Genome-wide association study reveals novel resistance loci to banana weevil (Cosmopolites sordidus) in Rwandan Musa cultivars

The banana weevil (Cosmopolites sordidus) poses a significant threat to banana production in Rwanda, causing annual yield losses of 30-60%. While traditional pest management strategies exist, genetic resistance offers a more sustainable long-term solution. This study aimed to identify genomic loci associated with banana weevil resistance in Rwandan Musa cultivars through genome-wide association study (GWAS) analysis. We conducted a comprehensive GWAS using 485 Musa accessions from Rwanda's national banana germplasm collection. Phenotypic evaluation involved controlled weevil infestation trials across three locations (Rubona, Karama, and Rwerere) over two seasons (2022-2023). Genotyping was performed using genotyping-by-sequencing (GBS), yielding 45,678 high-quality SNPs. Population structure, linkage disequilibrium, and association mapping were analyzed using TASSEL 5.0 and GAPIT3. Significant phenotypic variation was observed among cultivars (H2 = 0.74, p < 0.001). GWAS identified 23 significant SNPs (p < 2.19 × 10−6) associated with weevil resistance across chromosomes 2, 5, 8, and 11. The strongest association was found on chromosome 8 (SNP8_2347891, p = 4.32 × 10−9, R2 = 12.4%). Candidate genes within resistance loci included leucine-rich repeat receptor kinases, chitinases, and phenylpropanoid biosynthesis enzymes. Local Rwandan cultivars 'Injagi', 'Igikashi', and 'Intokatoke' demonstrated exceptional resistance levels (damage index < 2.0). This study provides the first comprehensive genetic analysis of banana weevil resistance in Rwandan germplasm, identifying novel resistance loci and candidate genes. These findings offer valuable resources for marker-assisted selection and breeding programs to develop weevil-resistant banana varieties adapted to Rwandan conditions.