TY - JOUR
T1 - Sliding window haplotype approaches overcome single SNP analysis limitations in identifying genes for meat tenderness in Nelore cattle
AU - Braz, Camila U.
AU - Taylor, Jeremy F.
AU - Bresolin, Tiago
AU - Espigolan, Rafael
AU - Feitosa, Fabieli L.B.
AU - Carvalheiro, Roberto
AU - Baldi, Fernando
AU - De Albuquerque, Lucia G.
AU - De Oliveira, Henrique N.
N1 - Funding Information:
This research was supported by the São Paulo Research Foundation (FAPESP) and National Council of Technological and Scientific Development (CNPq) grants: #2009/16118–5 and #480369/2009–7, respectively. São Paulo Research Foundation (FAPESP) also funds the scholarships #2013/00035–9 and 2014/23013–3 to Camila U. Braz.
Publisher Copyright:
© 2019 The Author(s).
PY - 2019/1/14
Y1 - 2019/1/14
N2 - Background: Traditional 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. Results: The 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. Conclusions: GWAA 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.
AB - Background: Traditional 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. Results: The 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. Conclusions: GWAA 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.
KW - Additive genetic variance
KW - Beef cattle
KW - GWAA
KW - Haplotype
KW - Meat tenderness
UR - http://www.scopus.com/inward/record.url?scp=85059949040&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85059949040&partnerID=8YFLogxK
U2 - 10.1186/s12863-019-0713-4
DO - 10.1186/s12863-019-0713-4
M3 - Article
C2 - 30642245
AN - SCOPUS:85059949040
SN - 1471-2156
VL - 20
JO - BMC genetics
JF - BMC genetics
IS - 1
M1 - 8
ER -