Copy number variation of N2091 in Iron Mountain Mimulus guttatus

Copy number variation is a major part of the genetic diversity segregating within populations, but remains poorly understood relative to single nucleotide variation. Here, we report on a tRNA ligase gene (RLG1a) exhibiting unprecedented, and fitness-relevant, CNV within an annual population of the yellow monkeyflower Mimulus guttatus. RLG1a variation was associated with multiple traits in pooled population sequencing scans of phenotypic and phenological cohorts. Resequencing of inbred lines revealed intermediate-frequency three-copy variants of RLG1a (trip+), and trip+ lines exhibited elevated RLG1a expression under multiple conditions. Trip+ carriers, in addition to being overrepresented in late-flowering and large-flowered PoolSeq populations, flowered later under stressful conditions in a greenhouse experiment. In wild population samples, we discovered an additional rare RLG1a variant (high+) that carries 250-300 copies of RLG1a totaling approximately 5.7 Mb (20 to 40 percent of a chromosome). In the progeny of a high+ carrier, Mendelian segregation of diagnostic alleles and qPCR-based copy counts indicate that high+ is a single tandem array unlinked to the single-copy RGL1a locus. In the wild, high+ carriers had highest fitness in two particularly dry and/or hot years, while single-copy individuals were twice as fecund as either CNV type in a lush year. Our results demonstrate fluctuation selection on CNVs affecting phenological traits in a wild population, suggest that plant tRNA ligases mediate stress-responsive and life-history traits, and introduce a novel system for investigating the molecular mechanisms of gene amplification.