Diversity and determinants of recombination landscapes in flowering plants

Abstract

During meiosis, crossover rates are not randomly distributed along the chromosome and therefore they locally influence the creation of novel genotypes and the efficacy of selection. To date, the broad diversity of recombination landscapes among plants has rarely been investigated, undermining the overall understanding of the constraints driving the evolution of crossover frequency and distribution. The determinants that shape the local crossover rate and the diversity of the resulting landscapes among species and chromosomes still need to be assessed in a formal comparative genomic approach. We gathered genetic maps and genomes for 57 flowering plant species, corresponding to 665 chromosomes, for which we estimated large-scale recombination landscapes. Chromosome length drives the basal recombination rate for each species, but within species we were intrigued to notice that the chromosome-wide recombination rate is proportional to the relative size of the chromosome. Moreover, for larger chromosomes, crossovers tend to accumulate at the ends of the chromosome leaving the central regions as recombination-free regions. Based on identified crossover patterns and testable predictions, we proposed a conceptual model explaining the broad-scale distribution of crossovers where both telomeres and centromeres are important. Finally, we qualitatively identified two recurrent crossover patterns among species and highlighted that these patterns globally correspond to the underlying gene distribution. In addition to the positive correlation between recombination and gene density, we argue that crossover patterns are essential for the efficiency of chromosomal genetic shuffling, even though the ultimate evolutionary potential forged by the diversity of recombination landscapes remains an open question.

Mating systems and recombination landscape strongly shape genetic diversity and selection in wheat relatives

“…We tested the hypothesis that selfing increases the effect of linked selection by comparing polymorphism patterns and recombination along chromosomes. Speciesspecific recombination maps were not available for most species, so we used the recombination map of the outgroup species Hordeum vulgare since synteny and recombination patterns at large scale are well conserved, in particular the sharp difference between a large central region almost devoid of recombination and highly recombining chromosome arms (Brazier & Glémin, 2022a; Mayer et al, 2011; but see Parisod & Badaeva, 2020). In addition, the outgroup has (on average) the same phylogentic distance to every Aegilops/Triticum species, avoiding to bias the analysis toward species closer to the reference.…”

The genomics of linkage drag in sunflower

“…Plant breeders typically monitor the size and location of introgressions with molecular markers and/or restrict pre-breeding efforts to fully compatible wild relatives (i.e., members of the primary gene pool; Harlan and de Wet 1971) to reduce the impact of the linkage drag (Young and Tanksley 1989; Tanksley and McCouch 1997; Frary et al 2004). However, in large plant genomes, regions of low recombination are widespread, making it difficult to reduce the sizes of some introgressions (Rodgers-Melnick et al 2015; Brazier and Glémin 2022; Huang et al 2022). Also, key traits may be found outside of the primary gene pool, making it necessary to tap less compatible wild relatives (e.g., Duriez et al 2019).…”

The genomics of linkage drag in inbred lines of sunflower

“…Plant breeders typically monitor the size and location of introgressions with molecular markers and focus their efforts on fully compatible wild relatives [i.e., members of the primary gene pool ( 26 )] to reduce the impact of the linkage drag ( 12 , 27 , 28 ). However, in large plant genomes, regions of low recombination are widespread, making it difficult to reduce the sizes of some introgressions ( 29 – 31 ). Also, key traits may be found outside of the primary gene pool, making it necessary to tap less compatible wild relatives (e.g., ref.…”