10 years of genomic selection: A quantum leap for pig breeding


Productivity & Profit

10 years ago, the DanBred breeding program was the first in the world to implement genomic selection for pigs, and today, genomic information is widely used for selection in most global-reaching pig breeding programs. Since its introduction, genomic selection has revolutionized pig breeding, as it ensures higher genetic gain at the same rate of inbreeding. The specific methods and technologies have undergone comprehensive developments throughout the years, and new breeding technologies are developing to increase long-term genetic gain.

By Tage Ostersen, Department Manager, and Lizette Vestergaard Pedersen, Consultant, Danish Pig Research Centre.

 

Increased genetic gain

Genomic information has revolutionized the pig breeding industry because it contributes to a more accurate prediction of breeding values, which in turn contributes directly to a higher genetic gain. As such, it has been instrumental for the high genetic gain we are continuously achieving. In the DanBred breeding program, we estimate that genomic selection increases genetic gain by 30 %, when all pigs are genotyped. These genetic improvements are cumulative and result in increased profits for pig producers each year.

The concept of genomic selection was first introduced in 2001 by Professor Theo Meuwissen and was implemented in the livestock industry relatively quickly. The basic principle in pig breeding remains the same. Pedigree and performance data are still essential, but genomic information provides an additional and more accurate source of information that can be utilized when calculating breeding values.

 

More accurate prediction of breeding values

The breeding value of a pig expresses the expected effect on the average performance (or phenotype) of its offspring. To calculate the breeding value before a pig has any offspring, we use advanced statistical mixed models that combine performance with relationship information. This elucidates which part of the performance expresses a pig’s genetic level and which part is simply random.

Before genomic selection was implemented, the relationships used in the statistical models were based on traditional pedigree. Pedigree relationships assume that two full sibs are always 50 % related. However, we know that the assumption of 50 % relatedness for full sibs is not entirely exact, it is just an average. It is a fact that each parent passes on half of its genes, but in one extreme scenario it is possible that two full sibs could receive the exact same half from their parents, meaning that they would be 100 % related. In the opposite extreme scenario, it is possible that two full sibs could receive the exact opposite halves from their parents, meaning that they would be 0 % related (i.e. unrelated).

Figure 1. The figure illustrates a simplified example of the fact that sibs can be more or less related genetically. The sow and the boar have their own individual DNA sets, and each pass on exactly half of their set to the offspring. But precisely which half is passed on to each piglet is random. In this example, piglet 1 has inherited a blue DNA-part from the boar and an orange DNA-part from the sow, whereas piglet 2 has inherited a green DNA-part from the boar and a red DNA-part from the sow. Evidently, both piglet 1 and 2 have inherited half of the genes from the boar and sow, but the parts are completely different. Consequently, piglets 1 and 2 are 0 % related to each other. The last offspring, piglet 3, has inherited half of each coloured DNA-part from the sow and boar, and is therefore 50 % related to piglet 1 and piglet 2.

 

With genomic information, we can measure the relatedness based on similarity at the genetic level, because we use thousands of markers across the genome to achieve this more precise measure of genomic relatedness. This is then utilized in our statistical models to distinguish the genetic part of the phenotype from the non-genetic part – i.e. to calculate more exact breeding values.

 

The Breeders Equation

More accurate predictions of breeding values contribute directly to a higher genetic gain. The Breeders Equation explains how different changes in the breeding scheme will affect genetic gain (∆G):

∆G= (r ∙i ∙s)/L

r is the accuracy of breeding values, i is the intensity of selection, s is the genetic standard deviation, and L is the generation interval. Genomic selection increases the accuracy and, thereby, contributes to an increased genetic gain.

 

Improving challenging traits

Genomic selection increases genetic gain for all traits included in the breeding goal, but especially challenging traits such as feed conversion and litter size benefit. Feed conversion is very costly to measure, and only some of the pigs are performance tested (phenotyped). Litter size is a lowly heritable trait measured after the pigs are selected for breeding.

