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Primarily as a result of very low LD in wild A. Gambiae, LD-based association mapping is challenging, but is feasible at least for major effect variants, especially where LD is enhanced by selective sweeps.
Our data illustrate that association mapping is difficult but feasible for wild A. gambiae populations, at least for major effect variants and especially, where LD is enhanced by selective sweeps.
Another interesting opportunity is the proposition of putative candidate genes for major effect QTLs.
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Oleuropein is the main secoiridoid, representing up to the 82% of total biophenols, known as the bitter principle of olives and responsible for major effects on human health and for releasing phytoalexins against plant pathogens [ 10].
Some of the observed changes may account for major effects on ethylene biosynthetic flux, e.g. the upregulation of a cystathionine γ-synthase, which catalyzes the first committed step in methionine biosynthesis and whose role as a key step in the regulation of ethylene metabolism has been proven in transgenic tobacco plants overexpressing a truncated cystathionine γ-synthase gene [ 40].
Linkage analysis is a useful method when looking for genes of major effect, especially if the same genes are involved in different families.
For major-effect QTLs, the LOD threshold was obtained based on a permutation test (1000 permutations, P = 0.05) for each dataset.
A dichotomous test of the extreme phenotype strains should reveal likely candidates for major-effect genes.
The genetic variants and trait-associated SNPs identified in this study will be useful for soybean cultivar improvement, especially for major-effect loci associated with PH that may have great potential for soybean yield improvement.
We and others have developed "nontemplate" GWA analyses to address highly heritable complex phenotypes for which there is little evidence for many genes of major effect.
We then reconducted GWAS for each trait with MLMM-identified SNPs included as covariates in the unified mixed linear model for better control of major effect loci.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com