Detection Of Meiotic Recombination Events In Populus Using Next Generation Sequencing Technology

The genus Populus is an important forest species with both economic and ecological values.In the field of forest biology,Populus was chosen as a model species for woody plants because of its small genome size and fast growth.During meiosis in Populus,double-strand breaks(DSBs)are repaired as crossover or noncrossover events.As the product of the noncrossover event,gene conversion could skew the segregation ratio of alleles in meiotic recombination.This may be related to segregation distortion for molecular markers,which appears frequently in linkage genetic mapping studies.In the past,gene conversion was difficult to be detected because of the low resolution of the traditional molecular markers.Next-generation sequencing technologies allow us to identify a large number of SNPs in a rapid and low-cost way,which can be used to detect gene conversion events.In this study,we use resequencing technology to detect meiotic recombination events in populus and study the relationship between segregation distortion of molecular markers and gene conversion events.Including the two parents,10 individuals were randomly selected as the materials from the F1 population crossed between P.deltodis(♀)and P.simonii(♂).Whole genome resequencing was performed on both parents and the 10 F1 individuals.We obtained 62.1Gb paired-end(PE)reads data with 101 bp in length for both parents and 137.69 Gb reads data with 126 bp in length for the 10 F1 individuals.PE reads of each individual were aligned to the reference genome of P.trichocarpa with the software BWA.By using the software Samtools,188,942 haplotype blocks for the male parent and 216,915 for the female were constructed.We chose those SNPs with segregation type of aa?ab for the male parent and ab?aa for the female,resulting in 20,153 and 41,877 haplotype blocks each containing 6 or more SNPs for the male and female,respectively.With the two parental-specific linkage maps constructed previously,we built long haplotypes corresponding to the 19 chromosomes for the male and female parents.The male long hapotypes contained 7,432 SNPs,while the female consisted of 10,164 SNPs.Haplotypes for all progeny were calculated after genotype calling for all loci in the haplotype blocks.By comparing the haplotypes between the progeny and their parents,2,355 gene conversions for male parent and 2,771 for female were detected per F1 individual.With the same method,21 and 18.8 crossovers in the male and female parents,respectively,were averagely detected through long haplotypes in each progeny.In order to uncover the relationship between gene conversion and distorted molecular markers,we identified 1,088 和 1,186 regions in the haplotypes of the male and female parents,respectively,each of which was detected to be a product of gene conversion in at least 5 progeny.By combining the use of RAD-seq data from 299 individuals in the same population,we found 372 SNPs in the 2,274 regions that each was genotyped in at least 100 progeny.Among those SNPs,298(80.1%)SNPs were significantly deviated from the expected segregation ratio(?2 test,p<0.05).The result demonstrated that there is a substential difference between the numbers of crossover and gene conversion events in Populus,and the segregation distortion of molecualr markers may be highly correlated with gene conversion events.This study provides a strategy to study meiotic recombination in forest trees,and an evidence for reference when dealing with distorted markers in genetic mapping of forest trees.