scholarly journals Quantitative trait loci associated with murine central corneal thickness

2010 ◽  
Vol 42 (2) ◽  
pp. 281-286 ◽  
Author(s):  
Geoffrey D. Lively ◽  
Demelza Koehn ◽  
Adam Hedberg-Buenz ◽  
Kai Wang ◽  
Michael G. Anderson
Keyword(s):  
Quantitative Trait ◽  
Central Corneal Thickness ◽  
Genetic Basis ◽  
Phenotypic Variability ◽  
Corneal Thickness ◽  
Biological Significance ◽  
Chromosome 7 ◽  
Structural Support ◽  
Trait Locus ◽  
Lines Of Evidence

The cornea is a specialized transparent tissue responsible for refracting light, serving as a protective barrier, and lending structural support to eye shape. Given its importance, the cornea exhibits a surprising amount of phenotypic variability in some traits, including central corneal thickness (CCT). More than a mere anatomic curiosity, differences in CCT have recently been associated with risk for glaucoma. Although multiple lines of evidence support a strong role for heredity in regulating CCT, the responsible genes remain unknown. To better understand the genetic basis of CCT variability, we conducted a genomewide quantitative trait locus (QTL) analysis with (C57BLKS/J × SJL/J) F2mice. This experiment identified a locus, Cctq1 (central corneal thickness QTL 1) on chromosome 7 (Chr 7; peak, 105 Mb), that is significantly associated with CCT. To independently test the biological significance of these results, (C57BLKS/J × NZB/B1NJ) F2mice were generated and analyzed for associations with Chr 7. This experiment identified a significant association at 131 Mb. Furthermore, low-generation congenic mice in which the Chr 7 QTL interval from the SJL strain was transferred onto the KS background had CCT values significantly higher than inbred KS mice. These results demonstrate that the genetic dependence of CCT in mice is a multigenic trait, which in these contexts is significantly regulated by a region on Chr 7. Future identification of the genes for these QTL will provide improved understanding of the processes regulating CCT and the pathophysiology of glaucoma.

scholarly journals Tyr is Responsible for the Cctq1a QTL and Links Developmental Environment to Central Corneal Thickness Determination

2021 ◽  
Author(s):  
Kacie J Meyer ◽  
Demelza R Larson ◽  
S Scott Whitmore ◽  
Carly J van der Heide ◽  
Adam Hedberg-Buenz ◽  
...  
Keyword(s):  
Quantitative Trait ◽  
Central Corneal Thickness ◽  
Light Exposure ◽  
Corneal Thickness ◽  
Causative Gene ◽  
Direct Function ◽  
Multiple Alleles ◽  
Albino Mice ◽  
Trait Locus ◽  
Derivatives Of

Central corneal thickness is a quantitative trait with important associations to human health. In a phenotype-driven approach studying corneal thickness of congenic derivatives of C57BLKS/J and SJL/J mice, the critical region for a quantitative trait locus influencing corneal thickness, Cctq1a, was delimited to a 10-gene interval. Exome sequencing, RNAseq, and studying independent mutations eliminated multiple candidate genes and confirmed one. Though the causative gene, Tyr, has no obvious direct function in the transparent cornea, studies with multiple alleles on matched genetic backgrounds, both in isolation and genetic complementation crosses, confirmed allelism of Tyr-Cctq1a; albino mice lacking Tyr function had thin corneas. Albino mice also had increased axial length. Because albinism exposes eyes to increased light, the effect of dark-rearing was tested and found to rescue central corneal thickness. In sum, the results point to an epiphenomenon; developmental light exposure interacts with genotype as an important determinate of adult corneal thickness.

scholarly journals Linkage mapping of quantitative trait loci for fiber yield and its related traits in the population derived from cultivated ramie and wild B. nivea var. tenacissima

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Zheng Zeng ◽  
Yanzhou Wang ◽  
Chan Liu ◽  
Xiufeng Yang ◽  
Hengyun Wang ◽  
...  
Keyword(s):  
Quantitative Trait ◽  
Linkage Mapping ◽  
Genetic Basis ◽  
Natural Fiber ◽  
Stem Bark ◽  
High Yield ◽  
Fiber Yield ◽  
Wild Allele ◽  
Trait Locus ◽  
Genomic Regions

AbstractRamie is an important natural fiber crop, and the fiber yield and its related traits are the most valuable traits in ramie production. However, the genetic basis for these traits is still poorly understood, which has dramatically hindered the breeding of high yield in this fiber crop. Herein, a high-density genetic map with 6,433 markers spanning 2476.5 cM was constructed using a population derived from two parents, cultivated ramie Zhongsizhu 1 (ZSZ1) and its wild progenitor B. nivea var. tenacissima (BNT). The fiber yield (FY) and its four related traits—stem diameter (SD) and length (SL), stem bark weight (BW) and thickness (BT)—were performed for quantitative trait locus (QTL) analysis, resulting in a total of 47 QTLs identified. Forty QTLs were mapped into 12 genomic regions, thus forming 12 QTL clusters. Among 47 QTLs, there were 14 QTLs whose wild allele from BNT was beneficial. Interestingly, all QTLs in Cluster 10 displayed overdominance, indicating that the region of this cluster was likely heterotic loci. In addition, four fiber yield-related genes underwent positive selection were found either to fall into the FY-related QTL regions or to be near to the identified QTLs. The dissection of FY and FY-related traits not only improved our understanding to the genetic basis of these traits, but also provided new insights into the domestication of FY in ramie. The identification of many QTLs and the discovery of beneficial alleles from wild species provided a basis for the improvement of yield traits in ramie breeding.

