Candidate genes and biological pathways associated with carcass quality traits in beef cattle

2013 ◽  
Vol 93 (3) ◽  
pp. 295-306 ◽  
Author(s):  
B. K. Karisa ◽  
J. Thomson ◽  
Z. Wang ◽  
H. L. Bruce ◽  
G. S. Plastow ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Association Analysis ◽  
Biological Pathways ◽  
Steroid Metabolism ◽  
Candidate Gene Approach ◽  
Carcass Quality ◽  
Quality Traits ◽  
Biological Processes ◽  
Positional Candidate

Karisa, B. K., Thomson, J., Wang, Z., Bruce, H. L., Plastow, G. S. and Moore, S. S. 2013. Candidate genes and biological pathways associated with carcass quality traits in beef cattle. Can. J. Anim. Sci. 93: 295–306. The objective of this study was to use the candidate gene approach to identify the genes associated with carcass quality traits in beef cattle steers at the University of Alberta Ranch at Kinsella, Canada. This approach involved identifying positional candidate genes and prioritizing them according to their functions into functional candidate genes before performing statistical association analysis. The positional candidate genes and single nucleotide polymorphisms (SNP) were identified from previously reported quantitative trait loci for component traits including body weight, average daily gain, metabolic weight, feed efficiency and energy balance. Positional candidate genes were then prioritized into functional candidate genes according to the associated gene ontology terms and their functions. A total of 116 genes were considered functional candidate genes and 117 functional SNPs were genotyped and used for multiple marker association analysis using ASReml®. Seven SNPs were significantly associated with various carcass quality traits (P≤0.005). The significant genes were associated with biological processes such as fat, glucose, protein and steroid metabolism, growth, energy utilization and DNA transcription and translation as inferred from the protein knowledgebase (UniprotKB). Gene network analysis indicated significant involvement of biological processes related to fat and steroid metabolism and regulation of transcription and translation of DNA.

Polymorphisms in positional candidate genes on BTA14 and BTA26 affect carcass quality in beef cattle

2009 ◽  
Vol 87 (8) ◽  
pp. 2475-2484 ◽  
Author(s):  
E. Marques ◽  
J. D. Nkrumah ◽  
E. L. Sherman ◽  
S. S. Moore
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Carcass Quality ◽  
Positional Candidate

scholarly journals Genome-wide association study to identify genomic regions and positional candidate genes associated with male fertility in beef cattle

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
H. Sweett ◽  
P. A. S. Fonseca ◽  
A. Suárez-Vega ◽  
A. Livernois ◽  
F. Miglior ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Male Fertility ◽  
Production Efficiency ◽  
Genome Wide Association Study ◽  
Gene Annotation ◽  
Enrichment Analysis ◽  
Single Step ◽  
Positional Candidate ◽  
Functional Candidate Gene

AbstractFertility plays a key role in the success of calf production, but there is evidence that reproductive efficiency in beef cattle has decreased during the past half-century worldwide. Therefore, identifying animals with superior fertility could significantly impact cow-calf production efficiency. The objective of this research was to identify candidate regions affecting bull fertility in beef cattle and positional candidate genes annotated within these regions. A GWAS using a weighted single-step genomic BLUP approach was performed on 265 crossbred beef bulls to identify markers associated with scrotal circumference (SC) and sperm motility (SM). Eight windows containing 32 positional candidate genes and five windows containing 28 positional candidate genes explained more than 1% of the genetic variance for SC and SM, respectively. These windows were selected to perform gene annotation, QTL enrichment, and functional analyses. Functional candidate gene prioritization analysis revealed 14 prioritized candidate genes for SC of which MAP3K1 and VIP were previously found to play roles in male fertility. A different set of 14 prioritized genes were identified for SM and five were previously identified as regulators of male fertility (SOD2, TCP1, PACRG, SPEF2, PRLR). Significant enrichment results were identified for fertility and body conformation QTLs within the candidate windows. Gene ontology enrichment analysis including biological processes, molecular functions, and cellular components revealed significant GO terms associated with male fertility. The identification of these regions contributes to a better understanding of fertility associated traits and facilitates the discovery of positional candidate genes for future investigation of causal mutations and their implications.

