Comparative RNA-seq analysis of resistant and susceptible banana genotypes reveals molecular mechanisms in response to banana bunchy top virus (BBTV) infection

Abstract

Bananas hold significant economic importance as an agricultural commodity, serving as a primary livelihood source, a favorite fruit, and a staple crop in various regions across the world. However, Banana bunchy top disease (BBTD), which is caused by banana bunchy top virus (BBTV), poses a considerable threat to banana cultivation. To understand the resistance mechanism and the interplay of host suitability factors in the presence of BBTV, we conducted RNA-seq-based comparative transcriptomics analysis on mock-inoculated and BBTV-inoculated samples from resistant (wild Musa balbisiana) and susceptible (Musa acuminata ‘Lakatan’) genotypes. We observed common patterns of expression for 62 differentially expressed genes (DEGs) in both genotypes, which represent the typical defense response of bananas to BBTV. Furthermore, we identified 99 DEGs exclusive to the 'Lakatan' banana cultivar, offering insights into the host factors and susceptibility mechanisms that facilitate successful BBTV infection. In parallel, we identified 151 DEGs unique to the wild M. balbisiana, shedding light on the multifaceted mechanisms of BBTV resistance, involving processes such as secondary metabolite biosynthesis, cell wall modification, and pathogen perception. Notably, our validation efforts via RT-qPCR confirmed the up-regulation of the glucuronoxylan 4-O-methyltransferase gene (14.28 fold-change increase), implicated in xylan modification and degradation. Furthermore, our experiments highlighted the potential recruitment of host's substrate adaptor ADO (30.31 fold-change increase) by BBTV, which may play a role in enhancing banana susceptibility to the viral pathogen. The DEGs identified in this work can be used as basis in designing associated gene markers for the precise integration of resistance genes in marker-assisted breeding programs. Furthermore, the findings can be applied to develop genome-edited banana cultivars targeting the resistance and susceptibility genes, thus developing novel cultivars that are resilient to important diseases.

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

“…Through extensive transcriptome analysis, the recent findings of Lantican et al (2023) have expanded our understanding on the molecular mechanisms underpinning BBTV resistance in bananas, paving the way for targeted genetic improvement to expedite the development of BBTV-resistant banana cultivars. To continue this initiative, we further investigated gene sequence diversity and polymorphisms of six RLK genes, the first line of plant defense against pathogens, across banana accessions at the NPGRL-IPB’s banana ex situ germplasm collection.…”

“…Six (6) upregulated receptor-like kinase ( RLK ) genes exclusive to wild M. balbisiana (BBTV-resistant) were obtained from the study of Lantican et al (2023), as summarized in Table 2, and their corresponding nucleotide sequences were retrieved from the Banana Genome Hub (https://banana-genome-hub.southgreen.fr/) platform. Sequencing primers per gene were designed using SnapGene software (from Insightful Science; accessible at snapgene.com) following the general guidelines for PCR primer design: primer length of 17-24 bases, 40-50% GC content, minimum T m mismatch of 2-3°C, G/C clamp at 3’ end, and avoidance of repeats and runs, as well as secondary structures (hairpin maximum ΔG: -0.3 kcal/mol; self-dimer maximum ΔG: -0.6 kcal/mol; and cross dimer maximum ΔG: -0.9 kcal/mol).…”

“…Resistance evaluations in the Philippines, however, have identified wild M. balbisiana accessions to have complete resistance or immunity to the virus (Dela Cueva et al 2023). Utilizing these germplasm materials, Lantican et al (2023) identified differentially expressed genes in two distinct banana genotypes: BBTV-resistant wild M. balbisiana (BBw) and susceptible M. acuminata cv. ‘Lakatan’ (AAA), making a significant stride in understanding the molecular basis of banana resistance against BBTV.…”

“…While RLKs have been studied in various plant species such as Arabidopsis (Shiu et al 2004; Jose et al 2020), soybean (Liu et al 2009), wheat (Yan et al 2023), and rice (Song et al 1995; Shiu et al 2004), their specific involvement in banana’s resistance to BBTV remains unexplored. By further investigating the differentially expressed banana RLK genes identified by Lantican et al (2023) using complementary approaches (i.e., genic variation identification, wet laboratory investigations, and genetic association studies), researchers can strengthen our understanding on their potential roles in defense mechanisms against BBTV infection and uncover other genetic factors influencing BBTD resistance of bananas.…”

“…List of upregulated receptor-like kinase (RLK) genes in BBTV-resistant wild Musa balbisiana accession(Lantican et al, 2023) and their functions.…”