Models and Tests of Linkage and Association Studies of Quantitative Trait Locus for Multi-Allele Marker Loci

2002 ◽  
Vol 53 (3) ◽  
pp. 130-145 ◽  
Author(s):  
Ruzong Fan ◽  
Joanna Floros ◽  
Momiao Xiong
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Association Studies ◽  
Marker Loci ◽  
Trait Locus

Identification of RAPD markers for percent hull in oat

Genome ◽  
1997 ◽  
Vol 40 (6) ◽  
pp. 873-878 ◽  
Author(s):  
P. S. Ronald ◽  
G. A. Penner ◽  
P. D. Brown ◽  
A. Brûlé-Babel
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Genetic Factors ◽  
Bulked Segregant Analysis ◽  
Multiple Time ◽  
Test Statistics ◽  
Marker Loci ◽  
Correct Determination ◽  
Trait Locus

Percent hull is an important physical parameter of oat grain quality, but it is affected by environment. Multiple time-consuming evaluations are required to obtain a correct determination of phenotype. The application of marker-assisted selection for the genes involved would greatly simplify the identification of desirable oat genotypes. Bulked segregant analysis, with selected progeny lines derived from a cross between Cascade and AC Marie (30 and 23% hull, respectively), was used to identify randomly amplified polymorphic DNA markers linked to genetic factors controlling primary kernel hull percentage in oat. Twelve polymorphisms, identified between bulks, were tested for linkage to genetic factors controlling hull percentage by genotyping 80 randomly selected F2-derived F8 lines from the progeny population. Three markers showed significant test statistics for quantitative trait locus effects, when tested with primary kernel percent hull data from two environments. Together, the unlinked marker loci OPC13800, OPD20600, and OPK71300 explained approximately 41% of the genetic variance in primary kernel percent hull, after accounting for the main effect of environment.Key words: Avena sativa, hull percentage, bulked segregant analysis, quantitative 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 Submergence Tolerance in Rice: Review of Mechanism, Breeding and, Future Prospects

2020 ◽  
Vol 12 (4) ◽  
pp. 1632 ◽  
Author(s):  
Yusuff Oladosu ◽  
Mohd Y. Rafii ◽  
Fatai Arolu ◽  
Samuel Chibuike Chukwu ◽  
Ismaila Muhammad ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Association Studies ◽  
Stem Elongation ◽  
Genome Wide Association Studies ◽  
Submergence Tolerance ◽  
Natural Ecosystems ◽  
Rice Varieties ◽  
Affected Plant ◽  
Trait Locus

Flooding or submergence is one of the major environmental stressors affecting many man-made and natural ecosystems worldwide. The increase in the frequency and duration of heavy rainfall due to climate change has negatively affected plant growth and development, which eventually causes the death of plants if it persists for days. Most crops, especially rice, being a semi-aquatic plant, are greatly affected by flooding, leading to yield losses each year. Genetic variability in the plant response to flooding includes the quiescence scheme, which allows underwater endurance of a prolonged period, escape strategy through stem elongation, and alterations in plant architecture and metabolism. Investigating the mechanism for flooding survival in wild species and modern rice has yielded significant insight into developmental, physiological, and molecular strategies for submergence and waterlogging survival. Significant progress in the breeding of submergence tolerant rice varieties has been made during the last decade following the successful identification and mapping of a quantitative trait locus for submergence tolerance, designated as SUBMERGENCE 1 (SUB1) from the FR13A landrace. Using marker-assisted backcrossing, the SUB1 QTL (quantitative trait locus) has been incorporated into many elite varieties within a short time and with high precision as compared with conventional breeding methods. Despite the advancement in submergence tolerance, for future studies, there is a need for practical approaches exploring genome-wide association studies (GWA) and QTL in combination with specific tolerance traits, such as drought, salinity, disease and insect resistance.

A Quantitative Trait Locus for Body Fat on Chromosome 1q43 in French Canadians: Linkage and Association Studies*

Obesity ◽  
2006 ◽  
Vol 14 (9) ◽  
pp. 1605-1615 ◽  
Author(s):  
Brahim Aissani ◽  
Louis Perusse ◽  
Gilles Lapointe ◽  
Yvon C. Chagnon ◽  
Luigi Bouchard ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Body Fat ◽  
Quantitative Trait ◽  
Association Studies ◽  
French Canadians ◽  
Trait Locus

scholarly journals Defining a rat blood pressure quantitative trait locus to a <81.8 kb congenic segment: comprehensive sequencing and renal transcriptome analysis

2010 ◽  
Vol 42A (2) ◽  
pp. 153-161 ◽  
Author(s):  
K. Gopalakrishnan ◽  
J. Saikumar ◽  
C. G. Peters ◽  
S. Kumarasamy ◽  
P. Farms ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Quantitative Trait Locus ◽  
Transcriptome Analysis ◽  
Quantitative Trait ◽  
Congenic Strain ◽  
Association Studies ◽  
Chromosome 9 ◽  
Genome Wide Association Studies ◽  
Congenic Strains ◽  
Trait Locus

Evidence from multiple linkage and genome-wide association studies suggest that human chromosome 2 (HSA2) contains alleles that influence blood pressure (BP). Homologous to a large segment of HSA2 is rat chromosome 9 (RNO9), to which a BP quantitative trait locus (QTL) was previously mapped. The objective of the current study was to further resolve this BP QTL. Eleven congenic strains with introgressed segments spanning <81.8 kb to <1.33 Mb were developed by introgressing genomic segments of RNO9 from the Dahl salt-resistant (R) rat onto the genome of the Dahl salt-sensitive (S) rat and tested for BP. The congenic strain with the shortest introgressed segment spanning <81.8 kb significantly lowered BP of the hypertensive S rat by 25 mmHg and significantly increased its mean survival by 45 days. In contrast, two other congenic strains had increased BP compared with the S. We focused on the <81.8 kb congenic strain, which represents the shortest genomic segment to which a BP QTL has been mapped to date in any species. Sequencing of this entire region in both S and R rats detected 563 variants. The region did not contain any known or predicted rat protein coding genes. Furthermore, a whole genome renal transcriptome analysis between S and the <81.8 kb S.R congenic strain revealed alterations in several critical genes implicated in renal homeostasis. Taken together, our results provide the basis for future studies to examine the relationship between the candidate variants within the QTL region and the renal differentially expressed genes as potential causal mechanisms for BP regulation.

scholarly journals Genetic architecture of growth traits in Populus revealed by integrated quantitative trait locus ( QTL ) analysis and association studies

2015 ◽  
Vol 209 (3) ◽  
pp. 1067-1082 ◽  
Author(s):  
Qingzhang Du ◽  
Chenrui Gong ◽  
Qingshi Wang ◽  
Daling Zhou ◽  
Haijiao Yang ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Qtl Analysis ◽  
Quantitative Trait ◽  
Genetic Architecture ◽  
Growth Traits ◽  
Association Studies ◽  
Trait Locus
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