scholarly journals Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle

2020 ◽  
Author(s):  
Bingxing An ◽  
Lei Xu ◽  
Jiangwei Xia ◽  
Xiaoqiao Wang ◽  
Jian Miao ◽  
...  
Keyword(s):  
Body Size ◽  
Beef Cattle ◽  
Candidate Genes ◽  
Association Analysis ◽  
Growth Traits ◽  
Association Studies ◽  
Growth Stages ◽  
Genome Wide Association Studies ◽  
Trait Analysis ◽  
Multiple Association

Abstract Background: Body size traits as one of the main breeding selection criteria was widely used to monitor cattle growth and to evaluate the selection response. In this study, body size was defined as body height (BH), body length (BL), hip height (HH), heart size (HS), abdominal size (AS), and cannon bone size (CS). We performed genome-wide association studies (GWAS) of these traits over the course of three growth stages (6, 12 and 18 months after birth) using three statistical models, single-trait GWAS, multi-trait GWAS and LONG-GWAS. The Illumina Bovine HD 770K BeadChip was used to identify genomic single nucleotide polymorphisms (SNPs) in 1217 individuals. Results: In total, 19, 29, and 10 significant SNPs were identified by the three models, respectively. Among these, 21 genes were promising candidate genes, including SOX2, SNRPD1, RASGEF1B, EFNA5, PTBP1, SNX9, SV2C, PKDCC, SYNDIG1, AKR1E2, and PRIM2 identified by single-trait analysis; SLC37A1, LAP3, PCDH7, MANEA, and LHCGR identified by multi-trait analysis; and P2RY1, MPZL1, LINGO2, CMIP, and WSCD1 identified by LONG-GWAS. Conclusions: Multiple association analysis was performed for six growth traits at each growth stage. These findings offer valuable insights for the further investigation of potential genetic mechanism of growth traits in Simmental beef cattle.

scholarly journals Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle

2020 ◽  
Author(s):  
Bingxing An ◽  
Lei Xu ◽  
Jiangwei Xia ◽  
Xiaoqiao Wang ◽  
Jian Miao ◽  
...  
Keyword(s):  
Body Size ◽  
Beef Cattle ◽  
Candidate Genes ◽  
Association Analysis ◽  
Growth Traits ◽  
Association Studies ◽  
Growth Stages ◽  
Genome Wide Association Studies ◽  
Trait Analysis ◽  
Multiple Association

Abstract Background: Body size traits as one of the main breeding selection criteria was widely used to monitor cattle growth and to evaluate the selection response. In this study, body size was defined as body height (BH), body length (BL), hip height (HH), heart size (HS), abdominal size (AS), and cannon bone size (CS). We performed genome-wide association studies (GWAS) of these traits over the course of three growth stages (6, 12 and 18 months after birth) using three statistical models, single-trait GWAS, multi-trait GWAS and LONG-GWAS. The Illumina Bovine HD 770K BeadChip was used to identify genomic single nucleotide polymorphisms (SNPs) in 1217 individuals. Results: In total, 19, 29, and 10 significant SNPs were identified by the three models, respectively. Among these, 21 genes were promising candidate genes, including SOX2, SNRPD1, RASGEF1B, EFNA5, PTBP1, SNX9, SV2C, PKDCC, SYNDIG1, AKR1E2, and PRIM2 identified by single-trait analysis; SLC37A1, LAP3, PCDH7, MANEA, and LHCGR identified by multi-trait analysis; and P2RY1, MPZL1, LINGO2, CMIP, and WSCD1 identified by LONG-GWAS. Conclusions: Multiple association analysis was performed for six growth traits at each growth stage. These findings offer valuable insights for the further investigation of potential genetic mechanism of growth traits in Simmental beef cattle.

scholarly journals Carcass quality traits of beef cattle with different DGAT1 genotypes

