Transgenic Cavendish bananas with resistance to Fusarium wilt tropical race 4

Plant growth promotion and biocontrol properties of a synthetic community in the control of apple disease

BACKGROUND

Apple Replant Disease (ARD) is common in major apple-growing regions worldwide, but the role of rhizosphere microbiota in conferring ARD resistance and promoting plant growth remains unclear.

RESULTS

In this study, a synthetic microbial community (SynCom) was developed to enhance apple plant growth and combat apple pathogens. Eight unique bacteria selected via microbial culture were used to construct the antagonistic synthetic community, which was then inoculated into apple seedlings in greenhouse experiments. Changes in the rhizomicroflora and the growth of aboveground plants were monitored. The eight strains, belonging to the genera Bacillus and Streptomyces, have the ability to antagonize pathogens such as Fusarium oxysporum, Rhizoctonia solani, Botryosphaeria ribis, and Physalospora piricola. Additionally, these eight strains can stably colonize in apple rhizosphere and some of them can produce siderophores, ACC deaminase, and IAA. Greenhouse experiments with Malus hupehensis Rehd indicated that SynCom promotes plant growth (5.23%) and increases the nutrient content of the soil, including soil organic matter (9.25%) and available K (1.99%), P (7.89%), and N (0.19%), and increases bacterial richness and the relative abundance of potentially beneficial bacteria. SynCom also increased the stability of the rhizosphere microbial community, the assembly of which was dominated by deterministic processes (|β NTI| > 2).

CONCLUSIONS

Our results provide insights into the contribution of the microbiome to pathogen inhibition and host growth. The formulation and manipulation of similar SynComs may be a beneficial strategy for promoting plant growth and controlling soil-borne disease.

Critical Secondary Metabolites Confer the Broad-Spectrum Pathogenic Fungi Resistance Property of a Marine-Originating Streptomyces sp. HNBCa1

Obtaining a microorganism strain with a broad-spectrum resistance property and highly efficient antifungal activity is important to the biocontrol strategy. Herein, a marine Streptomyces sp. HNBCa1 demonstrated a broad-spectrum resistance to 17 tested crop pathogenic fungi and exhibited a high biocontrol efficiency against mango anthracnose and banana fusarium wilt. To uncover the critical bioactive secondary metabolites basis, genome assembly and annotation, metabolomic analysis, and a semipreparative HPLC-based activity-guide method were employed. Finally, geldanamycin and ectoine involved in codifferential secondary metabolites were also found to be related to biosynthetic gene clusters in the genome of HNBCa1. Reblastatin and geldanamycin were uncovered in response to broad-spectrum resistance to the 17 crop pathogenic fungi. Our results suggested that reblastatin and geldanamycin were critical to maintaining the broad-spectrum resistance property and highly efficient antifungal activity of HNBCa1, which could be further developed as a biological control agent to control crop fungal diseases.

Molecular insights into the variability and pathogenicity of Fusarium odoratissimum, the causal agent of Panama wilt disease in banana

Fusarium wilt or Panama disease of banana caused by the hemibiotroph fungus, Fusarium odoratissimum, also known as F. oxysporum f.sp. cubense Tropical Race 4 is a serious threat to banana production worldwide. Being the world's largest grower and the origins of bananas in its northeast region, India is particularly vulnerable to this deadly fungus. In the present study, a total of 163 Fusarium isolates from infected banana were characterized for their pathogenic traits. Considering the variability in the Fusarium, the contaminated banana plants were collected from five districts of Uttar Pradesh and Bihar, two major primary infection states of India. All the isolates were screened using universal and specific primers to identify the F. odoratissimum strains. The identified F. odoratissimum strains were subjected to in vivo pathogenicity assessment using the susceptible banana cultivar 'Grand Naine'. The identified six most virulent strains were further characterized for their pathogenicity via in vivo bipartite interaction in terms of biochemical assays. Assessment of in vivo pathogenicity through qRT-PCR for three pathogenesis responsive genes, Six 1a (Secreted in xylem), Snf (Sucrose non-fermenting) and ChsV (Chitinase V), ascertained that the identified F. odoratissimum strains exhibit both intra- and inter-specific variability. The variability of F. odoratissimum strains signifies its importance for the assessment of spread of infection at specific sites to enable efficient management strategy of Fusarium wilt in banana.

Fusarium wilt pandemic: current understanding and molecular perspectives

Plant diseases pose a severe threat to the food security of the global human population. One such disease is Fusarium wilt, which affects many plant species and causes up to 100% yield losses. Fusarium pathogen has high variability in its genetic constitution; therefore, it has evolved into different physiological races to infect different plant species spread across the different geographical regions of the world. The pathogen mainly affects plant roots, leading to colonizing and blocking vascular bundle cells, specifically xylem vessels. This blocking results in chlorosis, vascular discoloration, leaf wilting, shortening of plant, and, in severe cases, premature plant death. Due to the soil-borne nature of the wilt pathogen, neither agronomic nor plant protection measures effectively reduce the incidence of the disease. Therefore, the most cost-effective management strategy for Fusarium wilt is developing varieties resistant to a particular race of the fungus wilt prevalent in a given region. This strategy requires understanding the pathogen, its disease cycle, and epidemiology with climate-changing scenarios. Hence, in the review, we will discuss the pathogenic aspect and genetics of the Fusarium wilt, including molecular interventions for developing climate-smart wilt tolerant/resistant varieties of crops. Overall, this review will add to our knowledge for advancing the breeding of resistance against the wilt pandemic.

Fine-mapping of a major locus for Fusarium wilt resistance in flax (Linum usitatissimum L.)

KEY MESSAGE

Fine-mapping of a locus on chromosome 1 of flax identified an S-lectin receptor-like kinase (SRLK) as the most likely candidate for a major Fusarium wilt resistance gene. Fusarium wilt, caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. lini, is a devastating disease in flax. Genetic resistance can counteract this disease and limit its spread. To map major genes for Fusarium wilt resistance, a recombinant inbred line population of more than 700 individuals derived from a cross between resistant cultivar 'Bison' and susceptible cultivar 'Novelty' was phenotyped in Fusarium wilt nurseries at two sites for two and three years, respectively. The population was genotyped with 4487 single nucleotide polymorphism (SNP) markers. Twenty-four QTLs were identified with IciMapping, 18 quantitative trait nucleotides with 3VmrMLM and 108 linkage disequilibrium blocks with RTM-GWAS. All models identified a major QTL on chromosome 1 that explained 20-48% of the genetic variance for Fusarium wilt resistance. The locus was estimated to span ~ 867 Kb but included a ~ 400 Kb unresolved region. Whole-genome sequencing of 'CDC Bethune', 'Bison' and 'Novelty' produced ~ 450 Kb continuous sequences of the locus. Annotation revealed 110 genes, of which six were considered candidate genes. Fine-mapping with 12 SNPs and 15 Kompetitive allele-specific PCR (KASP) markers narrowed down the interval to ~ 69 Kb, which comprised the candidate genes Lus10025882 and Lus10025891. The latter, a G-type S-lectin receptor-like kinase (SRLK) is the most likely resistance gene because it is the only polymorphic one. In addition, Fusarium wilt resistance genes previously isolated in tomato and Arabidopsis belonged to the SRLK class. The robust KASP markers can be used in marker-assisted breeding to select for this major Fusarium wilt resistance locus.

Origin and evolution of the triploid cultivated banana genome

Most fresh bananas belong to the Cavendish and Gros Michel subgroups. Here, we report chromosome-scale genome assemblies of Cavendish (1.48 Gb) and Gros Michel (1.33 Gb), defining three subgenomes, Ban, Dh and Ze, with Musa acuminata ssp. banksii, malaccensis and zebrina as their major ancestral contributors, respectively. The insertion of repeat sequences in the Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 RGA2 (resistance gene analog 2) promoter was identified in most diploid and triploid bananas. We found that the receptor-like protein (RLP) locus, including Foc race 1-resistant genes, is absent in the Gros Michel Ze subgenome. We identified two NAP (NAC-like, activated by apetala3/pistillata) transcription factor homologs specifically and highly expressed in fruit that directly bind to the promoters of many fruit ripening genes and may be key regulators of fruit ripening. Our genome data should facilitate the breeding and super-domestication of bananas.

