Sliding window haplotype approaches overcome single SNP analysis limitations in identifying genes for meat tenderness in Nelore cattle

Author(s)

Braz, Camila U. ^[1] ; Taylor, Jeremy F. ^[2] ; Bresolin, Tiago ^[1] ; Espigolan, Rafael ^[1] ; Feitosa, Fabieli L. B. ^[1] ; Carvalheiro, Roberto ^[1] ; Baldi, Fernando ^[1] ; de Albuquerque, Lucia G. ^[1] ; de Oliveira, Henrique N. ^[1]

Affiliation

^[1] Sao Paulo State Univ Unesp, Anim Sci Dept, BR-14488490 Jaboticabal, SP - Brazil

^[2] Univ Missouri, Div Anim Sci, Columbia, MO 65211 - USA

• Document type: Journal article
• Source: BMC GENETICS; v. 20, JAN 14 2019.
• Web of Science Citations: 2

Abstract

BackgroundTraditional single nucleotide polymorphism (SNP) genome-wide association analysis (GWAA) can be inefficient because single SNPs provide limited genetic information about genomic regions. On the other hand, using haplotypes in the statistical analysis may increase the extent of linkage disequilibrium (LD) between haplotypes and causal variants and may also potentially capture epistastic interactions between variants within a haplotyped locus, providing an increase in the power and robustness of the association studies. We performed GWAA (413,355 SNP markers) using haplotypes based on variable-sized sliding windows and compared the results to a single-SNP GWAA using Warner-Bratzler shear force measured in the longissimus thorasis muscle of 3161 Nelore bulls to ascertain the optimal window size for identifying the genomic regions that influence meat tenderness.ResultsThe GWAA using single SNPs identified eight variants influencing meat tenderness on BTA 3, 4, 9, 10 and 11. However, thirty-three putative meat tenderness QTL were detected on BTA 1, 3, 4, 5, 8, 9, 10, 11, 15, 17, 18, 24, 25, 26 and 29 using variable-sized sliding haplotype windows. Analyses using sliding window haplotypes of 3, 5, 7, 9 and 11 SNPs identified 57, 61, 42, 39, and 21% of all thirty-three putative QTL regions, respectively; however, the analyses using the 3 and 5 SNP haplotypes, cumulatively detected 88% of the putative QTL. The genes associated with variation in meat tenderness participate in myogenesis, neurogenesis, lipid and fatty acid metabolism and skeletal muscle structure or composition processes.ConclusionsGWAA using haplotypes based on variable-sized sliding windows allowed the detection of more QTL than traditional single-SNP GWAA. Analyses using smaller haplotypes (3 and 5 SNPs) detected a higher proportion of the putative QTL. (AU)

• FAPESP's process: 13/00035-9 - Detection of QTLs and search for causal mutations in candidate gene for meat tenderness in Nellore cattle
• Grantee: Camila Urbano Braz
• Support type: Scholarships in Brazil - Doctorate
• FAPESP's process: 14/23013-3 - Detection of QTL and search for causal mutations in candidate genes for meat tenderness in Nellore cattle
• Grantee: Camila Urbano Braz
• Support type: Scholarships abroad - Research Internship - Doctorate
• 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 type: Research Projects - Thematic Grants