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Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency

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posted on 21.06.2019, 10:43 by Laura-Jayne Gardiner, Luzie U. Wingen, Paul Bailey, Ryan Joynson, Thomas Brabbs, Jonathan Wright, James D. Higgins, Neil Hall, Simon Griffiths, Bernardo J. Clavijo, Anthony Hall
Background Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. A lack of recombination limits breeding efforts in crops; therefore, increasing recombination rates can reduce linkage drag and generate new genetic combinations. Results We use computational analysis of 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat (Triticum aestivum). We observe that high-frequency crossover sites are shared between populations and that closely related parents lead to populations with more similar crossover patterns. We demonstrate that gene conversion is more prevalent and covers more of the genome in wheat than in other plants, making it a critical process in the generation of new haplotypes, particularly in centromeric regions where crossovers are rare. We identify quantitative trait loci for altered gene conversion and crossover frequency and confirm functionality for a novel RecQ helicase gene that belongs to an ancient clade that is missing in some plant lineages including Arabidopsis. Conclusions This is the first gene to be demonstrated to be involved in gene conversion in wheat. Harnessing the RecQ helicase has the potential to break linkage drag utilizing widespread gene conversions.

Funding

DNA sequence was generated by the Earlham Institute-Genomic Pipelines (United Kingdom). We thank Robert King, Christian Schudoma, Cristobal Uauy, and Ksenia Krasileva for providing SNP calls and early access to these SNP calls for the Cadenza TILLING population overlaid onto the IWGSC RefSeq V1. We thank Simon Orford for his assistance obtaining the Paragon x Chinese Spring seeds at the John Innes Centre Germplasm Resources Unit. Assemblies of the Paragon cultivar were generated in the BBSRC funded Strategic LOLA project and we thank Mike Bevan and Bernardo Clavijo for authorizing and facilitating early access to this dataset. Funding This project was supported by the BBSRC via an ERA-CAPS grant BB/N005104/1, BB/N005155/1 (L.G, A.H), IWYP project grant BB/N020871/1 (R.J), BBSRC funded Strategic LOLA project BB/N002628/1 (JDH) and BBSRC Designing Future Wheat BB/P016855/1 (A.H, L.G). Assemblies of the Paragon cultivar were generated in the BBSRC funded Strategic LOLA project (BB/J003557/1).

History

Citation

Genome Biology, 2019, 20 (69)

Author affiliation

/Organisation/COLLEGE OF LIFE SCIENCES/Biological Sciences/Genetics and Genome Biology

Version

VoR (Version of Record)

Published in

Genome Biology

Publisher

BMC (part of Springer Nature)

issn

1474-760X

Acceptance date

13/03/2019

Copyright date

2019

Available date

21/06/2019

Publisher version

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1675-6

Notes

Availability of data and materials Genetic maps and 35K array data for the 13 populations used in this analysis are publicly available [16, 49] and at http://wisplandracepillar.jic.ac.uk/results/JIC_DFW_Watkins_ParWat_Ax_iS_maps.xlsx. The SNPs from the Cadenza TILLING lines are available publicly at https://plants.ensembl.org/Triticum_aestivum/Info/Annotation [26]. The skim sequencing datasets are available (study PRJEB28231) from the European Nucleotide Archive [13].

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en

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