Dirigent (DIR) proteins are important regulators of stereoselective lignan biosynthesis and play significant roles in lignification and plant defense against both biotic and abiotic stresses. However, the role of the DIR gene family in banana (Musa spp.) under such stress conditions remains largely unexplored. Therefore, a genome-wide analysis of the DIR gene family was undertaken to characterize these genes and to gain insights into their potential involvement in stress responses, with the aim of supporting the development of improved stress-resistant banana cultivars. A total of 26 DIR genes were identified in Musa acuminata (A genome) and 30 in M. balbisiana (B genome), and classified into nine subfamilies based on phylogenetic relationships. Duplication analysis indicated that purifying selection has played a major role in their evolution. Promoter analysis showed enrichment of hormone- and stress-responsive cis-elements, particularly those related to jasmonic acid, salicylic acid, and abscisic acid signaling. Expression profiling under Pseudocercospora eumusae, Pratylenchus coffeae, and moisture deficit stresses revealed that several dir genes, especially MaDIR-BD-unc4, were strongly induced in resistant cultivars at early stress stages. SNP analysis further identified resistance-associated variants in tolerant genotype. These findings provide a foundation for functional validation and highlight the potential of dir genes for improving stress resistance in banana through molecular breeding.

Pathogenesis-related protein 1 (PR-1) is a key plant defense protein, but its gene family evolution in Musa, Ensete, and Musella is not well understood. In this study, we conducted a comprehensive pangenome wide analysis of pr-1 genes across species, subspecies, and cultivars of Musa, Ensete and Musella using genomic datasets. A total of 104 pr-1 genes were identified and characterized through multiple in-silico comparative analyses. The PR-1 gene family exhibited notable variation in gene number reflecting extensive pangenome level diversity. Motif architecture and gene structure assessments revealed both conserved features and lineage-specific modifications among homoeologous pr-1 genes. Ka/Ks analysis indicated that pr-1 clade orthologs have predominantly undergone positive selection, followed by members of the intermediate clade. Collinearity analysis detected a single tandem duplication event in Musa textilis (abacá), while segmental duplications were predominant across other species. Promoter analysis revealed a wide array of cis-regulatory elements responsive to drought, cold, ethylene, methyl jasmonate (MeJA), abscisic acid (ABA), and gibberellic acid (GA). Transcriptome data mining further showed strong induction of several pr-1 genes under major biotic and abiotic stresses. Collectively, this study provides new insights into the evolutionary patterns, structural diversity, and functional specialization of the pr-1 gene family across Musa, Ensete and Musella. Importantly, it establishes the first pangenome resource for pr-1 genes in these genera, offering a valuable foundation for identifying key candidate genes that can be strategically utilized to enhance stress resilience in banana breeding programs.

Enhancing bananas (Musa sp.) through traditional breeding methods is difficult because of the intricate reproductive biology of the plant. This study evaluated the breeding potential of Kothia (ABB)-based progenies, which are typically discarded due to poor fruit filling. Hybridization of Kothia with diverse AA diploid accessions resulted in progenies with low seed set, poor regeneration rates (5.4%), and low frequency of parthenocarpy progenies (0.09%) reflecting inherent cross-compatibility limitations. Among 56 full-sib progenies (FSPs), only one exhibited parthenocarpy, while the rest were non-parthenocarpic with variable female fertility. Two parthenocarpic half-sib progenies (HSPs) were also obtained from these FSPs. Flow cytometry revealed ploidy variation, with most progenies being diploid, and some showing triploid or aneuploid status. Heterosis analysis found that most agronomic traits in FSPs had a negative relative heterosis, but HSPs showed positive heterosis for the number of hands per bunch. Interestingly, six FSPs and both HSPs were resistant to Fusarium wilt (Foc race 1), suggesting they could be useful in breeding programs for disease resistance. One HSP (Pr. 933) displayed a phenotype closely resembling the commercial cultivar Grand Nain (AAA). Another HSP (Pr. 932) showed significantly higher beta-carotene content than commercial cultivars and even surpassed some provitamin A-rich plantains. Volatile compound analysis revealed a unique aroma profile in Pr. 932, contributing to its superior flavor. This study shows that using non-parthenocarpic, poor-fruit-filling progenies can help increase the genetic diversity of bananas, allowing for the use of disease resistance, better nutrition, and unique taste qualities.