Improved abiotic stress tolerance in Arabidopsis by constitutive active form of a banana DREB2 type transcription factor, MaDREB20.CA, than its native form, MaDREB20

Banana is grown as one of the important fruit crops in tropical and subtropical regions of the world. In this study, we report induced expression of a dehydration responsive element binding 2 (DREB2) gene (MaDREB20) under individual heat, drought, and combined drought and heat stress in root of two banana genotypes Grand Nain (GN) and Hill Banana (HB). Motif analysis of MaDREB20 protein demonstrated the presence of a negative regulatory domain (NRD) or PEST motif between 150 and 184 amino acids. Transgenic Arabidopsis overexpressing MaDREB20 gene showed more survival rate, above-ground biomass, seed yield, leaf relative water content, and proline content but less ion leakage and malonaldehyde content, revealing improved tolerance against heat and drought as well as their combination than the wild-type. Overexpression of MaDREB20.CA (constitutive active form of MaDREB20 after removal of PEST region) showed better abiotic stress tolerance in Arabidopsis than its native form (MaDREB20). Transgenic Arabidopsis overexpressing MaDREB20 and MaDREB20.CA genes appeared to be associated with reduced stomatal densities under normal condition, better regulation of stomatal aperture under drought than in wild-type plants, and differential regulation of downstream target (AtTCH4 and AtIAA1) genes under heat, drought, and combined stress. Taken together, our findings revealed important functions of MaDREB20 in abiotic stress responses in transgenic Arabidopsis and could form a basis for CRISPR/Cas9-mediated removal of its NRD to enhance stress tolerance in banana.

Genetic improvement in Musa through modern biotechnological methods

Bananas, one of the most valued fruits worldwide, are produced in more than 135 countries in the tropics and subtropics for local consumption and export due to their tremendous nutritional value and ease of access. The genetic improvement of commercial crops is a crucial strategy for managing pests or other diseases and abiotic stress factors. Although conventional breeding has developed new hybrids with highly productive or agronomic performance characteristics, in some banana cultivars, due to the high level of sterility, the traditional breeding strategy is hampered. Therefore, modern biotechniques have been developed in a banana for genetic improvement. In vitro, culture techniques have been a basis for crop micropropagation for elite banana varieties and the generation of methods for genetic modification. This review includes topics of great interest for improving bananas and their products worldwide, from their origins to the different improvement alternatives. Keywords. Banana, genetic improvement, pest management, diseases, abiotic stress factors.

Identification of a Major QTL-Controlling Resistance to the Subtropical Race 4 of Fusarium oxysporum f. sp. cubense in Musa acuminata ssp. malaccensis

Vascular wilt caused by the ascomycete fungal pathogen Fusarium oxysporum f. sp. cubense (Foc) is a major constraint of banana production around the world. The virulent race, namely Tropical Race 4, can infect all Cavendish-type banana plants and is now widespread across the globe, causing devastating losses to global banana production. In this study, we characterized Foc Subtropical Race 4 (STR4) resistance in a wild banana relative which, through estimated genome size and ancestry analysis, was confirmed to be Musa acuminata ssp. malaccensis. Using a self-derived F₂ population segregating for STR4 resistance, quantitative trait loci sequencing (QTL-seq) was performed on bulks consisting of resistant and susceptible individuals. Changes in SNP index between the bulks revealed a major QTL located on the distal end of the long arm of chromosome 3. Multiple resistance genes are present in this region. Identification of chromosome regions conferring resistance to Foc can facilitate marker assisted selection in breeding programs and paves the way towards identifying genes underpinning resistance.

Biotechnological interventions in reducing losses of tropical fruits and vegetables

Tropical fruits and vegetables are predominantly cultivated in warm climate zones, resulting in cultivar diversity in terms of structure, features, and physiology. These constitute a variety of bioactive ingredients such as vitamins, minerals, phenolic acids, anthocyanins, flavonoids, fatty acids, fiber, and their distinctive appearances attract customers across the world. The global production of fruit and vegetables has been attained a tremendous increase for the last few decades. However, huge losses at pre- and postharvest levels are major constraints in their judicious use. Traditional breeding strategies were used to minimize these losses, but their functionality is limited due to their time and labor intensiveness. Recent biotechnological, computational, and multiomics approaches not only address the losses concern but also aid in boosting crop productivity and nutritional values. This article emphasizes molecular tools that have been used to reduce losses of tropical fruits and vegetables at pre- and postharvest levels.

A Perspective Review on Understanding Drought Stress Tolerance in Wild Banana Genetic Resources of Northeast India

The enormous perennial monocotyledonous herb banana (Musa spp.), which includes dessert and cooking varieties, is found in more than 120 countries and is a member of the order Zingiberales and family Musaceae. The production of bananas requires a certain amount of precipitation throughout the year, and its scarcity reduces productivity in rain-fed banana-growing areas due to drought stress. To increase the tolerance of banana crops to drought stress, it is necessary to explore crop wild relatives (CWRs) of banana. Although molecular genetic pathways involved in drought stress tolerance of cultivated banana have been uncovered and understood with the introduction of high-throughput DNA sequencing technology, next-generation sequencing (NGS) techniques, and numerous "omics" tools, unfortunately, such approaches have not been thoroughly implemented to utilize the huge potential of wild genetic resources of banana. In India, the northeastern region has been reported to have the highest diversity and distribution of Musaceae, with more than 30 taxa, 19 of which are unique to the area, accounting for around 81% of all wild species. As a result, the area is regarded as one of the main locations of origin for the Musaceae family. The understanding of the response of the banana genotypes of northeastern India belonging to different genome groups to water deficit stress at the molecular level will be useful for developing and improving drought tolerance in commercial banana cultivars not only in India but also worldwide. Hence, in the present review, we discuss the studies conducted to observe the effect of drought stress on different banana species. Moreover, the article highlights the tools and techniques that have been used or that can be used for exploring and understanding the molecular basis of differentially regulated genes and their networks in different drought stress-tolerant banana genotypes of northeast India, especially wild types, for unraveling their potential novel traits and genes.

Spatiotemporal biocontrol and rhizosphere microbiome analysis of Fusarium wilt of banana

The soil-borne fungus Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) causes Fusarium wilt of banana (FWB), which devastates banana production worldwide. Biocontrol is considered to be the most efficient approach to reducing FWB. Here we introduce an approach that spatiotemporally applies Piriformospore indica and Streptomyces morookaensis strains according to their respective strength to increase biocontrol efficacy of FWB. P. indica successfully colonizes banana roots, promotes lateral root formation, inhibits Foc TR4 growth inside the banana plants and reduces FWB. S. morookaensis strain Sm4-1986 secretes different secondary compounds, of which xerucitrinin A (XcA) and 6-pentyl-α-pyrone (6-PP) show the strongest anti-Foc TR4 activity. XcA chelates iron, an essential nutrient in pathogen-plant interaction that determines the output of FWB. 6-PP, a volatile organic compound, inhibits Foc TR4 germination and promotes banana growth. Biocontrol trials in the field demonstrated that application of S. morookaensis lead to improvement of soil properties and increase of rhizosphere-associated microbes that are beneficial to banana growth, which significantly reduces disease incidence of FWB. Our study suggests that optimal utilization of the two biocontrol strains increases efficacy of biocontrol and that regulating iron accessibility in the rhizosphere is a promising strategy to control FWB.

Antifungal effects and biocontrol potential of lipopeptide-producing Streptomyces against banana Fusarium wilt fungus Fusarium oxysporum f. sp. cubense

Fusarium wilt of banana (FWB), caused by Fusarium oxysporum f. sp. cubense (Foc), especially tropical race 4 (TR4), presents the foremost menace to the global banana production. Extensive efforts have been made to search for efficient biological control agents for disease management. Our previous study showed that Streptomyces sp. XY006 exhibited a strong inhibitory activity against several phytopathogenic fungi, including F. oxysporum. Here, the corresponding antifungal metabolites were purified and determined to be two cyclic lipopeptide homologs, lipopeptin A and lipopeptin B. Combined treatment with lipopeptin complex antagonized Foc TR4 by inhibiting mycelial growth and conidial sporulation, suppressing the synthesis of ergosterol and fatty acids and lowering the production of fusaric acid. Electron microscopy observation showed that lipopeptide treatment induced a severe disruption of the plasma membrane, leading to cell leakage. Lipopeptin A displayed a more pronounced antifungal activity against Foc TR4 than lipopeptin B. In pot experiments, strain XY006 successfully colonized banana plantlets and suppressed the incidence of FWB, with a biocontrol efficacy of up to 87.7%. Additionally, XY006 fermentation culture application improved plant growth parameters and induced peroxidase activity in treated plantlets, suggesting a possible role in induced resistance. Our findings highlight the potential of strain XY006 as a biological agent for FWB, and further research is needed to enhance its efficacy and mode of action in planta.

