Open Access Open Badges Research article

Genome-wide association analyses for carcass quality in crossbred beef cattle

Duc Lu12*, Mehdi Sargolzaei13, Matthew Kelly14, Gordon Vander Voort1, Zhiquan Wang2, Ira Mandell1, Stephen Moore24, Graham Plastow2 and Stephen Paul Miller12

Author Affiliations

1 Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada

2 Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, 1400 College Plaza, 8215 112 Street, Edmonton, Alberta T6G 2C8, Canada

3 L’Alliance Boviteq, 19320 Grand rang Saint-François, Saint-Hyacinthe, Quebec J2T 5H1, Canada

4 Centre for Animal Science, Queensland Alliance for Agriculture & Food Innovation, University of Queensland, St Lucia, Queensland 4072, Australia

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BMC Genetics 2013, 14:80  doi:10.1186/1471-2156-14-80

Published: 11 September 2013



Genetic improvement of beef quality will benefit both producers and consumers, and can be achieved by selecting animals that carry desired quantitative trait nucleotides (QTN), which result from intensive searches using genetic markers. This paper presents a genome-wide association approach utilizing single nucleotide polymorphisms (SNP) in the Illumina BovineSNP50 BeadChip to seek genomic regions that potentially harbor genes or QTN underlying variation in carcass quality of beef cattle.

This study used 747 genotyped animals, mainly crossbred, with phenotypes on twelve carcass quality traits, including hot carcass weight (HCW), back fat thickness (BF), Longissimus dorsi muscle area or ribeye area (REA), marbling scores (MRB), lean yield grade by Beef Improvement Federation formulae (BIFYLD), steak tenderness by Warner-Bratzler shear force 7-day post-mortem (LM7D) as well as body composition as determined by partial rib (IMPS 103) dissection presented as a percentage of total rib weight including body cavity fat (BDFR), lean (LNR), bone (BNR), intermuscular fat (INFR), subcutaneous fat (SQFR), and total fat (TLFR).


At the genome wide level false discovery rate (FDR < 10%), eight SNP were found significantly associated with HCW. Seven of these SNP were located on Bos taurus autosome (BTA) 6. At a less stringent significance level (P < 0.001), 520 SNP were found significantly associated with mostly individual traits (473 SNP), and multiple traits (47 SNP). Of these significant SNP, 48 were located on BTA6, and 22 of them were in association with hot carcass weight. There were 53 SNP associated with percentage of rib bone, and 12 of them were on BTA20. The rest of the significant SNP were scattered over other chromosomes. They accounted for 1.90 - 5.89% of the phenotypic variance of the traits. A region of approximately 4 Mbp long on BTA6 was found to be a potential area to harbor candidate genes influencing growth. One marker on BTA25 accounting for 2.67% of the variation in LM7D may be worth further investigation for the improvement of beef tenderness.


This study provides useful information to further assist the identification of chromosome regions and subsequently genes affecting carcass quality traits in beef cattle. It also revealed many SNP that acted pleiotropically to affect carcass quality. This knowledge is important in selecting subsets of SNP to improve the performance of beef cattle.

Single nucleotide polymorphism; Chromosome regions; Beef carcass quality