SNI1/NSE5 is a cold-sensitive brake on Class II crossovers

Temperature modulates meiotic recombination, but the genetic control and pathway choice remain unclear. Combining interval assays, genome-wide maps, QTL mapping and targeted genetics, we show that in Arabidopsis at 12 °C crossovers redistribute toward subtelomeres and increase via the Class II pathway. A temperature-responsive QTL on chromosome 4 (rQTL4) explains most variance and maps to a 15.6-kb interval encompassing SNI1/NSE5. Dosage and complementation tests identify SNI1 as a cold-sensitive brake: lowering SNI1 fixes a subtelomeric bias in inbreds and unmasks cold responsiveness in hybrids, with stronger effects for the Ler allele. In zip4 backgrounds, cold elevates chiasmata in a SNI1-dependent manner, and both cold and sni1-1 shorten the synaptonemal complex, linking loop–axis architecture to Class II usage. Inter-homolog polymorphism dampens Class II output in hybrids, explaining the inbred–hybrid split. These data nominate SNI1 as the driver of QTL4 and identify an environmental gate on meiotic pathway choice through SMC5/6.