single-pollen genotyping in rye

The core molecular machinery of meiosis is conserved deep across eukaryotic lineages. Nevertheless, meiotic genes and proteins show sequence variation even within species. Patterns of meiotic recombination vary at multiple scales, from chromosomes to populations, caused by alleles of meiotic genes or environmental factors. To improve our understanding of the causes and consequences of this variation, we need to identify the underlying genetic architecture. In this work, we explored the genetic basis and environmental plasticity of meiotic recombination in a large rye population grown under control and nutrient deficient conditions. We used single-pollen nuclei (SPN) genotyping to directly measure male meiotic crossovers in 2,,539 pollen nuclei from 476 individuals, and detected a significant reduction of crossovers in response to nutrient deficiency (-8%). The effect of nutrient deficiency on meiosis is known since the mid 20th century, but studies were limited to few genotypes per species. Here, by using population-wide SPN-genotyping, we uncovered the genetic basis of crossover count, crossover interference, and intra-chromosomal shuffling, which revealed an oligogenic architecture of these traits. Most loci associated with crossover traits were unique to control or nutrient deficient conditions, suggesting that alleles regulating crossover traits act in response to nutrient availability. We found a negative relationship between effect size and allele frequency of crossover loci, indicating that large effect crossover modifiers are kept under purifying selection. Finally, we revealed differences in recombination landscapes measured in pollen (i.e. before fertilization) and plants (i.e. after fertilization), which may be explained by a survivorship bias in meiosis.