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

Pena, Ramona Natacha; Ros-Freixedes, Roger; Tor, Marc; Estany, Joan
December 2016
International Journal of Molecular Sciences;Dec2016, Vol. 17 Issue 12, p2100
Academic Journal
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.


Related Articles

  • Molecular analysis of new sources of resistance to Pseudoperonospora cubensis (Berk. et Curt.) Rostovzev in cucumber. Szczechura, W.; Staniaszek, M.; Klosinska, U.; Kozik, E. // Russian Journal of Genetics;Oct2015, Vol. 51 Issue 10, p974 

    Downy mildew of cucumber ( Cucumis sativus L.), caused by Pseudoperonospora cubensis (Berk. et Curt.) Rostovzev, is one of the most important foliar diseases of cucurbit crops. Two parental lines resistant PI 197085, susceptible PI 175695 and their F2 generation were used in our study....

  • A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Hu, Hao; Roach, Jared C; Coon, Hilary; Guthery, Stephen L; Voelkerding, Karl V; Margraf, Rebecca L; Durtschi, Jacob D; Tavtigian, Sean V; Shankaracharya; Wu, Wilfred; Scheet, Paul; Wang, Shuoguo; Xing, Jinchuan; Glusman, Gustavo; Hubley, Robert; Li, Hong; Garg, Vidu; Moore, Barry; Hood, Leroy; Galas, David J // Nature Biotechnology;Jul2014, Vol. 32 Issue 7, p663 

    High-throughput sequencing of related individuals has become an important tool for studying human disease. However, owing to technical complexity and lack of available tools, most pedigree-based sequencing studies rely on an ad hoc combination of suboptimal analyses. Here we present...

  • Power and Predictive Accuracy of Polygenic Risk Scores. Dudbridge, Frank // PLoS Genetics;Mar2013, Vol. 9 Issue 3, Special section p1 

    Polygenic scores have recently been used to summarise genetic effects among an ensemble of markers that do not individually achieve significance in a large-scale association study. Markers are selected using an initial training sample and used to construct a score in an independent replication...

  • An approximate model of polygenic inheritance. Lange, Kenneth; Weir, B.S. // Genetics;Nov97, Vol. 147 Issue 3, p1423 

    Presents information regarding the approximate model of polygenic inheritance. Proven alternative of mixed model of polygenic and major gene inheritance; Implications of results; What does a simple numerical example illustrates.

  • Single-marker and multi-marker mixed models for polygenic score analysis in family-based data. Bohossian, Nora; Saad, Mohamad; Legarra, Andrés; Martinez, Maria // BMC Proceedings;6/17/2014, Vol. 9 Issue Supplement 5, p1 

    Genome-wide association studies have proven successful but they remain underpowered for detecting variants of weaker effect. Alternative methods propose to test for association by using an aggregate score that combines the effects of the most associated variants. The set of variants that are to...

  • Estimating Polygenic Effects Using Markers of the Entire Genome. Shizhong Xu // Genetics;Feb2003, Vol. 163 Issue 2, p789 

    Molecular markers have been used to map quantitative trait loci. However, they are rarely used to evaluate effects of chromosome segments of the entire genome. The original interval-mapping approach and various modified versions of it may have limited use in evaluating the genetic effects of the...

  • Polygenic susceptibility to breast cancer and implications for prevention. Pharoah, Paul D.P.; Antoniou, Antonis; Bobrow, Martin; Zimmern, Ron L.; Easton, Douglas F.; Ponder, Bruce A.J. // Nature Genetics;May2002, Vol. 31 Issue 1, p33 

    The knowledge of human genetic variation that will come from the human genome sequence makes feasible a polygenic approach to disease prevention, in which it will be possible to identify individuals as susceptible by their genotype profile and to prevent disease by targeting interventions to...

  • An evaluation of the variance components approach: type 1 error, power and size of the estimated effect. Yin Yao Shugart; O'Connell, Jeffrey R.; Wilson, Alexander F. // European Journal of Human Genetics;Feb2002, Vol. 10 Issue 2, p133 

    In order to evaluate the statistical properties of the variance components method implemented in SOLAR and GENEHUNTER2, the type I error rate, power and estimated size of modelled effects were determined using computer simulation. Results suggested that the type I error rate was quite...

  • QTL for the heritable inverted teat defect in pigs. Jonas, Elisabeth; Schreinemachers, Heinz-Josef; Kleinwächter, Tina; Ün, Cemal; Oltmanns, Ina; Tetzlaff, Sylvio; Jennen, Danyel; Tesfaye, Dawid; Ponsuksili, Siriluck; Murani, Eduard; Juengst, Heinz; Tholen, Ernst; Schellander, Karl; Wimmers, Klaus // Mammalian Genome;Feb2008, Vol. 19 Issue 2, p127 

    The mothering ability of a sow largely depends on the shape and function of the mammary gland. The aim of this study was to identify QTL for the heritable inverted teat defect, a condition characterized by disturbed development of functional teats. A QTL analysis was conducted in a porcine...

  • Polygenic inheritance of canopy wilting in soybean [ Glycine max (L.) Merr.]. Charlson, Dirk V.; Bhatnagar, Sandeep; King, C. Andy; Ray, Jeffery D.; Sneller, Clay H.; Carter Jr., Thomas E.; Purcell, Larry C. // Theoretical & Applied Genetics;Aug2009, Vol. 119 Issue 4, p587 

    As water demand for agriculture exceeds water availability, cropping systems need to become more efficient in water usage, such as deployment of cultivars that sustain yield under drought conditions. Soybean cultivars differ in how quickly they wilt during water-deficit stress, and this trait...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics