Using genotyping-by-sequencing to understand Musa diversity : [P449]

This project is part of a larger effort to apply genomics technologies to assess genetic diversity and to advance genetic improvement efforts in Musa (banana and plantain), a major staple food crop in the developing world. Most cultivated varieties of bananas result from intra- or inter-specific crosses of the wild diploid species, Musa acuminata (A genome) and Musa balbisiana (B genome). Somaclonal mutation and human selection has resulted in current day bananas with a wide morphological diversity. The Cavendish (AAA) subgroups are believed to have derived from an individual unique initial genotype, and similarly for the subgroup plantain (AAB). However, little or no genetic diversity can be detected within these groups using conventional molecular markers such as RFLP, SSR, DArT. To assess genetic diversity with an improved resolution, we have selected 65 accessions with diploid and triploid combinations of the A and/or B genomes including AAB plantains and AAA Cavendish, and cultivated or wild Musa accessions from the core collection at the Global Musa Genomics Consortium (GMGC) (http://www.musagenomics.org). We have used a high-throughput reduced representation genome sequencing approach - genotyping-by-sequencing (GBS) to obtain high density sequence markers. Genotypes are determined for each diploid and triploid accession, and dissimilarity computed across all accessions. We will discuss the value of GBS markers to characterize the genetic diversity of individual Musa subgroups with high resolution. This work is funded by the USAID linkage funds. (Texte intégral

Paleoploidization events in the Musa (banana) lineage

Bananas (Musa spp.) are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales. Cultivars are mainly triploid, from inter(sub)specific origin and clonally propagated. We sequenced the genome of a Musa acuminata doubled-haploid genotype (Pahang-HD) providing the first monocotyledon high-continuity whole-genome sequence reported outside Poales. The analysis of the genome revealed three rounds of whole genome duplications (WGD), denoted as alpha, beta and gamma (from the most recent event to the oldest). Based on Ks analyses and synteny relationships, twelve beta Musa ancestral blocks were constructed, representing the ancestral genome before alpha and beta duplications. Comparative genomics and phylogenetic approaches revealed that these three WGDs occurred in the Musa lineage independently of those described in the Poales lineage and the one that we detected in the Arecales lineage. Following WGDs, that are particularly frequent in the flowering plant lineages, most duplicated genes are deleted by intrachromosomal recombination, a process referred to as fractionation. We are currently analyzing the fractionation pattern following the Musa polyploidization events. Finally, this Musa reference sequence represents an invaluable reference for studying monocot evolution and associated genomic changes. (Résumé d'auteur

The Musa Germplasm Information System enhances knowledge of banana diversity

Bananas (Musa spp.) are a staple food and vital source of income for millions of people. These livelihoods in developing countries depend on over 1000 traditional varieties that are mostly consumed locally. Because Musa cultivars are usually seedless, their genetic diversity must be conserved as full-size plants or plantlets, in field collections or in in vitro genebanks. More than 6000 accessions are conserved in about 60 Musa national collections. The Global Musa Germplasm Collection (ITC) in Belgium, managed by Bioversity International, stores more than 1400 Musa germplasm accessions in trust. The utilization of the germplasm in the collection depends on the availability of information relating to the characteristics of each germplasm accession. In 1997, the Musa Germplasm Information System (MGIS) was developed. It is a global exchange system and the most extensive source of data on Musa genetic resources. It contains information on 5522 accessions managed in 22 banana collections, including passport data (where and when the germplasm accession was collected, donated or developed), botanical classification, morpho-taxonomic descriptors, and evaluation data (characteristics such as agronomic traits, disease, and stress tolerance) as well as many different photographs. Each participating collection enters and manages its own accession data, which is centralized by Bioversity. Links have been created to external data sources such as the System-wide Information Network for Genetic Resources (SINGER), under which FAO in-trust accessions held by ITC are published. MGIS has been recognised by the Generation Challenge Programme as a model system for storing accession-level data. However, it represents an incomplete dataset due to either the lack of capacity or motivation by several collections to contribute to it. The database has undergone two upgrades (see new release http://www.crop-diversity.org/banana/) and new features should be made available in the coming months, such as links to a molecular database (TropGENE DB), Geographic Information System (GIS) information, data quality control and inter-collection data comparison. (Texte intégral

Evolution of gene families involved in banana fruit development and ripening : W077

