Multidisciplinary perspectives on banana (Musa spp.) domestication.
Ontology highlight
ABSTRACT:
SUBMITTER: Perrier X
PROVIDER: S-EPMC3136277 | biostudies-literature | 2011 Jul
REPOSITORIES: biostudies-literature
Publications
Multidisciplinary perspectives on banana (Musa spp.) domestication.
Perrier Xavier X De Langhe Edmond E Donohue Mark M Lentfer Carol C Vrydaghs Luc L Bakry Frédéric F Carreel Françoise F Hippolyte Isabelle I Horry Jean-Pierre JP Jenny Christophe C Lebot Vincent V Risterucci Ange-Marie AM Tomekpe Kodjo K Doutrelepont Hugues H Ball Terry T Manwaring Jason J de Maret Pierre P Denham Tim T
Proceedings of the National Academy of Sciences of the United States of America 20110705 28
Original multidisciplinary research hereby clarifies the complex geodomestication pathways that generated the vast range of banana cultivars (cvs). Genetic analyses identify the wild ancestors of modern-day cvs and elucidate several key stages of domestication for different cv groups. Archaeology and linguistics shed light on the historical roles of people in the movement and cultivation of bananas from New Guinea to West Africa during the Holocene. The historical reconstruction of domestication ...[more]
Similar Datasets
Project description:BackgroundBananas (Musa spp.) are a globally significant crop and are severely afflicted by diseases for which there are no effective chemical controls. Banana microbiomes may provide novel solutions to these constraints but are difficult to manage due to their high diversity and variability between locations. Hence 'common core' taxa, which are a subset of the microbiome that frequent all, or most, individuals of a host species, represent logical targets for the development of microbiome management approaches. Here, we first performed a pot experiment to characterise the effects of two factors that are likely to differ between farms (viz. edaphic conditions and host genotype) on bacterial diversity in bulk soil and seven plant compartments. From this experiment, we created shortlisted core 'candidates' that were then refined using a survey of 52 field-grown Musa spp. We confirmed the importance of the core through network analysis and by comparing the sequences of our core taxa with those reported in 22 previous studies.ResultsDiversity was found to differ between plant compartments and soils, but not genotypes. Therefore, we identified populations that were frequent across most plants irrespective of the soil in which they were grown. This led to the selection of 36 'common core' bacteria, that represented 65-95% of the dominant taxa in field-grown plants and were identified as highly interconnected 'hubs' using network analysis - a characteristic shown to be indicative of microbes that influence host fitness in studies of other plants. Lastly, we demonstrated that the core taxa are closely related to banana-associated bacteria observed on five other continents.ConclusionsOur study provides a robust list of common core bacterial taxa for Musa spp. Further research may now focus on how changes in the frequencies and activities of these most persistent taxa influence host fitness. Notably, for several of our core taxa, highly similar populations have already been isolated in previous studies and may be amenable to such experimentation. This contribution should help to accelerate the development of effective Musa spp. microbiome management practices.
| S-EPMC9461194 | biostudies-literature
Project description:BackgroundIn plants, RNA- based gene silencing mediated by small RNAs functions at the transcriptional or post-transcriptional level to negatively regulate target genes, repetitive sequences, viral RNAs and/or transposon elements. Post-transcriptional gene silencing (PTGS) or the RNA interference (RNAi) approach has been achieved in a wide range of plant species for inhibiting the expression of target genes by generating double-stranded RNA (dsRNA). However, to our knowledge, successful RNAi-application to knock-down endogenous genes has not been reported in the important staple food crop banana.ResultsUsing embryogenic cell suspension (ECS) transformed with ß-glucuronidase (GUS) as a model system, we assessed silencing of gusAINT using three intron-spliced hairpin RNA (ihpRNA) constructs containing gusAINT sequences of 299-nt, 26-nt and 19-nt, respectively. Their silencing potential was analysed in 2 different experimental set-ups. In the first, Agrobacterium-mediated co-transformation of banana ECS with a gusAINT containing vector and an ihpRNA construct resulted in a significantly reduced GUS enzyme activity 6-8 days after co-cultivation with either the 299-nt and 19-nt ihpRNA vectors. In the second approach, these ihpRNA constructs were transferred to stable GUS-expressing ECS and their silencing potential was evaluated in the regenerated in vitro plants. In comparison to control plants, transgenic plants transformed with the 299-nt gusAINT targeting sequence showed a 4.5 fold down-regulated gusA mRNA expression level, while GUS enzyme activity was reduced by 9 fold. Histochemical staining of plant tissues confirmed these findings. Northern blotting used to detect the expression of siRNA in the 299-nt ihpRNA vector transgenic in vitro plants revealed a negative relationship between siRNA expression and GUS enzyme activity. In contrast, no reduction in GUS activity or GUS mRNA expression occurred in the regenerated lines transformed with either of the two gusAINT oligo target sequences (26-nt and 19-nt).ConclusionsRNAi-induced silencing was achieved in banana, both at transient and stable level, resulting in significant reduction of gene expression and enzyme activity. The success of silencing was dependent on the targeted region of the target gene. The successful generation of transgenic ECS for second transformation with (an)other construct(s) can be of value for functional genomics research in banana.
