Genomic features of meiotic crossovers in diploid potato

Abstract

Meiotic recombination plays an important role in genome evolution and crop improvement. Potato (Solanum tuberosum L.) is the most important tuber crop in the world, but research about meiotic recombination in potato is limited. Here, we resequenced 2163 F₂ clones derived from five different genetic backgrounds and identified 41 945 meiotic crossovers. Some recombination suppression in euchromatin regions was associated with large structural variants. We also detected five shared crossover hotspots. The number of crossovers in each F₂ individual from the accession Upotato 1 varied from 9 to 27, with an average of 15.5, 78.25% of which were mapped within 5 kb of their presumed location. We show that 57.1% of the crossovers occurred in gene regions, with poly-A/T, poly-AG, AT-rich, and CCN repeats enriched in the crossover intervals. The recombination rate is positively related with gene density, SNP density, Class II transposon, and negatively related with GC density, repeat sequence density and Class I transposon. This study deepens our understanding of meiotic crossovers in potato and provides useful information for diploid potato breeding.

Acknowledgements

This work was supported by the China National Key Research and Development Program (Grant Number 2019YFE0120500), the National Natural Science Foundation of China (32022075), the Natural Science Foundation of Shenzhen (JCYJ20190813142201666), the National Science Fund of Yunnan for Distinguished Young Scholars (Grant No. 202001AV070003), the Agricultural Science and Technology Innovation Program (CAAS-ZDRW202101), and Science Technology and Innovation Commission of Shenzhen Municipality of China (ZDSYS20200811142605017).

Author contributions

C.Z., G.Z., and L.G. designed the experiments; C.Z. and X.J. wrote the manuscripts; X.J. and C.Z. performed the bioinformatics analysis; X.J., D.L., H.D., and P.W. performed the experiments. All authors confirm their contributions and read and approved the final manuscript.

Data availability

All resequencing data have been deposited in the NCBI Sequence Read Archive under BioProject accession number PRJNA904517 (https://dataview.ncbi.nlm.nih.gov/object/PRJNA904517?reviewer=1eipbbj3d6qjbjktigm8l908h6).

Conflict of interest statement

The authors have no conflict of interest.

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