Preprint expands bovine transcript atlas with 13,000 novel isoforms via population-scale long-read RNA-seq

A preprint posted to bioRxiv presents a population-scale, multi-omics study of bovine complex traits, using matched whole-genome sequencing, Oxford Nanopore Technology (ONT) long-read RNA-seq, short-read RNA-seq, and metabolome data from 432 dairy cows sampled across four lactation stages. The authors report the identification of 13,177 novel transcript isoforms not present in current bovine reference annotations, and the fine-mapping of approximately 1.09 million regulatory effects across 11 diverse molecular phenotypes — including gene expression, alternative splicing, and metabolite levels.

The study addresses a recognised limitation of short-read RNA sequencing, which cannot reliably resolve full-length transcript isoforms or complex patterns of alternative splicing. Long-read sequencing of sufficient depth across a population enables researchers to attribute regulatory variation to specific isoforms rather than aggregating signal at the gene level, a distinction that matters when interpreting quantitative trait loci (QTL) for agricultural and biomedical traits.

Although conducted in cattle, the methodological approach — integrating population-scale long-read transcriptomics with genomic and metabolomic data — is broadly applicable to human and model-organism genetics. The dataset represents a substantial expansion of bovine molecular reference resources. The preprint has not yet been peer reviewed.