Fusarium wilt, caused by Fusarium oxysporum f.sp. cubense (Foc), poses a significant threat to banana crops. Circular RNAs (circRNAs), a newly discovered group of non-coding RNA, play a role in gene regulation. However, Musa spp. has not been explored for circRNA detection. This study presents the first identification of circRNAs in resistant and susceptible banana cultivars infected with Foc race 1 and TR4. A substantial number of circRNAs were identified from RNA-seq libraries of infected corm and root tissues. Differential expression analysis revealed specific circRNAs associated with Foc-resistant and susceptible cultivars. Functional annotation and pathway analysis highlighted involvement in secondary metabolite biosynthesis, Mitogen-activated protein kinases (MAPK) signalling pathway, and plant-pathogen interaction. Utilizing the differentially expressed circRNAs, we conducted a microRNA miRNA-mediated interaction analysis to identify potential sponge interactions. Subsequently, a comprehensive circRNA–miRNA–messenger RNA (mRNA) network was constructed, incorporating target genes directly or indirectly associated with plant resistance. This network sheds light on the intricate regulatory mechanisms underlying plant resistance to Fusarium wilt and provides valuable insights into the complex interplay between circRNAs, miRNAs, and mRNAs in banana defense responses.

Endogenous viral elements (EVEs) are virus-derived sequences integrated into host germline genomes, propagating across generations and potentially becoming fixed through natural selection or genetic drift. While extensively studied in animals, EVEs have been less frequently reported in plants. This study performed a comprehensive genome-wide analysis across 15 species, subspecies, and cultivars of Musa and Ensete to identify sequences associated with viral interactions. Our analysis revealed EVEs associated with four plant virus families: Tospoviridae, Caulimoviridae, Solemoviridae, and Mimiviridae. Phylogenetic analysis showed that these EVEs clustered with their corresponding viruses, with viruses from the same family grouping together. We identified 11 distinct Banana Streak Virus species across Musa genomes. Most corresponding EVEs were annotated as hypothetical proteins, while others aligned with functional proteins, including Polyprotein P3, movement protein, capsid protein, protease, reverse transcriptase, and ribonuclease H. These EVEs appear to be stable components of the Musa genome, which may potentially contribute to growth, development, metabolism, and stress responses. This study provides insights into virus-host interactions and evolutionary relationships among Musa and Ensete species, highlighting the prevalence and distribution of EVEs in Musa genomes and offering a foundation for future investigations into their functional roles and evolutionary significance.

Nudix hydrolases, which catalyze the hydrolysis of nucleoside diphosphate derivatives, play critical roles in plant detoxification and homeostasis. Despite their significance, a comprehensive analysis of the NUDX gene family in Musa spp. remains unexplored. This study identified 30 and 31 putative Nudix hydrolases in the A and B genomes of Musa spp., respectively, categorizing them into eight subfamilies based on substrate specificity. Segmental and tandem duplications have driven the expansion of these genes. Phylogenetic analysis identified that the NUDX genes Macma4_08_g27360, Macma4_04_g28130, and Macma4_10_g25320 are closely related to AtNUDT7, a known negative regulator of basal immunity. Transcriptome and real-time PCR analyses further revealed significant up-regulation of these NUDX genes in banana cultivars susceptible to Fusarium wilt and Eumusae leaf spot. These findings suggest that these genes may act as susceptibility factors, highlighting their potential role in plant immunity against these biotic stresses.

Several species of mealybugs infest various parts of bananas and plantains including foliage, fruits, rhizome and roots in all the major banana growing regions of India and cause moderate to occasionally serious damage but systematic attempts at documenting the mealybug pests of banana and their natural enemies are lacking in India. In this study, mealybugs infesting bananas and plantains in Tamil Nadu, South India, are documented along with their coccinellid predators and other natural enemies. The exotic Jack Beardsley mealybug, Pseudococcus jackbeardsleyi Gimpel & Miller, was found to be a major pest of banana bunches in all localities surveyed in Tamil Nadu and the grey pineapple mealybug, Dysmicoccus neobrevipes Beardsley, was a serious pest in some isolated pockets. Three coccinellids, Scymnus (Pullus) coccivora Ramakrishna Ayyar, Nephus regularis Sicard and Slipinskiscymnus saciformis (Motschulsky) were found to be the major predators of all species of mealybugs. Brumoides suturalis (Fabricius) was predatory on solenopsis mealybug (Phenacoccus solenopsis Tinsley) only and Hyperaspis maindroni Sicard was associated with solenopsis mealybug and pink pineapple mealybug (Dysmicoccus brevipes (Cockerell)). One new species, Scymnus (Pullus) spicatus sp. n., is described as a predator of Jack Beardsley mealybug and striped mealybug (Ferrisia virgata (Cockerell)). Scymnus (Pullus) syoitii Sasaji, 1971, a Japanese species, is recorded for the first time from India as a predator of banana root mealybugs in Tamil Nadu and on Planococcus citri (Risso) in Karnataka. Brief notes on the other natural enemies of banana mealybugs are also given with illustrations.

