Identification of the Loci Associated with Resistance to Banana <i>Xanthomonas</i> Wilt (<i>Xanthomonas vasicola</i> pv. <i>musacearum</i>) Using DArTSeq Markers and Continuous Mapping

Banana <i>Xanthomonas</i> wilt, caused by <i>Xanthomonas vasicola</i> pv. <i>musacearum</i> (<i>Xvm</i>), is a devastating disease that results in total yield loss of affected plants. Resistance to the disease is limited in <i>Musa acuminata</i>, but it has been identified so far in the <i>zebrina</i> subspecies. This study identified markers associated with tolerance to <i>Xvm</i> in Monyet, a tetraploid banana from the <i>zebrina</i> subspecies which was identified to be partially resistant to the bacterium. We used a triploid progeny of 135 F₁ hybrids resulting from a cross between Monyet (<i>Xvm</i> partially resistant) and Kokopo (diploid and <i>Xvm</i> susceptible). The F₁ hybrids were screened in pots for resistance to <i>Xvm</i>. The population was genotyped using the genotyping-by-sequencing platform of Diversity Array Technology (DArTSeq). The adjusted means of the phenotypic data were combined with the allele frequencies of the genotypic data in continuous mapping. We identified 25 SNPs associated with resistance to <i>Xvm</i>, and these were grouped into five quantitative traits loci (QTL) on chromosomes 2, 3, 6, and 7. For each marker, we identified the favorable allele and the additive effect of replacing the reference allele with the alternative allele. The comparison between weevil borer (<i>Cosmopolites sordidus</i> (Germar)) and <i>Xvm</i> QTL revealed one QTL shared between the two biotic stresses at the distal end of chromosome 6 but with a repulsion linkage. This linkage should be broken down by generating more recombinants in the region. We also identified 18 putative alleles in the vicinity of the SNPs associated with resistance to <i>Xvm</i>. Among the 18 putative genes, two particularly putative genes, namely, <i>Ma06_g13550</i> and <i>Ma06_g36840</i>, are most likely linked to disease resistance. This study is a basis for marker-assisted selection to improve banana resistance to banana Xanthomonas wilt, especially in East and Central Africa where the disease is still devastating the crop.