Pasi Rastas’s research while affiliated with University of Helsinki and other places

Meiotic recombination is an ubiquitous feature of sexual reproduction across eukaryotes. While recombination has been widely studied both theoretically and experimentally, the causes of its variation across species are still poorly understood. Composing a coherent view across species has been difficult because of the differences in recombination map generation and reporting of the results. Thus, fundamental questions like why recombination rates differ between sexes (heterochiasmy) in many but not all species remain unanswered. Here we present the first collection of recombination maps that allows quantitative comparisons across a diverse set of species. We generated sex-specific high-density linkage maps for 40 fish species using the same computational pipeline. Comparing the maps revealed that the higher genome-wide recombination rate in females compared to males was linked to the karyotype of the species. The difference between the sexes in the positioning of the crossovers was also highly variable and unrelated to the difference in their total number. Especially in males, CpG content of the sequence was a strong indicator of the broad scale distribution of crossovers between and within chromosomes. More generally, the collection of recombination landscapes can serve as a link between the theoretical and experimental work on recombination.

There is growing evidence from diverse taxa for sex differences in the genomic landscape of recombination, but the causes and consequences of these differences remain poorly understood. Strong recombination landscape dimorphism between the sexes could have important implications for the dynamics of sex chromosome evolution because low recombination in the heterogametic sex can favour the spread of sexually antagonistic alleles. Here, we present a sex-specific linkage map and revised genome assembly of Rumex hastatulus and provide the first evidence and characterization of sex differences in recombination landscape in a dioecious plant. We present data on significant sex differences in recombination, with regions of very low recombination in males covering over half of the genome. This pattern is evident on both sex chromosomes and autosomes, suggesting that pre-existing differences in recombination may have contributed to sex chromosome formation and divergence. Our analysis of segregation distortion suggests that haploid selection due to pollen competition occurs disproportionately in regions with low male recombination. We hypothesize that sex differences in the recombination landscape have contributed to the formation of a large heteromorphic pair of sex chromosomes in R. hastatulus , but more comparative analyses of recombination will be important to investigate this hypothesis further. This article is part of the theme issue ‘Sex determination and sex chromosome evolution in land plants’.

Good knowledge about genome properties of the populations helps to optimize breeding methods, particularly genomic selection (GS). In oil palm ( Elaeis guineensis Jacq.), the first global source of vegetable oil, GS gave promising results. The present study considered two complex oil palm breeding populations, Deli and La Mé, with 943 individuals and 7,324 single-nucleotide polymorphisms (SNPs) from genotyping-by-sequencing. Linkage disequilibrium (LD), haplotype sharing, effective size (N e ), and fixation index (F st ) were investigated. A genetic linkage map was constructed, including 4,252 SNPs and spanning 1,778.52 cM, with an average recombination rate of 2.85 cM/Mbp. The LD at r²=0.3, considered as the minimum to get reliable results for genomic predictions, spanned over 1.05 cM/0.22 Mbp in Deli and 0.9 cM/0.21 Mbp in La Mé. The significant degree of differentiation existing between Deli and La Mé was confirmed by the high Fst value (0.53), the pattern of correlation of SNP heterozygosity and allele frequency among populations, and the decrease of persistence of LD and of haplotype sharing among populations with increasing SNP distance. However, the level of resemblance between the two populations over short genomic distances (correlation of r values between populations >0.6 for SNPs separated by <0.5 cM or <1 kbp and percentage of common haplotypes >40% for haplotypes <3,600 bp or <0.20 cM) likely explains the superiority of GS models ignoring the parental origin of marker alleles over models taking this information into account. The two populations had low N e (<5). Population-specific genetic maps and reference genomes are needed for future studies.

There is growing evidence across diverse taxa for sex differences in the genomic landscape of recombination, but the causes and consequences of these differences remain poorly understood. Strong recombination landscape dimorphism between the sexes could have important implications for the dynamics of sex chromosome evolution and turnover because low recombination in the heterogametic sex can help favour the spread of sexually antagonistic alleles. Here, we present a sex-specific linkage map and revised genome assembly of Rumex hastatulus, representing the first characterization of sex differences in recombination landscape in a dioecious plant. We provide evidence for strong sex differences in recombination, with pericentromeric regions of highly suppressed recombination in males that cover over half of the genome. These differences are found on autosomes as well as sex chromosomes, suggesting that pre-existing differences in recombination may have contributed to sex chromosome formation and divergence. Analysis of segregation distortion suggests that haploid selection due to pollen competition occurs disproportionately in regions with low male recombination. Our results are consistent with the hypothesis that sex differences in the recombination landscape contributed to the formation of a large heteromorphic pair of sex chromosomes, and that pollen competition is an important determinant of recombination dimorphism.