scholarly journals Allelic association with SNPs: Metrics, populations, and the linkage disequilibrium map

2001 ◽  
Vol 17 (4) ◽  
pp. 255-262 ◽  
Author(s):  
A. Collins ◽  
S. Ennis ◽  
P. Taillon-Miller ◽  
P-Y. Kwok ◽  
N.E. Morton
Keyword(s):  
Linkage Disequilibrium ◽  
Allelic Association ◽  
Linkage Disequilibrium Map

scholarly journals A first-generation linkage disequilibrium map of human chromosome 22

Nature ◽  
2002 ◽  
Vol 418 (6897) ◽  
pp. 544-548 ◽  
Author(s):  
Elisabeth Dawson ◽  
Gonçalo R. Abecasis ◽  
Suzannah Bumpstead ◽  
Yuan Chen ◽  
Sarah Hunt ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Human Chromosome ◽  
First Generation ◽  
Chromosome 22 ◽  
Linkage Disequilibrium Map

Joint Linkage and Linkage Disequilibrium Mapping of Quantitative Trait Loci in Natural Populations

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 779-792 ◽  
Author(s):  
Rongling Wu ◽  
Chang-Xing Ma ◽  
George Casella
Keyword(s):  
Linkage Disequilibrium ◽  
Quantitative Trait Loci ◽  
Linkage Analysis ◽  
Quantitative Trait ◽  
Genome Mapping ◽  
Linkage Disequilibrium Mapping ◽  
Allelic Association ◽  
Mapping Strategy ◽  
Trait Loci ◽  
New Strategy

AbstractLinkage analysis and allelic association (also referred to as linkage disequilibrium) studies are two major approaches for mapping genes that control simple or complex traits in plants, animals, and humans. But these two approaches have limited utility when used alone, because they use only part of the information that is available for a mapping population. More recently, a new mapping strategy has been designed to integrate the advantages of linkage analysis and linkage disequilibrium analysis for genome mapping in outcrossing populations. The new strategy makes use of a random sample from a panmictic population and the open-pollinated progeny of the sample. In this article, we extend the new strategy to map quantitative trait loci (QTL), using molecular markers within the EM-implemented maximum-likelihood framework. The most significant advantage of this extension is that both linkage and linkage disequilibrium between a marker and QTL can be estimated simultaneously, thus increasing the efficiency and effectiveness of genome mapping for recalcitrant outcrossing species. Simulation studies are performed to test the statistical properties of the MLEs of genetic and genomic parameters including QTL allele frequency, QTL effects, QTL position, and the linkage disequilibrium of the QTL and a marker. The potential utility of our mapping strategy is discussed.

A Metric Linkage Disequilibrium Map of a Human Chromosome

2003 ◽  
Vol 67 (6) ◽  
pp. 487-494 ◽  
Author(s):  
W. J. Tapper ◽  
N. Maniatis ◽  
N. E. Morton ◽  
A. Collins
Keyword(s):  
Linkage Disequilibrium ◽  
Human Chromosome ◽  
Linkage Disequilibrium Map

Constructing Linkage Disequilibrium Map with Iterative Approach

2008 ◽  
Author(s):  
S. I. Ao ◽  
Sio-Iong Ao ◽  
Mahyar A. Amouzegar ◽  
Su-Shing Chen
Keyword(s):  
Linkage Disequilibrium ◽  
Iterative Approach ◽  
Linkage Disequilibrium Map

scholarly journals Inference of Population Genetic Structure and High Linkage Disequilibrium Among Alternaria spp. Collected from Tomato and Potato Using Genotyping by Sequencing

2019 ◽  
Author(s):  
Tika B. Adhikari ◽  
Brian J. Knaus ◽  
Niklaus J. Grünwald ◽  
Dennis Halterman ◽  
Frank J. Louws
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Plant Pathogens ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Allelic Association ◽  
Nucleotide Polymorphisms ◽  
Entire Genome ◽  
Genome Wide ◽  
A Genome

ABSTRACTGenotyping by sequencing (GBS) is considered a powerful tool to discover single nucleotide polymorphisms (SNPs), which are useful to characterize closely related genomes of plant species and plant pathogens. We applied GBS to determine genome-wide variations in a panel of 187 isolates of three closely related Alternaria spp. that cause diseases on tomato and potato in North Carolina (NC) and Wisconsin (WI). To compare genetic variations, reads were mapped to both A. alternata and A. solani draft reference genomes and detected dramatic differences in SNPs among them. Comparison of A. linariae and A. solani populations by principal component analysis revealed the first (83.8% of variation) and second (8.0% of variation) components contained A. linariae from tomato in NC and A. solani from potato in WI, respectively, providing evidence of population structure. Genetic differentiation (Hedrick’s G’ST) in A. linariae populations from Haywood, Macon, and Madison counties in NC were little or no differentiated (G’ST 0.0 - 0.2). However, A. linariae population from Swain county appeared to be highly differentiated (G’ST > 0.8). To measure the strength of the linkage disequilibrium (LD), we also calculated the allelic association between pairs of loci. Lewontin’s D (measures the fraction of allelic variations) and physical distances provided evidence of linkage throughout the entire genome, consistent with the hypothesis of non-random association of alleles among loci. Our findings provide new insights into the understanding of clonal populations on a genome-wide scale and microevolutionary factors that might play an important role in population structure. Although we found limited genetic diversity, the three Alternaria spp. studied here are genetically distinct and each species is preferentially associated with one host.

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