Genome-Wide Association Study for Carcass Traits in an Experimental Nelore Cattle Population

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de Oliveira Silva, Rafael Medeiros ; Stafuzza, Nedenia Bonvino ; Fragomeni, Breno de Oliveira ; Ferreira de Camargo, Gregorio Miguel ; Ceacero, Thais Matos ; dos Santos Goncalves Cyrillo, Joslaine Noely ; Baldi, Fernando ; Boligon, Arione Augusti ; Zerlotti Mercadante, Maria Eugenia ; Lourenco, Daniela Lino ; Misztal, Ignacy ; de Albuquerque, Lucia Galvao

• Document type: Journal article
• Source: PLoS One; v. 12, n. 1 JAN 24 2017.
• Web of Science Citations: 17

Abstract

The purpose of this study was to identify genomic regions associated with carcass traits in an experimental Nelore cattle population. The studied data set contained 2,306 ultrasound records for longissimus muscle area (LMA), 1,832 for backfat thickness (BF), and 1,830 for rump fat thickness (RF). A high-density SNP panel (BovineHD BeadChip assay 700k, Illumina Inc., San Diego, CA) was used for genotyping. After genomic data quality control, 437,197 SNPs from 761 animals were available, of which 721 had phenotypes for LMA, 669 for BF, and 718 for RF. The SNP solutions were estimated using a single-step genomic BLUP approach (ssGWAS), which calculated the variance for windows of 50 consecutive SNPs and the regions that accounted for more than 0.5% of the additive genetic variance were used to search for candidate genes. The results indicated that 12, 18, and 15 different windows were associated to LMA, BF, and RF, respectively. Confirming the polygenic nature of the studied traits, 43, 65, and 53 genes were found in those associated windows, respectively for LMA, BF, and RF. Among the candidate genes, some of them, which already had their functions associated with the expression of energy metabolism, were found associated with fat deposition in this study. In addition, ALKBH3 and HSD17B12 genes, which are related in fibroblast death and metabolism of steroids, were found associated with LMA. The results presented here should help to better understand the genetic and physiologic mechanism regulating the muscle tissue deposition and subcutaneous fat cover expression of Zebu animals. The identification of candidate genes should contribute for Zebu breeding programs in order to consider carcass traits as selection criteria in their genetic evaluation. (AU)

• FAPESP's process: 09/16118-5 - Genomic tools to genetic improvement of direct economic important traits in Nelore cattle
• Grantee: Lucia Galvão de Albuquerque
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 13/01228-5 - Genomic selection for feed efficiency traits in Nellore cattle
• Grantee: Rafael Medeiros de Oliveira Silva
• Support Opportunities: Scholarships in Brazil - Doctorate