Genomic Features Of Meiotic Crossovers In Diploid Potato

Meiotic recombination plays an important role in genome evolution and crop improvement.Potato（Solanum tuberosum L.）is the most important tuber crop in the world,but previous research about meiotic recombination in potato is limited.1.In this study,we resequenced 2,163 F₂ individuals derived from five different genetic backgrounds.We sequenced each F₂ individual from Upotato 1 to an average depth of 14íand those from the other four populations to a lower depth of 1.5íto3.0í.Based on the different genetic backgrounds,two methods were used to identify crossovers.We delimitated the crossover intervals of Upotato 1 F₂ plants into two flanking Single Nucleotide Polymorphisms（SNP）using deep sequencing data,while for the other four populations with low depth sequencing,we defined the crossovers between two bins.Finally,we identified 41,945 meiotic crossovers.2.We compared the recombination landscape among 5 populations.A recombination suppression in euchromatin regions of chromosome 3 was associated with large structural variations by comparative genomic analysis.False positive recombination suppression regions were also found in regions with low SNP density.We also detected five shared crossover hotspots.3.Then we found that the number of crossovers in each F₂ individual of Upotato 1varied from 9 to 27,with an average of 15.5,78.25%of which were mapped within 5kb of their presumed location.We show that 57.1%of the crossovers occurred in gene regions.We extracted 500 bp sequences flanked the midpoints of crossover intervals,and we found poly-A/T,poly-AG,AT-rich,and CCN repeats enriched in the crossover intervals.We explored the correlations between recombination rate and genomic features and found that recombination rate is positively related with gene density,SNP density,Class II transposon,and negatively related with GC density,repeat sequence density and Class I transposon.4.Statistics on the number of crossovers in Upotato 1 revealed that the data distribution was close to a normal distribution.Therefore,a genome-wide quantitative trait loci（QTL）scan was performed using the number of recombination per individual of Upotato 1 as the phenotype,and a QTL with a phenotypic variance explained of 5.6%was found on chromosome 11.We calculated the number of crossovers for the three genotypes（genotype AA from A6-26,hybrid genotype AB from A6-26 and E4-63,and genotype BB from E4-63）on this QTL and found that there was no difference in the number of crossovers between the AA and AB genotypes,while the crossover number of BB genotype was 12%less than AA,indicating that the A allele（A6-26 corresponds to the A allele）is the dominant QTL controlling the recombination rate in diploid potatoes.In summary,this study compared the differences in recombination landscapes among populations by analyzing the genomic features of diploid potatoes from five different genetic backgrounds,revealed the association between recombination rates and genomic features in diploid potatoes,and detected a dominant QTL that may influence the number of crossovers.This study deepens our understanding in potato meiosis and provides useful information for diploid potato breeding.