Abstract
Sequencing cohorts with long-read technology is crucial to understand the impact of structural variants (SVs) on complex traits. Here, we obtain 4.86 terabases of HiFi reads with an average read N50 of 16.3 Kb from 120 Bos taurus taurus bulls, yielding a mean coverage depth of 13.5-fold. We genotype 23.8 M small variants (SNPs and short INDELs) and 79.3 k SVs to perform association testing with molecular phenotypes derived from a subset of 117 bulls with total RNA sequencing data from testis tissue. We identify 27.3 k molecular QTL (molQTL) including 316 for which SVs were the most significant variant. This corresponds to a 2.1- and 5.6-fold enrichment of SVs among expression and splicing QTL, respectively. When considering SVs in perfect LD with the lead small variant, the enrichment increases to 6.1- and 12-fold for expression and splicing QTL in testis, respectively. Imperfect genotyping for SVs limits our ability to detect all SV molQTL, suggesting that the true enrichment of SVs among molQTL may be even higher. These results demonstrate that SVs have a profound impact on gene expression and splicing variation but highlight the necessity of improved SV genotyping to fully leverage long-read sequencing cohorts for dissecting complex traits.
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Data availability
DNA and RNA sequencing data of the analysed cohort are available in the ENA database at the study accessions PRJEB42335 (Long-read sequencing data from cattle for the purpose of de-novo genome assembly), PRJEB28191 (Short read sequencing of cattle) and PRJEB46995 (Testis transcriptome of mature bulls). Accession identifiers for all samples are available as Supplementary Data 1. Gene expression and splicing matrices, a VCF file of genome-wide small and structural variant genotypes used for e/sQTL mapping, a cross-table to link genotype and transcriptome data as well as results from e/sQTL mapping have been archived at zenodo (https://zenodo.org/records/15431126)79. The source data behind the graphs in the paper can be found in Supplementary Data 2 and at Zenodo (https://zenodo.org/records/15431126)79.
Code availability
Computational workflows are available through https://github.com/AnimalGenomicsETH/HiFi_cohort and are archived at zenodo (https://zenodo.org/records/18172395)80.
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Acknowledgements
This study was supported by an ETH Research Grant and a grant from the Swiss National Science Foundation (SNSF, grant-ID 204654). The funding bodies were neither involved in the design of the study and collection, analysis, and interpretation of data nor in writing the manuscript. We thank Eirini Lampraki from Pacific Biosciences for DNA fragment analysis and sequencing. We thank Audald Lloret-Villas and Qiongyu He for valuable discussions.
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X.M.M. sampled tissue and purified HMW DNA, aligned RNA reads against the reference, developed and applied workflows to quantify gene expression and splicing variation, conducted molecular QTL mapping, interpreted results, and drafted the manuscript; A.S.L. aligned DNA reads against the reference, called variants from short- and long-read alignments, interpreted results, and drafted the manuscript; H.P. conceived the study, contributed to the analysis of expression and splicing QTL, interpreted results, and contributed to the writing of the manuscript. All authors approved the final version of the manuscript.
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Mapel, X.M., Leonard, A.S. & Pausch, H. Molecular QTL are enriched for structural variants in a cattle long-read cohort. Commun Biol (2026). https://doi.org/10.1038/s42003-026-09596-w
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DOI: https://doi.org/10.1038/s42003-026-09596-w
