Modeling Recombination Rate as a Quantitative Trait Reveals New Insight into Selection in Humans

Mixed Outcomes in Recombination Rates After Domestication: Revisiting Theory and Data

The process of domestication has altered many phenotypes. Selection on these phenotypes has long been hypothesised to indirectly select for increases in the genome-wide recombination rate. This hypothesis is potentially consistent with theory on the evolution of the recombination rate, but empirical support has been unclear. We review relevant theory, lab-based experiments, and data comparing recombination rates in wild progenitors and their domesticated counterparts. We utilise population sequencing data and a deep learning method to infer genome-wide recombination rates for new comparisons of chicken/red junglefowl, sheep/mouflon, and goat/bezoar. We find evidence of increased recombination in domesticated goats compared to bezoars but more mixed results in chicken and generally decreased recombination in domesticated sheep compared to mouflon. Our results add to a growing body of literature in plants and animals that finds no consistent evidence of an increase in genome-wide recombination with domestication.

Genetics of Recombination Rate Variation Within and Between Species

Recombination diversifies the genomes of offspring, influences the evolutionary dynamics of populations, and ensures that chromosomes segregate properly during meiosis. Individuals recombine at different rates but observed levels of variation in recombination rate remain mostly unexplained. Genetic dissection of differences in recombination rate within and between species provides a powerful framework for understanding how this trait evolves. In this Perspective, I amalgamate published findings from genetic studies of variation in the genome-wide number of crossovers within and between species, and I use exploratory analyses to identify preliminary patterns. The narrow-sense heritability of crossover count is consistently low, indicating limited resemblance among relatives and predicting a weak response to short-term selection. Variants associated with crossover number within populations span the range of minor allele frequency. The size of the additive effect of recombination-associated variants, along with a negative correlation between this effect and minor allele frequency, raises the prospect that mutations inducing phenotypic shifts larger than a few crossovers are deleterious, though the contributions of methodological biases to these patterns deserve investigation. Quantitative trait loci that contribute to differences between populations or species alter crossover number in both directions, a pattern inconsistent with selection toward a constant optimum for this trait. Building on this characterization of genetic variation in crossover number within and between species, I describe fruitful avenues for future research. Better integrating recombination rate into quantitative genetics will reveal the balance of evolutionary forces responsible for genetic variation in this trait that shapes inheritance.

Metabolic stress-induced long ncRNA transcription governs the formation of meiotic DNA breaks in the fission yeast fbp1 gene

Meiotic recombination is a pivotal process that ensures faithful chromosome segregation and contributes to the generation of genetic diversity in offspring, which is initiated by the formation of double-strand breaks (DSBs). The distribution of meiotic DSBs is not uniform and is clustered at hotspots, which can be affected by environmental conditions. Here, we show that non-coding RNA (ncRNA) transcription creates meiotic DSBs through local chromatin remodeling in the fission yeast fbp1 gene. The fbp1 gene is activated upon glucose starvation stress, in which a cascade of ncRNA-transcription in the fbp1 upstream region converts the chromatin configuration into an open structure, leading to the subsequent binding of transcription factors. We examined the distribution of meiotic DSBs around the fbp1 upstream region in the presence and absence of glucose and observed several new DSBs after chromatin conversion under glucose starvation conditions. Moreover, these DSBs disappeared when cis-elements required for ncRNA transcription were mutated. These results indicate that ncRNA transcription creates meiotic DSBs in response to stress conditions in the fbp1 upstream region. This study addressed part of a long-standing unresolved mechanism underlying meiotic recombination plasticity in response to environmental fluctuation.