With genomic selection, however, additional information is used to estimate more accurate breeding values at an earlier point, thus leading to higher genetic gains – especially for these challenging traits, which would have otherwise been costly or slow to progress at the same level as achieved by using genomic selection.

 

The evolution of genomic selection

In the beginning, the cost of genotyping was high, resulting in a low proportion of genotyped pigs. In fact, the cost was 10-15 times higher in 2010 than it is today, and this expense was not offset by matching genetic gain for the most economically important traits. Consequently, advanced genotyping strategies were therefore developed in order to save costs. These genotyping strategies sought to maximize genetic gain through a balance of genotyping pigs that showed promise for breeding and pigs that could improve the prediction of other pigs – i.e. become “reference pigs”. We, therefore, partly genotyped the best-performing pigs, and partly genotyped pigs with abundant performance test information.

Today, the price of genotyping has decreased to a level where all global-reaching breeding programs genotype the majority of their breeding candidates, which has reduced the need to develop genotyping strategies. The genotyping process itself has also been developed and improved to the point, where the benefits in terms of genetic gain justify the inclusion of this extra step and cost. DanBred began to genotype 10 % of all selection candidates as early as in 2010, and since 2017, DanBred has genotyped 100 % of selection candidates. That is more than 100.000 pigs each year.

 

 

Cutting-edge computing power

The DanBred breeding program was the first to utilize genomic selection in pigs. As a result, Danbred were often the first to face new challenges, including those associated with the exponential growth in the number of genotyped pigs. During the first 10 years of genomic selection, the total number of genotyped pigs doubled approximately every second year. This led to considerable computational challenges. With standard genomic selection methods, doubling the number of genotyped pigs increases the computational load by a factor of between four and eight. The computational load has, therefore, increased several hundred times since DanBred began using genomic selection.

Figure 2. The graph shows the cumulative number of genotyped DanBred pigs over the years. Since 2017, DanBred has genotyped 100 % of all selection candidates.

 

To accommodate these challenges, DanBred has repeatedly doubled the computing power and implemented new methods to reduce the computational load. Most recently, DanBred has implemented the solver facilities from the Linear Models Toolbox (LMT), which is a generalized linear mixed model software frame developed and maintained by the Centre for Quantitative Genetics and Genomics (QGG) at Aarhus University, as a successor to its popular DMU package. In that regard, we are the first breeding company to replace DMU by LMT, and this has enabled DanBred to decrease the processing time by about 90 %.

 

Metabolomics as the next leap for pig breeding

Genomic selection has substantially enhanced the breeder’s toolbox, contributing with increased long-term genetic gain. Genomic selection is still developing, and other interesting breeding tools are also beginning to emerge. For instance, metabolomic selection which is a breeding technology that uses nuclear magnetic resonance data (or NMR).

NMR metabolomics measures all the metabolites in a sample from an individual. This complete set of metabolites – referred to as whole-metabolomic data – is associated with the level of physiological activity in biological pathways that are initiated at a DNA level and culminate in trait expression (performance). The level of physiological activity is, in turn, regulated by the genes that an individual has inherited from its parents, as well as by influence from its environment. This link between whole-metabolomic data and inherited genes may be exploited to increase the genetic potential for desirable traits such as feed efficiency in pigs.

To explore this potential next leap for pig breeding, DanBred, the Danish Pig Research Centre, Nordic Seed, and Aarhus University have partnered on a new a R&D metabolomics project, where whole-metabolomic data in combination with phenotypic, pedigree, and genomic data will be used to further investigate feed efficiency and meat quality traits, etc. Subsequently, the experts will conduct metabolomic analysis, develop statistical models, and plan the implementation of the findings into the DanBred breeding programme. The project is partially funded with ~ €1.1 million from the Green Development and Demonstration Programme under the Ministry of Environment and Food in Denmark.

This is an example of how partnerships of many expert actors are already busy taking the next great leap for pig genetics, thus driving the development of the industry towards a more efficient and sustainable global pig production.





