Françoise Carreel

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.

Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. 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 clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon–eudicotyledon divergence.

Multidisciplinary perspectives on banana (Musa spp.) domestication

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 processes is essential for breeding programs seeking to diversify and improve banana cvs for the future.

The interspecific genome structure of cultivated banana, Musa spp. revealed by genomic DNA in situ hybridization

Abstract In cultivated banana, Musa spp., there are four known genomes, A, B, S, and T. These correspond to the genetic constitutions of wild Eumusa species M. acuminata, M. balbisiana, M. schizocarpa and the Australimusa species, respectively. Most cultivated clones are triploid or diploid, they have been classified into genomic groups according to chromosome numbers and morphological traits. Genomic in situ hybridization (GISH) enabled us to differentiate the chromosomes of these four genomes; however, a distal portion of the chromosomes remained unlabelled. GISH was used to determine the exact genome structure of interspecific cultivated clones.In most cases the results were consistent with the chromosome constitution estimated by means of phenotypic descriptors.The one notable exception, the clone ’Pelipita’, has the 8 A and 25 B chromosomes instead of the predicted 11 A and 22 B. GISH also enabled us to determine the chromosome complement of a few clones that could not be classified only on the basis of phenotypic descriptors and chromosome counts. The rDNA sites were located in Musa species. They appeared to be often associated with satellites, which can be separated from the chromosomes, representing a potential source of error for chromosome counting using classical techniques.

Maternal inheritance of chloroplast genome and paternal inheritance of mitochondrial genome in bananas (Musa acuminata)

Restriction fragment length polymorphisms (RFLPs) were used as markers to determine the transmission of cytoplasmic DNA in diploid banana crosses. Progenies from two controlled crosses were studied with heterologous cytoplastmic probes. This analysis provided evidence for a strong bias towards maternal transmission of chloroplast DNA and paternal transmission of mitochondrial DNA in Musa acuminata. These results suggest the existence of two separate mechanisms of organelle transmission and selection, but no model to explain this can be proposed at the present time. Knowledge of the organelle mode of inheritance constitutes an important point for phylogeny analyses in bananas and may offer a powerful tool to confirm hybrid origins.

Identification of genetic markers linked to banana streak disease expression in inter-specific Musa hybrids

Abstract.Recently-introduced inter-specific Musa hybrids, bred for improved yield and resistance to diseases, have been found to be widely infected with banana streak virus (BSV), the causal agent of banana streak disease (BSD). One hypothesis suggests: (1) that BSD occurrence in these inter-specific hybrids results from activation of BSV-Ol endogenous pararetrovirus sequences (EPRV) integrated into the Musa genome rather than from external sources of infection, and (2) that the process of genetic hybridisation may be one factor involved in triggering episomal expression of the BSV integrants. In order to test this hypothesis we carried out a genetic analysis of BSD incidence in a F1 triploid (Musa AAB) population produced by inter-specific hybridisation between virus and disease-free diploid Musa balbisiana (BB) and tetraploid Musa acuminata (AAAA) parents. Half of the F1 progeny of this cross expressed BSV particles. Using PCR amplification to determine the presence or absence of BSV-Ol EPRVs, it was determined that this endogenous sequence was specific to the M. babisiana genome and occurred in a homozygous state. Using bulk segregant analysis, ten AFLP markers co-segregating with the absence and/or presence of BSV infection were identified in the M. balbisiana genome, but were absent from the M. acuminata genome. Seven of these markers segregated with the presence of a BSV particle and three with the absence of BSV particles. Analysis of the segregation of these markers using a test-cross configuration allowed the construction of a genetic map of the linkage group containing the locus associated with BSV infection in the F1 hybrid population. These data indicate that a genetic mechanism is involved in BSV appearance, and suggest that a monogenic allelic system confers the role of carrier to the M. balbisiana parent.

Genetic improvement of banana

World production of bananas, estimated at 106 million tons (Lescot 2006), ranks fourth in agricultural production. Bananas make up the largest production of fruits and the largest international trade, more than apple, orange, grape and melon. Bananas are cultivated in more than 120 countries in tropical and subtropical zones on 5 continents. Banana products represent an essential food resource and have an important socioeconomic and ecological role. Current varieties are generally seedless triploid clones either of the single genome A from the species Musa acuminata (group AAA) or of both genomes A and B from species M. acuminata and Musa balbisiana (groups AAB and ABB). More rarely, diploid varieties (AA and AB) and tetraploid clones are encountered. There are two major channels of banana production: those cultivated for export and those reserved for local markets. The main banana varieties cultivated for export, known as ‘Grande Naine’, ‘Poyo’ and ‘Williams’, belong to the monospecific triploid bananas (AAA) of the Cavendish sub-group. They differ from each other only in somatic mutations such as plant height or bunch and fruit shape. Their production relies on an intensive monoculture of the agro-industrial type, without rotation, and a high quantity of inputs. Banana cultivation for local consumption is based on a large number of varieties adapted to different conditions of production as well as the varied uses and tastes of consumers. Diploid bananas, close to the ancestral wild forms, are still cultivated in Southeast Asia. In other regions, triploid clones belonging to different sub-groups – Plantain, Silk, Lujugira, Gros Michel, Pisang Awak – are the most widely distributed. Bananas have many uses. They are not only consumed as fresh fruits but also cooked, like plantains. They are processed in various ways, into chips, fries, fritters,