Genome-wide identification, characterization, and evolutionary analysis of NBS genes and their association with disease resistance in Musa spp

Banana is an important food crop that is susceptible to a wide range of pests and diseases that can reduce yield and quality. The primary objective of banana breeding programs is to increase disease resistance, which requires the identification of resistance (R) genes. Despite the fact that resistant sources have been identified in bananas, the genes, particularly the nucleotide-binding site (NBS) family, which play an important role in protecting plants against pathogens, have received little attention. As a result, this study included a thorough examination of the NBS disease resistance gene family's classification, phylogenetic analysis, genome organization, evolution, cis-elements, differential expression, regulation by microRNAs, and protein-protein interaction. A total of 116 and 43 putative NBS genes from M. acuminata and M. balbisiana, respectively, were identified and characterized, and were classified into seven sub-families. Structural analysis of NBS genes revealed the presence of signal peptides, their sub-cellular localization, molecular weight and pI. Eight commonly conserved motifs were found, and NBS genes were unevenly distributed across multiple chromosomes, with the majority of NBS genes being located in chr3 and chr1 of the A and B genomes, respectively. Tandem duplication occurrences have helped bananas' NBS genes spread throughout evolution. Transcriptome analysis of NBS genes revealed significant differences in expression between resistant and susceptible cultivars of fusarium wilt, eumusae leaf spot, root lesion nematode, and drought, implying that they can be used as candidate resistant genes. Ninety miRNAs were discovered to have targets in 104 NBS genes from the A genome, providing important insights into NBS gene expression regulation. Overall, this study offers a valuable genomic resource and understanding of the function and evolution of NBS genes in relation to rapidly evolving pathogens, as well as providing breeders with selection targets for fast-tracking breeding of banana varieties with more durable resistance to pathogens.

Multi-site fungicides suppress banana Panama disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4

Global banana production is currently challenged by Panama disease, caused by Fusarium oxysporum f.sp. cubense Tropical Race 4 (FocTR4). There are no effective fungicide-based strategies to control this soil-borne pathogen. This could be due to insensitivity of the pathogen to fungicides and/or soil application per se. Here, we test the effect of 12 single-site and 9 multi-site fungicides against FocTR4 and Foc Race1 (FocR1) in quantitative colony growth, and cell survival assays in purified FocTR4 macroconidia, microconidia and chlamydospores. We demonstrate that these FocTR4 morphotypes all cause Panama disease in bananas. These experiments reveal innate resistance of FocTR4 to all single-site fungicides, with neither azoles, nor succinate dehydrogenase inhibitors (SDHIs), strobilurins or benzimidazoles killing these spore forms. We show in fungicide-treated hyphae that this innate resistance occurs in a subpopulation of "persister" cells and is not genetically inherited. FocTR4 persisters respond to 3 μg ml-1 azoles or 1000 μg ml-1 strobilurins or SDHIs by strong up-regulation of genes encoding target enzymes (up to 660-fold), genes for putative efflux pumps and transporters (up to 230-fold) and xenobiotic detoxification enzymes (up to 200-fold). Comparison of gene expression in FocTR4 and Zymoseptoria tritici, grown under identical conditions, reveals that this response is only observed in FocTR4. In contrast, FocTR4 shows little innate resistance to most multi-site fungicides. However, quantitative virulence assays, in soil-grown bananas, reveals that only captan (20 μg ml-1) and all lipophilic cations (200 μg ml-1) suppress Panama disease effectively. These fungicides could help protect bananas from future yield losses by FocTR4.

The Banana MaWRKY18, MaWRKY45, MaWRKY60 and MaWRKY70 Genes Encode Functional Transcription Factors and Display Differential Expression in Response to Defense Phytohormones

WRKY transcription factors (TFs) play key roles in plant defense responses through phytohormone signaling pathways. However, their functions in tropical fruit crops, especially in banana, remain largely unknown. Several WRKY genes from the model plants rice (OsWRKY45) and Arabidopsis (AtWRKY18, AtWRKY60, AtWRKY70) have shown to be attractive TFs for engineering disease resistance. In this study, we isolated four banana cDNAs (MaWRKY18, MaWRKY45, MaWRKY60, and MaWRKY70) with homology to these rice and ArabidopsisWRKY genes. The MaWRKY cDNAs were isolated from the wild banana Musa acuminata ssp. malaccensis, which is resistant to several diseases of this crop and is a progenitor of most banana cultivars. The deduced amino acid sequences of the four MaWRKY cDNAs revealed the presence of the conserved WRKY domain of ~60 amino acids and a zinc-finger motif at the N-terminus. Based on the number of WRKY repeats and the structure of the zinc-finger motif, MaWRKY18 and MaWRKY60 belong to group II of WRKY TFs, while MaWRKY45 and MaWRKY70 are members of group III. Their corresponding proteins were located in the nuclei of onion epidermal cells and were shown to be functional TFs in yeast cells. Moreover, expression analyses revealed that the majority of these MaWRKY genes were upregulated by salicylic acid (SA) or methyl jasmonate (MeJA) phytohormones, although the expression levels were relatively higher with MeJA treatment. The fact that most of these banana WRKY genes were upregulated by SA or MeJA, which are involved in systemic acquired resistance (SAR) or induced systemic resistance (ISR), respectively, make them interesting candidates for bioengineering broad-spectrum resistance in this crop.

Assessment of root-specific promoters in banana and tobacco and identification of a banana TIP2 promoter with strong root activity

Genetic modification is one possible strategy to generate bananas (Musa spp.) with resistance to the soil-borne pathogen causing Fusarium wilt. The availability of banana root-specific promoters to target transgene expression to the sites of infection would be beneficial. We have assessed 18 promoter sequences derived from a range of plant species for their expression profiles in banana tissues to identify those with root-specific activity. Promoter sequences were isolated and fused to the β-glucuronidase (GUS) gene to assess their expression levels and tissue specificity in both banana and the model plant tobacco. Two heterologous promoters conferring high root expression levels in banana were identified, including a β-glucosidase 1 (GLU1) promoter from maize and the RB7-type tonoplast intrinsic protein (TIP)-2 promoter from strawberry. Further, a novel Musa TIP2-2 promoter sequence was isolated and characterized which, when fused to the GUS gene, conferred very high GUS expression levels in banana roots. These promoters will expand the options for the control of gene expression in genetically modified bananas, providing a tool to develop plants with resistance not only to soil-borne diseases such as Fusarium wilt, but also for the improvement of other traits, such as nematode resistance, nutrition or abiotic stress resistance.

The banana genome hub: a community database for genomics in the Musaceae

The Banana Genome Hub provides centralized access for genome assemblies, annotations, and the extensive related omics resources available for bananas and banana relatives. A series of tools and unique interfaces are implemented to harness the potential of genomics in bananas, leveraging the power of comparative analysis, while recognizing the differences between datasets. Besides effective genomic tools like BLAST and the JBrowse genome browser, additional interfaces enable advanced gene search and gene family analyses including multiple alignments and phylogenies. A synteny viewer enables the comparison of genome structures between chromosome-scale assemblies. Interfaces for differential expression analyses, metabolic pathways and GO enrichment were also added. A catalogue of variants spanning the banana diversity is made available for exploration, filtering, and export to a wide variety of software. Furthermore, we implemented new ways to graphically explore gene presence-absence in pangenomes as well as genome ancestry mosaics for cultivated bananas. Besides, to guide the community in future sequencing efforts, we provide recommendations for nomenclature of locus tags and a curated list of public genomic resources (assemblies, resequencing, high density genotyping) and upcoming resources-planned, ongoing or not yet public. The Banana Genome Hub aims at supporting the banana scientific community for basic, translational, and applied research and can be accessed at https://banana-genome-hub.southgreen.fr.

