scholarly journals Multiple association analysis strategies identified loci and candidate genes for body size on three growth stages in Simmental beef cattle

2019 ◽  
Author(s):  
Bingxing An ◽  
Lei Xu ◽  
Jiangwei Xia ◽  
Tianpeng Chang ◽  
Xiaoqiao Wang ◽  
...  
Keyword(s):  
Body Size ◽  
Beef Cattle ◽  
Candidate Genes ◽  
Association Analysis ◽  
Growth Traits ◽  
Association Studies ◽  
Growth Stages ◽  
Genome Wide Association Studies ◽  
Multiple Association ◽  
Analysis Strategies

Abstract Background: Body size traits as one of the main breeding selection criteria have long since being widely used to monitor cattle growth and evaluate the selection response. Here the volume of body size is indicated by 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) for these traits to a broad spectrum of three growth stages (months 6, 12 and 18 after birth) under three statistical models: single-trait GWAS, multi-trait GWAS and LONG-GWAS. The whole genomic single nucleotide polymorphisms (SNPs) were obtained from the Illumina Bovine HD 770K BeadChip genotype on 1217 individuals. Results: In total, 19, 29, and 10 significant SNPs were identified by the three models, respectively. While 21 genes among in these loci appeared to be promising candidate genes, including SOX2, SNRPD1, RASGEF1B, EFNA5, PTBP1, SNX9, SV2C, PKDCC, SYNDIG1, AKR1E2 and PRIM2 detected by single-trait analyze; SLC37A1, LAP3, PCDH7, MANEA and LHCGR detected by multi-trait analyze; P2RY1, MPZL1, LINGO2, CMIP and WSCD1 detected by LONG-GWAS. Conclusions: Multiple association analysis strategies were performed for six growth traits on each stage. This research could offer valuable insights to further explore the potential 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 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 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.

Genome‐wide association studies revealed candidate genes for tail fat deposition and body size in the Hulun Buir sheep

2019 ◽  
Vol 136 (5) ◽  
pp. 362-370 ◽  
Author(s):  
Tongyu Zhang ◽  
Hongding Gao ◽  
Goutam Sahana ◽  
Yanjun Zan ◽  
Hongying Fan ◽  
...  
Keyword(s):  
Body Size ◽  
Candidate Genes ◽  
Association Studies ◽  
Fat Deposition ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals Association Analysis of Salt Tolerance in Asiatic cotton (Gossypium arboretum) with SNP Markers

2019 ◽  
Vol 20 (9) ◽  
pp. 2168 ◽  
Author(s):  
Tussipkan Dilnur ◽  
Zhen Peng ◽  
Zhaoe Pan ◽  
Koffi Palanga ◽  
Yinhua Jia ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Candidate Genes ◽  
Association Analysis ◽  
Association Studies ◽  
Snp Markers ◽  
Stem Length ◽  
Tolerance Index ◽  
Genome Wide Association Studies ◽  
Asiatic Cotton ◽  
Fundamental Information

Salinity is not only a major environmental factor which limits plant growth and productivity, but it has also become a worldwide problem. However, little is known about the genetic basis underlying salt tolerance in cotton. This study was carried out to identify marker-trait association signals of seven salt-tolerance-related traits and one salt tolerance index using association analysis for 215 accessions of Asiatic cotton. According to a comprehensive index of salt tolerance (CIST), 215 accessions were mainly categorized into four groups, and 11 accessions with high salinity tolerance were selected for breeding. Genome-wide association studies (GWAS) revealed nine SNP rich regions significantly associated with relative fresh weight (RFW), relative stem length (RSL), relative water content (RWC) and CIST. The nine SNP rich regions analysis revealed 143 polymorphisms that distributed 40 candidate genes and significantly associated with salt tolerance. Notably, two SNP rich regions on chromosome 7 were found to be significantly associated with two salinity related traits, RFW and RSL, by the threshold of −log10P ≥ 6.0, and two candidate genes (Cotton_A_37775 and Cotton_A_35901) related to two key SNPs (Ca7_33607751 and Ca7_77004962) were possibly associated with salt tolerance in G. arboreum. These can provide fundamental information which will be useful for future molecular breeding of cotton, in order to release novel salt tolerant cultivars.

scholarly journals Genome-Wide Association Studies Reveal Neurological Genes for Dog Herding, Predation, Temperament, and Trainability Traits

2021 ◽  
Vol 8 ◽  
Author(s):  
Shuwen Shan ◽  
Fangzheng Xu ◽  
Bertram Brenig
Keyword(s):  
Body Size ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Nervous System Development ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Behavioral Traits ◽  
Genome Wide ◽  
Dog Breed

Genome-wide association study (GWAS) using dog breed standard values as phenotypic measurements is an efficient way to identify genes associated with morphological and behavioral traits. As a result of strong human purposeful selections, several specialized behavioral traits such as herding and hunting have been formed in different modern dog breeds. However, genetic analyses on this topic are rather limited due to the accurate phenotyping difficulty for these complex behavioral traits. Here, 268 dog whole-genome sequences from 130 modern breeds were used to investigate candidate genes underlying dog herding, predation, temperament, and trainability by GWAS. Behavioral phenotypes were obtained from the American Kennel Club based on dog breed standard descriptions or groups (conventional categorization of dog historical roles). The GWAS results of herding behavior (without body size as a covariate) revealed 44 significantly associated sites within five chromosomes. Significantly associated sites on CFA7, 9, 10, and 20 were located either in or near neuropathological or neuronal genes including THOC1, ASIC2, MSRB3, LLPH, RFX8, and CHL1. MSRB3 and CHL1 genes were reported to be associated with dog fear. Since herding is a restricted hunting behavior by removing killing instinct, 36 hounds and 55 herding dogs were used to analyze predation behavior. Three neuronal-related genes (JAK2, MEIS1, and LRRTM4) were revealed as candidates for predation behavior. The significantly associated variant of temperament GWAS was located within ACSS3 gene. The highest associated variant in trainability GWAS is located on CFA22, with no variants detected above the Bonferroni threshold. Since dog behaviors are correlated with body size, we next incorporate body mass as covariates into GWAS; and significant signals around THOC1, MSRB3, LLPH, RFX8, CHL1, LRRTM4, and ACSS3 genes were still detected for dog herding, predation, and temperament behaviors. In humans, these candidate genes are either involved in nervous system development or associated with mental disorders. In conclusion, our results imply that these neuronal or psychiatric genes might be involved in biological processes underlying dog herding, predation, and temperament behavioral traits.

scholarly journals Genome-wide association studies for growth traits in broilers

2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Dachang Dou ◽  
Linyong Shen ◽  
Jiamei Zhou ◽  
Zhiping Cao ◽  
Peng Luan ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Candidate Genes ◽  
Rapid Growth ◽  
Genetic Parameters ◽  
Growth Traits ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Multiple Methods ◽  
Genome Wide

Abstract Background The identification of markers and genes for growth traits may not only benefit for marker assist selection /genomic selection but also provide important information for understanding the genetic foundation of growth traits in broilers. Results In the current study, we estimated the genetic parameters of eight growth traits in broilers and carried out the genome-wide association studies for these growth traits. A total of 113 QTNs discovered by multiple methods together, and some genes, including ACTA1, IGF2BP1, TAPT1, LDB2, PRKCA, TGFBR2, GLI3, SLC16A7, INHBA, BAMBI, APCDD1, GPR39, and GATA4, were identified as important candidate genes for rapid growth in broilers. Conclusions The results of this study will provide important information for understanding the genetic foundation of growth traits in broilers.

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