Multiparental RNA-seq driven eQTL screening identifies loci underlying host plant fitness in a generalist herbivore
- 1Ghent University
Abstract
The two-spotted spider mite (Tetranychus urticae) is an extremely polyphagous pest, yet the genetic basis of this adaptive potential remains to be fully elucidated. Since expression quantitative trait loci (eQTLs) provide the genetic basis of numerous phenotypes, we aimed to identify trans-eQTL hotspots underlying T. urticae fitness upon transfer from a common (bean) to a challenging (tomato) host plant. Nonetheless, the identification of trans-eQTLs is complex and often constrained by methodological challenges and high costs. Therefore, we employed a multiparental mapping strategy driven by RNA-seq, enabling us to leverage extensive genetic variation in a cost-efficient manner. A randomly mating population was generated on bean from a small number of genetically diverse, often heterozygous parents, and subsequently transferred to tomato prior to RNA-seq. Upon whole genome sequencing of the parents, RNA-seq of the mapping population individuals was sufficient to reconstruct their genomes as a combination of parental haploblocks. Subsequent eQTL mapping identified 23 distinct trans-eQTL hotspot regions associated with the expression of numerous target genes. The most prominent hotspot on chromosome 3 was associated with approximately 900 genes and showed enrichment for functions related to detoxification and digestion. Furthermore, 4 of these trans-eQTL hotspot genotypes explained significant variation in mite fitness on the challenging host plant. This contrasted a traditional QTL mapping approach, where these genotypes could not be detected due to multiple testing correction. Our study hence offers a powerful strategy for trans-eQTL hotspot screening and the discovery of trait-associated loci in complex, multiparental genetic backgrounds.
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BibTeX
@misc{graeve2026multiparental,
title = {{Multiparental RNA-seq driven eQTL screening identifies loci underlying host plant fitness in a generalist herbivore}},
author = {F. De Graeve and B. De Beer and S. De Rouck and S. Naessens and M. Herpoel and J. Fostier and R. Clark and T. Van Leeuwen and T. De Meyer},
howpublished = {bioRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.30.748081},
url = {https://www.biorxiv.org/content/10.64898/2026.08.30.748081v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - Multiparental RNA-seq driven eQTL screening identifies loci underlying host plant fitness in a generalist herbivore
AU - F. De Graeve
AU - B. De Beer
AU - S. De Rouck
AU - S. Naessens
AU - M. Herpoel
AU - J. Fostier
AU - R. Clark
AU - T. Van Leeuwen
AU - T. De Meyer
PY - 2026
DA - 2026/08/30
PB - bioRxiv
DO - 10.64898/2026.08.30.748081
UR - https://www.biorxiv.org/content/10.64898/2026.08.30.748081v1
AB - The two-spotted spider mite (Tetranychus urticae) is an extremely polyphagous pest, yet the genetic basis of this adaptive potential remains to be fully elucidated. Since expression quantitative trait loci (eQTLs) provide the genetic basis of numerous phenotypes, we aimed to identify trans-eQTL hotspots underlying T. urticae fitness upon transfer from a common (bean) to a challenging (tomato) host plant. Nonetheless, the identification of trans-eQTLs is complex and often constrained by methodological challenges and high costs. Therefore, we employed a multiparental mapping strategy driven by RNA-seq, enabling us to leverage extensive genetic variation in a cost-efficient manner. A randomly mating population was generated on bean from a small number of genetically diverse, often heterozygous parents, and subsequently transferred to tomato prior to RNA-seq. Upon whole genome sequencing of the parents, RNA-seq of the mapping population individuals was sufficient to reconstruct their genomes as a combination of parental haploblocks. Subsequent eQTL mapping identified 23 distinct trans-eQTL hotspot regions associated with the expression of numerous target genes. The most prominent hotspot on chromosome 3 was associated with approximately 900 genes and showed enrichment for functions related to detoxification and digestion. Furthermore, 4 of these trans-eQTL hotspot genotypes explained significant variation in mite fitness on the challenging host plant. This contrasted a traditional QTL mapping approach, where these genotypes could not be detected due to multiple testing correction. Our study hence offers a powerful strategy for trans-eQTL hotspot screening and the discovery of trait-associated loci in complex, multiparental genetic backgrounds.
ER -