A population-scale isoform atlas enables isoform-based trait association and regulatory analysis in lettuce

A pan isoform atlas built from 240 lettuce accessions contains 531,657 isoforms across 49,729 transcribed loci, enabling isoform-level trait and splicing genetics analyses.

• Why it matters: Genetic variation’s contribution to transcript isoform diversity is unclear at population scale, limiting isoform-based trait mapping and understanding of alternative splicing regulation.
• What they did: The study integrated accession transcriptomes with a lettuce pangenome to create the atlas, then developed ISONET-GWAS for isoform trait associations and sQTL mapping, including 10,498 sQTL associations.
• The result: ISONET-GWAS linked isoforms to traits and metabolites (455 associations across 77 metabolites) and found a trans-sQTL hotspot overlapping LsPPR, whose perturbation altered alternative splicing and delayed bolting and flowering.

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