| S-EPMC4177175 | biostudies-literature
Project description:The genetic diversity of endophytic bacteria in banana 'Prata Anã' roots was characterized. Two hundred and one endophytic bacteria were isolated, 151 of which were classified as Gram-positive and 50 as Gram-negative. No hypersensitivity response was observed in any of the isolates. The rep-PCR technique generated different molecular profiles for each primer set (REP, ERIC and BOX). Fifty readable loci were obtained and all of the fragments were polymorphic. Amplified ribosomal DNA restriction analysis (ARDRA) of the isolates based on cleavage with four restriction enzymes yielded 45 polymorphic bands and no monomorphic bands. PCR amplified the nifH gene in 24 isolates. 16S rDNA sequencing of the 201 bacterial isolates yielded 102 high-quality sequences. Sequence analyses revealed that the isolates were distributed among ten bacterial genera (Agrobacterium, Aneurinibacillus, Bacillus, Enterobacter, Klebsiella, Lysinibacillus, Micrococcus, Paenibacillus, Rhizobium and Sporolactobacillus) and included 15 species. The greatest number of isolates belonged to the genus Bacillus. The bacteria identified in this study may be involved in promoting growth, phosphate solubilization, biological control and nitrogen fixation in bananas.
| S-EPMC3715292 | biostudies-literature
Project description:Here, we report a metabarcoding (ITS2) study to define the common core fungal microbiome (mycobiome) of healthy Musa spp. (bananas and plantains). To identify a list of 21 core fungal taxa, we first characterised the effects of edaphic conditions and host genotype - two factors that are likely to differ between farms - on the diversity of fungal communities in bulk soil and seven plant compartments. This experiment facilitated shortlisting of core 'candidates', which were then elevated to full core status if also found to frequent a wide-range of field-grown Musa spp. and exhibit hub-like characteristics in network analyses. Subsequently, we conducted a meta-analysis of eleven publicly available datasets of Musa spp. associated fungi demonstrating that the core fungi identified in our study have close relatives in other countries. The diversity and composition of mycobiomes differed between plant compartments and soils, but not genotypes. The core mycobiome included Fusarium oxysporum and its relatives, which dominated all plant compartments, as well as members of the Sordariomycetes, Dothideomycetes, and Mortierellomycota. Our study provides a robust list of common core fungal taxa for Musa spp. Further studies may consider how changes in the frequencies and activities of these taxa influence host fitness and whether they can be managed to improve banana production.
| S-EPMC10098452 | biostudies-literature
Project description:Chikungunya and yellow fever virus cause vector-borne viral diseases in humans. There is currently no specific antiviral drug for either of these diseases. Banana plants are used in traditional medicine for treating viral diseases such as measles and chickenpox. Therefore, we tested selected banana cultivars for their antiviral but also cytotoxic properties. Different parts such as leaf, pseudostem and corm, collected separately and extracted with four different solvents (hexane, acetone, ethanol, and water), were tested for in vitro antiviral activity against Chikungunya virus (CHIKV), enterovirus 71 (EV71), and yellow fever virus (YFV). Extracts prepared with acetone and ethanol from leaf parts of several cultivars exhibited strong (EC50 around 10 ?g/mL) anti-CHIKV activity. Interestingly, none of the banana plant extracts (concentration 1-100 µg/mL) were active against EV71. Activity against YFV was restricted to two cultivars: Namwa Khom-Pseudostem-Ethanol (5.9 ± 5.4), Namwa Khom-Corm-Ethanol (0.79 ± 0.1) and Fougamou-Corm-Acetone (2.5 ± 1.5). In most cases, the cytotoxic activity of the extracts was generally 5- to 10-fold lower than the antiviral activity, suggesting a reasonable therapeutic window.
| S-EPMC7291111 | biostudies-literature
Project description:The "Cavendish" and "Prata" subgroups represent respectively 47% and 24% of the world banana production. Compared to world average progressing from 10.6 to 20.6 t ha-1 between 1961 and 2016, and despite sustained domestic demand and the introduction of new cultivars, banana yield in Brazil has stagnated around 14.5 t ha-1 mainly due to nutrient and water mismanagement. "Prata" is now the dominant subgroup in N-E Brazil and is fertigated at high costs. Nutrient balances computed as isometric log-ratios (ilr) provide a comprehensive understanding of nutrient relationships in the diagnostic leaf at high yield level by combining raw concentration data. Although the most appropriate method for multivariate analysis of compositional balances may be less efficient due to non-normal data distribution and limited nutrient mobility in the plant, robustness of the nutrient balance approach could be improved using Box-Cox exponents assigned to raw foliar concentrations. Our objective was to evaluate the accuracy of nutrient balances to diagnose fertigated "Prata" orchards. The dataset comprised 609 observations on fruit yields and leaf tissue compositions collected from 2010 to 2016 in Ceará state, N-E Brazil. Raw nutrient concentration ranges were ineffective as diagnostic tool due to considerable overlapping of concentration ranges for low- and high-yielding subpopulations at cutoff yield of 40 Mg ha-1. Nutrient concentrations were combined into isometric log-ratios (ilr) and normalized by Box-Cox corrections between 0 and 1 which may also account for restricted nutrient transfer from leaf to fruit. Despite reduced ilr skewness, Box-Cox coefficients did not improve model robustness measured as the accuracy of the Cate-Nelson partition between yield and the multivariate distance across ilr values. Sensitivity was 94%, indicating that low yields are attributable primarily to nutrient imbalance. There were 148 false-positive specimens (high yield despite nutrient imbalance) likely due to suboptimal nutrition, contamination, or luxury consumption. The profitability of "Prata" orchards could be enhanced by rebalancing nutrients using ilr standards with no need for Box-Cox correction.
