Another genomic tool for improving litter size

Dr. Chunyan Zhang, Phd,  Genetician Genesus Inc. 

czhang@genesus.com

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).

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.

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Genesus Welcomes Chunyan Zhang, PhD

Genesus is very pleased to announce the appointment of Dr. Chunyan Zhang, PhD to the position of Geneticist.  

Since receiving her PhD in 2010, Chunyan has worked in Dr. Graham Plastow’s program at Livestock Gentec, University of Alberta as a postdoctoral fellow and most recently as a research associate.

She has been actively engaged in several R&D projects focusing on genetic and genomic approaches to improving economically important traits in pork production. She has worked collaboratively with pig genetic companies in the conduct of industry-driven R&D projects.

In her new role, Chunyan will develop and conduct internally and externally funded R&D projects focused on increasing pig genetic improvement through incorporation of genomic technologies. As a member of the Genesus genetic program team she will collaborate with other team members and university personnel on R&D projects and technical services. Additionally, she will provide direct supervision and support to Genesus nucleus herds located in China and Asia as well as providing technical support for the Genesus sales team in China and Asia.

“We look forward to Chunyan’s contributions to our programs. We have worked collaboratively with her on several successful projects at Livestock Gentec. Her skill set, experience, and desire to be involved in the pork industry make her an excellent choice for this position. Our genetic improvement and R&D programs continue to expand and finding the right people to support and move these programs forward is a key to the future of Genesus” says Dr. Bob Kemp, Vice President of Genetic Programs and R&D.

Chunyan holds Bachelor and Doctoral degrees from Huazhong Agricultural University in China. She was awarded a Mitacs Elevate Postdoctoral Fellowship at the University of Alberta from 2014 to 2016. She has published over 20 articles in peer-reviewed scientific journals.

Chunyan resides in Edmonton, Alberta with her husband and two children.