A complex relationship : banana & Fusarium wilt in Indonesia

Banana is one of the most consumed fruits and also a staple in many countries. Sustaining banana production is important to supply domestic and international markets, which support the livelihood of millions of smallholder farmers. The most beloved fruit was and is currently devastated by one of the most threatening plant diseases in history called Fusarium wilt or Panama disease. The disease is caused by a suite of soil born fungi, previously collectively known as Fusarium oxysporum f. sp. cubense (Foc). A prime strategy to manage the ongoing pandemic of the disease that has devastated thousands of hectares of banana plantations in many countries is the generation of resistant banana varieties. Therefore, more knowledge on the diversity of the causal fungi is indispensable. Indonesia is the main centre of origin of banana where hundreds of wild and cultivated varieties are grown across the entire archipelago. Generally, the centres of diversity of hosts and pathogens overlap. Thus, Indonesia is the primary region to study the diversity of the pathogens causing Panama disease due to their co-evolution with the banana hosts. This thesis provides some of the most informative studies on the genetic diversity and phylogeny of Fusarium spp. associated with Panama disease. It contributes to the knowledge on the systematics of Fusarium species with pathogenicity to banana, their genotypic diversity and pathogenicity, as well as on non-pathogenic Fusarium spp. hitchhiking with pathogenic species in the interior of banana stems. In chapter 1, I describe the current state of art of banana research and the related Fusarium pathogens. Also, the history and early domestication of banana, its production and importance as a fruit crop commodity are described. This is then connected with Fusarium wilt as one of the main constraints, culminating in the importance and urgency of studying the diversity of the causal pathogens in Indonesia. Chapter 2 describes a sampling expedition to sample Fusarium wilt affected banana plants across 34 geographical locations of the main banana producing areas in Indonesia on Java, Flores, Kalimantan, Papua, Sumatra and Sulawesi. More than 200 Fusarium isolates were recovered from many local varieties that suffered from the disease. The identification and characterization of this collection represents the most extensive diversity analysis of Fusarium spp. associated with Panama disease. Using multi-gene phylogenetic analyses, I discovered nine distinct genetic lineages with pathogenicity to banana, which were recognised as new phylogenetic species in the Fusarium oxysporum species complex (FOSC), to which new names and taxonomic descriptions were assigned. The complexity and current status of Fusarium wilt disease in banana in Indonesia is also discussed. In Chapter 3, I expanded the diversity analyses by using whole genomic profiles generated by genotyping-by-sequencing using Diversity Array Technology (DArTseq) markers. Cluster analyses of Indonesian and global isolates revealed the widest genotypic diversity ever reported in Fusarium wilt pathogens of banana. More than half of the genotypes identified are present in Indonesia, suggesting that Fusarium spp. co-evolved with local banana varieties. I provide strong evidence that the so-called Tropical Race 4 (TR4) that kills Cavendish varieties, likely emerged from Indonesia, and is still evolving with many local varieties. In contrast, Race 1 isolates, which caused the first epidemic in Gros Michel bananas in the previous century display more genetic diversity. Such precise descriptions of genetic diversity are very important to further explore disease resistance in native and wild banana varieties. The reliability of DArTseq markers was demonstrated by their power to discriminate isolates below the Fusarium spp. level, which provided an unparalleled robustness of the proposed species concept. Chapter 4 focuses on the pathogenicity of the Indonesian collection of Fusarium spp. described in chapter 2 and 3. All isolates were phenotyped on Grand Naine, Gros Michel, the wild diploid Musa acuminata ssp. malaccensis (Pahang) and the diploid cultivated variety Pisang Rejang. This resulted in a large database with qualitative and quantitative variation for pathogenicity for the ten identified Fusarium spp. in Indonesia. Interestingly, TR4 isolates mapped to one species that I named Fusarium odoratissimum, whereas Race 1 strains belonged to six species. Chapter 5 describes the discovery of other non-pathogenic Fusarium species hitchhiking with pathogenic Fusarium spp. on banana. Multi-gene phylogenies revealed two new species in the F. fujikuroi species complex (FFSC), six new species in the F. incarnatum-equiseti species complex (FIESC) and one isolate of F. longipes in the F. sambucinum species complex (FSSC). The latter was never reported to be present in the pseudostem of banana plants. None of these species are pathogenic on banana and hence, these findings give an insight into the endophytic existence of Fusarium spp. in non-host plants and their potential role in the Fusarium wilt disease of banana. In chapter 6, the findings in all chapters are synthesized in an overarching discussion. The required taxonomic revision of the Fusarium wilt pathogens of banana is discussed with a proposition to place them in the Fusarium of banana complex (FuBC). The adopted approach of identification comprising molecular-based diversity analyses, which excels over phenotyped-based diversity analyses and the evidence of possible sources of genetic variation in these asexual fungi are also discussed. Despite the advances, the FuBC – banana pathosystem lacks a genetic basis and comparative analyses with other formae speciales might therefore be very useful as well as genetic studies in the host. With well-characterized Fusarium species, such studies become meaningful and will contribute to an overall strategy for developing new and resistant banana germplasm. The thesis ends with a complete overview of all cited references.