Biology subjects

Manohar, A. N. C.

Publications and source records attributed to Manohar, A. N. C..

6 recordsLinked to original sources

bioRxiv2023

Development and validation of allele specific RLK gene markers for banana bunchy top disease (BBTD) resistance in banana

As global demand for bananas rises, the threat of banana bunchy top disease (BBTD), caused by banana bunchy top virus (BBTV), poses a significant constraint to sustainable banana production. To circumvent this, it is critical to fast-track the development of BBTV-resistant banana cultivars. In a dataset of differentially expressed genes between BBTV-resistant and susceptible bananas, six RLK genes involved in plant defense against pathogens were exclusively upregulated in the BBTV-resistant wild Musa balbisiana compared to the BBTV-susceptible Musa acuminata cv. Lakatan. Here, two genic variants of RLKs, single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSR), were identified in 10 banana accessions representing major genomic groupings. Nine gene-specific markers were developed using three marker systems: SSR, allele-specific PCR, and tetra primer amplification refractory mutation system PCR markers. Six of these were polymorphic and successfully discriminated 117 Musa genotypes at the NPGRL-IPB ex situ germplasm, with an average polymorphism information content of 0.36 for SNP markers and 0.49 for SSR marker, both of which are moderately informative. These markers facilitated the construction of a dendrogram using the Unweighted Neighbor-Joining (UNJ) method with 1000 bootstrap iterations, identifying four major clades: M. acuminata spp. and other Musa spp. (I), wild M. balbisiana (BBw) and other accessions with high-proportion of B-genome (II & III), hybrid bananas (triploids and tetraploids) (IV), which revealed the genetic diversity and relationships among Musa accessions. Ultimately, this genomic resource will aid in positioning the Philippines as a key player in banana disease resistance breeding towards a food-secure banana industry.

genetics↗

bioRxiv2023

Comparative transcriptomics reveals the molecular mechanisms of maize in response to downy mildew caused by Peronosclerospora philippinensis (Weston) Shaw

Maize is the Philippines second most valuable staple crop based on overall value and total area planted. Yellow maize, which is the most important type, is utilized as feed for poultry and swine. Still, local maize production is hampered by the Philippine downy mildew (DM) disease caused by the pathogen Peronosclerospora philippinensis (Weston) Shaw, causing substantial losses in maize production annually. To comprehend the underlying resistance mechanisms upon the presence of the disease, we performed an RNA-Seq comparative transcriptomics approach between mock-inoculated and DM-inoculated susceptible and resistant yellow maize inbred lines. Among the identified differentially expressed genes (DEGs), we detected 43 DEGs shared in both genotypes which may play roles in the basal defense response of maize upon DM infection. We also identified 68 DEGs exclusive to the susceptible genotype, providing insights into the molecular responses underlying successful DM disease progression in maize. Further, we detected 651 DEGs unique to the resistant genotype. This set of genes revealed that the molecular basis of DM resistance in maize is governed by multi-faceted defense strategies. These include multi-process regulations such as programmed cell death (PCD), regulatory proteins, and transcription factors involved in pathogen defense mechanisms, cell wall organization, homeostasis, and many others. Out of 694 resistant DEGs detected, we narrowed down genes of interest, particularly those highly overexpressed and associated with disease resistance found in other crops. Finally, transcriptome-wide variants and their corresponding impact on gene function were detected for further application in targeted genotyping-by-sequencing, association studies, and marker-assisted DM resistance breeding.

genetics↗

bioRxiv2022

Comparative RNA-seq analysis of resistant and susceptible banana genotypes reveals molecular mechanisms in response to Banana bunchy top virus (BBTV)

Banana is a major fruit crop in the Philippines and remains to be a large contributor to the countrys dollar reserve. Among the main hindrances in global banana production, diseases such as Banana bunchy top disease (BBTD) caused by BBTV can bring catastrophic loss to any banana plantation. To elucidate the resistance mechanism and understand the interplay of host factors in the presence of the invading pathogen, we implemented RNA-seq-based comparative transcriptomics analyses of mock- and BBTV-inoculated resistant (wild M. balbisiana) and susceptible (M. acuminata Lakatan) banana genotypes. Similar patterns of expression for 119 differentially expressed genes (DEGs) were observed on both genotypes, representing the typical defense response of banana to BBTV. A set of 173 DEGs specific to the susceptible Lakatan banana cultivar revealed potential host factors and susceptibility mechanisms involved in successful BBTV infection. Further, differential transcriptomic analysis revealed 268 DEGs exclusive to the resistant wild M. balbisiana, unraveling insights into the complex resistance mechanisms involved in BBTV defense such as pathogen perception, phytohormone action, reactive oxygen species (ROS), hypersensitive response (HR), production of secondary metabolites and cell wall modification. The DEGs identified in this study will aid in the design of foreground markers for the precise integration of resistance genes during marker-assisted breeding programs. Furthermore, the application of these results will also enable the foreseen deployment of genome-edited banana cultivars targeting the resistance and host factor genes towards a future-proof banana industry.