Induced resistance to Fusarium wilt of banana caused by Tropical Race 4 in Cavendish cv Grand Naine bananas after challenging with avirulent Fusarium spp

In the last century, Fusarium wilt of banana (FWB) destroyed the banana cultivar Gros Michel. The Cavendish cultivars saved the global banana industry, and currently they dominate global production (~50%) and the export trade (~95%). However, a new strain called Tropical Race 4 (TR4) surfaced in the late 1960’s, spread globally and greatly damages Cavendish plantations as well as manifold local varieties that are primarily grown by small holders. Presently, there is no commercially available replacement for Cavendish and hence control strategies must be developed and implemented to manage FWB. Here, we studied whether it is possible to induce resistance to TR4 by pre-inoculations with different Fusarium spp. Only pre-treatments with an avirulent Race 1 strain significantly reduced disease development of TR4 in a Cavendish genotype and this effect was stable at various nutritional and pH conditions. We then used transcriptome analysis to study the molecular basis of this response. Several genes involved in plant defence responses were up-regulated during the initial stages of individual infections with TR4 and Race 1, as well as in combined treatments. In addition, a number of genes in the ethylene and jasmonate response pathways as well as several gibberellin synthesis associated genes were induced. We observed upregulation of RGA2 like genes in all treatments. Hence, RGA2 could be a key factor involved in both R1 and TR4 resistance. The data support the hypothesis that activating resistance to Race 1 in Cavendish bananas affects TR4 development and provide a first insight of gene expression during the interaction between various Fusarium spp. and banana.

Advances in Crop Breeding Through Precision Genome Editing

The global climate change and unfavourable abiotic and biotic factors are limiting agricultural productivity and therefore intensifying the challenges for crop scientists to meet the rising demand for global food supply. The introduction of applied genetics to agriculture through plant breeding facilitated the development of hybrid varieties with improved crop productivity. However, the development of new varieties with the existing gene pools poses a challenge for crop breeders. Genetic engineering holds the potential to broaden genetic diversity by the introduction of new genes into crops. But the random insertion of foreign DNA into the plant's nuclear genome often leads to transgene silencing. Recent advances in the field of plant breeding include the development of a new breeding technique called genome editing. Genome editing technologies have emerged as powerful tools to precisely modify the crop genomes at specific sites in the genome, which has been the longstanding goal of plant breeders. The precise modification of the target genome, the absence of foreign DNA in the genome-edited plants, and the faster and cheaper method of genome modification are the remarkable features of the genome-editing technology that have resulted in its widespread application in crop breeding in less than a decade. This review focuses on the advances in crop breeding through precision genome editing. This review includes: an overview of the different breeding approaches for crop improvement; genome editing tools and their mechanism of action and application of the most widely used genome editing technology, CRISPR/Cas9, for crop improvement especially for agronomic traits such as disease resistance, abiotic stress tolerance, herbicide tolerance, yield and quality improvement, reduction of anti-nutrients, and improved shelf life; and an update on the regulatory approval of the genome-edited crops. This review also throws a light on development of high-yielding climate-resilient crops through precision genome editing.

Genome-based high-resolution mapping of fusarium wilt resistance in sweet basil

Fusarium wilt of basil is a disease of sweet basil (Ocimum basilicum L.) plants caused by the fungus Fusarium oxysporum f. sp. basilici (FOB). Although resistant cultivars were released > 20 years ago, the underlying mechanism and the genes controlling the resistance remain unknown. We used genetic mapping to elucidate FOB resistance in an F₂ population derived from a cross between resistant and susceptible cultivars. We performed genotyping by sequencing of 173 offspring and aligning the data to the sweet basil reference genome. In total, 23,411 polymorphic sites were detected, and a single quantitative trait locus (QTL) for FOB resistance was found. The confidence interval was < 600 kbp, harboring only 60 genes, including a cluster of putative disease-resistance genes. Based on homology to a fusarium resistance protein from wild tomato, we also investigated a candidate resistance gene that encodes a transmembrane leucine-rich repeat - receptor-like kinase - ubiquitin-like protease (LRR-RLK-ULP). Sequence analysis of that gene in the susceptible parent vs. the resistant parent revealed multiple indels, including an insertion of 20 amino acids next to the transmembrane domain, which might alter its functionality. Our findings suggest that this LRR-RLK-ULP might be responsible for FOB resistance in sweet basil and demonstrate the usefulness of the recently sequenced basil genome for QTL mapping and gene mining.

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth’s biodiversity.

Turning promise into practice: Crop biotechnology for increasing genetic diversity and climate resilience

As climate change increasingly threatens agricultural production, expanding genetic diversity in crops is an important strategy for climate resilience in many agricultural contexts. In this Essay, we explore the potential of crop biotechnology to contribute to this diversification, especially in industrialized systems, by using historical perspectives to frame the current dialogue surrounding recent innovations in gene editing. We unearth comments about the possibility of enhancing crop diversity made by ambitious scientists in the early days of recombinant DNA and follow the implementation of this technology, which has not generated the diversification some anticipated. We then turn to recent claims about the promise of gene editing tools with respect to this same goal. We encourage researchers and other stakeholders to engage in activities beyond the laboratory if they hope to see what is technologically possible translated into practice at this critical point in agricultural transformation.

Will gene editing contribute to improved crop diversity and climate resilience? In this Essay, the authors look at lessons from past biotechnology efforts to inform action for the future.

Cultivar-specific markers, mutations, and chimerisim of Cavendish banana somaclonal variants resistant to Fusarium oxysporum f. sp. cubense tropical race 4

Background

The selection of tissue culture–derived somaclonal variants of Giant Cavendish banana (Musa spp., Cavendish sub-group AAA) by the Taiwan Banana Research Institute (TBRI) has resulted in several cultivars resistant to Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), a destructive fungus threatening global banana production. However, the mutations in these somaclonal variants have not yet been determined. We performed an RNA-sequencing (RNA-seq) analysis of three TBRI Foc TR4–resistant cultivars: ‘Tai-Chiao No. 5’ (TC5), ‘Tai-Chiao No. 7’ (TC7), and ‘Formosana’ (FM), as well as their susceptible progenitor ‘Pei-Chiao’ (PC), to investigate the sequence variations among them and develop cultivar-specific markers.

Results

A group of single-nucleotide variants (SNVs) specific to one cultivar were identified from the analysis of RNA-seq data and validated using Sanger sequencing from genomic DNA. Several SNVs were further converted into cleaved amplified polymorphic sequence (CAPS) markers or derived CAPS markers that could identify the three Foc TR4–resistant cultivars among 6 local and 5 international Cavendish cultivars. Compared with PC, the three resistant cultivars showed a loss or alteration of heterozygosity in some chromosomal regions, which appears to be a consequence of single-copy chromosomal deletions. Notably, TC7 and FM shared a common deletion region on chromosome 5; however, different TC7 tissues displayed varying degrees of allele ratios in this region, suggesting the presence of chimerism in TC7.

Conclusions

This work demonstrates that reliable SNV markers of tissue culture–derived and propagated banana cultivars with a triploid genome can be developed through RNA-seq data analysis. Moreover, the analysis of sequence heterozygosity can uncover chromosomal deletions and chimerism in banana somaclonal variants. The markers obtained from this study will assist with the identification of TBRI Cavendish somaclonal variants for the quality control of tissue culture propagation, and the protection of breeders’ rights.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08692-5.

Novel Fusarium wilt resistance genes uncovered in natural and cultivated strawberry populations are found on three non-homoeologous chromosomes

Several Fusarium wilt resistance genes were discovered, genetically and physically mapped, and rapidly deployed via marker-assisted selection to develop cultivars resistant to Fusarium oxysporum f. sp. fragariae, a devastating soil-borne pathogen of strawberry. Fusarium wilt, a soilborne disease caused by Fusarium oxysporum f. sp. fragariae, poses a significant threat to strawberry (Fragaria [Formula: see text] ananassa) production in many parts of the world. This pathogen causes wilting, collapse, and death in susceptible genotypes. We previously identified a dominant gene (FW1) on chromosome 2B that confers resistance to race 1 of the pathogen, and hypothesized that gene-for-gene resistance to Fusarium wilt was widespread in strawberry. To explore this, a genetically diverse collection of heirloom and modern cultivars and octoploid ecotypes were screened for resistance to Fusarium wilt races 1 and 2. Here, we show that resistance to both races is widespread in natural and domesticated populations and that resistance to race 1 is conferred by partially to completely dominant alleles among loci (FW1, FW2, FW3, FW4, and FW5) found on three non-homoeologous chromosomes (1A, 2B, and 6B). The underlying genes have not yet been cloned and functionally characterized; however, plausible candidates were identified that encode pattern recognition receptors or other proteins known to confer gene-for-gene resistance in plants. High-throughput genotyping assays for SNPs in linkage disequilibrium with FW1-FW5 were developed to facilitate marker-assisted selection and accelerate the development of race 1 resistant cultivars. This study laid the foundation for identifying the genes encoded by FW1-FW5, in addition to exploring the genetics of resistance to race 2 and other races of the pathogen, as a precaution to averting a Fusarium wilt pandemic.

