Identification of recombination events in outbred species with next-generation sequencing data

Abstract

Background: Meiotic recombination events include crossovers and non-crossovers or gene conversions. Although the rate of crossovers is often used for genetic mapping, the gene conversion events are not well studied especially in outbred species, which could produce distorted markers and thus affect the precision of genetic maps.

Results: We proposed a strategy for identifying gene conversion events in Populus with the next-generation sequencing (NGS) data from the two parents and their progeny in an F₁ hybrid population. The strategy first involved phasing the heterozygous SNPs of the parents to obtain the parental haplotype blocks by NGS analytical tools, permitting to identify the parental gene conversion events with progeny genotypes. By incorporating available genetic linkage maps, longer haplotype blocks each corresponding to a chromosome can be created, not only allowing to detect crossover events but also possibly to locate a crossover in a small region. Our analysis revealed that gene conversions are more abundant than crossovers in Populus, with a higher probability to generate distorted markers in the regions involved than in the other regions on genome. The analytical procedures were implemented with Perl scripts as a freely available package, findGCO at https://github.com/tongchf/findGCO .

Conclusions: The novel strategy and the new developed Perl package permit to identify gene conversion events with the next-generation sequencing technology in a hybrid population of outbred species. The new method revealed that in a genetic mapping population some distorted genetic markers are possibly due to the gene conversion events.

Keywords: Crossover; Gene conversion; Haplotype block; Next-generation sequencing; Populus.

Fig. 1

Merger of two haplotype blocks with linkage information. Two different alleles are denoted by ‘a’ and ‘b’ for all SNPs in the haplotype blocks. a The two SNPs, namely C01_400706 and C01_666847 with a repulsion linkage phase, are found in (b) haplotype blocks 1 and 2. c According to the linkage phase, the two blocks can be merged into a longer one (dark brown), with another one on the homologous chromosome

Fig. 2

Procedures for identifying recombination events with a haplotype block inherited from one parent. a The haplotype blocks at the same SNP sites for two parents are shown. At these sites, the genotypes are all heterozygous in the female P. deltoides, but homozygous in the male P. simonii. b The homozygous allele is denoted by ‘a’ and the other allele in a heterozygote by ‘b’ at each SNP. c One progeny is genotyped with notations of ‘aa’ and ‘ab’ at those SNPs. d The haplotype blocks of this progeny can be discriminated, one (blue) from the male parent and the other (yellow/red) from the female. The haplotype block from the female carries recombinant information, in which the first red fragment (< 2 kb) from the top is considered to be a product of gene conversion and the junction between the second yellow and red fragments (> 10 kb) a crossover. e The alleles on the haplotype blocks of the progeny are labelled with base notations as they were

Fig. 3

Bar charts of the number of haplotype blocks against the number of individuals in which one or more GC events were detected in the same haplotype block for the female (a) and male (b) parents

Fig. 4

CO patterns identified in each progeny on chromosome 1 for the female (a) and male (b) parents. The red and blue bars represent two homologous chromosomes and the junction between the two colors is detected as a CO location