Success of banana (Musa acuminata L.) breeding mainly depends on the male diploid parents used in the hybridization program. Developing intermediate diploid breeding lines with fertile pollen production ability, resistance to biotic and abiotic stresses, and fruit quality through the diploid x diploid strategy is the key step in improving commercial cultivars. Till now, at the global level only a limited number of diploid accessions is being used in banana breeding programs. In the present study, through the diploid x diploid breeding strategy, the genetic diversity of diploids has been broadened by developing nine polleniferous biotic-stress-resistant diploid lines. Among these, except for two progenies (P), all were resistant to the eumusae leaf spot disease. A single progeny (P 134) showed resistance to root-lesion and root-knot nematodes, whereas P 148 showed moderate resistance to root-knot nematodes alone. Three progenies of cv. Rose x Pisang Lilin (P 427, P 428 and P 429) were moderately resistant to banana stem weevil. Irrespective of cross combinations, barring two, all other progenies exhibited resistant reactions to fusarium wilt, Foc race 1 under both hot spot and pot culture screening. Among the nine diploid progenies, P 427, P 428 and P 429 were the best prospects to contribute multiple resistance against pests (banana stem weevil) and diseases (eumusae leaf spot and Foc race 1), whereas P 134 could be used as the resistant source for root-knot nematodes. The pyramiding of resistant/defense-related alleles in the progenies has been confirmed through SSR markers associated with Foc resistance. These polleniferous resistant improved diploid progenies are the potential source for accelerating the banana breeding program for improving biotic resistances in the triploid commercial cultivars through reconstructive breeding and/or for stacking the resistant genes in other genetic backgrounds.

Background Pathogen-related proteins (PR) are pivotal in plant defense, combating diverse biotic and abiotic stresses. While multiple gene families contribute to banana resistance against Fusarium oxysporum f sp. cubense (Foc), Pseudocercospora eumusae , and Pratylenchus coffeae , the significance of PR-1 genes in defense is paramount. Methods Three PR-1 genes, up-regulated under diverse biotic stresses, were cloned from both resistant and susceptible cultivars of Foc, P. eumusae , and P. coffeae . Molecular characterization, phylogenetic analysis, and docking studies with the Foc TR4 CP gene were conducted. Results Through transcriptomic and real-time studies, three PR-1 genes (Ma02_g15050, Ma02_g15060, and Ma04_g34800) from Musa spp. were identified. These genes exhibited significant up-regulation in resistant cultivars when exposed to Foc, P. eumusae , and P. coffeae . Cloning of these genes was successfully performed from both resistant and susceptible cultivars of Foc race 1 and TR4, P. eumusae , and P. coffeae . Distinct characteristics were observed among the PR-1 genes, with groups 1 and 2 being acidic with signal peptides, and group 3 being basic without signal peptides. All cloned PR-1 proteins belonged to the CAP superfamily (PF00188). Phylogenetic analysis revealed clustering patterns for acidic PR-1 proteins, and KEGG orthology showed associations with vital pathways, including MAPK signaling, plant hormone signal transduction, and plant-pathogen interaction. Secondary and tertiary structure analyses confirmed sequence conservation across studied species. Docking studies explored interactions between the cerato-platanin (CP) gene from Foc TR4 and Ma02_g15060 from banana, suggesting the potential hindrance of PR-1 antifungal activity through direct interaction. Conclusions The findings underscore the crucial role of cloned PR-1 genes in banana plant defense mechanisms against a broad spectrum of biotic stresses. These genes, especially those in groups 1 and 2, hold promise as candidates for developing stress-tolerant banana cultivars. The study provides valuable insights into the molecular aspects of banana defense strategies, emphasizing the potential applications of PR-1 genes in enhancing banana resilience.

