Animal Molecular Breeding 2024, Vol.14, No.2, 154-164 http://animalscipublisher.com/index.php/amb 158 Overall, the choice of breeding strategy depends on the specific goals of the breeding program, the traits of interest, and the available resources. While traditional methods and MAS can still play a role in certain contexts, GS represents the most advanced and effective approach for improving complex traits such as carcass quality in pigs. 4 Case Study: Application of Quantitative Genetics in Pig Breeding Programs 4.1 Description of the breeding program The breeding program under consideration involves a comprehensive approach to improving carcass traits in pigs through the application of quantitative genetics. This program integrates various genetic and phenotypic data to enhance economically important traits such as backfat thickness, loin depth, and carcass daily gain. For instance, in a study involving crossbred pigs, a reference population was used to evaluate the predictive ability of different models for carcass traits, with data collected from over 130 000 animals (Bergamaschi et al., 2019). Another breeding program focused on a three-generation experimental cross between Meishan and Large White pig breeds, analyzing 15 different carcass composition traits (Milan et al., 2002). These breeding programs typically involve large-scale phenotypic measurements and genotyping efforts. For example, in the Duroc × Pietrain resource population, 510 F2 animals were genotyped for 124 microsatellite markers, and various carcass and meat quality traits were evaluated (Edwards et al., 2008). Similarly, a study on Duroc pigs estimated genetic parameters for 39 traits, including growth, conventional carcass traits, and novel carcass traits, using data from 2 583 purebred Duroc gilts (Willson et al., 2020). 4.2 Implementation of quantitative genetic methods Quantitative genetic methods are implemented in these breeding programs through genome-wide association studies (GWAS), quantitative trait locus (QTL) mapping, and the estimation of genetic parameters. For instance, a GWAS conducted on pooled F2 designs led to the identification of numerous significantly associated variant clusters for traits such as average daily gain, backfat thickness, and carcass length (Falker-Gieske et al., 2019). In another study, QTL mapping in a Landrace pig population identified QTL for carcass weight, cutlet weight, and backfat thickness, among other traits (Vidal et al., 2005). The use of genetic markers and heritability estimates is also crucial. In a study on the endangered German pig breed ‘Bunte Bentheimer’, genetic markers at the ryanodine receptor 1 (RYR1) locus were used alongside phenotypic data to design breeding strategies for meat quality improvement (Biermann et al., 2015). Additionally, heritability estimates for various traits, such as meat lightness, loin pH, and marbling, were found to be moderate to high, indicating that these traits can be genetically improved if included in selection schemes (Willson et al., 2019). 4.3 Outcomes and improvements in carcass traits The application of quantitative genetics in these breeding programs has led to significant improvements in carcass traits. For example, the pooling of four large F2 designs in a GWAS study resulted in the discovery of more than 32 million variants, including 8 million previously unreported ones, and the identification of new candidate genes such as BMP2 (Falker-Gieske et al., 2019). In another study, the inclusion of records from different finishing flows in the training set increased the prediction accuracy of carcass traits by approximately 6% (Bergamaschi et al., 2019). Moreover, the identification of significant QTL for traits like backfat thickness, loin depth, and carcass daily gain has facilitated the fine mapping of genes controlling these traits, enabling their incorporation into marker-assisted selection programs (Edwards et al., 2008). The use of genetic parameters in Duroc pigs has also shown that genetic progress can be achieved for a wide range of traits, including novel carcass traits, without undesirable impacts on growth rate and carcass leanness (Willson et al., 2020). 4.4 Lessons learned and future perspectives One of the key lessons learned from these breeding programs is the importance of integrating both phenotypic and
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