AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Traditional genetic mapping relies heavily on reference genome assemblies for variant calling and map construction.
• The absence of a reference genome poses a significant challenge for genetic analysis and map development in many species.
• Existing methods can be limited by the quality and completeness of available genome assemblies.

Purpose of the Study:

• To introduce and validate an assembly-free linkage analysis pipeline (AFLAP) for constructing high-density genetic maps.
• To demonstrate the utility of AFLAP in generating unbiased genetic maps without requiring a reference genome.
• To showcase AFLAP's capability in facilitating chromosome-scale genome assembly.

Main Methods:

• AFLAP identifies segregating markers as k-mers directly from raw sequencing reads.
• The pipeline bypasses the need for a reference genome for variant calling and genotype table generation.
• AFLAP was validated using simulated data and applied to whole genome sequencing and genotype-by-sequencing data from plant populations (F1, F2, RILs).

Main Results:

• AFLAP successfully generated unbiased, high-density genetic maps for two plant species, which were concordant with existing genome assemblies.
• The pipeline proved effective across different population types (F1, F2, RILs) and sequencing strategies (WGS, GBS).
• An AFLAP-derived genetic map for *Bremia lactucae* enabled the successful production of a chromosome-scale genome assembly.

Conclusions:

• AFLAP provides a robust, reference-free approach for genetic map construction, significantly advancing genetic analysis in non-model organisms.
• The pipeline overcomes limitations associated with the lack of a reference genome, enabling high-resolution mapping.
• AFLAP is a valuable tool for accelerating genome assembly and understanding the genetic architecture of traits in diverse species.