Which genomic technique would best identify candidate genes for armor variation in sticklebacks?

• A. Karyotype analysis.
• B. Targeted Sanger sequencing of known armor genes.
• C. Genome-wide association studies (GWAS) or QTL mapping combined with whole-genome sequencing.
• D. Expression profiling using microarrays.

Answer: (C)

Identifying how natural variation in a trait is wired to the genome requires linking genetic differences to the phenotype across many individuals and then zooming in on the exact DNA changes. For armor variation in sticklebacks, a combination of genome-wide association studies or quantitative trait locus mapping with whole-genome sequencing is ideal because GWAS or QTL mapping scans the genome to find regions where genetic variation co-segregates with armor patterns, while whole-genome sequencing provides the detailed sequence within those regions to pinpoint candidate genes and variants. Other approaches miss key pieces: karyotype analysis only reveals chromosome structure and cannot identify gene-level contributors to variation; targeted sequencing of known armor genes looks only at a predefined set of loci and may miss other important regions; expression profiling shows which genes are active but not which DNA changes cause the trait, and it may overlook regulatory variants or differences that affect armor without changing expression in the sampled tissue. The pooled strategy of GWAS/QTL mapping plus comprehensive sequencing therefore offers the broad discovery and precise narrowing needed to identify candidate genes for armor variation.