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Int. J. Mol. Sci. 2016, 17(12), 2100; doi:10.3390/ijms17122100

Genetic Marker Discovery in Complex Traits: A Field Example on Fat Content and Composition in Pigs

1
Departament de Ciència Animal, Universitat de Lleida—Agrotecnio, 25198 Lleida, Spain
2
The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland EH25 9RG, UK
*
Author to whom correspondence should be addressed.
Academic Editor: Sabrina Angelini
Received: 3 November 2016 / Revised: 6 December 2016 / Accepted: 7 December 2016 / Published: 14 December 2016
(This article belongs to the Special Issue Exploring the Genotype–Phenotype Map to Explain Complex Traits)
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Abstract

Among the large number of attributes that define pork quality, fat content and composition have attracted the attention of breeders in the recent years due to their interaction with human health and technological and sensorial properties of meat. In livestock species, fat accumulates in different depots following a temporal pattern that is also recognized in humans. Intramuscular fat deposition rate and fatty acid composition change with life. Despite indication that it might be possible to select for intramuscular fat without affecting other fat depots, to date only one depot-specific genetic marker (PCK1 c.2456C>A) has been reported. In contrast, identification of polymorphisms related to fat composition has been more successful. For instance, our group has described a variant in the stearoyl-coA desaturase (SCD) gene that improves the desaturation index of fat without affecting overall fatness or growth. Identification of mutations in candidate genes can be a tedious and costly process. Genome-wide association studies can help in narrowing down the number of candidate genes by highlighting those which contribute most to the genetic variation of the trait. Results from our group and others indicate that fat content and composition are highly polygenic and that very few genes explain more than 5% of the variance of the trait. Moreover, as the complexity of the genome emerges, the role of non-coding genes and regulatory elements cannot be disregarded. Prediction of breeding values from genomic data is discussed in comparison with conventional best linear predictors of breeding values. An example based on real data is given, and the implications in phenotype prediction are discussed in detail. The benefits and limitations of using large SNP sets versus a few very informative markers as predictors of genetic merit of breeding candidates are evaluated using field data as an example. View Full-Text
Keywords: meat quality; intramuscular fat; candidate gene; pork; oleic acid; monounsaturated fatty acid meat quality; intramuscular fat; candidate gene; pork; oleic acid; monounsaturated fatty acid
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Pena, R.N.; Ros-Freixedes, R.; Tor, M.; Estany, J. Genetic Marker Discovery in Complex Traits: A Field Example on Fat Content and Composition in Pigs. Int. J. Mol. Sci. 2016, 17, 2100.

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