Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination

Hequan Sun,Bruno Huettel,Ronny Brandt,Beth A Rowan,Korbinian Schneeberger,Pádraic J Flood,Angela M Hancock,Janina Fuss,Richard W Michelmore

doi:10.1038/s41467-019-12209-2

Abstract

Meiotic crossovers (COs) ensure proper chromosome segregation and redistribute the genetic variation that is transmitted to the next generation. Large populations and the demand for genome-wide, fine-scale resolution challenge existing methods for CO identification. Taking advantage of linked-read sequencing, we develop a highly efficient method for genome-wide identification of COs at kilobase resolution in pooled recombinants. We first test this method using a pool of Arabidopsis F2 recombinants, and recapitulate results obtained from the same plants using individual whole-genome sequencing. By applying this method to a pool of pollen DNA from an F1 plant, we establish a highly accurate CO landscape without generating or sequencing a single recombinant plant. The simplicity of this approach enables the simultaneous generation and analysis of multiple CO landscapes, accelerating the pace at which mechanisms for the regulation of recombination can be elucidated through efficient comparisons of genotypic and environmental effects on recombination.

Highlights

Meiotic crossovers (COs) ensure proper chromosome segregation and redistribute the genetic variation that is transmitted to the generation
The availability of an efficient method to assess the genome-wide distribution and frequency of COs at a high resolution would greatly enhance our understanding of the processes that govern meiotic recombination
We investigate the use of linked-read sequencing of bulk recombinants for high-throughput genome-wide determination of COs in Arabidopsis thaliana

Summary

Introduction

Meiotic crossovers (COs) ensure proper chromosome segregation and redistribute the genetic variation that is transmitted to the generation. We first develop and assess this approach using bulked F2 individuals within known recombination sites and apply this method to hybrid pollen to generate a genome-wide CO map with a single sequencing experiment and without even growing a single recombinant plant These results show that the time and effort needed to generate genome-wide CO maps can be reduced to sequencing and analyzing a single DNA library, making it feasible to compare multiple CO maps and thereby determine the effect of genetic and environmental factors within a single study. We believe that this method will be widely applicable to different organisms and will have a sizeable impact on the design of experiments aiming to decipher how meiotic recombination is regulated

Methods

Results

Conclusion