Multi-trait GWAS using high-density genotypes identifies genes associated with body traits in Nile tilapia

Multi-trait GWAS using imputed high-density genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia

10.21203/rs.3.rs-48903/v3 ◽

2020 ◽

Author(s):

Grazyella Yoshida ◽

José Manuel Yáñez

Keyword(s):

Quantitative Trait Loci ◽

Candidate Genes ◽

Quantitative Trait ◽

Nile Tilapia ◽

Statistical Power ◽

Association Studies ◽

Genome Wide Association ◽

Whole Genome ◽

Genome Wide ◽

Trait Loci

Abstract Background: Body traits are generally controlled by several genes in vertebrates (i.e. polygenes), which in turn make them difficult to identify through association mapping. Increasing the power of association studies by combining approaches such as genotype imputation and multi-trait analysis improves the ability to detect quantitative trait loci associated with polygenic traits, such as body traits. Results: A multi-trait genome-wide association study (mtGWAS) was performed to identify quantitative trait loci (QTL) and genes associated with body traits in Nile tilapia (Oreochromos niloticus) using genotypes imputed to whole-genome sequence (WGS). To increase the statistical power of mtGWAS for the detection of genetic associations, summary statistics from single-trait genome-wide association studies (stGWAS) for eight different body traits recorded in 1,309 animals were used. The mtGWAS increased the statistical power from the original sample size from 13% to 44%, depending on the trait analyzed. The better resolution of the WGS data combined with the increased power of the mtGWAS approach, allowed the detection of significant markers not previously found in the stGWAS. Some lead single nucleotide polymorphisms (SNPs) were found within important functional candidate genes previously associated with growth-related traits. For instance, we identified SNP within the α1,6-fucosyltransferase (FUT8), solute carrier family 4 member 2 (SLC4A2), A disintegrin and metalloproteinase with thrombospondin motifs 9 (ADAMTS9) and heart development protein with EGF like domains 1 (HEG1) genes, which have been associated with average daily gain in sheep, osteopetrosis in cattle, chest size in goats, and growth and meat quality in sheep, respectively. Conclusions: The high-resolution mtGWAS presented, allowed identification of significant SNPs, linked to strong functional candidate genes, associated with body traits in Nile tilapia. These results provide further insights about the genetic variants and genes underlying body trait variation in cichlid fish with high accuracy and strong statistical support.

Download Full-text

Multi-trait GWAS using imputed high-density genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia

BMC Genomics ◽

10.1186/s12864-020-07341-z ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Grazyella M. Yoshida ◽

José M. Yáñez

Keyword(s):

Quantitative Trait Loci ◽

Candidate Genes ◽

Quantitative Trait ◽

Nile Tilapia ◽

Statistical Power ◽

Association Studies ◽

Genome Wide Association ◽

Whole Genome ◽

Genome Wide ◽

Trait Loci

Abstract Background Body traits are generally controlled by several genes in vertebrates (i.e. polygenes), which in turn make them difficult to identify through association mapping. Increasing the power of association studies by combining approaches such as genotype imputation and multi-trait analysis improves the ability to detect quantitative trait loci associated with polygenic traits, such as body traits. Results A multi-trait genome-wide association study (mtGWAS) was performed to identify quantitative trait loci (QTL) and genes associated with body traits in Nile tilapia (Oreochromis niloticus) using genotypes imputed to whole-genome sequences (WGS). To increase the statistical power of mtGWAS for the detection of genetic associations, summary statistics from single-trait genome-wide association studies (stGWAS) for eight different body traits recorded in 1309 animals were used. The mtGWAS increased the statistical power from the original sample size from 13 to 44%, depending on the trait analyzed. The better resolution of the WGS data, combined with the increased power of the mtGWAS approach, allowed the detection of significant markers which were not previously found in the stGWAS. Some of the lead single nucleotide polymorphisms (SNPs) were found within important functional candidate genes previously associated with growth-related traits in other terrestrial species. For instance, we identified SNP within the α1,6-fucosyltransferase (FUT8), solute carrier family 4 member 2 (SLC4A2), A disintegrin and metalloproteinase with thrombospondin motifs 9 (ADAMTS9) and heart development protein with EGF like domains 1 (HEG1) genes, which have been associated with average daily gain in sheep, osteopetrosis in cattle, chest size in goats, and growth and meat quality in sheep, respectively. Conclusions The high-resolution mtGWAS presented here allowed the identification of significant SNPs, linked to strong functional candidate genes, associated with body traits in Nile tilapia. These results provide further insights about the genetic variants and genes underlying body trait variation in cichlid fish with high accuracy and strong statistical support.