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.

The prized Red banana, selected for superior qualities, demands strong genetic uniformity for successful clonal propagation and preservation. Ensuring this uniformity early in the growth of in vitro Red banana plants is essential, as gene mutations and chromosome rearrangements during tissue culture can jeopardize both cloning and germplasm conservation. In this situation, molecular markers play a pivotal role in confirming genetic stability. Thus the study aims to discover a marker that identifies tissue-cultured Red bananas from their virescent variants during initial sub-culturing. A marker linked to anthocyanin has been identified which effectively differentiated Red bananas from virescent variants and it was further validated in various banana cultivars, ornamental Musa species and their interspecific hybrids. The PCR-based marker showed remarkable specificity, discerning Red bananas from virescent variants during tissue culture. It also distinguished green and red offspring, cutting time and resource costs, and shortening the banana breeding cycle.

Bananas are an important staple food and cash crop, but they are vulnerable to a variety of pests and diseases that substantially reduce yield and quality. Banana diseases are challenging to control and necessitate an integrated strategy, and development of resistant cultivars is one of the effective ways of managing diseases. Lasting disease resistance is the main goal in crop improvement and resistance mediated by a single resistant (R) gene mostly lack durability. However, long-term resistance can be obtained by inactivating susceptibility factors (S), which facilitate pathogen infection and proliferation. Identification and inactivation of susceptibility factors against the major pathogens like Fusarium oxysporum f. sp. cubense (Foc), Pseudocercospora eumusae and Pratylenchus coffeae in banana will be an effective way in developing banana varieties with more durable resistance. Downy mildew resistance 6 (DMR6) and DMR-like oxygenases (DLO1) are one such susceptibility factors and they belong to 2-oxoglutarate Fe(II) dependent oxygenases (2OGD) superfamily. 2OGDs are known to catalyze a plethora of reactions and also confer resistance to different pathogens in various crops, but not much is known about the 2OGD in Musa species. Through a comprehensive genome-wide analysis, 133 and 122 potential 2OGDs were systematically identified and categorized from the A and B genomes of banana, respectively. Real time expression of dmr6 and dlo1 genes showed positive correlation with transcriptome data upon Foc race1 and TR4 infection and examination of expression pattern of Macma4_04_g22670 (Ma04_g20880) and Macma4_02_g13590 (Ma02_g12040) genes revealed their involvement in Foc race1 and TR4 infections, respectively. Further the expression profile of 2OGDs, specifically Macma4_04_g25310 (Ma04_g23390), Macma4_08_g11980 (Ma08_g12090) and Macma4_04_g38910 (Ma04_g36640) shows that they may play a significant role as a susceptibility factor, particularly against P. eumusae and P. coffeae , implying that they can be exploited as a candidate gene for editing in developing resistant cultivars against these diseases. In summary, our findings contribute to a deeper comprehension of the evolutionary and functional aspects of 2OGDs in Musa spp. Furthermore, they highlight the substantial functions of these family constituents in the progression of diseases. These insights hold significance in the context of enhancing the genetic makeup of bananas to attain extended and more durable resistance against pathogens.

Micraspis discolor (Fabricius, 1798) (Coleoptera: Coccinellidae), a widely studied complex of externally similar species, is known to be distributed in all the major rice growing countries of the Oriental region. It consists of disjunct populations that have been treated as a single taxonomic entity, but these are not conspecific and show disparities in their morphology. In this paper, we establish the identity of the true M. discolor based on Fabricius's type material from Tamil Nadu, Southern India, and redescribe it with illustrations of the diagnostic characters and the life stages. A lectotype is designated for M. discolor from Fabricius's type material (lectotype designation). Coccinella tenuilinea Walker, 1859, a sympatric species closely related to M. discolor and omitted from Korschefsky's World Catalogue of Coccinellidae, is transferred to Micraspis (new combination) and a lectotype is designated for it. It is found to be the most predominant species in South India and redescribed with illustrations of the genitalia and the life stages. COI sequences of M. discolor, M. tenuilinea and M. yasumatsui Sasaji based on the material collected in India are given. Phylogenetic analysis of the COI sequences of Indian M. discolor and other Asian 'M. discolor'sequences confirm that the Indian M. discolor is a distinct species and all Micraspis spp. from South and southeast Asian countries not matching the true M. discolor described here need to be reexamined and renamed if necessary. Brief illustrated accounts of other Micraspis spp. known from the paddy ecosystems of India are also given. Alesia guerini Mulsant, 1850, currently placed in Micraspis, is transferred to Oenopia Mulsant (new combination) and Coelophora walteri Sicard, 1913 is a new junior synonym of O. guerini (new synonym).

