Frédéric Bakry

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.

A molecular marker-based linkage map of diploid bananas (Musa acuminata).

A partial molecular linkage map of the Musa acuminata diploid genome is presented. This map is based on 58 RFLP, four isozyme and 28 RAPD markers segregating in an F2 population of 92 individuals. A total of 90 loci was detected, 77 of which were placed on 15 linkage groups while 13 segregated independently. Segregation distortions were shown by 36% of all loci, mostly favoring the male parent. Chromosome structural rearrangements were believed to be one of the main causes of these distortions. The use of genetic linkage data to further the genetic and evolutionary knowledge of the genus Musa, as well as to help improve the design of breeding strategies, is discussed.

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.

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.

Foundation characteristics of edible Musa triploids revealed from allelic distribution of SSR markers

Background and Aims The production of triploid banana and plantain (Musa spp.) cultivars with improved characteristics (e.g. greater disease resistance or higher yield), while still preserving the main features of current popular cultivars (e.g. taste and cooking quality), remains a major challenge for Musa breeders. In this regard, breeders require a sound knowledge of the lineage of the current sterile triploid cultivars, to select diploid parents that are able to transmit desirable traits, together with a breeding strategy ensuring final triploidization and sterility. Highly polymorphic single sequence repeats (SSRs) are valuable markers for investigating phylogenetic relationships. Methods Here, the allelic distribution of each of 22 SSR loci across 561 Musa accessions is analysed. Key Results and Conclusions We determine the closest diploid progenitors of the triploid ‘Cavendish’ and ‘Gros Michel’ subgroups, valuable information for breeding programmes. Nevertheless, in establishing the likely monoclonal origin of the main edible triploid banana subgroups (i.e. ‘Cavendish’, ‘Plantain’ and ‘Mutika-Lujugira’), we postulated that the huge phenotypic diversity observed within these subgroups did not result from gamete recombination, but rather from epigenetic regulations. This emphasizes the need to investigate the regulatory mechanisms of genome expression on a unique model in the plant kingdom. We also propose experimental standards to compare additional and independent genotyping data for reference.

Evidence for non-disomic inheritance in a Citrus interspecific tetraploid somatic hybrid between C. reticulata and C. limon using SSR markers and cytogenetic analysis

Artificial tetraploid somatic hybrids have been developed for sterile triploid citrus breeding by sexual hybridization between diploid and tetraploid somatic hybrids. The genetic structure of diploid gametes produced by tetraploid genotypes depends on the mode of chromosome association at meiosis. In order to evaluate tetraploid inheritance in a tetraploid interspecific somatic hybrid between mandarin and lemon, we performed segregation studies using cytogenetic and single sequence repeat molecular markers. Cytogenetic analysis of meiosis in the somatic hybrid revealed 11% tetravalents and 76% bivalents. Inheritance of the tetraploid hybrid was analyzed by genotyping the triploid progeny derived from a cross between a diploid pummelo and the tetraploid somatic hybrid, in order to derive genotypes of the meiospores produced by the tetraploid. A likelihood-based approach was used to distinguish between disomic, tetrasomic, and intermediate inheritance models and to estimate the double reduction rate. In agreement with expectations based the cytogenetic data, marker segregation was largely compatible with tetrasomic and inheritance intermediate between disomic and tetrasomic, with some evidence for preferential pairing of homoeologous chromosomes. This has important implications for the design of breeding programs that involve tetraploid hybrids, and underscores the need to consider inheritance models that are intermediate between disomic and tetrasomic.

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 and challenges of varietal improvement strategies

Agricultural production and supply chains are facing major challenges in the form of increasing demand for food products, a diversified use of agricultural products including for non-food purposes, ecologically intensive agriculture, and the necessity of taking climate change into account. The creation and adoption of new varieties that are productive, diversified, better adapted, and more environmentally friendly can help cropping systems that seek to address these issues become more efficient. Plant breeding efforts must anticipate the needs of the end users and adapt to very different agri-chains, illustrated in this chapter by two examples: first, an agri-chain that is highly structured around targeted export products, for example, the dessert banana, which requires ideotypes that meet the requirements of production and marketing systems; and second, an emerging agri-chain for multi-use sorghum, characterized by new production objectives of increased energy potential and production of biomaterials, sometimes without compromising with the requirement of high grain yields. To meet the objectives and the sustainability of agri-chains, research into genetic improvement must propose new approaches, new tools, and innovative breeding methods. The objectives, and sometimes the entire breeding process, are shared with all the actors, especially the end users, as part of an enhanced partnership within agri-chains. The breeding strategy also depends on ease of access, better use of available and useful genetic resources, in-depth knowledge of the structure and diversity of these resources, genetic determinism of desirable traits, and pre-breeding approaches. All these scientific and partnership innovations ensure the necessary responsiveness to support the execution of current breeding processes and the identification of new varieties that meet current and future uses and services.