title: Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle.
abstract: Average daily gain (ADG) is the most economically important trait in beef cattle industry. Using genome-wide association study (GWAS) approaches, previous studies have identified several causal variants within the PLAG1, NCAPG and LCORL genes for ADG in cattle. Multi-strategy GWASs were implemented in this study to improve detection and to explore the causal genes and regions. In this study, we conducted GWASs based on the genotypes of 1,173 Simmental cattle. In the SNP-based GWAS, the most significant SNPs (rs109303784 and rs110058857, P = 1.78 × 10-7) were identified in the NCAPG intron on BTA6 and explained 4.01% of the phenotypic variance, and the independent and significant SNP (rs110406669, P = 5.18 × 10-6) explained 3.32% of the phenotypic variance. Similarly, in the haplotype-based GWAS, the most significant haplotype block, Hap-6-N1416 (P = 2.56 × 10-8), spanned 12.7 kb on BTA6 and explained 4.85% of the phenotypic variance. Also, in the gene-based GWAS, seven significant genes were obtained which included DCAF16 and NCAPG. Moreover, analysis of the transcript levels confirmed that transcripts abundance of NCAPG (P = 0.046) and DCAF16 (P = 0.046) were significantly correlated with the ADG trait. Overall, our results from the multi-strategy GWASs revealed the DCAF16-NCAPG region to be a susceptibility locus for ADG in cattle.
authors.affiliation: Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
authors.forename: Wengang
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
authors.forename: Junya
authors.initials: J
authors.lastname: Li
authors.affiliation: Animal Science and Technology College, Beijing University of Agriculture (BUA), Beijing 102206, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
authors.forename: Lupei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
authors.forename: Lingyang
authors.initials: L
authors.lastname: Xu
authors.affiliation: Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
authors.forename: Xue
authors.initials: X
authors.lastname: Gao
authors.affiliation: Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Zhu
authors.affiliation: Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
authors.forename: Huijiang
authors.initials: H
authors.lastname: Gao
authors.affiliation: Animal Science and Technology College, Beijing University of Agriculture (BUA), Beijing 102206, China.
authors.forename: Hemin
authors.initials: H
authors.lastname: Ni
authors.affiliation: Cattle Genetics and Breeding Group, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Chen
mesh_terms: D000818:Animals; D002352:Carrier Proteins / Q000235:genetics*; D002417:Cattle; D018797:Cell Cycle Proteins / Q000235:genetics*; D002874:Chromosome Mapping; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D006239:Haplotypes; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D015430:Weight Gain / Q000235:genetics*
chemical_list: D002352:Carrier Proteins; D018797:Cell Cycle Proteins