A reference genome sequence of banana was recently obtained from a Musa acuminata doubled-haploid accession (DH-Pahang, 523 Mb) and organized into eleven pseudomolecules. This genome opens brand new perspectives for the identification of genes underlying key physiological processes and agricultural traits in this economically important species. To identify genes involved in banana fruit development and ripening, we used a whole genome-scale approach combining phylogenomic analyses and gene expression profiling. Global analysis of gene expression in banana fruits in response to ethylenic treatment was performed using RNA-seq. In parallel, gene families involved in core ethylene biosynthesis/signaling pathways and starch/sucrose metabolism were identified in the Musa genome using comparative genomics and phylogenomic analyses with eleven plant species. Our results showed a progressive global reprogramming of banana fruits during ripening characterized by an inhibition of the downstream ethylene signaling pathway. In addition, we identified expansions of gene families encoding transcriptional regulation elements of the ethylene signaling pathway in Musa. These expansions are currently analyzed in relation to Musa whole genome duplications. Finally, the combined structural and gene expression analyses led to the identification of candidate genes and gene family members involved in banana fruit ripening. (Résumé d'auteur

Comparison of hom(oe)ologous regions containing clusters of duplicated RGAs within Musa species and with rice

Understanding structure and evolution of genomic regions coding for proteins of agronomical interest is an important objective for crop improvement. We compare hom(oe)ologous regions within monocot genomes through BAC annotation. Here, we present putative orthologous and paralogous relationships of a highly duplicated Resistance Gene Analog (RGA) locus within Musa species and between Musa and rice species. (Résumé d'auteur

Banana and plantain (Musa spp.) cultivar preference, local processing techniques and consumption patterns in Eastern Democratic Republic of Congo

This cross-sectional study carried out in North Kivu (NK) and South Kivu (SK) of the Eastern Democratic Republic of Congo aimed to identify the most preferred Musa cultivars, their processing/cooking methods and Musa consumption patterns among rural households. Our results showed that the preferred cooking banana varieties included yellow-pulped AAA-East African Highland bananas [EAHB] 'Nshikazi' (SK) and 'Vulambya' (NK), which were valued for their cooking qualities, large bunches and suitability for production of banana beer. The preferred plantains were orange-pulped and included 'Musheba' (SK) and 'Musilongo' (NK) and were preferred for their short maturation period, large bunches and higher market prices. Over 60% of the households examined had consumed EAHB within 24 hours, whereas <10% had consumed plantains. The most common cooking method was simple boiling of bananas/plantains and main accompaniments include beans and amaranth leaves. Over 69% of surveyed households that had consumed Musa products had con-sumed them boiled. The majority of the households (90%) obtained banana/plantains from their farms, and >55% of households from SK and NK consumed banana products between 2 and 4 times/week. This information will be used to help direct researchers on the Musa cultivars that could be further sampled for carotenoid analysis and those found to be rich could be used in the fast-tracking approach to reduce Vitamin A deficiency. (Résumé d'auteur

The exploration of the pathosystem BSV/Musa sp. : How does it work?

As several other plants, the genome of banana and plantain contains integrations of Banana streak virus (BSV) sequences even though integration is not an essential step in the replication cycle of this virus. In banana two types of BSV integrants exist. Ones are non functional sequences present in both common Musa species, Musa acuminata (denoted A) and Musa balbisiana (denoted B) and it is now assumed that the integrants of the other type, containing the complete viral genome and restricted to M. balbisiana genome, become infectious by reconstituting a complete replication-competent viral genome. Thereby, an increasing record of BSV outbreaks was observed fifteen years ago among banana breeding lines and micro propagated inter-specific Musa hybrids, worldwide. Today, three widespread BSV species, Banana streak Obino l'Ewai virus (BSOIV), Banana streak Imové virus (BSImV) and Banana streak Golfinger virus (BSGfV) are known to occur as infectious integrants in the M. balbisiana genome. However, even though such integrations are known to be infectious, their presence is not sufficient to induce infection. We demonstrated that the process of genetic hybridization and abiotic stresses such as micropropagation by in vitro culture contributed in triggering episomal expression from EPRVs. Two mechanisms at least are involved in the BSV expression: the ploidy of the M. balbisiana in Musa genotypes and an additional genetic factor called BEL for BSV expressed locus concerning the triploids (Musa AAB) resulting from inter-species genetic crosses between virus-free diploid M. balbisiana (BB) and tetraploid M acuminata (AAAA) parents. Then, diploids M. balbisiana such as PKW and Pisang Batu harboring pathogenic BSV EPRVs are resistant to any multiplication of BSV while haploid genotypes such as triploids (AAB, French clair) or tetraploids (AAAB, FHIA 21) expressed BSV. Thereby, we characterized the segregation of three BSV species appearance among the AAB F1 progeny as a monogenic allelic system conferring the role of carrier to the M. balbisiana diploid parent. BSOIV and BSImV appeared in almost all infected hybrids (50% of the progeny) depending of BEL regulation while BSGfV are restricted in only half of these hybrids and subordinated by BEL. Three BAC libraries from accession of M.acuminata Cavendish subgroup cv petite naine (AAA), a wild M. acuminata subsp burmannicoides Calcutta 4 (AA) and a wild M. balbisiana PKW (BB) are explored for the pattern of integration of infectious BSV EPRVs by testing a set of different viral probes representing each time the BSOIV, lm and Gf complete genome. BSV positive BAC clones are characterised by RFLP fingerprints approaches. This analysis revealed that the three BSV species represent low-copy loci and their integration is specific to the PKW Musa balbisiana genome. BSGfV EPRVs in PKW is twice and are fully annotated after sequencing. Each BSGfV is composed of back-to-back viral sequences representing more than a whole BSV genome very similar each other. We developed molecular markers (PCR, PCR-RFLP) to distinguish each others and analysed the BSGfV EPRV segregation in the AAB F1 progeny. BSGfV EPRVs are found to be allelic, located at the same locus. In theory, both allelic EPRVs could be involved in the restitution of virions through a set of recombination events. (Texte intégral