Slipinskiscymnus gen. nov. (Coleoptera: Coccinellidae) is proposed to accommodate two anomalous species of Scymnini, namely, Scymnus pallidicollis Mulsant, 1853 (= Slipinskiscymnus pallidicollis (Mulsant), comb. nov.) and Scymnus saciformis Motschulsky, 1858 (=Slipinskiscymnus saciformis (Motschulsky), comb. nov.) and five new species, Slipinskiscymnus confertus Peng et Chen sp. nov., S. siculiformis Peng et Chen sp. nov., S. spiculatus Peng et Chen sp. nov., S. interstricus Peng et Chen sp. nov. and S. keralensis Poorani sp. nov., described from China and India. A lectotype is designated for Scymnus saciformis Motschulsky, 1858 (lectotype designation). Descriptive accounts of these species with illustrations of adult habitus, male genitalia and other diagnostic characters are given with a key to species. Notes on the status of the genus Keiscymnus Sasaji, 1971, are also provided.

In this investigation, the study focused on the RNAseq data generated in response to Fusarium oxysporum f.sp. cubense (Foc) race1 (Cavendish infecting strain VCG 0124), targeting both resistant (cv. Rose, AA) and susceptible cultivars (Namarai, AA), and Tropical Race 4 (TR4, strain VCG 01213/16), involving resistant (cv. Rose, AA) and susceptible cultivars (Matti, AA). The respective contrasting cultivars were independently challenged with Foc race1 and TR4, and the root and corm samples were collected in two replications at varying time intervals [0th (control), 2nd, 4th, 6th, and 8th days] in duplicates. The RNA samples underwent stringent quality checks, with all 80 samples meeting the primary parameters, including a satisfactory RNA integrity number (>7). Subsequent library preparation and secondary quality control steps were executed successfully for all samples, paving the way for the sequencing phase. Sequencing generated an extensive amount of data, yielding a range of 10 to 31 million paired-end raw reads per sample, resulting in a cumulative raw data size of 11-50 GB. These raw reads were aligned against the reference genome of Musa acuminata ssp. malaccensis version 2 (DH Pahang), as well as the pathogen genomes of Foc race 1 and Foc TR4, using the HISAT2 alignment tool. The focal point of this study was the investigation of differential gene expression patterns of Musa spp. upon Foc infection. In Foc race1 resistant and susceptible root samples across the designated day intervals, a significant number of genes displayed up-regulation (ranging from 1 to 228) and down-regulation (ranging from 1 to 274). In corm samples, the up-regulated genes ranged from 1 to 149, while down-regulated genes spanned from 3 to 845. For Foc TR4 resistant and susceptible root samples, the expression profiles exhibited a notable up-regulation of genes (ranging from 31 to 964), along with a down-regulation range of 316-1315. In corm samples, up-regulated genes ranged from 57 to 929, while down-regulated genes were observed in the range of 40-936. In addition to the primary analysis, a comprehensive secondary analysis was conducted, including Gene Ontology (GO), euKaryotic Orthologous Groups (KOG) classification, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and investigations into Simple Sequence Repeats (SSRs), Single Nucleotide Polymorphisms (SNPs), and microRNA (miRNA). The complete dataset was carefully curated and housed at ICAR-NRCB, Trichy, ensuring its accuracy and accessibility for the duration of the study. Further, the raw transcriptome read datasets have been successfully submitted to the National Center for Biotechnology Information - Sequence Read Archive (NCBI-SRA) database, ensuring the accessibility and reproducibility of this valuable dataset for further research endeavors.

