Association Mapping: Critical Considerations Shift from Genotyping to Experimental Design

By S. Myles, Jason Peiffer, P. Brown, Elhan Ersoz, Zhiwu Zhang, D. Costich, Edward S. Buckler. The Plant Cell Online, 2009

843 citations recorded by the source corpus.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/ff1c58c4895ce35c43bfd4acdb1691ad57b4df64

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

Citations in the corpus

Genetic structure and domestication history of the grape (2011, background): “For this reason, we conclude that wellpowered GWA studies in the grape will require whole-genome sequencing, as in other high-diversity plants with rapid LD decay (19).”
Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm (2011, background): “Some alleles are not under selection in common growth conditions and, therefore, their frequency is low in the populatio”
Molecular marker-assisted breeding options for maize improvement in Asia (2010, background): “As suggested by Myles et al. (2009), researchers must be concerned with determining and using appropriate experimental designs that maximize the reliability of their phenotyping efforts.”
Marker-Assisted Plant Breeding: Principles and Practices (2015, background): “lation structure, and the genetic architecture of the traits of interest (Myles et al. 2009).”
Perspectives for Genomic Selection Applications and Research in Plants (2015, background): “, 2011), emphasis should be shifted to maximizing the value of expensive phenotypes (Myles et al., 2009).”
Zinc nutrition in wheat-based cropping systems (2017, methodology): “Quantitative trait loci are mapped using two methods viz. association and linkage mapping (Zhu et al. 2008; Myles et al. 2009).”
Genetic mapping of quantitative trait loci in crops (2017, background): “difference between the two methods will disappear [14].”
Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize (2011, background): “…and selection by breeders, complex patterns of genetic relatedness are common in maize association panels, generating numerous spurious associations (Yu and Buckler 2006; Zhu et al. 2008; Myles et al. 2009), which makes correcting spurious associations a major challenge for association mapping.”
Abiotic stresses, constraints and improvement strategies in chickpea (2014, background): “Therefore, it can be postulated that growing approaches such as MARS, GS and genome wise association (GWA) studies (Syvanen 2005, Myles et al. 2009, Rafalski 2010) would be more relevant than the family-based genetic linkage mapping because the former methods require phenotyping only once while…”
Field-based phenomics for plant genetics research (2012, background): “Practical application through genomic selection (Goddard nd Hayes, 2007; Jannink et al., 2010) or genome-wide associaion studies (Myles et al., 2009) will similarly involve phenotyping housands of genetically distinct lines (reference or association opulations) grown in replication across multiple…”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, positive): “Association mapping by screening for phenotype–genotype associations in a general population of individuals, whose degree of relatedness or pedigree is unknown, is also becoming more popular and useful in plant systems (Myles et al., 2009).”
Natural variations and genome-wide association studies in crop plants. (2014, background): “A matter requiring attention in crop GWAS is the need to account for the massive population structure, including weighing the trade-offs of increased false-negative and decreased false-positive rates from accounting for that structure (55, 77, 85, 112).”
Association Mapping in Plant Genomes (2012, background): “The mating system has profound effects on LD (Myles et al., 2009).”
Accuracy of Genomewide Selection for Different Traits with Constant Population Size, Heritability, and Number of Markers (2013, background): “While there has been much research on the inl uence of genetic architecture on QTL mapping (Holland, 2007) and association mapping (Myles et al., 2009), further studies are needed on why some traits are predicted more accurately than others in genomewide prediction (Meuwissen, 2012).”