Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc), is the most lethal soil-borne fungal pathogen infecting bananas. Foc race 1 (R1) and 4 (R4) are the two most predominant races affecting the economically important Cavendish group of bananas in India. A total of seven vegetative compatibility groups (VCGs) from three pathogenic races were isolated during our field survey and were found to be highly virulent towards cv. Grande Naine. According to comparative genome analyses, these Indian Foc VCGs were diverse in genomic organization and effector gene profiles. As a result, false-positive results were obtained with currently available molecular markers. In this context, the study has been initiated to develop PCR-based molecular markers for the unambiguous identification of Indian Foc R1 and R4 isolates. Whole-genome sequences of Foc R1 (GCA_011316005.3), Foc TR4 (GCA_014282265.3), and Foc STR4 (GCA_016802205.1), as well as the reference genomes of Foc (ASM799451v1) and F. oxysporum f. sp. lycopersici (Fol; ASM14995v2), were aligned to identify unique variable regions among the Foc races. Using putative chromosome and predicted gene comparison, race-specific unique Foc virulence genes were identified. The putative lineage-specific identified genes encoding products secreted in xylem (SIX) that may be necessary for disease development in the banana. An in silico analysis was performed and primers were designed from a region where sequences were dissimilar with other races to develop a specific marker for Foc R1, R4, TR4, and STR4. These race-specific markers allowed target amplification in the characterized highly virulent Foc isolates, and did not show any cross-amplification to any other Foc races, VCGs or banana pathogens, Fusarium species, and non-pathogenic Fusarium oxysporum isolates. The study demonstrated that the molecular markers developed for all the three Foc races of India could detect the pathogen in planta and up to 0.025 pg µL⁻¹ DNA levels. Thus, the markers developed in this study are novel and could potentially be useful for the accurate diagnosis and detection of the Indian Foc races which are important for the effective management of the disease.

The effect of application of different biocontrol agents (Trichoderma spp (eight isolates), Pseudomonas fluorescens (four isolates) and Bacillus subtilis (two isolates)) was tested against head rot fungus, Sclerotinia sclerotiorum and root-knot nematode, Meloidogyne incognita complex diseases. In vitro studies showed that three Trichoderma isolates (Tvc1, Tvc2 and Thc) were effective in inhibition of mycelial growth of the fungus as well as egg hatching ability of the nematode. Application of talc based formulation of biocontrol agents (bioformulations) individually as well as in mixtures with or without chitin was tested against head rot–root-knot disease complex under greenhouse conditions. The combined application of bioformulation mixture (Tvc1, Tvc2 and Thc) along with chitin reduced the incidence of the complex diseases and induced significantly increased activities of phenylalanine ammonia-lyase (PAL), peroxidase (PO), polyphenol oxidase (PPO) and chitinase in cabbage. Activities of PAL and chitinase reached maximum levels within 10 – 20 d, while the activity of PAL continued to be maintained up to 40 d after the application of Tvc1 + Tvc2 + Thc + chitin. Isozyme analyses observed that unique PO (PO1, PO2 PO3 and PO4) and PPO (PPO1, PPO2 and PPO3) enzymes were induced after 10 d in cabbage plants treated with Tvc1 + Tvc2 + Thc + chitin upon challenge inoculation with head rot–root-knot pathogens. Similarly, the bioformulation mixture with chitin was successful at reducing the incidence of head rot–root-knot apart from enhancing the crop yield under field conditions. The mechanism associated with reduced incidence of head rot–root-knot in cabbage may be due to induction of defense proteins (PAL, PO, PPO and chitinase) in the crop.

Fusarium wilt, caused by the fungus Fusarium oxysporum f. sp. cubense, is the most serious pandemic disease of banana. In this study, we report the draft genome of F. oxysporum f. sp. cubense vegetative compatibility group (VCG) 01213/16 of strain tropical race 4 (TR4) that infects the Cavendish (AAA) group of banana collected from the subtropical region in India. The genome assembly of SFoc TR4 comprises 47,384,463 bp with 4,034 contigs and 15,508 protein-coding regions. Based on VCG analysis, the fungal isolate belongs to F. oxysporum f. sp. cubense TR4 but the genome sequence of SFoc TR4 shows differences in secreted-in-xylem (SIX) protein gene clusters (specifically, SIX8) in comparison with the reference genome of F. oxysporum f. sp. lycopersici and F. oxysporum f. sp. cubense TR4.