Abstract
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.
Highlights
Banana and plantain (Musa spp.) are the most important fruit crop in the world and approximately 148 million tones are produced annually from 135 countries [1]
A total of 21,842 intact protein-coding genes were predicted from the consensus gene sets of the Fusarium oxysporum sp. cubense (Foc) race 1 (R1) genome assembly, while, the Foc STR4 and TR4 genome assemblies contain 17,118 and 17,745 protein-coding regions, respectively
The results revealed that the Foc R1 contained a maximum of 524 tRNAs and 223 rRNAs, TR4 has a maximum of 358 tRNAs and 134 rRNAs, and STR4 has a total of 304 tRNAs and 121 rRNAs in the genome
Summary
Banana and plantain (Musa spp.) are the most important fruit crop in the world and approximately 148 million tones are produced annually from 135 countries [1]. It serves as a staple food for more than 400 million people worldwide and a source of income to many developing countries. Several hundreds of varieties are grown in different parts of the world, the Cavendish group of bananas contributes to 47% of global. J. Fungi 2022, 8, 53 parts of the world, the Ca parts of the world, the Cavendish group of bananas contributes to 47% tion, of global with producan export of 22. Fusarium wilt is cau ever, Fusarium wilt is caused by a soil-borne fungal disease Fusarium oxysporum sp. cubense (Foc)f.and is becomin production, with export of
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