2021 ◽  
Vol 624 ◽  
pp. 012148
Author(s):  
T A Sedykh ◽  
L A Kalashnikova ◽  
R S Gizatullin
Keyword(s):  
Beef Cattle ◽  
Carcass Quality ◽  
Quality Traits

scholarly journals Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle

2020 ◽  
Author(s):  
Bingxing An ◽  
Lei Xu ◽  
Jiangwei Xia ◽  
Xiaoqiao Wang ◽  
Jian Miao ◽  
...  
Keyword(s):  
Body Size ◽  
Beef Cattle ◽  
Candidate Genes ◽  
Association Analysis ◽  
Growth Traits ◽  
Association Studies ◽  
Growth Stages ◽  
Genome Wide Association Studies ◽  
Trait Analysis ◽  
Multiple Association

Abstract Background: Body size traits as one of the main breeding selection criteria was widely used to monitor cattle growth and to evaluate the selection response. In this study, body size was defined as body height (BH), body length (BL), hip height (HH), heart size (HS), abdominal size (AS), and cannon bone size (CS). We performed genome-wide association studies (GWAS) of these traits over the course of three growth stages (6, 12 and 18 months after birth) using three statistical models, single-trait GWAS, multi-trait GWAS and LONG-GWAS. The Illumina Bovine HD 770K BeadChip was used to identify genomic single nucleotide polymorphisms (SNPs) in 1217 individuals. Results: In total, 19, 29, and 10 significant SNPs were identified by the three models, respectively. Among these, 21 genes were promising candidate genes, including SOX2, SNRPD1, RASGEF1B, EFNA5, PTBP1, SNX9, SV2C, PKDCC, SYNDIG1, AKR1E2, and PRIM2 identified by single-trait analysis; SLC37A1, LAP3, PCDH7, MANEA, and LHCGR identified by multi-trait analysis; and P2RY1, MPZL1, LINGO2, CMIP, and WSCD1 identified by LONG-GWAS. Conclusions: Multiple association analysis was performed for six growth traits at each growth stage. These findings offer valuable insights for the further investigation of potential genetic mechanism of growth traits in Simmental beef cattle.

scholarly journals Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle

2020 ◽  
Author(s):  
Bingxing An ◽  
Lei Xu ◽  
Jiangwei Xia ◽  
Xiaoqiao Wang ◽  
Jian Miao ◽  
...  
Keyword(s):  
Body Size ◽  
Beef Cattle ◽  
Candidate Genes ◽  
Association Analysis ◽  
Growth Traits ◽  
Association Studies ◽  
Growth Stages ◽  
Genome Wide Association Studies ◽  
Trait Analysis ◽  
Multiple Association

Abstract Background: Body size traits as one of the main breeding selection criteria was widely used to monitor cattle growth and to evaluate the selection response. In this study, body size was defined as body height (BH), body length (BL), hip height (HH), heart size (HS), abdominal size (AS), and cannon bone size (CS). We performed genome-wide association studies (GWAS) of these traits over the course of three growth stages (6, 12 and 18 months after birth) using three statistical models, single-trait GWAS, multi-trait GWAS and LONG-GWAS. The Illumina Bovine HD 770K BeadChip was used to identify genomic single nucleotide polymorphisms (SNPs) in 1217 individuals. Results: In total, 19, 29, and 10 significant SNPs were identified by the three models, respectively. Among these, 21 genes were promising candidate genes, including SOX2, SNRPD1, RASGEF1B, EFNA5, PTBP1, SNX9, SV2C, PKDCC, SYNDIG1, AKR1E2, and PRIM2 identified by single-trait analysis; SLC37A1, LAP3, PCDH7, MANEA, and LHCGR identified by multi-trait analysis; and P2RY1, MPZL1, LINGO2, CMIP, and WSCD1 identified by LONG-GWAS. Conclusions: Multiple association analysis was performed for six growth traits at each growth stage. These findings offer valuable insights for the further investigation of potential genetic mechanism of growth traits in Simmental beef cattle.

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