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Resultados de producción medios conseguidos por las cerdas jóvenes de DanBred en núcleos

  • Ganancia media diaria, g/día; 30 kg – sacrificio 1103
  • Ganancia de peso diaria, g/día; nacimiento – 30 kg 367
  • Porcentaje de carne magra 62,2
  • Conformación, puntos 3,15
  • Medición de escaneo, mm 7,9
  • Peso de escaneo, kg 98,0

Gennemsnitlige resultater for DanBred orner afprøvet på forsøgsstationen Bøgildgård

  • Daglig tilvækst, g/dag 30 kg – slagtning 1258
  • Foderudnyttelse, FEs/kg Tilvækst, 30 kg – slagtning 1,96
  • Kødprocent (%) 63,0
  • Styrke, point 2,88
  • Slagtesvind (%) 25,2
  • Rygspæk, mm 6,0
  • Scanningsvægt, kg 101,7

Resultados promedio de producción conseguidos por los verracos DanBred en núcleos

  • Ganancia media diaria, g/día; 30 kg – sacrificio 1322
  • Ganancia media diaria, g/día; nacimiento – 30 kg 409
  • Porcentaje de carne magra 62,0
  • Conformación, puntos 2,87
  • Medición de escaneo, mm 6,8
  • Peso de escaneo, kg 99,1

Gemiddeld productieresultaat behaald door beren van DanBred in kernbedrijven

  • Dagelijkse groei (g/dag), 30 kg – slacht 1322
  • Dagelijkse groei (g/dag), geboorte – 30 kg 409
  • Mager-vleespercentage (%) 62,0
  • Conformatie (punten) 2,87
  • Rugspekdiktemeting (mm) 6,8
  • Levend Scangewicht (kg) 99,1

Producción media en la central de pruebas de verracos de Bøgildgaard

  • Ganancia media diaria, g/día; 30 kg – sacrificio 1258
  • Índice de Conversión, kg pienso/kg ganancia; 30 kg – sacrificio 1,83
  • Porcentaje de carne magra 63,0
  • Conformación, puntos 2,88
  • Pérdida al sacrificio (Rendimiento canal) 25,2
  • Medición de escaneo, mm 6,0
  • Peso de escaneo, kg 101,7

Gemiddelde productie resultaten van berenteststation Bøgildgård

  • Dagelijkse groei (g/dag), 30 kg – slacht 1258
  • Voederconversie, kg voer//kg gewichtstoename, 30 kg – slacht 1,83
  • Mager-vleespercentage (%) 63,0
  • Conformatie (punten) 2,88
  • Slachtrendement (zonder kop) 25,2
  • Rugspekdiktemeting (mm) 6,0
  • Levend Scangewicht (kg) 101,7

Gennemsnitlige resultater for DanBred polte afprøvet i avlsbesætningerne

  • Daglig tilvækst, g/dag 30 kg – slagtning 1222
  • Daglig tilvækst, g/dag Fødsel – 30 kg 413
  • Kødprocent (%) 62,4
  • Styrke, point 2,94
  • Rygspæk, mm 6,4
  • Scanningsvægt, kg 99,3

Gennemsnitlige resultater for DanBred orner afprøvet i avlsbesætningerne

  • Daglig tilvækst, g/dag 30 kg – slagtning 1322
  • Daglig tilvækst, g/dag Fødsel – 30 kg 409
  • Kødprocent (%) 62,0
  • Styrke, point 2,87
  • Rygspæk, mm 6,8
  • Scanningsvægt, kg 99,1

Average production results achieved by DanBred females (gilts) in Nucleus herds

  • Daily gain, g/day, 30 kg – slaughter 1222
  • Daily gain, g/day, birth – 30 kg 413
  • Lean meat perctentage 62.4
  • Conformation, points 2.94
  • Scanning measurement, mm 6.4
  • Scanning weight, kg 99.3

Average production results achieved by DanBred boars in Nucleus herds

  • Daily gain, g/day, 30 kg – slaughter 1322
  • Daily gain, g/day, birth - 30kg 409
  • Lean meat perctentage 62.0
  • Conformation, points 2.87
  • Scanning measurement, mm 6.8
  • Scanning weight, kg 99.1

