RADtyping

RADtyping performs de novo genotyping from Restriction-site Associated DNA sequencing (RAD-Seq) data to enable construction of high-density genetic linkage maps and downstream QTL analysis.

Key Features:

• De Novo Genotyping: Performs genotyping without a reference genome and supports both codominant and dominant marker typing.
• Dominant Marker Statistical Framework: Implements a statistical framework to genotype dominant markers arising from recognition site disruptions in eukaryotic genomes.
• High Genotyping Accuracy: Delivers high accuracy on both simulated and real mapping datasets.
• RAD-Seq Format Support: Processes single-end and paired-end RAD sequencing data.
• Integrated Algorithms: Integrates algorithms for simultaneous codominant and dominant marker analysis for linkage mapping.

Scientific Applications:

• Genetic Linkage Mapping: Constructs high-resolution linkage maps, exemplified by a map with unprecedented marker density in Chlamys farreri covering nearly the entire genome.
• Quantitative Trait Locus (QTL) Mapping: Facilitates identification of QTLs, including growth-related regions and potential sex-determination areas, and has been used to identify the candidate gene PROP1 linked to growth hormone regulation.
• Genomic Resource Integration: Supports linkage mapping and genome survey sequencing to improve genome assembly and unify genomic resources in non-model organisms lacking extensive genomic data.

Methodology:

Applies a statistical framework for de novo genotyping of codominant and dominant markers, models dominant markers caused by recognition site disruptions, and processes RAD-Seq reads from single-end and paired-end sequencing formats.