Two sides to every coin: reciprocal introgression line populations in Caenorhabditis elegans

Quantitative genetics seeks to understand the role of allelic variation in trait differences. Introgression lines (ILs) contain a single genetic locus introgressed into another genetic background, and are one of the most powerful quantitative trait locus (QTL) mapping designs. However, albeit useful for QTL discovery, this homogenous background confounds genetic interactions. Here, we created an IL population with N2 segments in a CB4856 background (ILCB4856), reciprocal to an N2 background with CB4856 introgressions population (ILN2). The ILCB4856 panel comprises a population of 145 strains with sequencing confirmed N2 introgressions in a CB4856 background. A core set of 87 strains covering the entire genome was selected. We present three experiments demonstrating the power of the reciprocal IL panels. First, we performed QTL mapping identifying new regions associated with lifespan. Second, the existence of opposite-effect loci regulating heat-stress survival is demonstrated. Third, by combining ILN2 and ILCB4856 strains, an interacting expression QTL was uncovered. In conclusion, the reciprocal IL panels are a unique and ready-to-use resource to identify, resolve, and refine complex trait architectures in C. elegans.

set, a core set of 87 strains was assembled, covering the entire C. elegans genome with N2 conclusion, this set of strains can be used as resource for QTL exploration in C. elegans.
To facilitate integrated analyses using IL populations, we created and tested the power background IL population (IL N2 ) (DOROSZUK et al. 2009). To complete the IL N2 genetic map, we sequenced 29 of the IL N2 strains, to supplement the 57 IL N2 strains that were sequenced previously (THOMPSON et al. 2015). By integrating the IL CB486 , IL N2 with the genetic map of table 4). We used this map for power analyses of the core sets of the two IL populations.

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With the establishment of an IL CB4856 population, we could simulate its ability to detect QTL 3 6 9 when combined with the IL N2 population (Supplementary figure 2; Figure 1C). Using 3 7 0 simulations, we found that three replicates are sufficient to detect 50% of the interacting QTL 3 7 1 explaining at least 35% of variance. Therefore, this analytical design can effectively uncover 3 7 2 local genetic interactions. (no label, each row represents a single strain). The blue colours indicate the CB4856 genotype, and the orange colours indicate the N2 genotype. (C) In silico power analysis of the detection of background interactions when combining the IL CB4856 with the previously constructed IL N2 panel. On the x-axis, the number of replicates per IL is plotted against the percentage of the simulated QTL detected on the y-axis. The colours indicate the amount of variance explained (h 2 ) per simulated interaction QTL. To investigate QTL detection using real data in the newly generated IL CB4856 strains, we the QTL architectures (DOROSZUK et al. 2009). In the previous panel, six QTL for mean 3 8 0 lifespan were detected. When we measured lifespan, we found that the N2 strain lived longer 3 8 1 than the CB4856 strain on average, which was in line with previous results (Figure 2A On the x-axis, the physical position in million bases (Mb) is shown. On the y-axis, the statistical significance of the association. The dashed horizontal line indicates the FDR = 0.05 threshold (based on 1,000 permutations). The red triangles indicate the peaks that were called, the asterisk indicates that this peak was mapped previously in the IL N2 panel (C) The trait values under the chromosome IV peak (7), where we found that the ILs with an introgression on the site (N2 genotype) had an increased lifespan compared to the CB4856 parental strain. The most common usage of ILs is in fine mapping or experimental validation of previously  KAMMENGA et al. 2007;MCGRATH et al. 2009;BENDESKY et al. 2011;FREZAL et al. 2018;3 9 6 ANDERSEN AND ROCKMAN 2022)). We used a set of ILs that could validate the detected QTL 3 9 7 on chromosome IV in the heat-stress response. Chromosome IV was previously implicated in 3 9 8 fitness (reproduction) after heat shock, and a heat-shock expression QTL hotspot was found 3 9 9 on chromosome IV (RODRIGUEZ et al. 2012;SNOEK et al. 2017;STERKEN et al. 2020 Figure 3A). We observed that the ILs typically showed a decreased survival when 4 1 0 compared with the parental lines ( Figure 3B). When we used these data for bin mapping, 18  Figure 3C). One locus, a QTL around 12.6 Mb was associated with a decrease in survival in 4 1 3 both N2 and CB4856 ILs, this was also the QTL we mapped in the previously published data opposite-effect QTL in that region ( Figure 3D and E). Therefore, we concluded that the use 4 1 6 of strains from both IL panels is useful to uncover background-effects.  population.

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We measured the expression of the two isoforms of clec-62 in 47 RILs, 42 IL N2 therefore the analysis was performed using the higher expressed isoform A. We also found a  IL N2 and IL CB4856 panels, we identified two loci with significant interaction effects: one on shown in million bases (Mb). On the y-axis the significance of the association is shown (log 10 (p)). The dashed horizontal line indicates the FDR = 0.05 threshold. The red triangles indicate QTL-peaks. (C) The split-out of the chromosome IV peak from panel (B). Where both parental lines (PL) and the IL CB4856 population have a similar clec-62 expression, the IL N2 (CB4856 introgression at the locus) has a lower clec-62 expression. (D) As in (C), but for the chromosome X peak. Here we presented a novel whole-genome N2>CB4856 IL population in C. elegans. This new 4 5 7 IL CB4856 population is reciprocal to the previous IL N2 population (DOROSZUK et al. 2009). The novel population in various QTL approaches. We present three such approaches in this paper: The IL CB4856 panel for use in QTL mapping The IL CB4856 panel is mostly free from large-effect laboratory-derived alleles that segregate in IL N2 population QTL in these ILs can now also be pinpointed to a narrower locus. Therefore, panel are shown. The 100, 500, and 1000 bp bands of the 1kb+ marker are indicated.

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