Academic journal article Genetics

Substantial Heritable Variation in Recombination Rate on Multiple Scales in Honeybees and Bumblebees

Academic journal article Genetics

Substantial Heritable Variation in Recombination Rate on Multiple Scales in Honeybees and Bumblebees

Article excerpt

MEIOSIS, which results in the production of haploid germ cells, is an essential process in sexually reproducing organisms. Recombination is a key mechanism that ensures accurate segregation of homologous chromosomes during meiosis by forming at least one crossover (CO) event per chromosome arm (or chromosome) in sexual eukaryotes (Mézard et al. 2015). Although many genes involved in recombination are highly conserved (Baudat et al. 2013; Wang and Copenhaver 2018), the genomic distribution of recombination events is not uniform across the genome, and this distribution is also highly variable between species (Serrentino and Borde 2012; de Boer et al. 2015). A range of taxa, including most birds and mammals, possess distinct recombination hotspots in their genomes, where recombination rate is several orders of magnitudes higher than the surrounding regions, while other species, such as fruit flies and nematodes, do not have such distinct recombination hotspots (reviewed in Smukowski and Noor 2011; Stapley et al. 2017). Furthermore, both the number and distribution of recombination events varies between individuals and between populations, in addition to between species (Auton et al. 2012; Comeron et al 2012; Hunter et al. 2016; Kawakami et al. 2017). However, the extent of this variation and its genetic and environmental determinants are still not fully understood.

Meiotic recombination entails the repair of doublestranded breaks (DSBs) by several distinct pathways (Gray and Cohen 2016; Wang and Copenhaver 2018). Outcomes of these DSB repair pathways are either COs, which involve a reciprocal exchange of chromatid arms, or noncrossovers (NCOs), which do not involve such a reciprocal exchange. Both of these outcomes can be associated with gene conversion events, by which genetic materials are exchanged unidirectionally between homologous chromosomes (Chen et al. 2007; Duret and Galtier 2009). Recombination can vary in several quantifiable ways between individuals and between species, including the total number of COs and NCOs, the ratio of these two outcomes (CO:NCO), and the genomic distribution of recombination events (Cole et al. 2014). The genomic distribution can be quantified by the degree of clustering of COs or their tendency to localize in certain genomic regions or motifs (Myers et al. 2010; Auton et al. 2012). These variables can be used to determine the factors that influence localization of DSBs in the genome, factors that cause variation in usage of DSB repair pathways and the mechanisms involved in these processes.

Variation in recombination has a heritable component, and genes with large effects on recombination rate have been identified in some species. In mammals, several lines of evidence led to the identification of a major role of the PR domain zinc finger protein 9 (PRDM9) in determining the location of recombination hotspots through binding to specific sequence motifs (Myers etal. 2005, 2010; Parvanov etal. 2010). Furthermore, quantitative genetic analyses have identified several genes associated with variation in CO number in humans, cattle, and Soay sheep, such as REC8 and RNF212 (Sandor et al. 2012; Ma et al. 2015; Johnston et al. 2016, 2018).

This genetic architecture of recombination rate variation appears to be fundamentally different between mammalian and nonmammalian species, given the absence ofthese mammalian recombination-associated genes and the differences in distribution or the lack of recombination hotspots in nonmammalian genomes (Pan etal. 2011; Choi etal. 2013; Lake etal. 2015; Singhal etal. 2015). For example, agenome-wide association study using 205 lines of the Drosophila melanogaster Genetic Reference Panel identified five genes associated with variation in the recombination rate, but these genes likely influence local rather than genome-wide variation, and it is possible that there is little genetic control of the variation in total CO number (Hunter etal. 2016). In red deer and mice, the recombination rate is highly variable between individuals, with an approximately twofold difference between the highest and lowest rates, but narrow-sense heritability is low to modest (h2 = 0. …

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