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

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. How...

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Bibliographic Details
Published in:Breeding Science 2023, Vol.73(2), pp.168-179
Main Authors: Akai, Kotaro, Asano, Kenji, Suzuki, Chika, Shimosaka, Etsuo, Tamiya, Seiji, Suzuki, Takako, Takeuchi, Toru, Ohki, Takehiro
Format: Article
Language:English
Subjects:
Assembly
Autotetraploid
Binding sites
Chromosome 9
de novo assembly
Dihaploid
Disease resistance
Gene clusters
gene isolation
Gene mapping
Gene sequencing
Genes
Genomes
Interleukin 1
Interleukins
Leucine
Nucleotides
polyploidy
Potatoes
Repetitive structures
Research Paper
resistance gene
Rychc
Target recognition
third-generation sequencing
Vegetables
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Summary: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 Rychc as a model. The assembled contig containing Rychc-linked markers was 3.3 Mb in length and could be joined with gene location information from the fine mapping analysis. Rychc 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.
ISSN:1344-7610
1347-3735
DOI:10.1270/jsbbs.22078