Bananas are vital for food security in many countries, and half of banana production relies solely on ‘Cavendish’ (AAA), which is presently threatened by the fungal pathogenFusarium oxysporumf. sp.cubense(Foc) tropical race 4. This particular virulentFocstrain was also found to attack other banana varieties of commercial importance. As there is no single effective management practice available so far, this study was undertaken to determine resistant sources from the genotype collection available at the ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu, India for direct use by farmers and/or in breeding programmes to develop resistant hybrids. A total of 258 genotypes of different ploidies and genomic constitutions were tested againstFocrace 1 (VCG 0124). In total, 19 genotypes (AA Unique-6, BB type-2, AAA Unique-1, AAA Cavendish-1, AAB Mysore-3, AAB Pome-1, AAB Plantain-4 and AAAB-1) were found to be immune; eight genotypes (AA Unique-1, BB type-3, AAA Cavendish-1, AAB Mysore-1, AAB Unique-1, AAB Plantain-1) were highly resistant; and nine genotypes (AA Unique-1, AAA Cavendish-3, AAB Silk-1, AAB Pome-4) were resistant. The genotypes that are resistant to the virulentFocrace 1 (VCG 0124) strain can be exploited directly for commercialization and/or in breeding programs to develop resistant hybrids.

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.

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.

Fusarium wilt of banana is a major production constraint in India, prompting banana growers to replace bananas with less remunerative crops. Effective disease management practices thus need to be developed and implemented to prevent further spread and damage caused by Fusarium oxysporum f. sp. cubense (Foc), the cause of Fusarium wilt. Currently, knowledge of disease incidence, affected varieties, and the geographical spread of Foc races in India are only scantily available. An extensive field survey was conducted in 53 districts of 16 major banana-growing states of and one union territory of India that covered both tropical and subtropical regions. Disease incidence ranged from 0 to 95% on farms, with Cavendish bananas (AAA) most affected. No Fusarium wilt symptoms due to Foc R1 were observed in Nendran (AAB) or Red Banana (AAA) in South India. During the survey, 293 Foc isolates were collected from Cavendish, Pisang Awak (ABB), Silk (AAB), Monthan (ABB), Neypoovan (AB), and Mysore (AAB) bananas. Isolate diversity was assessed through Vegetative Compatibility Group (VCG) analyses, sequencing of EF1α gene sequences, phylogenetic analyses, and characterisation by SIX gene composition. Thirteen VCGs were identified, of which VCGs 0124, 0125, 01220, and 01213/16 were dominant and infected Cavendish bananas. Phylogenetic analysis divided the Indian Foc isolates into race 1 (R1), subtropical race 4 (STR4), and tropical race 4 (TR4). Secreted in Xylem (SIX) gene analyses indicated that the effector genes SIX4 and SIX6 were present in the VCGs 0124, 0124/5, 0125, and 01220 of race 1, SIX7 was present only in Foc STR4, and SIX8 was found only in Foc R4 (TR4 and STR4) isolates. Insights into the geographical distribution of Foc races, and their interactions with banana varieties, can guide integrated disease management intervention strategies across India.