Download Full-text

Multi-trait GWAS using imputed high-density genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia

10.21203/rs.3.rs-48903/v2 ◽

2020 ◽

Author(s):

Grazyella Yoshida ◽

José Manuel Yáñez

Keyword(s):

Quantitative Trait Loci ◽

Candidate Genes ◽

Quantitative Trait ◽

Nile Tilapia ◽

Statistical Power ◽

Association Studies ◽

Genome Wide Association ◽

Whole Genome ◽

Genome Wide ◽

Trait Loci

Abstract Background: Body traits are generally controlled by several genes in vertebrates (i.e. polygenes), which in turn make them difficult to identify through association mapping. Increasing the power of association studies by combining approaches such as genotype imputation and multi-trait analysis improves the ability to detect quantitative trait loci associated with polygenic traits, such as body traits.Results: A multi-trait genome-wide association study (mtGWAS) was performed to identify quantitative trait loci (QTL) and genes associated with body traits in Nile tilapia (Oreochromos niloticus) using genotypes imputed to whole-genome sequence (WGS). To increase the statistical power of mtGWAS for the detection of genetic associations, summary statistics from single-trait genome-wide association studies (stGWAS) for eight different body traits recorded in 1,309 animals were used. The mtGWAS increased the statistical power from the original sample size from 13% to 44%, depending on the trait analyzed. The better resolution of the WGS data combined with the increased power of the mtGWAS approach, allowed the detection of significant markers not previously found in the stGWAS. Some lead single nucleotide polymorphisms (SNPs) were found within important functional candidate genes previously associated with growth-related traits. For instance, we identified SNP within the α1,6-fucosyltransferase (FUT8), solute carrier family 4 member 2 (SLC4A2), A disintegrin and metalloproteinase with thrombospondin motifs 9 (ADAMTS9) and heart development protein with EGF like domains 1 (HEG1) genes, which have been associated with average daily gain in sheep, osteopetrosis in cattle, chest size in goats, and growth and meat quality in sheep, respectively.Conclusions: The high-resolution mtGWAS presented, allowed identification of significant SNPs, linked to strong functional candidate genes, associated with body traits in Nile tilapia. These results provide further insights about the genetic variants and genes underlying body trait variation in cichlid fish with high accuracy and strong statistical support.

Download Full-text

Identification, deployment, and transferability of quantitative trait loci from genome-wide association studies in plants

Current Plant Biology ◽

10.1016/j.cpb.2020.100145 ◽

2020 ◽

Vol 24 ◽

pp. 100145 ◽

Cited By ~ 2

Author(s):

Mohsen Mohammadi ◽

Alencar Xavier ◽

Travis Beckett ◽

Savannah Beyer ◽

Liyang Chen ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Trait Loci

Download Full-text

Detection of quantitative trait loci in Bos indicus and Bos taurus cattle using genome-wide association studies

Genetics Selection Evolution ◽

10.1186/1297-9686-45-43 ◽

2013 ◽

Vol 45 (1) ◽

Cited By ~ 30

Author(s):

Sunduimijid Bolormaa ◽

Jennie E Pryce ◽

Kathryn E Kemper ◽

Ben J Hayes ◽

Yuandan Zhang ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Bos Taurus ◽

Association Studies ◽

Bos Indicus ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Trait Loci

Download Full-text

Genome-wide Association Study for Carcass Primal Cut Yields Using Single-step Bayesian Approach in Hanwoo Cattle

Frontiers in Genetics ◽

10.3389/fgene.2021.752424 ◽

2021 ◽

Vol 12 ◽

Author(s):

Masoumeh Naserkheil ◽

Hossein Mehrban ◽

Deukmin Lee ◽

Mi Na Park

Keyword(s):

Quantitative Trait Loci ◽

Candidate Genes ◽

Quantitative Trait ◽

Single Step ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Trait Loci ◽

Genomic Regions ◽

Hanwoo Cattle

The importance of meat and carcass quality is growing in beef cattle production to meet both producer and consumer demands. Primal cut yields, which reflect the body compositions of carcass, could determine the carcass grade and, consequently, command premium prices. Despite its importance, there have been few genome-wide association studies on these traits. This study aimed to identify genomic regions and putative candidate genes related to 10 primal cut traits, including tenderloin, sirloin, striploin, chuck, brisket, top round, bottom round, shank, flank, and rib in Hanwoo cattle using a single-step Bayesian regression (ssBR) approach. After genomic data quality control, 43,987 SNPs from 3,745 genotyped animals were available, of which 3,467 had phenotypic records for the analyzed traits. A total of 16 significant genomic regions (1-Mb window) were identified, of which five large-effect quantitative trait loci (QTLs) located on chromosomes 6 at 38–39 Mb, 11 at 21–22 Mb, 14 at 6–7 Mb and 26–27 Mb, and 19 at 26–27 Mb were associated with more than one trait, while the remaining 11 QTLs were trait-specific. These significant regions were harbored by 154 genes, among which TOX, FAM184B, SPP1, IBSP, PKD2, SDCBP, PIGY, LCORL, NCAPG, and ABCG2 were noteworthy. Enrichment analysis revealed biological processes and functional terms involved in growth and lipid metabolism, such as growth (GO:0040007), muscle structure development (GO:0061061), skeletal system development (GO:0001501), animal organ development (GO:0048513), lipid metabolic process (GO:0006629), response to lipid (GO:0033993), metabolic pathways (bta01100), focal adhesion (bta04510), ECM–receptor interaction (bta04512), fat digestion and absorption (bta04975), and Rap1 signaling pathway (bta04015) being the most significant for the carcass primal cut traits. Thus, identification of quantitative trait loci regions and plausible candidate genes will aid in a better understanding of the genetic and biological mechanisms regulating carcass primal cut yields.

Download Full-text