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BREEDING & GENETICS ▶▶▶


Metabolomics: The missing link in genetic selection


Metabolomic selection can improve genetic gain in difficult-to-measure traits by combining whole- metabolomic data with phenotypic, pedigree and genomic data. The metabolome is the complete set of metabolites in a sample and forms a link in the chain between DNA and phenotype.


BY HELLE PALMØ, CHIEF GENETICIST, DANBRED N


ew breeding technologies such as genomic selec- tion, whole-genome sequencing, optimal contri- bution selection and gene editing are developing at an increasing pace. Metabolomic selection is an


emerging breeding technology based on a new source of in- formation, namely nuclear magnetic resonance (NMR) me- tabolomics. NMR metabolomics measures all metabolites in a sample from an individual. That complete set of metabolites – referred to as whole-me- tabolomic data – is associated with the level of physiological activity in biological pathways that are initiated at DNA level and culminate in trait expression. The level of physiological activity is, in turn, regulated by the genes that an individual has inherited from its parents, as well as by cues from its envi- ronment. This link between whole-metabolomic data and in-


Whole-metabolomic data


Whole-metabolomic data – or the metabolome – is the full collection or net- work of metabolites identified at a certain time in a specific tissue or blood sam- ple from an individual. Metabolites are the small molecules that result from metabolic reactions within the body and reflect physiological activity. The me- tabolome can be measured on a large scale using nuclear magnetic resonance (NMR) spectroscopy. The NMR measurement can be made based on, for exam- ple, blood samples from pigs.


28 ▶PIG PROGRESS | Volume 36, No. 9, 2020


herited genes may be exploited to increase the genetic potential for desirable phenotypic traits, such as feed efficiency and meat quality in pigs.


Increasing the genetic potential Selective breeding increases the genetic potential of pigs by choosing genetically superior selection candidates as parents of the next generation. The resulting increase in genetic po- tential – hereafter referred to as genetic gain – is a direct re- sult of the accuracy by which we can predict the breeding values of selection candidates in each generation. The more accurate the breeding values, the higher the probability that we will select the genetically superior candidates, thus result- ing in higher genetic gain. Unfortunately, the accuracy of breeding values is low for the majority of traits in pigs, as well as in other species. The range is 10–40% for most traits, which highlights that we are only realising a small proportion of the genetic gain that is theo- retically possible. The main reason is that the information cur- rently used to predict breeding values – phenotypic, pedigree and genomic data – does not adequately describe the genet- ic potential of the pigs. Other sources of information are clearly needed, and this is where whole-metabolomic data comes into play.


Increasing genetic gain for feed efficiency Previous research suggests that metabolomic selection can increase genetic gain. For feed efficiency in pigs, the gain could be as much as 25%. Feed efficiency is an evident trait for which whole-metabolomic data may contribute infor- mation that has not yet been exploited due to the expense and difficulty in taking accurate measurements at the indi- vidual level. In fact, most pig breeding programmes do not record phenotypic feed efficiency information for all selection candidates.


Potential benefits for meat quality Achieving genetic gain for difficult-to-measure traits is chal- lenging because without accurate phenotypes, the genetic


PHOTO: SWEDISH NMR CENTRE


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