De novo genome assembly of the partial homozygous dihaploid potato identified PVY resistance gene (Rychc) derived from Solanum chacoense

Kotaro Akai; Kenji Asano; Chika Suzuki; Etsuo Shimosaka; Seiji Tamiya; Takako Suzuki; Toru Takeuchi; Takehiro Ohki

doi:10.1270/jsbbs.22078

Research Papers

De novo genome assembly of the partial homozygous dihaploid potato identified PVY resistance gene (Ry_chc) derived from Solanum chacoense

Kotaro Akai, Kenji Asano, Chika Suzuki, Etsuo Shimosaka, Seiji Tamiya, Takako Suzuki, Toru Takeuchi, Takehiro Ohki

Author information

Kotaro Akai
Memuro Upland Farming Research Division, Hokkaido Agricultural Research Center, National Agricultural Research Organization
Research Faculty of Agriculture, Hokkaido University
Kenji Asano
Memuro Upland Farming Research Division, Hokkaido Agricultural Research Center, National Agricultural Research Organization
Chika Suzuki
Hokkaido Research Organization, Central Agricultural Experiment Station
Present address: Hokkaido Research Organization, Tokachi Agricultural Experiment Station
Etsuo Shimosaka
Memuro Upland Farming Research Division, Hokkaido Agricultural Research Center, National Agricultural Research Organization
Seiji Tamiya
Memuro Upland Farming Research Division, Hokkaido Agricultural Research Center, National Agricultural Research Organization
Present address: National Agriculture and Food Research Organization, Tohoku Agricultural Research Center
Takako Suzuki
Hokkaido Research Organization, Central Agricultural Experiment Station
Toru Takeuchi
Hokkaido Research Organization, Central Agricultural Experiment Station
Present address: National Agriculture and Food Research Organization, Headquarters
Takehiro Ohki
Research Faculty of Agriculture, Hokkaido University
National Agriculture and Food Research Organization, Hokkaido Agricultural Research Center

Keywords: gene isolation, resistance gene, Ry_chc, polyploidy, de novo assembly, third-generation sequencing

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Supplementary material

2023 Volume 73 Issue 2 Pages 168-179

DOI https://doi.org/10.1270/jsbbs.22078

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Abstract

The isolation of disease resistance genes introduced from wild or related cultivated species is essential for understanding their mechanisms, spectrum and risk of breakdown. To identify target genes not included in reference genomes, genomic sequences with the target locus must be reconstructed. However, de novo assembly approaches of the entire genome, such as those used for constructing reference genomes, are complicated in higher plants. Moreover, in the autotetraploid potato, the heterozygous regions and repetitive structures located around disease resistance gene clusters fragment the genomes into short contigs, making it challenging to identify resistance genes. In this study, we report that a de novo assembly approach of a target gene-specific homozygous dihaploid developed through haploid induction was suitable for gene isolation in potatoes using the potato virus Y resistance gene Ry_chc as a model. The assembled contig containing Ry_chc-linked markers was 3.3 Mb in length and could be joined with gene location information from the fine mapping analysis. Ry_chc was successfully identified in a repeated island located on the distal end of the long arm of chromosome 9 as a Toll/interleukin-1 receptor-nucleotide-binding site-leucine rich repeat (TIR-NBS-LRR) type resistance gene. This approach will be practical for other gene isolation projects in potatoes.

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