Genome-Wide Analysis of the LRR-RLP Gene Family in a Wild Banana (Musa acuminata ssp. malaccensis) Uncovers Multiple Fusarium Wilt Resistance Gene Candidates

Banana is the most popular fruit in the world, with a relevant role in food security for more than 400 million people. However, fungal diseases cause substantial losses every year. A better understanding of the banana immune system should facilitate the development of new disease-resistant cultivars. In this study, we performed a genome-wide analysis of the leucine-rich repeat receptor-like protein (LRR-RLP) disease resistance gene family in a wild banana. We identified 78 LRR-RLP genes in the banana genome. Remarkably, seven MaLRR-RLPs formed a gene cluster in the distal part of chromosome 10, where resistance to Fusarium wilt caused by Foc race 1 has been previously mapped. Hence, we proposed these seven MaLRR-RLPs as resistance gene candidates (RGCs) for Fusarium wilt. We also identified seven other banana RGCs based on their close phylogenetic relationships with known LRR-RLP proteins. Moreover, phylogenetic analysis of the banana, rice, and Arabidopsis LRR-RLP families revealed five major phylogenetic clades shared by these plant species. Finally, transcriptomic analysis of the MaLRR-RLP gene family in plants treated with Foc race 1 or Foc TR4 showed the expression of several members of this family, and some of them were upregulated in response to these Foc races. Our study provides novel insights into the structure, distribution, evolution, and expression of the LRR-RLP gene family in bananas as well as valuable RGCs that will facilitate the identification of disease resistance genes for the genetic improvement of this crop.

Food biodiversity: Quantifying the unquantifiable in human diets

Dietary diversity is an established public health principle, and its measurement is essential for studies of diet quality and food security. However, conventional between food group scores fail to capture the nutritional variability and ecosystem services delivered by dietary richness and dissimilarity within food groups, or the relative distribution (i.e., evenness or moderation) of e.g., species or varieties across whole diets. Summarizing food biodiversity in an all-encompassing index is problematic. Therefore, various diversity indices have been proposed in ecology, yet these require methodological adaption for integration in dietary assessments. In this narrative review, we summarize the key conceptual issues underlying the measurement of food biodiversity at an edible species level, assess the ecological diversity indices previously applied to food consumption and food supply data, discuss their relative suitability, and potential amendments for use in (quantitative) dietary intake studies. Ecological diversity indices are often used without justification through the lens of nutrition. To illustrate: (i) dietary species richness fails to account for the distribution of foods across the diet or their functional traits; (ii) evenness indices, such as the Gini-Simpson index, require widely accepted relative abundance units (e.g., kcal, g, cups) and evidence-based moderation weighting factors; and (iii) functional dissimilarity indices are constructed based on an arbitrary selection of distance measures, cutoff criteria, and number of phylogenetic, nutritional, and morphological traits. Disregard for these limitations can lead to counterintuitive results and ambiguous or incorrect conclusions about the food biodiversity within diets or food systems. To ensure comparability and robustness of future research, we advocate food biodiversity indices that: (i) satisfy key axioms; (ii) can be extended to account for disparity between edible species; and (iii) are used in combination, rather than in isolation.Supplemental data for this article is available online at https://doi.org/10.1080/10408398.2022.2051163 .

Quantitative Trait Locus Mapping and Identification of Candidate Genes for Resistance to Fusarium Wilt Race 7 Using a Resequencing-Based High Density Genetic Bin Map in a Recombinant Inbred Line Population of Gossypium barbadense

Fusarium wilt caused by Fusarium oxysporum f. sp. vasinfectum (FOV) is one of the most destructive diseases in cotton (Gossypium spp.) production, and use of resistant cultivars is the most cost-effective method managing the disease. To understand the genetic basis of cotton resistance to FOV race 7 (FOV7), this study evaluated a recombinant inbred line (RIL) population of 110 lines of G. barbadense from a cross between susceptible Xinhai 14 and resistant 06-146 in eight tests and constructed a high-density genetic linkage map with resequencing-based 933,845 single-nucleotide polymorphism (SNP) markers covering a total genetic distance of 2483.17 cM. Nine quantitative trait loci (QTLs) for FOV7 resistance were identified, including qFOV7-D03-1 on chromosome D03 in two tests. Through a comparative analysis of gene expression and DNA sequence for predicted genes within the QTL region between the two parents and selected lines inoculated with FOV7, GB_D03G0217 encoding for a calmodulin (CaM)-like (CML) protein was identified as a candidate gene. A further analysis confirmed that the expression of GB_D03G0217 was suppressed, leading to increased disease severity in plants of the resistant parent with virus induced gene silencing (VIGS).

The pangenome of banana highlights differences between genera and genomes

Banana (Musaceae family) has a complex genetic history and includes a genus Musa with a variety of cultivated clones with edible fruits, Ensete species that are grown for their edible corm, and monospecific Musella whose generic status has been questioned. The most commonly exported banana cultivars belong to Cavendish, a subgroup of Musa triploid cultivars, which is under threat by fungal pathogens, though there are also related species M. balbisiana Colla (B genome), M. textilis Née (T genome), and M. schizocarpa N. W. Simmonds (S genome), along with hybrids of these genomes, which potentially host genes of agronomic interest. Here we present the first cross-genus pangenome of banana, which contains representatives of the Musa and Ensete genera. Clusters based on gene presence-absence variation (PAV) clearly separate Musa and Ensete, while Musa is split further based on species. These results present the first pangenome study across genus boundaries and identifies genes that differentiate between Musaceae species, information that may support breeding programs in these crops.

Vacuolar Processing Enzymes Modulating Susceptibility Response to Fusarium oxysporum f. sp. cubense Tropical Race 4 Infections in Banana

Fusarium oxysporum f. sp. cubense tropical race 4 (FocTR4) is a destructive necrotrophic fungal pathogen afflicting global banana production. Infection process involves the activation of programmed cell death (PCD). In this study, seven Musa acuminata vacuolar processing enzyme (MaVPE1-MaVPE7) genes associated with PCD were successfully identified. Phylogenetic analysis and tissue-specific expression categorized these MaVPEs into the seed and vegetative types. FocTR4 infection induced the majority of MaVPE expressions in the susceptible cultivar "Berangan" as compared to the resistant cultivar "Jari Buaya." Consistently, upon FocTR4 infection, high caspase-1 activity was detected in the susceptible cultivar, while low level of caspase-1 activity was recorded in the resistant cultivar. Furthermore, inhibition of MaVPE activities via caspase-1 inhibitor in the susceptible cultivar reduced tonoplast rupture, decreased lesion formation, and enhanced stress tolerance against FocTR4 infection. Additionally, the Arabidopsis VPE-null mutant exhibited higher tolerance to FocTR4 infection, indicated by reduced sporulation rate, low levels of H₂O₂ content, and high levels of cell viability. Comparative proteomic profiling analysis revealed increase in the abundance of cysteine proteinase in the inoculated susceptible cultivar, as opposed to cysteine proteinase inhibitors in the resistant cultivar. In conclusion, the increase in vacuolar processing enzyme (VPE)-mediated PCD played a crucial role in modulating susceptibility response during compatible interaction, which facilitated FocTR4 colonization in the host.

