polymapR

polymapR constructs linkage maps for outcrossing autopolyploid species (e.g., potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato, kiwifruit, rose) by analyzing marker dosage scores to enable genetic mapping across triploid, tetraploid, and hexaploid datasets.

Key Features:

• Genetic Linkage Analysis: polymapR creates linkage maps by analyzing marker dosage scores derived from F1 crosses between two heterozygous parents in bi-parental populations.
• Integrated Genetic Map Construction: polymapR integrates marker data across different ploidy levels, enabling construction of comprehensive integrated linkage maps for triploid, tetraploid, and hexaploid datasets.
• Preferential Chromosome Pairing Detection and Correction: polymapR estimates preferential chromosome pairing and applies corrections to account for nonrandom pairing in polyploids.
• High-Density Marker Dataset Compatibility: polymapR supports high-density marker datasets and has been tested on datasets from potato, rose, and chrysanthemum.

Scientific Applications:

• Breeding and Genetic Research: polymapR supports breeding programs and genetic research in polyploid crops by enabling linkage map construction from marker dosage data produced by modern genotyping platforms to aid trait improvement such as yield, disease resistance, and environmental adaptability.
• Crop-Specific Linkage Mapping: polymapR enables high-resolution linkage mapping and inheritance analysis in polyploid crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato, kiwifruit, and rose.

Methodology:

Analyzes bi-parental F1 populations of outcrossing autopolyploids using marker dosage scores from two heterozygous parents to construct linkage maps, integrate data across ploidies, detect and estimate preferential chromosome pairing, and apply corrections.