Average production for boar testing station Bøgildgård

  • Daily gain, g/day, 30 kg – slaughter 1258
  • Feed conversion, kg feed/kg gain, 30 kg – slaughter 1.83
  • Lean meat perctentage 63.0
  • Conformation, points 2.88
  • Killing out percentage 25.2
  • Scanning measurement, mm 6.0
  • Scanning weight, kg 101.7

Average production results achieved by DanBred gilts in Nucleus herds

  • Daily gain, g/day, 30 kg – slaughter 1089
  • Daily gain, g/day, birth – 30 kg 386
  • Lean meat perctentage 64.5
  • Conformation, points 3.05
  • Scanning measurement, mm 6.2
  • Scanning weight, kg 98.9

Average production results achieved by DanBred boars in Nucleus herds

  • Daily gain, g/day, 30 kg – slaughter 1143
  • Daily gain, g/day, birth – 30 kg 382
  • Lean meat perctentage 64.2
  • Conformation, points 2.87
  • Scanning measurement, mm 6.5
  • Scanning weight, kg 98.8

Average production for boar testing station Bøgildgård

  • Daily gain, g/day, 30 kg – slaughter 1107
  • Feed conversion, kg feed/kg gain, 30 kg – slaughter 1.94
  • Lean meat perctentage 65.1
  • Conformation, points 2.90
  • Killing out percentage 26.3
  • Scanning measurement, mm 5.4
  • Scanning weight, kg 99.1

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Resultados promedio de producción conseguidos por los verracos DanBred en núcleos

  • Ganancia media diaria, g/día; 30 kg – sacrificio 1135
  • Ganancia media diaria, g/día; nacimiento – 30 kg 360
  • Porcentaje de carne magra 62,6
  • Conformación, puntos 3,08
  • Medición de escaneo, mm 7,2
  • Peso de escaneo, kg 98,3

Durchschnittliche Produktionsergebnisse von DanBred-Weibchen (Jungsauen) in Nukleusherden

Producción media en la central de pruebas de verracos de Bøgildgaard

  • Ganancia media diaria, g/día; 30 kg – sacrificio 1097
  • Índice de Conversión, kg pienso/kg ganancia; 30 kg – sacrificio 1,93
  • Porcentaje de carne magra 63,2
  • Conformación, puntos 3,06
  • Pérdida al sacrificio (Rendimiento canal) 26,6
  • Medición de escaneo, mm 6,0
  • Peso de escaneo, kg 97,8

Resultados de producción medios conseguidos por las cerdas jóvenes de DanBred en núcleos

  • Ganancia media diaria, g/día; 30 kg – sacrificio 1089
  • Ganancia de peso diaria, g/día; nacimiento – 30 kg 386
  • Porcentaje de carne magra 64,5
  • Conformación, puntos 3,05
  • Medición de escaneo, mm 6,2
  • Peso de escaneo, kg 98,9

Resultados promedio de producción conseguidos por los verracos DanBred en núcleos

  • Ganancia media diaria, g/día; 30 kg – sacrificio 1143
  • Ganancia media diaria, g/día; nacimiento – 30 kg 382
  • Porcentaje de carne magra 64,2
  • Conformación, puntos 2,87
  • Medición de escaneo, mm 6,5
  • Peso de escaneo, kg 98,8

Producción media en la central de pruebas de verracos de Bøgildgaard

  • Ganancia media diaria, g/día; 30 kg – sacrificio 1107
  • Índice de Conversión, kg pienso/kg ganancia; 30 kg – sacrificio 1,94
  • Porcentaje de carne magra 65,1
  • Conformación, puntos 2,90
  • Pérdida al sacrificio (Rendimiento canal) 26,3
  • Medición de escaneo, mm 5,4
  • Peso de escaneo, kg 99,1

Gemiddeld productieresultaat behaald door jonge
zeugen (< 1 jaar) van DanBred in kernbedrijven

