Searching for new loci and candidate genes for economically important traits through gene-based association analysis of Simmental cattle.
Single-marker genome-wide association study (GWAS) is a convenient strategy of genetic analysis that has been successful in detecting the association of a number of single-nucleotide polymorphisms (SNPs) with quantitative traits. However, analysis of individual SNPs can only account for a small proportion of genetic variation and offers only limited knowledge of complex traits. This inadequacy may be overcome by employing a gene-based GWAS analytic approach, which can be considered complementary to the single-SNP association analysis. Here we performed an initial single-SNP GWAS for bone weight (BW) and meat pH value with a total of 770,000 SNPs in 1141 Simmental cattle. Additionally, 21836 cattle genes collected from the Ensembl Genes 83 database were analyzed to find supplementary evidence to support the importance of gene-based association study. Results of the single SNP-based association study showed that there were 11 SNPs significantly associated with bone weight (BW) and two SNPs associated with meat pH value. Interestingly, all of these SNPs were located in genes detected by the gene-based association study.
Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China.
Jiangwei
J
Xia
Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China.
Huizhong
H
Fan
Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China.
Tianpeng
T
Chang
Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China.
Lingyang
L
Xu
Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China.
Wengang
W
Zhang
Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China.
Yuxin
Y
Song
Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China.
Bo
B
Zhu
Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China.
Lupei
L
Zhang
Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China.
Xue
X
Gao
Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China.
Yan
Y
Chen
Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China.
Junya
J
Li
Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China.
Huijiang
H
Gao
D000003:Abattoirs; D000818:Animals; D001842:Bone and Bones / Q000033:anatomy & histology / Q000378:metabolism*; D001947:Breeding; D002417:Cattle; D030541:Databases, Genetic; D005819:Genetic Markers; D055106:Genome-Wide Association Study; D006863:Hydrogen-Ion Concentration; D008460:Meat / Q000032:analysis*; D009929:Organ Size; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable
D005819:Genetic Markers