PolyHaplotyper

PolyHaplotyper reconstructs haplotypes in polyploid organisms from bi-allelic marker dosage data to enable accurate genetic analyses such as linkage mapping, QTL mapping, and genome-wide association studies.

Key Features:

• Haplotype reconstruction from SNP dosage: Reconstructs haplotypes and phased haploblocks from bi-allelic SNP (single nucleotide polymorphism) dosage data obtained from genotyping arrays.
• Support for multi-allelic markers: Leverages phased haploblocks derived from closely-linked SNP markers to represent multi-allelic marker information.
• Use of full-sib family information: Utilizes full-sib family relationships among samples to guide haplotype inference and improve accuracy.
• Polyploid applicability: Applied to and demonstrated with experimental hexaploid data and simulated tetraploid data.
• Comparative performance: Shows superior performance relative to existing polyploid haplotyping software in scenarios with one or more full-sib families.

Scientific Applications:

• Linkage mapping: Provides phased haplotypes that can be used for constructing linkage maps in polyploid species.
• QTL mapping: Supplies haplotype-resolution marker data to support quantitative trait loci mapping in polyploids.
• Genome-wide association studies (GWAS): Generates multi-allelic haplotype markers suitable for association analyses in polyploid genomes.

Methodology:

Reconstructs haplotypes from SNP dosage data derived from genotyping arrays, uses phased haploblocks from closely-linked SNP markers, and incorporates full-sib family relationships to guide haplotype inference; evaluated on experimental hexaploid and simulated tetraploid datasets.