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SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids


Many plant species of great economic value (e.g., potato, wheat, cotton and sugarcane) are polyploids. Despite the essential roles of autopolyploid plants in human activities, our genetic understanding of these species is still very poor. The huge recent progress in instrumentation and biochemical manipulation has led to the accumulation of an incredible amount of genomic data. Herein, we demonstrate for the first time a successful genetic analysis in a highly polyploidy genome (sugarcane) by quantitative analysis of single nucleotide polymorphism (SNP) allelic dosage, and application of a new data analysis framework. This provides a better understanding of autopolyploid genomic structure and is a sound basis for genetic studies. The proposed methods can be employed to analyse any autopolyploid and will permit the future development of high-quality genetic maps to assist in the assembly of reference genome sequences for polyploid species. (AU)