Development and validation of allele specific RLK gene markers for banana bunchy top disease (BBTD) resistance in banana

As global demand for bananas rises, the threat of banana bunchy top disease (BBTD), caused by banana bunchy top virus (BBTV), poses a significant constraint to sustainable banana production. To circumvent this, it is critical to fast-track the development of BBTV-resistant banana cultivars. In a dataset of differentially expressed genes between BBTV-resistant and susceptible bananas, six RLK genes involved in plant defense against pathogens were exclusively upregulated in the BBTV-resistant wild Musa balbisiana compared to the BBTV-susceptible Musa acuminata cv. Lakatan. Here, two genic variants of RLKs, single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSR), were identified in 10 banana accessions representing major genomic groupings. Nine gene-specific markers were developed using three marker systems: SSR, allele-specific PCR, and tetra primer amplification refractory mutation system PCR markers. Six of these were polymorphic and successfully discriminated 117 Musa genotypes at the NPGRL-IPB ex situ germplasm, with an average polymorphism information content of 0.36 for SNP markers and 0.49 for SSR marker, both of which are moderately informative. These markers facilitated the construction of a dendrogram using the Unweighted Neighbor-Joining (UNJ) method with 1000 bootstrap iterations, identifying four major clades: M. acuminata spp. and other Musa spp. (I), wild M. balbisiana (BBw) and other accessions with high-proportion of B-genome (II & III), hybrid bananas (triploids and tetraploids) (IV), which revealed the genetic diversity and relationships among Musa accessions. Ultimately, this genomic resource will aid in positioning the Philippines as a key player in banana disease resistance breeding towards a food-secure banana industry.