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

Abstract

ABSTRACTAs global demand for bananas rises, the threat of banana bunchy top disease (BBTD), caused bybanana 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, sixRLKgenes involved in plant defense against pathogens were exclusively upregulated in the BBTV-resistant wildMusa balbisianacompared to the BBTV-susceptibleMusa acuminatacv. ’Lakatan’. Here, two genic variants ofRLKs, 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 117Musagenotypes at the NPGRL-IPBex situgermplasm, 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. acuminataspp. and otherMusaspp. (I), wildM. 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 amongMusaaccessions. 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.