Identification of a new quantitative trait locus on Chromosome 7 controlling disease severity of collagen-induced arthritis in rats

1999 ◽  
Vol 49 (9) ◽  
pp. 787-791 ◽  
Author(s):  
Svetlana V. Dracheva ◽  
Elaine F. Remmers ◽  
Pércio S. Gulko ◽  
Yutaka Kawahito ◽  
Ryan E. Longman ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Disease Severity ◽  
Quantitative Trait ◽  
Chromosome 7 ◽  
Collagen Induced Arthritis ◽  
Trait Locus

scholarly journals Barcoded Bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast

2021 ◽  
Author(s):  
Alex N. Nguyen Ba ◽  
Katherine R. Lawrence ◽  
Artur Rego-Costa ◽  
Shreyas Gopalakrishnan ◽  
Daniel Temko ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Qtl Mapping ◽  
Quantitative Trait ◽  
Complex Traits ◽  
Large Scale ◽  
Genetic Basis ◽  
Association Studies ◽  
Model Organisms ◽  
Genome Wide Association Studies ◽  
Trait Locus

Mapping the genetic basis of complex traits is critical to uncovering the biological mechanisms that underlie disease and other phenotypes. Genome-wide association studies (GWAS) in humans and quantitative trait locus (QTL) mapping in model organisms can now explain much of the observed heritability in many traits, allowing us to predict phenotype from genotype. However, constraints on power due to statistical confounders in large GWAS and smaller sample sizes in QTL studies still limit our ability to resolve numerous small-effect variants, map them to causal genes, identify pleiotropic effects across multiple traits, and infer non-additive interactions between loci (epistasis). Here, we introduce barcoded bulk quantitative trait locus (BB-QTL) mapping, which allows us to construct, genotype, and phenotype 100,000 offspring of a budding yeast cross, two orders of magnitude larger than the previous state of the art. We use this panel to map the genetic basis of eighteen complex traits, finding that the genetic architecture of these traits involves hundreds of small-effect loci densely spaced throughout the genome, many with widespread pleiotropic effects across multiple traits. Epistasis plays a central role, with thousands of interactions that provide insight into genetic networks. By dramatically increasing sample size, BB-QTL mapping demonstrates the potential of natural variants in high-powered QTL studies to reveal the highly polygenic, pleiotropic, and epistatic architecture of complex traits.Significance statementUnderstanding the genetic basis of important phenotypes is a central goal of genetics. However, the highly polygenic architectures of complex traits inferred by large-scale genome-wide association studies (GWAS) in humans stand in contrast to the results of quantitative trait locus (QTL) mapping studies in model organisms. Here, we use a barcoding approach to conduct QTL mapping in budding yeast at a scale two orders of magnitude larger than the previous state of the art. The resulting increase in power reveals the polygenic nature of complex traits in yeast, and offers insight into widespread patterns of pleiotropy and epistasis. Our data and analysis methods offer opportunities for future work in systems biology, and have implications for large-scale GWAS in human populations.

scholarly journals Limited genetic parallels underlie convergent evolution of quantitative pattern variation in mimetic butterflies

2020 ◽  
Author(s):  
Hannah E. Bainbridge ◽  
Melanie N. Brien ◽  
Carlos Morochz ◽  
Patricio A. Salazar ◽  
Pasi Rastas ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Qtl Analysis ◽  
Quantitative Trait ◽  
Convergent Evolution ◽  
Genetic Basis ◽  
Major Effect ◽  
Multivariate Approach ◽  
Trait Variation ◽  
Heliconius Melpomene ◽  
Trait Locus

AbstractMimetic systems allow us to address the question of whether the same genes control similar phenotypes in different species. Although widespread parallels have been found for major effect loci, much less is known about genes that control quantitative trait variation. In this study, we identify and compare the loci that control subtle changes in the size and shape of forewing pattern elements in two Heliconius butterfly co-mimics. We use quantitative trait locus (QTL) analysis with a multivariate phenotyping approach to map the variation in red pattern elements across the whole forewing surface of Heliconius erato and Heliconius melpomene. These results are compared to a QTL analysis of univariate trait changes, and show that our resolution for identifying small effect loci is improved with the multivariate approach. QTL likely corresponding to the known patterning gene optix were found in both species but otherwise, a remarkably low level of genetic parallelism was found. This lack of similarity indicates that the genetic basis of convergent traits may not be as predictable as assumed from studies that focus solely on Mendelian traits.

scholarly journals Genetic Basis of Climatic Adaptation in Scots Pine by Bayesian Quantitative Trait Locus Analysis

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1309-1322 ◽  
Author(s):  
Päivi Hurme ◽  
Mikko J Sillanpää ◽  
Elja Arjas ◽  
Tapani Repo ◽  
Outi Savolainen
Keyword(s):  
Quantitative Trait Locus ◽  
Scots Pine ◽  
Quantitative Trait ◽  
Genetic Basis ◽  
Natural Populations ◽  
Backcross Progeny ◽  
Mapping Method ◽  
Frost Hardiness ◽  
Bud Set ◽  
Trait Locus

Abstract We examined the genetic basis of large adaptive differences in timing of bud set and frost hardiness between natural populations of Scots pine. As a mapping population, we considered an “open-pollinated backcross” progeny by collecting seeds of a single F1 tree (cross between trees from southern and northern Finland) growing in southern Finland. Due to the special features of the design (no marker information available on grandparents or the father), we applied a Bayesian quantitative trait locus (QTL) mapping method developed previously for outcrossed offspring. We found four potential QTL for timing of bud set and seven for frost hardiness. Bayesian analyses detected more QTL than ANOVA for frost hardiness, but the opposite was true for bud set. These QTL included alleles with rather large effects, and additionally smaller QTL were supported. The largest QTL for bud set date accounted for about a fourth of the mean difference between populations. Thus, natural selection during adaptation has resulted in selection of at least some alleles of rather large effect.

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