The animal article of the month for November is ‘Genotype imputation from various low-density SNP panels and its impact on accuracy of genomic breeding values in pigs

The rapid increase in the world population, which is expected to reach 9.8 billion in 2050, needs to be accompanied by a substantial increase in food production. At the same time, consumers require tasty and high-quality food, produced under exemplary welfare and health conditions, all at a minimized cost. Pork is among the most consumed meat globally and, therefore, in order to meet this increasing demand, the swine industry seeks for innovative strategies, technologies, and breeding tools to increase the production efficiency.

Selective breeding has been an efficient way to improve animal performance in a sustainable production system. Over the past decade, the use of genomic information to select high genetic merit animals for breeding was proven to substantially increase genetic progress for economically important traits in various livestock species. However, the cost for generating a large number of genotyped individuals is still the major limitation for the uptake of genomic selection (i.e., selection of breeding candidates based on genomic information) by the pig industry.

As a large number of genomic markers (over 60K) are needed to accurately predict the genetic merit of breeding animals, a possible way to reduce the cost is to genotype a lower number of markers in a so-called low-density panel, and infer the untyped markers using imputation techniques (i.e., filling the missing markers). To design an optimal low-density panel, our study investigated a wide range of combinations of different scenarios in order to systematically identify the one that balances imputation accuracy, precision of breeding values based on genomic information, and the number of markers present in the genotyping panel which is directly related to the genotyping costs. The study of various low-density panels with increasing number of markers distributed along the whole genome allowed for assessing the trend in imputation accuracy in the three most popular commercial pig breeds (Duroc, Landrace, and Yorkshire). In addition, scenarios with different levels of the availability of parental genotype information were evaluated in order to provide practical recommendations to pig breeders. In summary, using a reference population of animals genotyped with a dense genotyping panel and with available phenotypes, a low-density panel of at least 3,000 genomic markers is recommended for an accurate genotype imputation and a precise prediction of the genetic merit of animals when the parents’ genotypes are not available. If both parents’ genotypes are available in the reference population, the panel density can be as low as 1,000. Our research points out the advantage of using low-density genotyping panels with imputation to lower the genomic evaluation cost and widen the application of genomic selection in the swine breeding industry. As a result, this strategy may greatly improve the overall pork production efficiency and quality.

This article is freely available for one month: ‘‘Genotype imputation from various low-density SNP panels and its impact on accuracy of genomic breeding values in pigs‘.

Author: Daniela Grossi et al.

The animal Article of the Month is selected by the Editor-in-Chief and is freely available for one month. View the recent selections


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