Metafounders: The Future of Swine Genetic Evaluation

Everestus Akanno, PhD., Geneticist, Genesus Inc.

The breeding objective of nucleus swine breeding programs is to improve performance of commercial crossbred pigs. However, what appear to be the same traits (e.g., growth rate) may be expressed differently at the commercial and nucleus herd levels and thus may not be genetically the same due to differences in management, production environment, etc.

Consequently, genetic progress achieved in the nucleus may not be directly observed at the commercial herd. Therefore, current research efforts are focused on evaluating the possibility of incorporating commercial data into nucleus genetic evaluation programs to predict breeding values of nucleus animals for crossbred performance (Christensen et al. Genet. Sel. Evol. (2015) 47:98, doi: 10.1186/s12711-015-0177-6). This requires collecting additional pedigree information from the nucleus through to the commercial pig so that the genetic relationships among commercial and nucleus pigs can be tracked.

Traditional approaches of tracking sire and dam information at multiplier and commercial levels can be expensive and usually requires cooperative commercial research herds which themselves may not be truly representative of typical commercial herds. One way to deal with this issue is to utilise genomic information on the crossbred and nucleus animals to create a combined genetic relationship across the different herd levels. An important question for genomic evaluation using this type of data is how to define the genetic relationships within and across the base generations of multiple populations (e.g., purebreds, F1(Y-L) crossbreds and 3-way (D(Y-L)) crossbreds).

What are metafounders?

Metafounders are a group of individuals, with unknown parents which are considered ancestral founders from which the oldest animals may have originated (Legarra et al. Genetics, Vol. 200, 455–468 June 2015, doi: 10.1534/genetics.115.177014). A metafounder group is created based on some form of similarity such as genetic line, sex, or age. They are considered as being related among themselves and their relationship among themselves is derived from the genomic relationship of all their descendants.

Using metafounders in genetic evaluation

The plan to use data from all levels of production for the purpose of conducting combined purebred-crossbred genetic evaluation has opened opportunity for developing a combined and complete relationship for multiple pedigreed populations. Where pedigree is available like in the nucleus, each contributing breed has its own oldest animals, and they are assumed to be unrelated with the oldest animals from other purebred populations.

In this scenario, metafounders are used to create a relationship across all the oldest animals from different breeds, thus, linking the datasets from the various breeds together. Genomic information is used to estimate these relationships for commercial crossbred data and thus connect the metafounders and all data sources together.

As an example, Table 1 shows the pedigree setup for 11 pigs drawn from all levels of production. Three metafounders each for Landrace (AF-L), Yorkshire (AF-Y) and Duroc (AF-D) were created to connect all three breeds. Individuals 1-6 represent the purebred founders for Landrace, Yorkshire and Duroc breeds and are assumed to originate from each of the three metafounders. Individuals 7-9 represents all purebred pigs born and raised in the nucleus. Individual 10 represent all maternal F1 crossbred pigs (L-Y) at the multiplier level while individual 11 represents the three-way terminal cross (D(L-Y)) at the commercial level.

Creating a complete pedigree in this way ensures that all data coming out of the various production systems are linked to one another and used for genetic evaluation purpose. The caveat with this effort is the extra cost associated with genotyping animals at all levels of production to be able to establish a good and complete relationship.

Impact of metafounders on breeding value prediction

Besides the obvious impact of performing genetic evaluation using a large dataset from all levels of the industry, early research results (Xiang et al. J Anim Sci. 2017 Apr;95(4):1472-1480. doi: 10.2527/jas.2016.1155; van Grevenhof et al. J. Anim. Sci. 2019.97:548–558, doi: 10.1093/jas/sky433) have shown:

Improved accuracy of breeding values and improvement in the rate of genetic gain.
Improvement in the ranking of selection candidates.
Decrease in inbreeding.

The Genesus Research and Development Team is continuously researching and reviewing the genetic evaluation system and presently acquiring genotypes and phenotypes from all levels of production to implement a genomic purebred-crossbred evaluation for all nucleus animals. This effort will ensure that Genesus Inc. continues to take a leadership position in improving the genetic merit of Genesus breeding stock to meet the needs of all customers.