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

• Published in: Nature communications Vol. 10; no. 1; pp. 4310 - 9
• Main Authors: Sun, Hequan, Rowan, Beth A., Flood, Pádraic J., Brandt, Ronny, Fuss, Janina, Hancock, Angela M., Michelmore, Richard W., Huettel, Bruno, Schneeberger, Korbinian
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 20.09.2019; Nature Publishing Group; Nature Portfolio
• Subjects: 45/23; 631/114; 631/1647/1513/2192; 631/1647/2217; 631/1647/514/1948; 631/208/8; Arabidopsis - genetics; Chromosome Breakpoints; Chromosomes; Computational Biology - methods; Crossing Over, Genetic; Crossovers; Deoxyribonucleic acid; DNA; DNA Methylation; DNA sequencing; Environmental effects; Gametes; Genetic diversity; Genome, Plant - genetics; Genomes; Genomics; Genotype; Genotyping Techniques - methods; Germ Cells; Haplotypes; Homologous Recombination - genetics; Humanities and Social Sciences; Identification methods; Meiosis; multidisciplinary; Pollen; Pollen - genetics; Recombinants; Recombination; Recombination, Genetic; Science; Science (multidisciplinary); Sequence Analysis, DNA; Test procedures; Whole Genome Sequencing - methods
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-12209-2

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 F 2 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 F 1 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. Meiotic crossovers (COs) generate genetic variation and ensure proper chromosome segregation. Here, the authors develop a method for identifying COs at kilobase resolution in pooled recombinants using linked-read sequencing data, and apply it to investigate genome-wide CO landscapes of Arabidopsis thaliana .