Banana is one of the major food crops and its production is subject to many pests and diseases. Banana breeding exploits wild relatives and progenitor species for the introgression of resistant genes (R) into cultivated varieties to overcome these hurdles. With advances in sequencing technologies, whole-genome sequences are available for many Musa spp. and many of them are potential donors of disease resistance genes. Considering their potential role, R genes from these species were explored to develop an user-friendly open-access database that will be useful for studying and implementing disease resistance in bananas. MusaRgene database is complemented with complete details of 3598 R genes identified from eight Musa spp. and rice, Arabidopsis, sorghum along with its classification and separate modules on its expression under various stresses in resistant and susceptible cultivars and corresponding SSRs are also provided. This database can be regarded as the primary resource of information on R genes from bananas and their relatives. R genes from other allele mining studies are also incorporated which will enable the identification of its homolog in related Musa spp. MusaRgene database will aid in the identification of genes and markers associated, cloning of full-length R genes, and genetic transformation or gene editing of the R genes in susceptible cultivars. Multiple R genes can also be identified for pyramiding the genes to increase the level of resistance and durability. Overall, this database will facilitate the understanding of defense mechanisms in bananas against biotic or abiotic stresses leading to the development of promising disease-resistant varieties.

Pathogenesis related protein-1 (PR-1) is the most abundantly produced protein during defense response against many biotic and abiotic stresses. However, knowledge on PR-1 gene family and its evolutionary relationship in banana is very limited. In order to study the potential role of PR-1 genes in banana, genome wide identification, structure analysis and expressions were performed. A total of 15 and 11 PR-1 genes were identified from A and B genomes of banana and the proteins encoded by this gene family are of varying lengths and harbor conserved domains and motifs. PR-1 genes are unevenly dispersed on 11 chromosomes with segmental duplication in both A and B genome, suggesting an important contribution of duplication in expansion of PR-1 gene family in banana. qRT-PCR analysis of PR-1 gene showed positive correlation with the RNAseq data under various stresses and examination of expression pattern of selected MaPR-1 genes in banana revealed its role in biotic and abiotic stresses in general and fusarium wilt in particular. This study provides significant insight into the functions of PR-1 genes which can be further exploited as a promising candidate for developing multiple stress tolerant banana varieties.

Banana, a major global food crop and the most important fruit crop, provides nutrition and food security to many developed and developing countries. Monoculturing of the commercial cultivars over a long period led their vulnerability to pest and diseases. This situation is threatening the food and livelihood security. Being a vegetatively propagated crop, and its inherent problem of seed setting owing to polyploidy, parthenocarpy, and sterility, tailoring a variety with desirable traits through conventional breeding is a challenge to the breeders. This can be achieved through molecular breeding approaches demanding basic and complete understanding of molecular mechanisms involved in trait expression in mind, cost-effective next-generation sequencing technologies have been exploited for unraveling the molecular mechanisms of various traits, ripening, biotic and abiotic stresses tolerance/resistance, etc., at genomic and transcriptomic levels. The remaining “omics” approaches aimed to study the complex interactions between genes, proteins, and metabolites within the resulting phenotype to open new avenues for breeding better bananas. Research on “omics” of pest and diseases also paved a way to reveal the host pathogen interactions, to develop strategies for management. This chapter tries to cover all the “omics platforms” for various traits and their applications in banana improvement program.

Expansin, a cell wall-modifying gene family, has been well characterized and its role in biotic and abiotic stress resistance has been proven in many monocots, but not yet studied in banana, a unique model crop. Banana is one of the staple food crops in developing countries and its production is highly influenced by various biotic and abiotic factors. Characterizing the expansin genes of the ancestor genome (M. acuminata and M. balbisiana) of present day cultivated banana will enlighten their role in growth and development, and stress responses. In the present study, 58 (MaEXPs) and 55 (MbaEXPs) putative expansin genes were identified in A and B genome, respectively, and were grouped in four subfamilies based on phylogenetic analysis. Gene structure and its duplications revealed that EXPA genes are highly conserved and are under negative selection whereas the presence of more number of introns in other subfamilies revealed that they are diversifying. Expression profiling of expansin genes showed a distinct expression pattern for biotic and abiotic stress conditions. This study revealed that among the expansin subfamilies, EXPAs contributed significantly towards stress-resistant mechanism. The differential expression of MaEXPA18 and MaEXPA26 under drought stress conditions in the contrasting cultivar suggested their role in drought-tolerant mechanism. Most of the MaEXPA genes are differentially expressed in the root lesion nematode contrasting cultivars which speculated that this expansin subfamily might be the susceptible factor. The downregulation of MaEXPLA6 in resistant cultivar during Sigatoka leaf spot infection suggested that by suppressing this gene, resistance may be enhanced in susceptible cultivar. Further, in-depth studies of these genes will lead to gain insight into their role in various stress conditions in banana.