The genomic improvement of meat quality traits in pigs

• Author / Creator

  Kristin Lee

• Meat and carcass quality traits are of increasing interest to the swine industry due to their influence on customer purchasing and repurchasing decisions. However, meat quality traits must be measured post-mortem, meaning that these traits cannot be measured on the potential breeding candidates themselves, instead they must be measured on their siblings. For this reason, selection of meat quality traits using traditional selection methods is difficult, expensive, and lowly accurate, which is preventing the practical use of many of these traits in breeding programs today. Alternatively, genomic selection (GS) can be implemented for the improvement of meat quality traits. Using GS, breeding values are estimated using genomic relationships or genomic effects, providing a higher selection accuracy and an increased rate of genetic gain compared to traditional selection methods. Therefore, GS provides a significant opportunity to improve and predict meat and carcass quality. The main goal of this thesis was to improve our current understanding of the genetic and biological factors underlying meat and carcass quality traits to aid in the implementation of GS methods. In part 1 of this thesis, variance component estimates were used to calculate genetic parameters for meat quality traits in pigs. These results could be used to directly incorporate meat quality traits into selection procedures, including both traditional or GS methods. Secondly, the biological factors underlying meat quality traits were explored. In part 2, a genome wide association study (GWAS) was used to identify quantitative trait loci (QTL) and genes associated with drip loss (DL). Following this, in part 3, a single-SNP association analysis was used to determine the effects of two potential causative mutations on meat colour phenotypes. These two analyses were intended to contribute to an improved understanding of the genes and mutations underlying meat quality traits, which would not only improve the biological knowledge for meat quality traits, but also facilitate the future implementation of alternative methods of GS that incorporate biological knowledge. Phenotypes were collected from either a purebred Duroc (n = 997), or commercial crossbred pig population (Duroc X Landrace/Large White, n = 1098). Meat quality traits included various colour measurements (Minolta L, a, and b*) from multiple muscle types, including the longissimus thoracis et lumborum (loin; LOINL, LOINA, and LOINB), loin fat (LOINFATL, LOINFATA, LOINFATB), ham gluteus medius (GLUTL, GLUTA, GLUTB), ham quadriceps femoris (QUADL, QUADA, QUADB), and ham iliopsoas (ILIOL, ILIOA, ILIOB), as well as drip loss (DL), and ultimate pH. Further, carcass traits included muscle depth (MD), fat depth (FD), loin eye area (LEA), and intramuscular fat (NSIF IMF). In part 1 of this thesis, meat colour traits showed heritabilities ranging between low to moderate (0.06±0.05 for QUADB to 0.44±0.09 for LOINA) and remaining meat quality traits showed moderate heritabilities, including DL (0.23±0.08) and pH (0.28±0.08). All carcass quality traits analyzed had moderate heritabilities, including MD (0.33±0.08), FD (0.39±0.08), LEA (0.39±0.09), and NSIF IMF (0.43±0.09). Moderate to high genetic correlations were observed between the same colour measurements from different muscle types (ranging between 0.50 to 0.96) and different colour measurements from the same muscle types (ranging between 0.56 to 0.92). Colour measurements also showed moderate to high genetic correlations with pH (ranging between -0.54 to -0.80) and DL (ranging between 0.38 to 0.69). The remaining meat quality traits showed a high negative correlation, between DL and pH (-0.65±0.16). Carcass quality traits showed moderate to high correlations, including LEA and MD (0.94±0.04), and FD and NSIF IMF (0.36±0.15). In addition, very few unfavorable correlations were observed between the meat and carcass quality traits. Overall, these results show that meat and carcass quality traits can be improved by genetic selection, to produce a high quality and lean pork product. In the remaining studies of this thesis, parts 2 and 3, the biological factors underlying meat quality traits were explored. However, both studies proved underpowered in their ability to identify genes and causative mutations that were significantly associated with meat quality traits. Nonetheless, the results from these studies provide a basis upon which future work can built.

• Subjects / Keywords

  • GWAS
  • Genomic selection
  • Pigs
  • Genetic parameter
  • Meat quality

• Graduation date

  Fall 2020

• Type of Item

  Thesis

• Degree

  Master of Science

• DOI

  https://doi.org/10.7939/r3-5mdd-fg77

• License

  Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.