Polyploidy is widely recognized as a major source of novel genetic material, which can undergo mutation and selection to give rise to new or specialized functions to aid adaptation86,87. To assess the impact of both negative and positive selection on sites located in different-copy (one-, two...
which are required for the positive regulation of seed dormancy [50] (Additional file23: Table S20). For instance, the gene encoding an AP2/ethylene response factor (ERF1, Gh_D10G1537) was
Linking biology to treatment response through Networks Using the factors identified in the response prediction and their top enriched functions and tissue types (FDR < 0.2 from GSEA and CSEA, respectively), we further explored the underlying biology. For Afatinib, there were four factors associat...
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Inference and broad impact of genome-wide introgression Estimated mean uncorrected distance betweenL. granatensisandL. timiduswas 0.69%, and mean genome-wide FSTper site was 0.35. As expected given estimates of effective population size [34],L. timiduswas found to be more polymorphic thanL. gr...
To gain insight into the impact of repetitive elements on genome structure of dioeciousAmaranthusspecies, we subjected subsampled read pairs of the nine dioecious species to RepeatExplorer2 [57], a graph-based repetitive sequence clustering and characterization tool for Illumina raw reads. Subsampled...
(1:24). However, one could create a different reference sample using other cell lines. For more detailed recommendations and information related to creating a reference sample with low allele frequency variants, including the impact of the number of cell lines to admix, see Additional file3: ...
The deflation/inflation factor (λ) calculated for all association analyses was lower than 1.1 (Additional files1,2,3,4,5and6), which was considered acceptable and can be used on genomic control correction approach (GC). The P-values of SNPs along the chromosomes are shown in the form of...
Nielsen, J. B. et al. Biobank-driven genomic discovery yields new insight into atrial fibrillation biology.Nat. Genet.50, 1234–1239 (2018). CASPubMedPubMed CentralGoogle Scholar Inouye, M. et al. Genomic risk prediction of coronary artery disease in 480,000 adults: implications for primary...
(Fig.1a). While previous genetic mapping studies in allopolyploid wheat identified several genes where regulatory variants associated with adaptive and domestication traits21,22,23,24also change the relative levels of homoeolog expression, the overall impact of genomic variants on the population-scale ...