genomics↗

bioRxiv2021

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

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 ({pi}) of 0.00721, average number of nucleotide differences (k) of 5.51984, and haplotype diversity (hd) of 0.971. Neutrality tests using Fus Fs and Tajimas 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.

genetics↗

bioRxiv2020

Reference-Aided Full-length Transcript Assembly, cDNA Cloning, and Molecular Characterization of 1 Coronatine-insensitive 1b (COI1b) Gene in Coconut (Cocos nucifera L.)

In the Philippines, 26% of the total agricultural land is devoted to coconut production making coconut one of the most valuable industrial crop in the country. However, the countrys multimillion-dollar coconut industry is threatened by the outbreak of coconut-scale insect (CSI) and other re-emerging insect pests promoting national research institutes to work jointly on developing new tolerant coconut varieties. Here, we report the cloning and characterization of coronatine-insensitive 1 (COI1) gene, one of the candidate insect defense genes, using Catigan Green Dwarf (CATD) genome sequence assembly as reference. Two (2) splicing variants were identified and annotated - CnCOI1b-1 and CnCOI1b-2. The full-length cDNA of CnCOI1b-1 was 7,919 bp with an ORF of 1,176 bp encoding for a deduced protein of 391 amino acids while CnCOI1b-2 has 2,360 bp full-length cDNA with an ORF of 1,743 bp encoding a deduced protein of 580 amino acids. The 3D structural model for the two (2) isoforms were generated through homology modelling. Functional analysis revealed that both isoforms are involved in various physiological and developmental plant processes including defense response of plants to insects and pathogens. Phylogenetic analysis confirms high degree of COI1 protein conservation during evolution, especially among monocot species. Key MessageThis paper reports the molecular cloning and characterization of corononatine-insensitive I (COI1) gene in coconut using reference-guided transcript assembly approach. As a well-known insect defense-response gene in other crops, the results of this study are expected to assist in the development of new resistant coconut varieties as one of the strategies to address threats in coconut production.

genomics↗

bioRxiv2020

Transcriptome-wide analysis of expressed resistance gene analogs (RGAs) in mango

Mango is an economically important fruit crop largely cultivated in the (sub)tropics and thus, is constantly challenged by a myriad of insect pests and diseases. Here, we identified and characterized the resistance gene analogs (RGAs) of mango from de novo assembly of transcriptomic sequences. A core RGA database of mango with 747 protein models was established and classified based on conserved domains and motifs: 53 nucleotide binding site proteins (NBS); 27 nucleotide binding site-leucine rich repeat proteins (NBS-LRR); 17 coiled-coil NBS-LRR (CNL); 2 toll/interleukin-1 receptor NBS-LRR (TNL); 29 coiled-coil NBS (CN); 4 toll/interleukin-1 receptor NBS (TN); 17 toll/interleukin-1 receptor with unknown domain (TX); 158 receptor-like proteins (RLP); 362 receptor-like kinases (RLK); 72 transmembrane coiled-coil domain protein (TM-CC), and 6 NBS-encoding proteins with other domains. The various molecular functions, biological processes, and cellular localizations of these RGAs were functionally well-annotated through gene ontology (GO) analysis, and their expression profiles across different mango varieties were also determined. Phylogenetic analysis broadly clustered the core RGAs into 6 major clades based on their domain classification, while TM-CC proteins formed subclades all across the tree. The phylogenetic results suggest highly divergent functions of the RGAs which also provide insights into the mango-pest co-evolutionary arms race. From the mango RGA transcripts, 134 unique EST-SSR loci were identified, and primers were designed targeting these potential markers. To date, this is the most comprehensive analysis of mango RGAs which offer a trove of markers for utilization in resistance breeding of mango.

molecular biology↗