Genotyping single nucleotide polymorphisms and inferring ploidy by amplicon sequencing for polyploid, ploidy-variable...

Area of Science:

• Genetics
• Evolutionary Biology
• Genomics

Background:

• Whole genome duplication (polyploidy) is a significant evolutionary force in vertebrates, yet many polyploid species remain.
• Modern genetic techniques struggle with polyploid genotyping due to ploidy variability.
• White sturgeon (Acipenser transmontanus) is a ploidy-variable, imperiled species requiring effective genetic management.

Purpose of the Study:

• To develop a high-throughput genotyping strategy for polyploid organisms using amplicon sequencing.
• To create a generalized method for inferring individual ploidy from amplicon sequencing data.
• To enable simultaneous ploidy inference and ploidy-aware genotyping for polyploid species.

Main Methods:

• Developed an amplicon sequencing panel of single nucleotide polymorphisms (SNPs) for polyploid genotyping.
• Created a generalized method to infer ploidy from amplicon sequencing data, independent of heterozygote identification.
• Applied and validated the combined approach using white sturgeon (octoploid, decaploid, dodecaploid).

Main Results:

• Generated an amplicon sequencing panel of 325 loci for polyploid genotyping.
• Validated SNP loci inheritance in known-cross families.
• Demonstrated accurate ploidy inference and genotyping in white sturgeon, including ploidy-variable individuals.

Conclusions:

• The developed amplicon sequencing panel and ploidy inference method effectively genotype polyploid organisms.
• This approach empowers genetic studies in naturally or artificially polyploid species.
• Facilitates conservation and management of ploidy-variable species like white sturgeon.