Biocontrol Potential of Endophytic Streptomyces malaysiensis 8ZJF-21 From Medicinal Plant Against Banana Fusarium Wilt Caused by Fusarium oxysporum f. sp. cubense Tropical Race 4

Banana (Musa spp.) is an important fruit crop cultivated in most tropical countries. Banana Fusarium wilt caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is the most destructive fungal disease. Biocontrol using endophytic microorganisms is considered as a safety and sustainable strategy. Actinomycetes have a potential for the production of diverse metabolites. Isolation of endophytic actinomycetes with high efficiency and broad-spectrum antagonism is key for exploring biocontrol agents. Our previous study showed that a total of 144 endophytic actinomycetes were isolated from different tissues of medicinal plants in Hainan, China. Especially, strain 8ZJF-21 exhibited a broad-spectrum antifungal activity. Its morphological, physiological, and biochemical characteristics were consistent with the genus Streptomyces. The phylogenetic tree demonstrated that strain 8ZJF-21 formed a distinct clade with Streptomyces malaysiensis. Average nucleotide identity (ANI) was 98.49% above the threshold of novel species. The pot experiment revealed that endophytic Streptomyces malaysiensis 8ZJF-21 could improve the plant resistance to Foc TR4 by enhancing the expression levels of defense-related and antioxidant enzyme genes. It also promoted the plant growth by producing several extracellular enzymes and metabolites. Antifungal mechanism assays showed that S. malaysiensis 8ZJF-21 extract inhibited mycelial growth and spore germination of Foc TR4 in vitro. Pathogenic cells occurred cytoplasmic heterogeneity, disappeared organelles, and ruptured ultrastructure. Sequencing and annotation of genome suggested that S. malaysiensis 8ZJF-21 had a potential of producing novel metabolites. Nineteen volatile organic compounds were obtained from the extract by Gas Chromatography-Mass Spectrometry (GC-MS). Hence, endophytic Streptomyces strains will become essential biocontrol agents of modern agricultural practice.

Exploring diverse roles of micro RNAs in banana: Current status and future prospective

Micro RNAs (miRNAs) are 20-24 nucleotides long non-coding RNA sequences identified and characterized in multiple plant and animal systems. miRNAs play multifarious roles ranging from plant development to stress tolerance by synchronizing physiological processes at the level of transcription and translation. Banana is a major horticultural crop with colossal production worldwide. Despite the recent encouraging developments, the information on functions of miRNAs in banana plants is still in its infancy. The available literature pertaining to miRNAs in banana plants hints towards their contribution as master regulators in crucial physiological processes for instance abiotic stress responses, pathogenic defence response, fruit ripening and so on. This review is focused on biogenesis of miRNAs, their identification and deciphering their respective roles in banana plants with special emphasis on abiotic stress responses, plant immune responses, fruit ripening and storage. Based on the prior reports, we identified a few miRNAs with prospective roles in stress tolerance and illustrated the potential applications of miRNAs in banana crop improvement utilizing recent biotechnological tools such as CRISPR cas9, RNAi and the nano particle based foliar spray of miRNAs. The review briefly explained the future directions in banana research with a special emphasis on miRNA regulatory networks and agronomic traits improvement. Finally, future domains in miRNA research in plants and their possible applications towards crop improvement in agriculture are described briefly.

Current technological interventions and applications of CRISPR/Cas for crop improvement

Efficient and innovative breeding strategies are immensely required to meet the global food demand, nutritional security and sustainable agriculture. Genome editing tools have emerged as an effective technology for site-directed genome modification causing the change in gene expression and protein function for the improvement of various important traits in particular the CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein). As the technology evolved with time, advances have been observed like prime editing, base editing, PAMless editing, Drosha based editing with multiple targets having the potential to fulfill the regulatory processes around the world. These recent interventions are highly proficient, cost-efficient, user-friendly, and holds promise for a major revolution in basic and applied plant biology research in the ever-evolving climatic conditions. In the review, we have discussed the most recent technologies and advances for CRISPR/Cas editing in plants.

Transcription factor MaMADS36 plays a central role in regulating banana fruit ripening

Bananas are model fruits for studying starch conversion and climactericity. Starch degradation and ripening are two important biological processes that occur concomitantly in banana fruit. Ethylene biosynthesis and postharvest fruit ripening processes, i.e. starch degradation, fruit softening, and sugar accumulation, are highly correlated and thus could be controlled by a common regulatory switch. However, this switch has not been identified. In this study, we transformed red banana (Musa acuminata L.) with sense and anti-sense constructs of the MaMADS36 transcription factor gene (also MuMADS1, Ma05_g18560.1). Analysis of these lines showed that MaMADS36 interacts with 74 other proteins to form a co-expression network and could act as an important switch to regulate ethylene biosynthesis, starch degradation, softening, and sugar accumulation. Among these target genes, musa acuminata beta-amylase 9b (MaBAM9b, Ma05_t07800.1), which encodes a starch degradation enzyme, was selected to further investigate the regulatory mechanism of MaMADS36. Our findings revealed that MaMADS36 directly binds to the CA/T(r)G box of the MaBAM9b promoter to increase MaBAM9b transcription and, in turn, enzyme activity and starch degradation during ripening. These results will further our understanding of the fine regulatory mechanisms of MADS-box transcription factors in regulating fruit ripening, which can be applied to breeding programs to improve fruit shelf-life.

Analysis of banana and cocoa export commodities in food system transformation, with special reference to certification schemes as drivers of change

Food systems analysis is increasingly being applied to understand relations between production, distribution, and consumption of food products, the drivers that influence the system, and the outcomes that show how well the food system performs on health and nutrition, on environmental sustainability, and on income and inclusiveness. Little attention has gone to the position of global export commodities, where production and consumption are far apart. Banana in Costa Rica and cocoa in Cote d’Ivoire were the subject of this study to find out what major drivers determine the functioning of these systems. Next to identifying drivers such as population growth and increased plant disease pressure, it was found that the typical far-away setting and different living conditions between producer and consumer countries required a special eye on governance as a tripartite arena (government, private sector, civil society) with their power relations, and on certification schemes as a driver that follows from corporate social responsibility. The certification schemes addressed cover all food system outcomes, although health and nutrition in a less conspicuous way. The descriptions of the functioning of the schemes were also linked to living wages and incomes for banana plantation workers in Costa Rica and cocoa smallholder farmers in Côte d’Ivoire. Although very meaningful, certification schemes so far do not prove to be a silver bullet, but they do have the potential, in combination with other measures, to help positive food system transformations.

A Novel Antifungal Actinomycete Streptomyces sp. Strain H3-2 Effectively Controls Banana Fusarium Wilt

Banana Fusarium wilt disease caused by Fusarium oxyspoum f. sp. cubense (Foc) seriously threatens the banana industry. Foc tropical race 4 (Foc TR4) can infect almost all banana cultivars. Compared with traditional physical and chemical practices, biocontrol strategy using beneficial microbes is considered as an environmentally sound option to manage fungal disease. In this study, a strain, H3-2, isolated from a non-infected banana orchard, exhibited high antifungal activity against Foc TR4. According to its morphological, physiological, and biochemical characteristics, the strain H3-2 was identified as Streptomyces sp. and convinced by the polymorphic phylogenic analysis of 16S rRNA sequences. Extracts of the strain H3-2 suppressed the growth and spore germination of Foc TR4 in vitro by destroying cell membrane integrity and mycelial ultrastructure. Notably, the strain and its extracts showed broad-spectrum antifungal activity against the selected seven fungal phytopathogens. Fourteen chemical compounds in the extracts were identified by gas chromatography–mass spectrometer (GC-MS), primarily phenolic compounds. Additional pot inoculation experiment demonstrated that the fermentation broth of the strain H3-2 promoted the growth of banana seedlings by efficiently inhibiting the spread of banana Fusarium wilt disease. This study demonstrated the potential application of the novel Streptomyces sp. H3-2 for the management of banana Fusarium wilt.

Banana Cultivar Field Screening for Resistance to Fusarium oxysporum f.sp. cubense Tropical Race 4 in the Northern Territory

Fusarium oxysporum f.sp. cubense, causal agent of Panama disease, is one of the biggest threats to global banana production, particularly the Cavendish competent tropical race 4 (Foc TR4). It continues to spread globally with detections occurring in regions of the Middle East and new continents such as Africa and South America in the last decade. As the search was on for new management strategies and resistant cultivars to combat the disease, a banana cultivar-screening trial took place in the Northern Territory of Australia, which examined the responses of 24 banana cultivars to the soil borne fungus. These cultivars included material from TBRI, FHIA and selections from Thailand, Indonesia and Australia and evaluated for their resistance to tropical race 4 for two cropping cycles. Several cultivars displayed considerable resistance to Foc TR4, including several FHIA parental lines and hybrids, the Cavendish (AAA) selections GCTCV 215 and GCTCV 247 from TBRI and an Indonesian selection CJ19 showed either very little to no plant death due to the disease.

