Genesus Global Technical Report: Another genomic tool for improving litter size

Tue, 05 Jun 2018

Litter size is a very important factor determining sow profitability. A major limitation for increasing litter size is embryonic loss that occurs during the 2nd to 3rd week of gestation (Geisert and Schmitt, 2002, J Anim Sci. 80, E54-E65).

by Dr Chunyan Zhang, Phd, Genetician Genesus Inc.

Many factors may contribute to this loss and one possible cause of early embryonic mortality may be the existence of some harmful alleles (different forms of a gene) for essential genes that lead to fetal death shortly after a female becomes pregnant. The frequency of these harmful alleles might be reduced in a population after long-term selection for large litter size, such as in maternal breeds. However, in breeds that have not been selected for increased litter size (eg. Duroc), these harmful alleles may be ignored (or hidden) and at a higher frequency compared to that in the selected populations.

Usually these harmful alleles cause the fetus to die when they are present in the homozygous state (called recessive, one harmful copy from each parent, e.g aa). When they are present in the heterozygous state (the alleles inherited from the dam and sire are different, such as Aa), the individual survives and is phenotypically normal. This heterozygous animal, known as a carrier is very difficult to identify and thus can continue to spread the harmful alleles in the population.

Genomic technology now provides a state-of-the-art approach to detect such harmful alleles that are expected to be relatively common in an unselected population but never occur in the recessive homozygote state in live animals. This approach only requires genotype data on phenotypically normal (i.e. live) individuals to detect the harmful alleles through statistical analysis. This approach was initially used in dairy cattle and detected alleles associated with fertility defects (VanRaden et al., 2011, J Dairy Sci. 94, 6153-6161). More recent studies have begun to look in pigs and found some alleles associated with smaller litters and more stillborn piglets in dam lines and/or commercial lines (Häggman and Uimari, 2017, J Anim Breed Genet. 134, 129-135; Howard et al., 2017, GSE. 49, 57; Derks et al., 2017, BMC Genomics. 18, 858).

In the Genesus genomic database, we have thousands of pigs with informative genotype data (60K, 80K, 650K and sequence wide) which enable us to search for these potentially harmful alleles related to litter size, and further estimate their effects on boar fertility through our large set of phenotypes. Our initial effort focused on Duroc boars using 650K SNP genotypes. Several regions of the genome were found to potentially harbour harmful alleles. As an example, for the most significant SNP we predicted that there should be 45 homozygous recessive (aa) individuals but none was observed. The region containing this SNP was significantly associated with more mummified fetuses (P < 0.001).

Compared with the previous reports in pigs (see above), the identified genomic regions seem to be somewhat breed or popualtion specific, although we did see a few regions that may overlap with the previous findings.

These findings provide valuable information to potentially increase litter size in the Genesus Duroc population. This would lead to not only more pigs produced but increased genetic improvement through higher selection intensity. Approaches for reducing the frequency of these harmful alleles include genomic selection and genomic-based mating plans using the Genesus custom SNP chip.

Implementation of such research findings will contribute significantly to the Genesus goal of increasing value and profitability for Genesus customers.