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Genetic Structure and Diversity of Banana Bunchy Top Virus (BBTV) in the Philippines

Jay-Vee S. Mendoza, Fe M. dela Cueva, View ORCID ProfileCris Q. Cortaga, Anand Noel C. Manohar, View ORCID ProfileRoanne R. Gardoce, Grace C. Lachica, Maricel C. Gonzales, John E. Thomas, View ORCID ProfileDarlon V. Lantican
doi: https://doi.org/10.1101/2021.05.11.442582
Jay-Vee S. Mendoza
1Institute of Plant Breeding, College of Agriculture and Food Science
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Fe M. dela Cueva
1Institute of Plant Breeding, College of Agriculture and Food Science
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  • For correspondence: fmdelacueva@up.edu.ph dvlantican@up.edu.ph
Cris Q. Cortaga
1Institute of Plant Breeding, College of Agriculture and Food Science
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  • ORCID record for Cris Q. Cortaga
Anand Noel C. Manohar
1Institute of Plant Breeding, College of Agriculture and Food Science
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Roanne R. Gardoce
1Institute of Plant Breeding, College of Agriculture and Food Science
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Grace C. Lachica
1Institute of Plant Breeding, College of Agriculture and Food Science
2Philippine Genome Center-Agriculture, Livestock & Fisheries Program University of the Philippines Los Baños (UPLB), College, Laguna 4031, Philippines
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Maricel C. Gonzales
1Institute of Plant Breeding, College of Agriculture and Food Science
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John E. Thomas
3The University of Queensland Ecosciences Precinct, Level 2C west, GPO Box 267, Brisbane, Queensland 4001, Australia
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Darlon V. Lantican
1Institute of Plant Breeding, College of Agriculture and Food Science
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  • For correspondence: fmdelacueva@up.edu.ph dvlantican@up.edu.ph
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Abstract

Banana bunchy top virus (BBTV) is an important disease of banana in the Philippines and in other banana-producing countries. This study was conducted to investigate the genetic structure and diversity of Philippine BBTV isolates which remain unexplored in the country. BBTV-infected plant tissues were sampled from banana-growing provinces (i.e., Cagayan, Isabela, Quirino, Batangas, Laguna, Rizal, Quezon, Palawan, Cebu, Leyte, and Davao del Sur) and the partial DNA-R gene of BBTV was sequenced. Analysis of all local BBTV isolates showed a nucleotide diversity (π) of 0.00721, average number of nucleotide differences (k) of 5.51984, and haplotype diversity (hd) of 0.971. Neutrality tests using Fu’s Fs and Tajima’s D showed significant and highly negative values which suggest an excess number of rare alleles due to recent population expansion or from genetic hitchhiking. Haplotype network and phylogenetic analyses revealed that the local BBTV isolates were closely related to Southeast Asian (SEA) group and exhibited a monophyletic clade with distinct haplotype grouping from other SEA sequences. However, some Indonesian and Indian reference sequences were also clustered within the Philippine BBTV group suggesting sequence homology. Results also showed that the local BBTV isolates may be categorized into three major haplotype groups (HA, HB, and HC) but only the HC group remained distinct upon comparison with other Philippine and SEA reference sequences. BBTV isolates from Quezon were the most diverse while isolates from Palawan displayed low genetic diversity indices and belonged only in the HC group. The assessment of the degree of variability among Philippine BBTV isolates will provide a reference towards the development of high-throughput BBTV detection systems as well as enable to devise plant breeding strategies to manage the current BBTV spread and variations.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted May 12, 2021.
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Genetic Structure and Diversity of Banana Bunchy Top Virus (BBTV) in the Philippines
Jay-Vee S. Mendoza, Fe M. dela Cueva, Cris Q. Cortaga, Anand Noel C. Manohar, Roanne R. Gardoce, Grace C. Lachica, Maricel C. Gonzales, John E. Thomas, Darlon V. Lantican
bioRxiv 2021.05.11.442582; doi: https://doi.org/10.1101/2021.05.11.442582
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Genetic Structure and Diversity of Banana Bunchy Top Virus (BBTV) in the Philippines
Jay-Vee S. Mendoza, Fe M. dela Cueva, Cris Q. Cortaga, Anand Noel C. Manohar, Roanne R. Gardoce, Grace C. Lachica, Maricel C. Gonzales, John E. Thomas, Darlon V. Lantican
bioRxiv 2021.05.11.442582; doi: https://doi.org/10.1101/2021.05.11.442582

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