  • Dagelijkse groei (g/dag), 30 kg – slacht 1089
  • Dagelijkse groei (g/dag), geboorte – 30 kg 386
  • Mager-vleespercentage (%) 64,5
  • Conformatie (punten) 3,05
  • Rugspekdiktemeting (mm) 6,2
  • Levend Scangewicht (kg) 98,9

Gemiddelde productie van berenteststation Bøgildgård

  • Dagelijkse groei (g/dag), 30 kg – slacht 1107
  • Voederconversie, kg voer//kg gewichtstoename, 30 kg – slacht 1,94
  • Mager-vleespercentage (%) 65,1
  • Conformatie (punten) 2,90
  • Slachtrendement (zonder kop) 26,3
  • Rugspekdiktemeting (mm) 5,4
  • Levend Scangewicht (kg) 99,1

Gemiddeld productieresultaat behaald door jonge
zeugen (< 1 jaar) van DanBred in kernbedrijven

  • Dagelijkse groei (g/dag), 30 kg – slacht 1103
  • Dagelijkse groei (g/dag), geboorte – 30 kg 367
  • Mager-vleespercentage (%) 62,2
  • Conformatie (punten) 3,15
  • Rugspekdiktemeting (mm) 7,9
  • Levend Scangewicht (kg) 98,0

Gemiddeld productieresultaat behaald door beren van DanBred in kernbedrijven

  • Dagelijkse groei (g/dag), 30 kg – slacht 1135
  • Dagelijkse groei (g/dag), geboorte – 30 kg 360
  • Mager-vleespercentage (%) 62,6
  • Conformatie (punten) 3,08
  • Rugspekdiktemeting (mm) 7,2
  • Levend Scangewicht (kg) 98,3

Gemiddelde productie van berenteststation Bøgildgård

  • Dagelijkse groei (g/dag), 30 kg – slacht 1097
  • Voederconversie, kg voer//kg gewichtstoename, 30 kg – slacht 1,93
  • Mager-vleespercentage (%) 63,2
  • Conformatie (punten) 3,06
  • Slachtrendement (zonder kop) 25,6
  • Rugspekdiktemeting (mm) 6,0
  • Levend Scangewicht (kg) 97,8

Durchschnittliche Produktionsergebnisse von DanBred-Weibchen (Jungsauen) in Nukleusherden

  • Tageszunahme 30 kg – Schlachtung (g/Tag) 1103
  • Tageszunahme Geburt – Schlachtung (g/Tag) 367
  • Magerfleischanteil 62,2
  • Fundament, Punkte 3,15
  • Rückenspeck, mm 7,9
  • Gescanntes Gewicht, kg 98,0

Durchschnittliche Produktionsergebnisse von DanBred-Ebern in Nukleusherden

  • Tageszunahme 30 kg – Schlachtung (g/Tag) 1135
  • Tageszunahme Geburt – Schlachtung (g/Tag) 360
  • Magerfleischanteil 62,6
  • Fundament, Punkte 3,08
  • Rückenspeck, mm 7,2
  • Gescanntes Gewicht, kg 98,3

Durchschnittsproduktion laut Eberprüfstation Bøgildgård

  • Tageszunahme 30 kg – Schlachtung (g/Tag) 1097
  • Futterverwertung 30 kg – Schlachtung (kg Futter / kg Tageszunahme) 2,06
  • Magerfleischanteil 63,2
  • Fundament, Punkte 3,06
  • Anteil geschlachteter Tiere (%) 26,6
  • Rückenspeck, mm 6,0
  • Gescanntes Gewicht, kg 97,8

Durchschnittliche Produktionsergebnisse von DanBred-Ebern in Nukleusherden

  • Tageszunahme 30 kg – Schlachtung (g/Tag) 1143
  • Tageszunahme Geburt – Schlachtung (g/Tag) 382
  • Magerfleischanteil 64,2
  • Fundament, Punkte 2,87
  • Rückenspeck, mm 6,5
  • Gescanntes Gewicht, kg 98,8

