Jean-Christophe Glaszmann

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.

Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics

Cultivated sugarcane clones (Saccharum spp., 2n=100 to 130) are derived from complex interspecific hybridizations between the speciesS. officinarum andS. spontaneum. Using comparative genomic DNA in situ hybridization, we demonstrated that it is possible to distinguish the chromosomes contributed by these two species in an interspecific F1 hybrid and a cultivated clone, R570. In the interspecific F1 studied, we observed n+n transmission of the parental chromosomes instead of the peculiar 2n+n transmission usually described in such crosses. Among the chromosomes of cultivar R570 (2n=107–115) about 10% were identified as originating fromS. spontaneum and about 10% were identified as recombinant chromosomes between the two speciesS. officinarum andS. spontaneum. This demonstrated for the first time the occurrence of recombination between the chromosomes of these two species. The rDNA sites were located by in situ hybridization in these two species and the cultivar R570. This supported different basic chromosome numbers and chromosome structural differences between the two species and provided a first bridge between physical and genetical mapping in sugarcane.

Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). I. Genome mapping with AFLP markers

Abstract Sugarcane cultivars are polyploid, aneuploid clones derived from interspecific hybridization between Saccharum officinarum and S. spontaneum. Their genome has recently started to be unravelled as a result of the development of molecular markers. We constructed an AFLP genetic map based on a selfing population of a specific cultivar, R570.Using 37 AFLP primer pairs, we detected 1,185 polymorphic markers of which 939 were simplex (segregated 3:1); these were used to construct the map. Of those 939, 887 were distributed on 120 cosegregation groups (CGs) based on linkages in coupling, while 52 remained unlinked. The cumulative length of all the groups was 5,849 cM, which is probably around one-third of the total genome length. Comparison with reference S. officinarum clones enabled us to assign 11 and 79 CGs to S. spontaneum and S. officinarum,respectively, whereas 11 CGs were probably derived from recombination between chromosomes of the two ancestral species. The patchy size of the groups, which ranges from 1 to 232 cM, illustrates the difficulty to access large portions of chromosomes, particularly those inherited from S. officinarum. Repulsion phase linkages suggested a high preferential pairing for 13 CG pairs. Out of the 120 CGs, 34 could be assigned to one of the 10 homo(eo)logy groups already defined in a previous RFLP map owing to the use of a small common marker set. The genome coverage was significantly increased in the map reported here. Implications for quantitative trait loci (QTL) research and marker-assisted breeding perspectives are discussed.

Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid

Abstract A sorghum composite linkage map was constructed with two recombinant inbred line populations using heterologous probes already mapped on maize and sugarcane. This map includes 199 loci revealed by 188 probes and distributed on 13 linkage groups. A comparison based on 84 common probes was performed between the sorghum composite map and a map of a sugarcane (Saccharum spp.) cultivar being developed and presently comprising 10 tentative linkage groups. A straight synteny was observed for 2 pairs of linkage groups; in two cases, 1 sorghum linkage group corresponded to 2 or 3 sugarcane linkage groups, respectively; in two cases 1 sugarcane link- age group corresponded to 2 separate sorghum linkage groups; for 2 sorghum linkage groups, no complete correspondance was found in the sugarcane genome. In most cases loci appeared to be colinear between homoeologous chromosomal segments in sorghum and sugarcane. These results are discussed in relation to published data on sorghum genomic maps, with specific reference to the genetic organization of sugarcane cultivars, and they, illustrate how investigations on relatively simple diploid genomes as sorghum will facilitate the mapping of related polyploid species such as sugarcane.

Identification and characterisation of sugarcane intergeneric hybrids, Saccharum officinarum x Erianthus arundinaceus, with molecular markers and DNA in situ hybridisation

Molecular markers were used to characterise sugarcane intergeneric hybrids between S. officinarum and E. arundinaceus. Very simple diagnostic tools for hybrid identification among the progeny were derived from isozyme electrophoresis and a sequence-tagged PCR. Two enzyme systems (GOT and MDH B) and PCR amplification revealing spacer-size variation in the 5s-rDNA cluster were found most convenient. Specific characterisation of the two genomic components was possible using RFLP and in situ hybridisation. The strong molecular differentiation between S. officinarum and E. arundinaceus allows the identification of numerous Erianthus-specific RFLP bands in the hybrids. Genomic DNA in situ hybridisation allows for the differentiation of the chromosomes contributed by S. officinarum and E. arundinaceus in chromosome preparations of the hybrids. In situ hybridisation with the 18s-5.8s-25s rDNA probe highlights the basic chromosome numbers in the two parental species. The potential of these techniques to monitor the Erianthus genome during the introgression process is discussed.

Relationships among ancestral species of sugarcane revealed with RFLP using single copy maize nuclear probes

SummaryDNA restriction fragment length polymorphism (RFLP) analysis was performed on 50 wild and old cultivated sugarcane accessions. Ninety-four maize low copy nuclear DNA sequences of known chromosomal position were screened for hybridization to digested sugarcane genomic DNA blots. Seventy-five (80%) gave very strong hybridization signals and usually yielded many bands and detected profuse polymorphism. Twenty-nine probes and 36 probe/enzyme combinations were selected on the basis of the scorability of the banding profiles. A total of 1110 fragments were separately identified among the 50 genotypes. Multivariate analyses of the data allowed the separation of the three basic species, Saccharum spontaneum, S. robustum and S. officinarum, showed that S. spontaneum had structure which could be related to the geographic origin of the clones and supported current hypotheses on the origin of secondary species S. barberi and S. sinense. The use of more probes did not improve the resolution between the various species examined but identified a few key polymorphisms which were not accounted for by current phylogenetic hypotheses and can guide future analyses. RFLPs in sugarcane will be useful essentially for depicting the genomic constitution of modern varieties of interspecific origin.

