Genome-wide association study for carcass traits in a composite beef cattle breed

• Published in: Livestock science 2018-07, Vol.213, p.35-43
• Main Authors: Hay, El Hamidi, Roberts, Andy
• Format: Article
• Language: English
• Subjects: Beef cattle; Carcass traits; GWAS; QTL
• ISSN: 1871-1413; 1878-0490
• DOI: 10.1016/j.livsci.2018.04.018

•Three GWAS methods were conducted for carcass traits in a beef cattle breed.•This study identified several SNP windows associated with carcass traits.•The five highest SNP windows explained a small percentage of the genetic variation.•The results were not consistent across the three GWAS methods. Improvement of carcass traits is highly emphasized in beef cattle production in order to meet consumer demands. Discovering and understanding genes and genetic variants that control these traits is of paramount importance. In this study, different genome wide association approaches (single step GBLUP GWAS, Bayes A and Bayes B) were implemented and compared for three ultrasound carcass traits: fat thickness (FAT), intramuscular fat (IMF) and ribeye area (REA) of a composite beef cattle breed. The results showed different SNP marker windows associated with carcass traits explaining a small percentage of the genetic variance. The SNP marker window with the highest percentage of genetic variance (1.83%) associated with FAT was located on BTA14 in position 24 Mb. Surveying candidate genes in the regions associated with these traits revealed genes such as LYPLA, and LYN genes which have been associated with feed intake and growth in beef cattle. This study supported previous results from GWAS of carcass traits and revealed additional regions in the bovine genome associated with these economically important traits. Comparing the top 5 SNP windows for each trait across the GWAS methods revealed that only a few of these windows overlap.