Selection indexes – Possibilities in the genomic era

Dr. Dinesh Thekkoot PhD, Genesus Genetics

Selection is the process by which we choose animals that become parents of the next generation, and we have been doing this since domestication. The important question is not whether selection is practiced but what is the goal of the selection.  In today’s pork industry the goal needs to be maximizing profit. Therefore, identifying the best animal or animals that maximize profit is the key part of the selection process

Traditional selection systems require parentage recording and performance testing of many pigs for multiple traits across various stages of life and in multiple environments /locations. This process is extremely time consuming and has large economic implications. With the recent advancement in the genomic technologies and methods, it is now possible to overcome many of these restrictions. Genomic applications offer opportunities for collecting new, more detailed and complex information/traits from a wider population of pigs. This, along with other factors like an improved understanding of animal biology, development of new sensing/recording technologies, etc. enables us to define and measure new traits and enhance current traits used in selection indexes.

Current index traits that benefit most by these new technologies:

Health and fitness traits: This is one area that has benefitted significantly with advancing genomic and related technologies. For example, PRRS and PED are economically significant diseases impacting the swine industry around the world. While vaccination and biosecurity measures have played a significant role in controlling the disease outbreaks, the variability and infectiousness of the virus strains have hampered the effectiveness of these steps. Producers also face increasing pressure from consumers and regulatory bodies to reduce antibiotic use and provide better animal welfare. These factors along with increased costs associated with reduced productivity and increased labor and veterinary cost require organizations to include health traits in selection index. Genomic advancements provide more efficient opportunities to include these traits in the selection indexes. Genesus has started implementing this and is using a Single Nucleotide Polymorphism (SNP) marker associated with tolerance to PRRS disease in the selection process.

Carcass and meat quality traits: Genesus is committed to carcass and meat quality improvement. Since 1998 Genesus has conducted a weekly carcass and meat quality testing program and has included these traits in the selection process. Because of this, Genesus pigs continue to excel in carcass, meat and eating quality traits. The incorporation of genomics in the selection program has helped us to improve these traits in a more efficient and effective manner. For example, Estimated Breeding Value (EBV) accuracies increased by an average of 76% for meat quality traits (color, marbling, pH etc.) and by 137% for carcass traits (carcass back fat, carcass loin and hot carcass weight).

Feed intake traits: Genesus has been recording growing pig and sow lactation feed intake for many years and have been using that in the selection program. Again incorporating genomics and automated recording technologies increases EBV accuracies by more than 30%, thereby increasing genetic improvement rate.

Growth and Reproductive traits: Our studies to validate the increase of EBV accuracies incorporating genomic information has shown that, the average prediction accuracies for growth traits (age to 120 kg, back fat and loin depth etc.) increased by 47%, 101% and 60% for Yorkshire, Landrace, and Durocs respectively. Similarly using genomics increased the EBV accuracies for total born by more than 100% in both Yorkshire and Landrace populations. These accuracy increases translate to improved genetic response and profitability of Genesus customers.

New traits that can be added in future:

The focus of genetic improvement needs to be on crossbred pigs raised in commercial production herds. Using genomics will help to add Information from crossbred animals in commercial herds to the evaluation of purebred animals in a nucleus herd. Currently, Genesus is conducting a large research project in collaboration with University of Alberta and Iowa State University to determine the advantages of genomic technologies for incorporating commercial crossbred information in the nucleus selection process. A recent Genesus technical report on the Gut microbiome, outlined a project related to pig disease resilience in which the gut microbiome is also a component. If economically important, these traits will be included in the future selection indexes. In addition to the traits involved in direct and indirect measurement of pig performance, a new set of data called “Omics data” is being collected from studies of functional biology. Examples are information about which genes are expressed in specific tissues in different stages of development, protein structure, methylation status, interaction of regulatory elements, etc. All these data can be used as better predictors in identifying a better and more robust pig. Genesus is keeping a close eye on these areas and is participating in many research projects being conducted in this area in various research universities in Canada and USA.  If found economical these “traits” will be included in the routine selection programs in future.

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This post was written by Genesus