Molecular diversity and genome structure in modern sugarcane varieties

SummaryRFLP analysis was performed on 40 sugarcane cultivated varieties. Twenty-two maize low copy DNA clones located on different regions of the 10 maize chromosomes were used as probes to survey variability among the sugarcane varieties. A total of 425 fragments, 411 of which were polymorphic, were identified for 22 probe/enzyme combinations. Each variety displayed an average of 7.28 fragments per combination, revealing the complex polyploid origin of modern sugarcane varieties. The average genetic similarity between sugarcane varieties was 0.61. Although cultivated varieties appear closely related to S. officinarum clones, the genes of S. spontaneum seem to constitute the principal component of varietal diversity. A very weak global structuring among the 40 varieties is observed, in agreement with the profuse exchanges of parental materials between sugarcane breeding stations. Traces of linkage disequilibrium can be attributed to the distribution of S. spontaneum chromosomes among sugarcane varieties. The possibility of using modern varieties as a population for detecting associations between molecular markers and agronomic traits is suggested.

A putative major gene for rust resistance linked with a RFLP marker in sugarcane cultivar 'R570'

Inheritance of resistance to rust was investigated in the self progeny of the sugarcane cultivar ‘R570’ also used to build a RFLP genetic map. Resistance was evaluated through both field and controlled greenhouse trials. A clear-cut 3 (resistant) ∶ 1 (susceptible) segregation indicative of a probable dominant resistant gene was observed. This is the first documented report of a monogenic inheritance for disease resistance in sugarcane. This gene was found linked at 10 cM with an RFLP marker revealed by probe CDSR29. Other minor factors involved in the resistance were also detected.

Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). II. Detection of QTLs for yield components

Abstract.The genetics of current sugarcane cultivars (Saccharum spp.) is outstandingly complex, due to a high ploidy level and an interspecific origin which leads to the presence of numerous chromosomes belonging to two ancestral genomes. In order to analyse the inheritance of quantitative traits, we have undertaken an extensive Quantitative Trait Allele (QTA) mapping study based on a population of 295 progenies derived from the selfing of cultivar R570, using about 1,000 AFLP markers scattered on about half of the genome. The population was evaluated in a replicated trial for four basic yield components, plant height, stalk number, stalk diameter and brix, in two successive crop-cycles. Forty putative QTAs were found for the four traits at P = 5 × 10–3, of which five appeared in both years. Their individual size ranged between 3 and 7% of the whole variation. The stability across years was improved when limiting threshold stringency. All these results depict the presence in the genome of numerous QTAs, with little effects, fluctuating slightly across cycles, on the verge to being perceptible given the experimental resolution. Epistatic interactions were also explored and 41 independent di-genic interactions were found at P = (5 × 10–3)2. Altogether the putative genetic factors revealed here explain from 30 to 55% of the total phenotypic variance depending on the trait. The tentative assignment of some QTAs to the ancestral genomes showed a small majority of contributions as expected from the ancestral phenotypes. This is the first extensive QTL mapping study performed in cultivated sugarcane.

The relationship between population structure and aluminum tolerance in cultivated sorghum.

Background Acid soils comprise up to 50% of the worlds arable lands and in these areas aluminum (Al) toxicity impairs root growth, strongly limiting crop yield. Food security is thereby compromised in many developing countries located in tropical and subtropical regions worldwide. In sorghum, SbMATE, an Al-activated citrate transporter, underlies the AltSB locus on chromosome 3 and confers Al tolerance via Al-activated root citrate release. Methodology Population structure was studied in 254 sorghum accessions representative of the diversity present in cultivated sorghums. Al tolerance was assessed as the degree of root growth inhibition in nutrient solution containing Al. A genetic analysis based on markers flanking AltSB and SbMATE expression was undertaken to assess a possible role for AltSB in Al tolerant accessions. In addition, the mode of gene action was estimated concerning the Al tolerance trait. Comparisons between models that include population structure were applied to assess the importance of each subpopulation to Al tolerance. Conclusion/Significance Six subpopulations were revealed featuring specific racial and geographic origins. Al tolerance was found to be rather rare and present primarily in guinea and to lesser extent in caudatum subpopulations. AltSB was found to play a role in Al tolerance in most of the Al tolerant accessions. A striking variation was observed in the mode of gene action for the Al tolerance trait, which ranged from almost complete recessivity to near complete dominance, with a higher frequency of partially recessive sources of Al tolerance. A possible interpretation of our results concerning the origin and evolution of Al tolerance in cultivated sorghum is discussed. This study demonstrates the importance of deeply exploring the crop diversity reservoir both for a comprehensive view of the dynamics underlying the distribution and function of Al tolerance genes and to design efficient molecular breeding strategies aimed at enhancing Al tolerance.