Deep sequencing of 3,367 maize genomes uncovers substantial contribution of rare variants to agronomic traits.

Deep whole-genome sequencing of 3,367 diverse elite maize inbred lines uncovered 75.3 million variants, with 79.2% rare, and 411 independent association signals across 10 agronomic traits.

• Why it matters: Rare variants are abundant, but their genome-wide contributions to agronomic traits in plants have remained elusive, limiting understanding of complex trait genetic architecture.
• What they did: The study sequenced 3,367 elite maize inbred lines and performed frequency-stratified GREML analyses plus conventional variant-level GWAS and gene-based tests, totaling 75.3 million variants and 411 association signals.
• The result: Globally rare variants accounted for 359 signals, with rare variants showing effect sizes ~2.4 times those of common variants, and GREML indicated substantial phenotypic variance for traits under strong adaptive selection.