Predicting ascites incidence in a simulated altitude-challenge using single nucleotide polymorphisms identified in multi-generational genome wide association studies

Tarrant, Katy; Fulton, Janet E.; Lund, Ashlee R.; Rhoads, David B.; Anthony, Nicholas B.

doi:10.3382/ps/pey273

“…These SNPs are in the intergenic region, 3.5 kbp from the 3' end of the LRRTM4 gene. The exonuclease assay was used to genotype more than 600 archived DNA samples from REL birds previously phenotyped for AS susceptibility in the hypobaric chamber [30,34,35]. The observed genotype frequencies were in agreement with calculated genotype frequencies (computed from allele frequencies) consistent with Hardy Weinberg Equilibrium (HWE) which implies that the quantitative Polymerase Chain Reaction (qPCR) genotyping is valid, there are no significant issues with null alleles, and that the samples of DNA utilized was non-biased.…”

Section: Whole Genome Resequencing and Templated Assemblymentioning

confidence: 62%

“…None of the current regions reported above have appeared in any previous GWAS studies on AS [31][32][33][34]. Identification of the CPQ gene [35] and now LRRTM4 demonstrates WGR to be an effective and robust method for high-resolution mapping of QTLs for complex traits.…”

Section: Discussionmentioning

confidence: 93%

“…Multiple Single Nucleotide Polymorphism (SNP) panel based genome wide association studies (GWAS) were used to identify potential genetic markers on chromosome 1, 2, 4, 9, and Z for this disease [29][30][31][32][33][34]. Unfortunately, further genotyping or marker assisted selection have only shown a marginal/minimal association between these regions and AS (unpublished).…”

Section: Introductionmentioning

confidence: 99%

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Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing.

Parveen

¹

,

Jackson

²

,

Dey

³

et al. 2020

Preprint

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0

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Background Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. The association was confirmed through further genotyping in multiple broiler populations. Results The whole genome resequencing analyses have now been extended to the current chicken genome assembly. DNA samples were pooled according to gender and phenotype and the pools subjected to next generation sequencing. Loci were identified as clusters of single nucleotide polymorphisms where frequencies of the polymorphisms differed between resistant and susceptible chickens. The chickens are an unselected line descended from a commercial elite broiler line. Regions identified were specific to one or both genders. The data identify a total of 28 regions as potential quantitative trait loci for ascites. The genes from these regions have been associated with hypertensive-related traits in human association studies. One region on chicken chromosome 28 contains the LRRTM4 gene. Additional genotyping for the LRRTM4 region demonstrates an epistatic interaction with the CPQ region for ascites phenotype. Conclusions The 28 regions identified were not previously identified in a multi-generational genome wide association study using 60k Single Nucleotide Polymorphism panels. This work demonstrates the utility of whole genome resequencing as a cost effective, direct, and efficient method for identifying specific gene regions affecting complex traits. The approach is applicable to any organism with a genome assembly and requires no a priori assumptions.

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“…were used to elucidate the polygenic nature of ascites and identify potential genetic markers for breeding for resistance to this disease [29][30][31][32][33][34]. The analyses from these studies identified potential regions on chromosome 1, 2, 4, 9, and Z, as possibly associated with AS phenotype.…”

Section: Multiple Single Nucleotide Polymorphism (Snp) Panel Based Gementioning

confidence: 99%

Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing.

Parveen

¹

,

Jackson

²

,

Dey

³

et al. 2020

Preprint

Self Cite

0

View full text Add to dashboard Cite

Background Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. The association was confirmed through further genotyping in multiple broiler populations. Results The whole genome resequencing analyses have now been extended to the current chicken genome assembly. DNA samples were pooled according to gender and phenotype and the pools subjected to next generation sequencing. Loci were identified as clusters of single nucleotide polymorphisms where frequencies of the polymorphisms differed between resistant and susceptible chickens. The chickens are an unselected line descended from a commercial elite broiler line. Regions identified were specific to one or both genders. The data identify a total of 28 regions as potential quantitative trait loci for ascites. The genes from these regions have been associated with hypertensive-related traits in human association studies. One region on chicken chromosome 28 contains the LRRTM4 gene. Additional genotyping for the LRRTM4 region demonstrates an epistatic interaction with the CPQ region for ascites phenotype. Conclusions The 28 regions identified were not previously identified in a multi-generational genome wide association study using 60k Single Nucleotide Polymorphism panels. This work demonstrates the utility of whole genome resequencing as a cost effective, direct, and efficient method for identifying specific gene regions affecting complex traits. The approach is applicable to any organism with a genome assembly and requires no a priori assumptions.

show abstract

“…Multiple Single Nucleotide Polymorphism (SNP) panel based genome wide association studies (GWAS) were used to identify potential genetic markers on chromosome 1, 2, 4, 9, and Z for this disease [28][29][30][31][32][33]. Unfortunately, further genotyping or marker assisted selection have only shown a marginal/minimal association between these regions and AS (unpublished).…”

Section: Introductionmentioning

confidence: 99%

Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing

Parveen

¹

,

Jackson

²

,

Dey

³

et al. 2020

View full text Add to dashboard Cite

Background: Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. The association was confirmed through further genotyping in multiple broiler populations. Results: The whole genome resequencing analyses have now been extended to the current chicken genome assembly. DNA samples were pooled according to gender and phenotype and the pools subjected to next generation sequencing. Loci were identified as clusters of single nucleotide polymorphisms where frequencies of the polymorphisms differed between resistant and susceptible chickens. The chickens are an unselected line descended from a commercial elite broiler line. Regions identified were specific to one or both genders. The data identify a total of 28 regions as potential quantitative trait loci for ascites. The genes from these regions have been associated with hypertensive-related traits in human association studies. One region on chicken chromosome 28 contains the LRRTM4 gene. Additional genotyping for the LRRTM4 region demonstrates an epistatic interaction with the CPQ region for ascites phenotype. Conclusions: The 28 regions identified were not previously identified in a multi-generational genome wide association study using 60k Single Nucleotide Polymorphism panels. This work demonstrates the utility of whole genome resequencing as a cost effective, direct, and efficient method for identifying specific gene regions affecting complex traits. The approach is applicable to any organism with a genome assembly and requires no a priori assumptions.

show abstract

Predicting ascites incidence in a simulated altitude-challenge using single nucleotide polymorphisms identified in multi-generational genome wide association studies

Cited by 3 publications

References 39 publications

Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing.

Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing.

Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing.

Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing

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