Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing.

Abstract

Background Karyotype, as a basic characteristic of species, provides valuable information for fundamental theoretical research and germplasm resource innovation. However, traditional karyotyping techniques, including fluorescence in situ hybridization (FISH), are challenging and low in efficiency, especially when karyotyping aneuploid and polyploid plants. The use of low coverage whole-genome resequencing (lcWGR) data for karyotyping was explored, but existing methods are complicated and require control samples. Results In this study, a new protocol for molecular karyotype analysis was provided, which proved to be a simpler, faster, and more accurate method, requiring no control. Notably, our method not only provided the copy number of each chromosome of an individual but also an accurate evaluation of the genomic contribution from its parents. Moreover, we verified the method through FISH and published resequencing data. Conclusions This method is of great significance for species evolution analysis, chromosome engineering, crop improvement, and breeding.

Plant phenotyping relevance

植物個体の染色体コピー数と親由来ゲノム寄与を推定する分子カリオタイピング法を開発し、FISHおよび公開データで検証しており、植物の状態・特性取得法が研究の中心である。

Code and data availability

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