CLARITY

CLARITY provides aligned high-resolution bovine genetic and physical maps that integrate Illumina BovineSNP50-based linkage maps from German Holstein and German/Austrian Fleckvieh pedigrees with the ARS-UCD1.2 chromosome-level assembly to support recombination and marker-placement analyses.

Key Features:

• Genetic and physical map visualization: Presents genetic (linkage) and physical coordinates with inter-marker distances in base pairs and recombination rates between marker pairs.
• High-resolution genetic maps: Uses pedigree-derived linkage data from large German Holstein and German/Austrian Fleckvieh datasets built on the Illumina BovineSNP50 genotyping array and aligned to ARS-UCD1.2.
• Recombination hotspot landscapes: Provides recombination-rate profiles and hotspot identification across whole chromosomes and specific chromosomal regions.
• Genetic map function analysis: Evaluates which commonly used genetic-map functions best fit local recombination data.
• Auxiliary marker placement information: Reports markers that may be misplaced relative to the ARS-UCD1.2 assembly.
• Cross-breed data integration: Integrates ongoing data from multiple cattle breeds to enable comparative genomic analyses.

Scientific Applications:

• QTL fine-mapping: Supports high-resolution localisation of quantitative trait loci using combined linkage and physical coordinates.
• Assembly curation and marker placement: Aids identification and correction of marker misplacements in the ARS-UCD1.2 assembly.
• Comparative bovine genomics: Enables comparison of recombination landscapes and marker order between German Holstein and German/Austrian Fleckvieh datasets.
• Recombination biology and evolutionary studies: Facilitates analysis of recombination rate variation and hotspot distribution for evolutionary and breeding research.

Methodology:

Constructs pedigree-based genetic maps from Illumina BovineSNP50 genotype data derived from German Holstein and German/Austrian Fleckvieh cohorts and aligns these linkage maps to the ARS-UCD1.2 chromosome-level genome assembly.