| S-EPMC6177482 | biostudies-literature
Project description:Plant casein kinase II (CKII) plays an essential role in regulating plant growth and development, and responses to biotic and abiotic stresses. Here, we report the identification and characterization of the CKII family genes in Musa spp. cv. 'Tianbaojiao' (AAA group) and the wild banana (Musa itinerans). The 13 cDNA sequences of the CKII family members were identified both in 'Tianbaojiao' and wild banana, respectively. The differences between CKII α and CKII β members are corroborated through the subcellular localizations, phosphorylation sites and gene structures. The cloning of CKII β-like-2 gDNA sequences in wild banana and 'Tianbaojiao' and the analysis of gene structures showed MiCKIIβ-like-2b and MaCKIIβ-like-2 are likely alternatively spliced transcripts, which were derived from the alternative splicing events that involved exon deletion. The qPCR validation showed differential expression CKII family members in response to cold stress and also in all tested tissues (leaf, pseudostem and root) of wild banana. In particular, the normal transcript MiCKIIβ-like-2a was highly expressed in response to cold stress in wild banana; oppositely, the alternatively spliced transcript MiCKIIβ-like-2b was quite lowly expressed. The complex origin and long-term evolution of Musa lineage might explain the alternative splicing events of CKII β-like-2.
| S-EPMC6040749 | biostudies-literature
Project description:Fertigation management of banana plantations at a plot scale is expanding rapidly in Brazil. To guide nutrient management at such a small scale, genetic, environmental and managerial features should be well understood. Machine learning and compositional data analysis (CoDa) methods can measure the effects of feature combinations on banana yield and rank nutrients in the order of their limitation. Our objectives are to review ML and CoDa models for application at regional and local scales, and to customize nutrient diagnoses of fertigated banana at the plot scale. We documented 940 "Prata" and "Cavendish" plot units for tissue and soil tests, environmental and managerial features, and fruit yield. A Neural Network informed by soil tests, tissue tests and other features was the most proficient learner (AUC up to 0.827). Tissue nutrients were shown to have the greatest impact on model accuracy. Regional nutrient standards were elaborated as centered log ratio means and standard deviations of high-yield and nutritionally balanced specimens. Plot-scale diagnosis was customized using the closest successful factor-specific tissue compositions identified by the smallest Euclidean distance from the diagnosed composition using centered or isometric log ratios. Nutrient imbalance differed between regional and plot-scale diagnoses, indicating the profound influence of local factors on plant nutrition. However, plot-scale diagnoses require large, reliable datasets to customize nutrient management using ML and CoDa models.
| S-EPMC7692714 | biostudies-literature
Project description:https://www.crop-diversity.org/mgis/.
| S-EPMC5502358 | biostudies-literature
Project description:Satellite DNA sequences consist of tandemly arranged repetitive units up to thousands nucleotides long in head-to-tail orientation. The evolutionary processes by which satellites arise and evolve include unequal crossing over, gene conversion, transposition and extra chromosomal circular DNA formation. Large blocks of satellite DNA are often observed in heterochromatic regions of chromosomes and are a typical component of centromeric and telomeric regions. Satellite-rich loci may show specific banding patterns and facilitate chromosome identification and analysis of structural chromosome changes. Unlike many other genomes, nuclear genomes of banana (Musa spp.) are poor in satellite DNA and the information on this class of DNA remains limited. The banana cultivars are seed sterile clones originating mostly from natural intra-specific crosses within M. acuminata (A genome) and inter-specific crosses between M. acuminata and M. balbisiana (B genome). Previous studies revealed the closely related nature of the A and B genomes, including similarities in repetitive DNA. In this study we focused on two main banana DNA satellites, which were previously identified in silico. Their genomic organization and molecular diversity was analyzed in a set of nineteen Musa accessions, including representatives of A, B and S (M. schizocarpa) genomes and their inter-specific hybrids. The two DNA satellites showed a high level of sequence conservation within, and a high homology between Musa species. FISH with probes for the satellite DNA sequences, rRNA genes and a single-copy BAC clone 2G17 resulted in characteristic chromosome banding patterns in M. acuminata and M. balbisiana which may aid in determining genomic constitution in interspecific hybrids. In addition to improving the knowledge on Musa satellite DNA, our study increases the number of cytogenetic markers and the number of individual chromosomes, which can be identified in Musa.
| S-EPMC3553004 | biostudies-literature