The M35 Metalloprotease Effector FocM35_1 Is Required for Full Virulence of Fusarium oxysporum f. sp. cubense Tropical Race 4

Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) causes Fusarium wilt of banana, the most devastating disease on a banana plant. The genome of Foc TR4 encodes many candidate effector proteins. However, little is known about the functions of these effector proteins on their contributions to disease development and Foc TR4 virulence. Here, we discovered a secreted metalloprotease, FocM35_1, which is an essential virulence effector of Foc TR4. FocM35_1 was highly upregulated during the early stages of Foc TR4 infection progress in bananas. The FocM35_1 knockout mutant compromised the virulence of Foc TR4. FocM35_1 could interact with the banana chitinase MaChiA, and it decreased banana chitinase activity. FocM35_1 induced cell death in Nicotiana benthamiana while suppressing the INF1-induced hypersensitive response (HR), and its predicted enzymatic site was required for lesion formation and the suppression to INF1-induced HR on N. benthamiana leaves. Importantly, treatment of banana leaves with recombinant FocM35_1 accelerates Foc TR4 infection. Collectively, our study provides evidence that metalloprotease effector FocM35 seems to contribute to pathogen virulence by inhibiting the host immunity.

Preliminary Study on Tracing the Origin and Exploring the Relations between Growing Conditions and Isotopic and Elemental Fingerprints of Organic and Conventional Cavendish Bananas (Musa spp.)

The stable isotopic ratios and elemental compositions of 120 banana samples, Musa spp. (AAA Group, Cavendish Subgroup) cultivar Williams, collected from six countries (Colombia, Costa Rica, Dominica Republic, Ecuador, Panama, Peru), were determined by isotope ratio mass spectrometry and inductively coupled plasma mass spectrometry. Growing conditions like altitude, temperature, rainfall and production system (organic or conventional cultivation) were obtained from the sampling farms. Principal component analysis (PCA) revealed separation of the farms based on geographical origin and production system. The results showed a significant difference in the stable isotopic ratios (δ¹³C, δ¹⁵N, δ¹⁸O) and elemental compositions (Al, Ba, Cu, Fe, Mn, Mo, Ni, Rb) of the pulp and peel samples. Furthermore, δ¹⁵N was found to be a good marker for organically produced bananas. A correlation analysis was conducted to show the linkage of growing conditions and compositional attributes. The δ¹³C of pulp and peel were mainly negatively correlated with the rainfall, while δ¹⁸O was moderately positively (R values ~0.5) correlated with altitude and temperature. A moderate correlation was also found between temperature and elements such as Ba, Fe, Mn, Ni and Sr in the pulp and peel samples. The PCA results and correlation analysis suggested that the differences of banana compositions were combined effects of geographical factors and production systems. Ultimately, the findings contribute towards understanding the compositional differences of bananas due to different growing conditions and production systems linked to a defined origin; thereby offering a tool to support the traceability of commercial fruits.

Earthworm species in Musa spp. plantations in Brazil and worldwide

Bananas and plantains are major commodity/food crops that represent an important habitat for earthworms, although so far, no review is available on earthworm communities associated with banana/plantain crops worldwide. The Vale do Ribeira region is among the largest banana producing areas in Brazil, but little is known of the earthworms living there. Hence, the present study assessed earthworm populations and species in three banana plantations and adjacent Atlantic forest fragments along the Ribeira de Iguape River using standard (hand sorting) methodologies. Furthermore, we review earthworm populations reported in banana/plantain plantations worldwide. Only two species (Pontoscolex corethrurus, Amynthas gracilis) belonging to two families (Rhinodrilidae, Megascolecidae) were found in the Ribeira River valley, occurring concurrently. Abundance was low (< 13 indiv. m-2) compared with other banana plantations worldwide, that frequently surpassed 100 indiv. m-2. More than 70 studies reported earthworms from >200 banana plantations in 28 countries, and mean species richness was 2.7 per site, ranging from 1 to 10 species. Exotics predominated in most sites and P. corethrurus was the most prevalent species encountered. Overall, more than 104 species from 10 families were reported, with around 61 native and 43 exotic widespread species, mainly of the Megascolecidae, Lumbricidae and Acanthodrilidae families. Richness was highest in India (27 spp.) and the Canary Islands (25 spp.), but native species dominated only in a few countries and sites, while exotics were prevalent especially in island countries and Brazil. Lower-input practices appear to be important for earthworm communities and banana plantations can have large earthworm populations in some cases, which may be contributing to soil processes and plant production, topics that deserve further attention. However, many important banana-producing countries have not yet been evaluated, so further work is warranted, both in terms of applied ecology and biodiversity.

Male meiosis and pollen morphology in diploid Indonesian wild bananas and cultivars

Breeding of banana is hampered by its genetic complexity, structural chromosome rearrangements and different ploidy levels. Various scientific disciplines, including cytogenetics, linkage mapping, and bioinformatics, are helpful tools in characterising cultivars and wild relatives used in crossing programs. Chromosome analysis still plays a pivotal role in studying hybrid sterility and structural and numerical variants. In this study, we describe the optimisation of the chromosome spreading protocol of pollen mother cells focusing on the effects of standard fixation methods, duration of the pectolytic enzyme treatment and advantages of fluorescence microscopy of DAPI stained cell spreads. We demonstrate the benefits of this protocol on meiotic features of five wild diploid Musa acuminata bananas and a diploid (AA) cultivar banana “Rejang”, with particular attention on pairing configurations and chromosome transmission that may be indicative for translocations and inversions. Pollen slides demonstrate regular-shaped spores except “Rejang”, which shows fertile pollen grains of different size and sterile pollen grains, suggesting partial sterility and unreduced gamete formation that likely resulted from restitutional meiotic divisions.

Improvements in the Resistance of the Banana Species to Fusarium Wilt: A Systematic Review of Methods and Perspectives

The fungus Fusarium oxysporum f. sp. cubense (FOC), tropical race 4 (TR4), causes Fusarium wilt of banana, a pandemic that has threatened the cultivation and export trade of this fruit. This article presents the first systematic review of studies conducted in the last 10 years on the resistance of Musa spp. to Fusarium wilt. We evaluated articles deposited in different academic databases, using a standardized search string and predefined inclusion and exclusion criteria. We note that the information on the sequencing of the Musa sp. genome is certainly a source for obtaining resistant cultivars, mainly by evaluating the banana transcriptome data after infection with FOC. We also showed that there are sources of resistance to FOC race 1 (R1) and FOC TR4 in banana germplasms and that these data are the basis for obtaining resistant cultivars, although the published data are still scarce. In contrast, the transgenics approach has been adopted frequently. We propose harmonizing methods and protocols to facilitate the comparison of information obtained in different research centers and efforts based on global cooperation to cope with the disease. Thus, we offer here a contribution that may facilitate and direct research towards the production of banana resistant to FOC.

Transgenic Expression of dsRNA Targeting the Pentalonia nigronervosa acetylcholinesterase Gene in Banana and Plantain Reduces Aphid Populations

The banana aphid, Pentalonia nigronervosa, is the sole insect vector of banana bunchy top virus (BBTV), the causal agent of banana bunchy top disease. The aphid acquires and transmits BBTV while feeding on infected banana plants. RNA interference (RNAi) enables the generation of pest and disease-resistant crops; however, its effectiveness relies on the identification of pivotal gene sequences to target and silence. Acetylcholinesterase (AChE) is an essential enzyme responsible for the hydrolytic metabolism of the neurotransmitter acetylcholine in animals. In this study, the AChE gene of the banana aphid was targeted for silencing by RNAi through transgenic expression of AChE dsRNA in banana and plantain plants. The efficacy of dsRNA was first assessed using an artificial feeding assay. In vitro aphid feeding on a diet containing 7.5% sucrose, and sulfate complexes of trace metals supported aphid growth and reproduction. When AChE dsRNA was included in the diet, a dose of 500 ng/μL was lethal to the aphids. Transgenic banana cv. Cavendish Williams and plantain cvs. Gonja Manjaya and Orishele expressing AChE dsRNA were regenerated and assessed for transgene integration and copy number. When aphids were maintained on elite transgenic events, there was a 67.8%, 46.7%, and 75.6% reduction in aphid populations growing on Cavendish Williams, Gonja Manjaya, and Orishele cultivars, respectively, compared to those raised on nontransgenic control plants. These results suggest that RNAi targeting an essential aphid gene could be a useful means of reducing both aphid infestation and potentially the spread of the disease they transmit.

