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. 2023 Aug 17;14:4990. doi: 10.1038/s41467-023-40778-w

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — a Genomic region at and nearby the 200 kb HS1 window (12.4–12.6 Mb) on chromosome 1 showing the extent of the introgressed R haplotype in A-NIL-HS1^RR and B-NIL-HS1^RR (legend, upper left). The numbers of genes within the introgressed regions are indicated at the bottom. b Venn diagram showing the number and overlap of differentially expressed genes (adj-p < 0.01, and see Methods) in the comparison of A-NIL-HS1^RR versus A-NIL-HS1^SS (denoted A-NIL-HS1), B-NIL-HS1^RR versus B-NIL-HS1^SS (denoted B-NIL-HS1), and those genes with trans control originating from HS1 as determined by eQTL mapping (denoted eQTL-HS1). Numbers of detoxification genes are given in parentheses, and overlap classes are color coded. c For genes with trans eQTLs overlapping the HS1 window (genotype bins are in alternating gray and white, and bin midpoints in kb are indicated at bottom), log₂ fold changes (log₂FC) attributable to the respective genotypes at the trans eQTL loci at HS1 are shown on the y-axis. Within a bin, trans regulated genes (circles) are jittered to prevent plotting overlap, and are color coded after panel b. Detoxification genes are denoted with filled circles (legend, top left). d Scatter plot showing log₂FC values for differentially expressed genes (from b) in either the A-NIL-HS1^RR versus A-NIL-HS1^SS or the B-NIL-HS1^RR versus B-NIL-HS1^SS comparisons (x-axis and y-axis, respectively; genes are color coded based on b). e Relative expression levels for a subset of highly differentially expressed detoxification genes in NIL-HS1^RR and NIL-HS1^SS for the A and B NIL sets along with the respective values for F1s. To facilitate comparisons, expression was normalized to values from A-NIL-HS1^RR and B-NIL-HS1^RR. Significant differences are indicated by asterisks (adj-p < 0.05*, DESeq2; n.s., not significant). For the bar plot, means, error bars of ±2 standard error, and all data points are shown. The differential gene expression analyses for NILs in b, e used p-values adjusted for multiple tests (adj-p values) as output by DESeq2 (n = 5 biologically independent replicates, except for B-NIL-HS1^RR, for which n = 4 biologically independent replicates).