Extreme copy number variation at a tRNA ligase gene affecting phenology and fitness in yellow monkeyflowers

Abstract

Copy number variation ( CNV ) 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 (Migut.N02091; RLG 1a) exhibiting unprecedented, and fitness‐relevant, CNV within an annual population of the yellow monkeyflower Mimulus guttatus . RLG 1a variation was associated with multiple traits in pooled population sequencing (PoolSeq) scans of phenotypic and phenological cohorts. Resequencing of inbred lines revealed intermediate‐frequency three‐copy variants of RLG 1a ( trip+; 5/35 = 14%), and trip+ lines exhibited elevated RLG 1a expression under multiple conditions. trip+ carriers, in addition to being over‐represented in late‐flowering and large‐flowered PoolSeq populations, flowered later under stressful conditions in a greenhouse experiment ( p RLG 1a variant ( high+ ) that carries 250–300 copies of RLG 1a totalling ~5.7 Mb (20–40% 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 RLG 1a locus. In the wild, high+ carriers had highest fitness in two particularly dry and/or hot years (2015 and 2017; both p CNV type in a lush year (2016: p CNV s affecting phenological traits in a wild population, suggest that plant tRNA ligases mediate stress‐responsive life‐history traits, and introduce a novel system for investigating the molecular mechanisms of gene amplification.

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