Catcher in the rye: museomics reveals the identity of cereal remains recovered from a late nineteenth century antique furniture

Abstract

Historical crop remains preserved in everyday objects are an underused archive of agrobiodiversity change, yet their degraded DNA resists conventional analysis. We recovered cereal grains and straws used as upholstery padding in a Central European settee dated to about 1870 to 1900. We identified and characterized the specimen by genome skimming. Damage-aware sequencing confirmed authentic historical DNA of modest, late nineteenth-century age. The assembled plastome placed the specimen securely within rye, and a genome-wide SNP panel of rye landraces resolved it inside cultivated Secale cereale subsp. cereale, closest to a Hungarian bred rye and a Slovak upland landrace and remote from wild or eastern lineages. Screening 192 stress-associated loci recovered the structural machinery of resistance, abiotic stress and aluminum tolerance pathways, while heading-date genotyping showed the Weining earliness allele at Hd2R already present. Divergence across 36 domestication sweep regions concentrated at a few improvement loci. Integrating these genomic signals with genebank passport data and an 1891 newspaper record, we interpret the specimen as a tall Central European rye at the threshold between landrace and improved variety. Historical crop material, read this way, preserves both genomes and the traces of human agricultural practice.