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No epistasis between the main effect loci were detected.> -wrap-foot> aChromosome number.
Of note, the issue of loci interaction is independent from consideration of main effect: loci that strongly interact may or may not be associated individually with the trait.
All epistatic interactions between the cytoplasmic genomic variation and nuclear loci (as labeled in Figure 2 ) are plotted as lines connecting the main effect loci as nodes.
Only three intQTL (int.13, int.107, and int. 42) overlap with the main effect loci in the same population (Lbn2.1c, Lbn3.2a, and Lbn18.1a [ Norgard et al. 2011]).
We did not extend this analysis to a full genome survey of all possible loci because these surveys do not account for existing main effect loci.
Among all detected QTLs, only 10 main effect loci overlapped for the same variable in both tissues: 1 for concB, 2 for concK, 1 for epiEx, 1 for galEx, 2 for catT, 1 for epiT, 1 for mDP and 1 for Ftranscis_T (see Figure 5 for some examples).
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A genome scan to identify main-effect loci affecting 24 growth-related traits revealed nine distinct QTL on six chromosomes.
We could also place robust candidate genes for several main-effect loci in an attempt to find the gene lying beneath the QTL.
In contrast, for the ColxKas population epistatic interactions are important, with heritabilities as high as those seen in individual main-effect loci (Additional File 2).
Only three rQTL overlap with main-effect loci, which were reported for this population in Norgard et al. (2011): r.4 for humerus/femur, r.23 for tibia/ulna, and r.28 for femur/humerus overlap with main-effect loci Lbn4.3 for femur and humerus, Lbn1.3 for tibia, and Lbn14.1 for femur and humerus.
These results show that there is one novel allele for each main-effect locus or one novel allele combination for each epistatic QTL.
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