The Arabidopsis leucine-rich repeat receptor-like kinase MIK2 is a crucial component of early immune responses to a fungal-derived elicitor

Fusarium spp. cause severe economic damage in many crops, exemplified by Panama disease of banana or Fusarium head blight of wheat. Plants sense immunogenic patterns (termed elicitors) at the cell surface to initiate pattern-triggered immunity (PTI). Knowledge of fungal elicitors and corresponding plant immune-signaling is incomplete but could yield valuable sources of resistance. We characterized Arabidopsis thaliana PTI responses to a peptide elicitor fraction present in several Fusarium spp. and employed a forward-genetic screen using plants containing a cytosolic calcium reporter to isolate fusarium elicitor reduced elicitation (fere) mutants. We mapped the causal mutation in fere1 to the leucine-rich repeat receptor-like kinase MDIS1-INTERACTING RECEPTOR-LIKE KINASE 2 (MIK2) and confirmed a crucial role of MIK2 in fungal elicitor perception. MIK2-dependent elicitor responses depend on known signaling components and transfer of AtMIK2 is sufficient to confer elicitor sensitivity to Nicotiana benthamiana. Arabidopsis senses Fusarium elicitors by a novel receptor complex at the cell surface that feeds into common PTI pathways. These data increase mechanistic understanding of PTI to Fusarium and place MIK2 at a central position in Arabidopsis elicitor responses.

Ancient genomes reveal early Andean farmers selected common beans while preserving diversity

All crops are the product of a domestication process that started less than 12,000 years ago from one or more wild populations^1,2. Farmers selected desirable phenotypic traits (such as improved energy accumulation, palatability of seeds and reduced natural shattering³) while leading domesticated populations through several more or less gradual demographic contractions^2,4. As a consequence, the erosion of wild genetic variation⁵ is typical of modern cultivars, making them highly susceptible to pathogens, pests and environmental change^6,7. The loss of genetic diversity hampers further crop improvement programmes to increase food production in a changing world, posing serious threats to food security^8,9. Using both ancient and modern seeds, we analysed the temporal dynamics of genetic variation and selection during the domestication process of the common bean (Phaseolus vulgaris) in the southern Andes. Here, we show that most domestic traits were selected for before 2,500 years ago, with no or only minor loss of whole-genome heterozygosity. In fact, most of the changes at coding genes and linked regions that differentiate wild and domestic genomes are already present in the ancient genomes analysed here, and all ancient domestic genomes dated between 600 and 2,500 years ago are highly variable (at least as variable as modern genomes from the wild). Single seeds from modern cultivars show reduced variation when compared with ancient seeds, indicating that intensive selection within cultivars in the past few centuries probably partitioned ancestral variation within different genetically homogenous cultivars. When cultivars from different Andean regions are pooled, the genomic variation of the pool is higher than that observed in the pool of ancient seeds from north and central western Argentina. Considering that most desirable phenotypic traits are probably controlled by multiple polymorphic genes¹⁰, a plausible explanation of this decoupling of selection and genetic erosion is that early farmers applied a relatively weak selection pressure² by using many phenotypically similar but genetically diverse individuals as parents. Our results imply that selection strategies during the past few centuries, as compared with earlier times, more intensively reduced genetic variation within cultivars and produced further improvements by focusing on a few plants carrying the traits of interest, at the cost of marked genetic erosion within Andean landraces.

What is the elephant in the room when considering new therapies for fungal diseases?

The global scenario of antimicrobial resistance is alarming, and the development of new drugs has not appeared to make substantial progress. The constraints on drug discovery are due to difficulties in finding new targets for therapy, the high cost of development, and the mismatch between the time of drug introduction in a clinic and microorganism adaptation to a drug. Policies to address neglected diseases miss the broad spectrum of mycosis. Society is not aware of the actual threat represented by fungi to human health, food security, and biodiversity. The evidence discussed here is critical for warning governments to establish effective surveillance policies for fungi.HIGHLIGHTSFungal diseases are ignored even among neglected disease classifications.There are few options to treat mycoses, which is an increasing concern regarding fungal resistance to drugs, as evidenced by the spread of Candida auris.Fungal diseases represent a real threat to human health and food security.Investment in research to investigate the potential of repurposing drugs already in use could obtain results in the short term.

Using Genetic Engineering Techniques to Develop Banana Cultivars With Fusarium Wilt Resistance and Ideal Plant Architecture

Bananas (Musa spp.) are an important fruit crop worldwide. The fungus Fusarium oxysporum f. sp. cubense (Foc), which causes Fusarium wilt, is widely regarded as one of the most damaging plant diseases. Fusarium wilt has previously devastated global banana production and continues to do so today. In addition, due to the current use of high-density banana plantations, desirable banana varieties with ideal plant architecture (IPA) possess high lodging resistance, optimum photosynthesis, and efficient water absorption. These properties may help to increase banana production. Genetic engineering is useful for the development of banana varieties with Foc resistance and ideal plant architecture due to the sterility of most cultivars. However, the sustained immune response brought about by genetic engineering is always accompanied by yield reductions. To resolve this problem, we should perform functional genetic studies of the Musa genome, in conjunction with genome editing experiments, to unravel the molecular mechanisms underlying the immune response and the formation of plant architecture in the banana. Further explorations of the genes associated with Foc resistance and ideal architecture might lead to the development of banana varieties with both ideal architecture and pathogen super-resistance. Such varieties will help the banana to remain a staple food worldwide.

Evolutionary developmental biology and sustainability: A biology of resilience

Evolutionary developmental biology, and especially ecological developmental biology, is essential for discussions of sustainability and the responses to global climate change. First, this paper explores examples of animals that have successfully altered their development to accommodate human-made changes to their environments. We next document the ability of global warming to disrupt the development of those organisms with temperature-dependent sex-determination or with phenologies coordinating that organism's development with those of other species. The thermotolerance of Homo sapiens is also related to key developmental factors concerning brain development and maintenance, and the development of corals, the keystone organisms of tropical reefs, is discussed in relation to global warming as well as to other anthropogenic changes. While teratogenic and endocrine-disrupting compounds are not discussed in this essay, the ability of glyphosate herbicides to block insect development is highlighted. Last, the paper discusses the need to creatively integrate developmental biology with ecological, political, religious, and economic perspectives, as the flourishing of contemporary species may require altering the ways that Western science has considered the categories of nature, culture, and self.

Swedish consumers´ attitudes and values to genetic modification and conventional plant breeding - The case of fruit and vegetables

This study examined public attitudes to genetic modification (GM) and conventional plant breeding and explored general differences in attitudes to these two types of breeding concepts, including the effect of individual personal characteristics such as gender and age. It also sought to identify the influence of personal values linked to attitudes to GM crops and conventional plant breeding, following Schwartz value theory. Relations between specific values and attitudes to GM organisms (GMOs) have been studied previously, but not gender- and age-specific relations between specific values and attitudes to conventional plant breeding. Data were collected in this study using a questionnaire completed on-line by 1500 Swedish consumers in 2019. The questionnaire covered three different aspects: 1) sociodemographic data, including gender and age; 2) attitudes to GMO/conventional plant breeding; and 3) values, measured using the human values scale. It was found that consumers expressed more positive attitudes to conventional plant breeding than to GMO, men expressed more positive attitudes to both conventional plant breeding and GMO than women did, and younger consumers expressed more positive attitudes to GMO than older consumers did. A negative correlation between attitudes to conventional plant breeding and the value ‘tradition’, but no correlation to ‘universalism’, ‘benevolence’, ‘power’ or ‘achievement’, was identified for men. For women, correlations between attitudes to conventional plant breeding and ‘benevolence’ (neg.) and ‘achievement’ (pos.) were found. For both men and women, attitudes to GMO were negatively influenced by ‘universalism’ and ‘benevolence’, and positively influenced by ‘power’ and ‘achievement’. The implications of these results are discussed.