methods are used in the future, breeding for improved longevity in sows requires better recording and analysis of the sows' individual longevity, and longevity must be quantified as, for instance, the sow's age, the total number of pigs born or total number of litters.

Breeding against shoulder lesions

There has been a great deal of focus on shoulder lesions in sows over recent years. Danish pig producers are therefore greatly interested in whether it is possible prevent shoulder lesions through breeding. To investigate this, comprehensive recordings are being made of sows on nine commercial farms. The animals are of known origin, and kinship can be traced back to parents and grand parents.

In 2007-2009, the occurrence of shoulder lesions was recorded on LY or YL sows on these nine commercial farms. A technician from the Department of Breeding & Genetics visited the farms every week and recorded the diameter of lesions and visually evaluated the sows' body condition.

Regardless of parity and age of the sows, the technician recorded shoulder lesions in the farrowing house. Body condition and shoulder lesions were scored at each visit, i.e. data was recorded for each sow four or five times in each lactation period.

The final data was recorded in February 2010, and a total of 77,300 evaluations will have been recorded from approximately 17,091 lactation periods and from 8,790 individual sows. If a shoulder lesion is defined as a lesion of minimum 1-cm in diameter, lesions were recorded in any part of lactation in 20.1 per cent of all 17,091 lactation periods. The probability of a sow developing a shoulder lesion between her first and last parity is 27.1 per cent.

The material will now be genetically analysed. Genetic parameters for shoulder lesions will be calculated and the phenotypic correlation between shoulder lesions, body condition, herd and season will be calculated. If high heritability for shoulder lesions is established, it will be possible through selection to increase resistance to shoulder lesions in Danish pig production.

This is one of several projects on shoulder lesions under Pig Research Centre, and is financially supported by the Rural Development Programme under by the Danish Food Industry Agency.

Breeding for FCR

As opposed to, for instance, litter size, genetic progress in feed conversion ratio is difficult to measure and assess for the individual pig producer. There are several reasons for this; factors such as feed, feeding strategy, lay-out of the accommodation and recording methods must be identical over several years before it is possible to determine whether changes are attributed to genetic progress or to other factors.

Seen on a year-to-year basis, only marginal progress can be achieved through breeding. This is one of the reasons it is difficult to see the effect of breeding for feed conversion ratio in production herds, and why the subject is still being discussed.

Genetic progress is ensured by recording the feed conversion ratio of every single animal that is performance-tested at Bøgildgård. The genetic correlation between feed conversion ratio and the traits gain and lean meat percentage is also utilised.

To be able to document that breeding based on recordings of individual animals can be transferred to group level, the correlation between breeding values and the actual feed conversion ratio at group level is investigated. The most efficient way to do this is by recording the feed conversion ratio of purebred Landrace boars in a nucleus herd.

Compilation of data for the trial began at the end of 2007. The Landrace boars are weighed in the pens and feed consumption from each feeder is recorded. The final data was compiled in the autumn 2009.

Preliminary analyses demonstrate that breeding values for feed conversion are, on average, dependent 1:1 with the feed conversion ratios actually recorded at pen level. There are, however, large variations as the recordings are based on pen averages.

Pigs and Health

In the project 'Pigs and Health', the aim is two-fold: partly to develop healthier pigs for meat production and partly to develop model pigs for medical research in human diseases. These are two separate projects that have nothing in common except for the pig and its genome. The project runs for four years (2007-2010) and has an overall budget of DKK50 million of which the Danish National Advanced Technology Foundation funds half.

There are eight parties in the project: the Faculty of Life Sciences at Copenhagen University; the Technical University of Denmark; Leo Pharma; PixieGene; Ellegaard Göttingen Minipigs; the Faculty of Health Sciences at Copenhagen University; and the Faculty of Agricultural Sciences at Aarhus University, and Pig Research Centre heading the management of the project.

In the project 'Healthy Pigs', the aim is to identify the genes that affect production pigs' resistance to diseases, primarily various types of respiratory disorders.

Parallel with the mapping of the pig genome, more than 10,000 pigs were followed from birth to slaughter in a comprehensive study. The pigs were reared under identical conditions, and disease, gain and other traits were recorded.

Currently, four regions in the genetic mass have been identified for pneumonia in pigs that seem to influence resistance to this type of disease. The genetic mass will now be analysed in detail to find the genes that trigger this resistance.

Preliminary results show that certain regions in the genetic mass affect pneumonia in pigs. In the final part of the project, this result will be verified by analysing DNA from fathers for lung recordings from 9,000 production pigs. If this turns out a success, pigs can be tested for these genes and it can thereby be guaranteed through breeding that the trait is passed on to future generations of pigs.

The result will be healthier pigs, lower consumption of medication and an improved economy in pig production.

The genes will be identified by scientists from Aarhus University, the Technical University of Denmark and Copenhagen University, while Pig Research Centre will conduct the practical testing of the effects in live pigs.

The other project, 'Model Pigs', aims at improving human health. This project concerns development of special model pigs for use in the pharmaceutical industry. Pigs are actually much more suitable for pharmaceutical trials than traditional experimental animals as pigs' organ development, physiology and metabolism have clear resemblances to those of humans.

The project focuses on developing model pigs for testing of treatment for, for instance, psoriasis, arteriosclerosis and Alzheimer's.

Several lines of cloned pigs that are likely to have genes that are sensitive to Alzheimer's and arteriosclerosis have now been made. Several sows are also pregnant with cloned psoriasis pigs of which the first were born in spring 2010. The cloned pigs that have been born will then be verified, i.e. the pharmaceutical industry will test the pigs' suitability as experimental animals. The project is expected to end in 2011.

Further Reading

- Go to our previous article on this report by clicking here.


September 2011