The Banana (Musa acuminata) genome and the evolution of monocotyledonous plants : W401

Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the Zingiberales order, a sister group to the well-studied Poales. We sequenced and assembled the 520 Mb genome of a doubled-haploid of the accession 'Pahang'. This accession belongs to the Musa acuminata species (AA genome) malaccensis subspecies. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it sheds new light on the monocotyledon lineage, reveals Poaceae specific features and has led to the discovery of conserved noncoding sequences predating monocotyledon-eudicotyledon divergence. The complete list of authors involved in this work can be found in D'Hont et al. Nature. 2012 Aug 9; 488(7410):213-7 (Résumé d'auteur

Sequencing the banana genome (W069)

Bananas (Musa) are the fourth most important crop in developing countries. They are important as an export crop but also play a major role in local food security. Crops of Musa are susceptible to an ever increasing range of diseases requiring massive use of pesticides that have dramatic environmental and health impacts and threaten the sustainability of the crop. There is thus an urgent need for a wider diversity of genetically improved banana cultivars with more robust disease resistance, increased productivity and better adaptability to a large range of growing conditions. The production of export dessert bananas relies on very few related genotypes of the Cavendish subgroup with an AAA genome constitution. However, numerous dessert and cooking types with an AAA, AAB (including plantain) or ABB genome constitution are grown for local consumption. The Musa accession selected for sequencing is a doubled haploid of the accession 'Pahang' (DH Pahang). This accession belongs to the Musa acuminata species (AA genome) malaccensis subspecies. We generated 20x coverage using paired and single 454 reads, complemented by Sanger BESs and ~50 x coverage of Illumina shotgun data. The assembly was performed with Newbler, and the scaffolds were anchored to a genetic map. Genes were predicted using a reconciliation approach taking ESTs, protein sequences and ab initio data as input. A genetic map of the parent accession 'Pahang' was developed with SSR and DArT markers to assemble the scaffolds in pseudo-molecules. (Texte intégral

Energy and carbon footprints of biofuel systems using banana and plantain waste

Waste that accumulates in Musa production systems (up to 40% of total fruit biomass) has a great potential to be processed into bioethanol due to high sugar contents of fruits, and can open new energy sources and markets for small-scale banana and plantain producers. However, the economical and ecological sustainability of biofuel systems strongly depends on how they are produced. The present study aimed to analyse energy and carbon footprints of Musa bioethanol production systems using a life cycle approach. The study compares three case studies differing in management practices, which are (1) a coffee producer's cooperative in Costa Rica using Musa as shade trees, (2) organic banana producers from Ecuador, and (3) conventional banana producers from Ecuador. The best net-energy balance (19.3 MJ L-1) was obtained for the case study from Costa Rica, closely followed by the organic producers from Ecuador (17.1 MJ L-1), which are Musa production systems operating with low external inputs. The net-energy balance for the conventional banana farms in Ecuador was significantly lower (7.2 MJ L?1), mainly due to the high amount of energy required for producing external inputs such as mineral fertilisers and pesticides. All three case studies yielded avoided carbon emissions (C emissions that are avoided when biofuels are used instead of petroleum based fuel), with the best value obtained for the Costa Rican case study (0.48 kg C L?1), followed by the organic (0.44 kg L?1) and the conventional (0.34 kg L?1) banana producers from Ecuador. 40-100% of gasoline consumption of farm households could be replaced by bioethanol, thereby saving C emissions in the range of 226-1038 kg yr-1. The study clearly showed the need to conduct feasibility studies that consider economic as well as ecological aspects. Biofuel systems should aim at having more favourable energy and carbon balances than fossil fuels, which will open opportunities for carbon credits and new markets. (Résumé d'auteur