Diploid ancestors of triploid export banana cultivars: molecular identification of 2n restitution gamete donors and n gamete donors

The origin of triploid export banana cultivars was investigated. They all belong to Cavendish and Gros Michel subgroups of triploid clones and have a monospecific Musa acuminata origin. The appearance of these cultivars is thought to be result of hybridization between partially sterile diploid cultivars producing non reduced gametes and fertile diploids producing normal haploid gametes. To trace these diploid ancestors we compared the RFLP patterns, revealed by 36 probe/enzyme combinations, of 176 diploid clones representing the worldwide available variability with that of clones from the Cavendish and Gros Michel subgroups. This lead us to the identification of the common putative diploid ancestor of cultivars from Cavendish and Gros Michel subgroups which contributed to triploid cultivar formation through the production of 2n restitution gametes. For cultivars of Gros Michel subgroup we also propose a normal gamete donor that may have complemented the triploid allele set.

Evolution of Endogenous Sequences of Banana Streak Virus: What Can We Learn from Banana (Musa sp.) Evolution?

ABSTRACT Endogenous plant pararetroviruses (EPRVs) are viral sequences of the family Caulimoviridae integrated into the nuclear genome of numerous plant species. The ability of some endogenous sequences of Banana streak viruses (eBSVs) in the genome of banana (Musa sp.) to induce infections just like the virus itself was recently demonstrated (P. Gayral et al., J. Virol. 83:6697-6710, 2008). Although eBSVs probably arose from accidental events, infectious eBSVs constitute an extreme case of parasitism, as well as a newly described strategy for vertical virus transmission in plants. We investigated the early evolutionary stages of infectious eBSV for two distinct BSV species—GF (BSGFV) and Imové (BSImV)—through the study of their distribution, insertion polymorphism, and structure evolution among selected banana genotypes representative of the diversity of 60 wild Musa species and genotypes. To do so, the historical frame of host evolution was analyzed by inferring banana phylogeny from two chloroplast regions—matK and trnL-trnF—as well as from the nuclear genome, using 19 microsatellite loci. We demonstrated that both BSV species integrated recently in banana evolution, circa 640,000 years ago. The two infectious eBSVs were subjected to different selective pressures and showed distinct levels of rearrangement within their final structure. In addition, the molecular phylogenies of integrated and nonintegrated BSVs enabled us to establish the phylogenetic origins of eBSGFV and eBSImV.

Homoeologous chromosome pairing between the A and B genomes of Musa spp. revealed by genomic in situ hybridization.

BACKGROUND AND AIMS Most cooking banana and several desert bananas are interspecific triploid hybrids between Musa acuminata (A genome) and Musa balbisiana (B genome). In addition, M. balbisiana has agronomical characteristics such as resistance to biotic and abiotic stresses that could be useful to improve monospecific acuminata cultivars. To develop efficient breeding strategies for improving Musa cultivars, it is therefore important to understand the possibility of chromosome exchange between these two species. METHODS A protocol was developed to prepare chromosome at meiosis metaphase I suitable for genomic in situ hybridization. A series of technical challenges were encountered, the main ones being the hardness of the cell wall and the density of the microsporocytes cytoplasm, which hampers accessibility of the probes to the chromosomes. Key parameters in solving these problems were addition of macerozyme in the enzyme mix, the duration of digestion and temperature during the spreading phase. RESULTS AND CONCLUSIONS This method was applied to analyse chromosome pairing in metaphase from triploid interspecific cultivars, and it was clearly demonstrated that interspecific recombinations between M. acuminata and M. balbisiana chromosomes do occur and may be frequent in triploid hybrids. These results provide new insight into Musa cultivar evolution and have important implications for breeding.

Evolution of the Banana Genome (Musa acuminata) Is Impacted by Large Chromosomal Translocations

Abstract Most banana cultivars are triploid seedless parthenocarpic clones derived from hybridization between Musa acuminata subspecies and sometimes M. balbisiana. M. acuminata subspecies were suggested to differ by a few large chromosomal rearrangements based on chromosome pairing configurations in intersubspecies hybrids. We searched for large chromosomal rearrangements in a seedy M. acuminata ssp. malaccensis banana accession through mate-pair sequencing, BAC-FISH, targeted PCR and marker (DArTseq) segregation in its progeny. We identified a heterozygous reciprocal translocation involving two distal 3 and 10 Mb segments from chromosomes 01 and 04, respectively, and showed that it generated high segregation distortion, reduced recombination and linkage between chromosomes 01 and 04 in its progeny. The two chromosome structures were found to be mutually exclusive in gametes and the rearranged structure was preferentially transmitted to the progeny. The rearranged chromosome structure was frequently found in triploid cultivars but present only in wild malaccensis ssp. accessions, thus suggesting that this rearrangement occurred in M. acuminata ssp. malaccensis. We propose a mechanism for the spread of this rearrangement in Musa diversity and suggest that this rearrangement could have played a role in the emergence of triploid cultivars.