Durchschnittsproduktion laut Eberprüfstation Bøgildgård

  • Tageszunahme 30 kg – Schlachtung (g/Tag) 1107
  • Futterverwertung 30 kg – Schlachtung (kg Futter / kg Tageszunahme) 2.08
  • Magerfleischanteil 65,1
  • Fundament, Punkte 2,90
  • Anteil geschlachteter Tiere (%) 26,3
  • Rückenspeck, mm 5,4
  • Gescanntes Gewicht, kg 99,1

Gennemsnitlige resultater for DanBred polte afprøvet i avlsbesætningerne

  • Daglig tilvækst, g/dag 30 kg – slagtning 1103
  • Daglig tilvækst, g/dag Fødsel – 30 kg 367
  • Kødprocent (%) 62,2
  • Styrke, point 3,15
  • Rygspæk, mm 7,9
  • Scanningsvægt, kg 98,0

Gennemsnitlige resultater for DanBred orner afprøvet i avlsbesætningerne

  • Daglig tilvækst, g/dag 30 kg – slagtning 1135
  • Daglig tilvækst, g/dag Fødsel – 30 kg 360
  • Kødprocent (%) 62,6
  • Styrke, point 3.08
  • Scanning measurement, mm 7,2
  • Rygspæk, mm 98,3

Gennemsnitlige resultater for DanBred orner afprøvet i avlsbesætningerne

  • Daglig tilvækst, g/dag 30 kg – slagtning 1143
  • Daglig tilvækst, g/dag Fødsel – 30 kg 382
  • Kødprocent (%) 64,2
  • Styrke, point 2,87
  • Rygspæk, mm 6,5
  • Scanningsvægt, kg 98,8

Gennemsnitlige resultater for DanBred polte afprøvet i avlsbesætningerne

Gennemsnitlige resultater for DanBred orner afprøvet på forsøgsstationen Bøgildgård

Average production results achieved by DanBred gilts in nucleus herds

  • Daily gain, g/day, 30 kg – slaughter 1103
  • Daily gain, g/day, birth - 30kg 367
  • Lean meat perctentage 62.2
  • Conformation, points 3.15
  • Scanning measurement, mm 7.9
  • Scanning weight, kg 98.0

Average production results achieved by DanBred boars in Nucleus herds

  • Daily gain, g/day, 30 kg – slaughter 1135
  • Daily gain, g/day, birth - 30kg 360
  • Lean meat perctentage 62.6
  • Conformation, points 3.08
  • Scanning measurement, mm 7.2
  • Scanning weight, kg 98.3

Average production for boar testing station Bøgildgård

  • Daily gain, g/day, 30 kg – slaughter 1097
  • Feed conversion, kg feed/kg gain, 30 kg – slaughter 1.93
  • Lean meat perctentage 63.2
  • Conformation, points 3.06
  • Killing out percentage 26.6
  • Scanning measurement, mm 6.0
  • Scanning weight, kg 97.8

Resultados de producción medios conseguidos por las cerdas jóvenes de DanBred en núcleos

  • Ganancia media diaria, g/día; 30 kg – sacrificio 1222
  • Ganancia de peso diaria, g/día; nacimiento – 30 kg 413
  • Porcentaje de carne magra 62,4
  • Conformación, puntos 2,94
  • Medición de escaneo, mm 6,4
  • Peso de escaneo, kg 99,3

Gemiddeld productieresultaat behaald door jonge
zeugen (< 1 jaar) van DanBred in kernbedrijven

  • Dagelijkse groei (g/dag), 30 kg – slacht 1222
  • Dagelijkse groei (g/dag), geboorte – 30 kg 413
  • Mager-vleespercentage (%) 62,4
  • Conformatie (punten) 2,94
  • Rugspekdiktemeting (mm) 6,4
  • Levend Scangewicht (kg) 99,3

cONTACT danbred

We can help you transition to DanBred genetics, technical services, transport and more. Book a time with us, and we will call you when it suits you.

danbred