Molecular and cytogenetic characterization of wild Musa species

All relevant data are within the paper and its Supporting Information files.The production of bananas is threatened by rapid spreading of various diseases and adverse environmental conditions. The preservation and characterization of banana diversity is essential for the purposes of crop improvement. The world's largest banana germplasm collection maintained at the Bioversity International Transit Centre (ITC) in Belgium is continuously expanded by new accessions of edible cultivars and wild species. Detailed morphological and molecular characterization of the accessions is necessary for efficient management of the collection and utilization of banana diversity. In this work, nuclear DNA content and genomic distribution of 45S and 5S rDNA were examined in 21 diploid accessions recently added to ITC collection, representing both sections of the genus Musa. 2C DNA content in the section Musa ranged from 1.217 to 1.315 pg. Species belonging to section Callimusa had 2C DNA contents ranging from 1.390 to 1.772 pg. While the number of 45S rDNA loci was conserved in the section Musa, it was highly variable in Callimusa species. 5S rRNA gene clusters were found on two to eight chromosomes per diploid cell. The accessions were genotyped using a set of 19 microsatellite markers to establish their relationships with the remaining accessions held at ITC. Genetic diversity done by SSR genotyping platform was extended by phylogenetic analysis of ITS region. ITS sequence data supported the clustering obtained by SSR analysis for most of the accessions. High level of nucleotide diversity and presence of more than two types of ITS sequences in eight wild diploids pointed to their origin by hybridization of different genotypes. This study significantly expands the number of wild Musa species where nuclear genome size and genomic distribution of rDNA loci is known. SSR genotyping identified Musa species that are closely related to the previously characterized accessions and provided data to aid in their classification. Sequence analysis of ITS region provided further information about evolutionary relationships between individual accessions and suggested that some of analyzed accessions were interspecific hybrids and/or backcross progeny

Molecular and cytological characterization of the global Musa germplasm collection provides insights into the treasure of banana diversity

Bananas (Musa spp.) are one of the main fruit crops grown worldwide. With the annual production reaching 144 million tons, their production represents an important contribution to the economies of many countries in Asia, Africa, Latin-America and Pacific Islands. Most importantly, bananas are a staple food for millions of people living in the tropics. Unfortunately, sustainable banana production is endangered by various diseases and pests, and the breeding for resistant cultivars relies on a far too small base of genetic variation. Greater diversity needs to be incorporated in breeding, especially of wild species. Such work requires a large and thoroughly characterized germplasm collection, which also is a safe depository of genetic diversity. The largest ex situ Musa germplasm collection is kept at the International Transit Centre (ITC) in Leuven (Belgium) and currently comprises over 1500 accessions. This report summarizes the results of systematic cytological and molecular characterization of the Musa ITC collection. By December 2015, 630 accessions have been genotyped. The SSR markers confirmed the previous morphological based classification for 84% of ITC accessions analyzed. The remaining 16% of the genotyped entries may need field verification by taxonomist to decide if the unexpected classification by SSR genotyping was correct. The ploidy level estimation complements the molecular data. The genotyping continues for the entire ITC collection, including newly introduced accessions, to assure that the genotype of each accession is known in the largest global Musa gene bank

Brane versus shell cosmologies in Einstein and Einstein-Gauss-Bonnet theories

We first illustrate on a simple example how, in existing brane cosmological models, the connection of a 'bulk' region to its mirror image creates matter on the 'brane'. Next, we present a cosmological model with no $Z_2$ symmetry which is a spherical symmetric 'shell' separating two metrically different 5-dimensional anti-de Sitter regions. We find that our model becomes Friedmannian at late times, like present brane models, but that its early time behaviour is very different: the scale factor grows from a non-zero value at the big bang singularity. We then show how the Israel matching conditions across the membrane (that is either a brane or a shell) have to be modified if more general equations than Einstein's, including a Gauss-Bonnet correction, hold in the bulk, as is likely to be the case in a low energy limit of string theory. We find that the membrane can then no longer be treated in the thin wall approximation. However its microphysics may, in some instances, be simply hidden in a renormalization of Einstein's constant, in which cases Einstein and Gauss-Bonnet membranes are identical.Comment: 15 pages, submitted to Phys. Rev.

Characterisation of accessions held at the International Musa Genebank

The International Transit Centre (ITC) managed by the Bioversity International is the largest ex situ collection of Musa germplasm. The genebank is hosted by Katholieke Universiteit Leuven in Belgium and maintains in vitro more than 1500 accessions, which include cultivated clones of banana, improved materials and wild Musa species. Efficient conservation of plant germplasm and use in breeding programs depends on proper identification and in-depth characterisation at the phenotypic and genotypic level. We have been involved in the cytogenetic and molecular characterisation of the ITC accessions. This included estimation of nuclear genome size and/or ploidy level using flow cytometry, chromosome number, characterisation of the karyotype and genomic constitution by fluorescence in situ hybridization as well as genotyping with molecular markers. Here we report on the application of a standard Musa genotyping platform which enables discrimination between individual Musa species, subspecies and subgroups. This platform is based on 19 microsatellite markers which are scored using fluorescently labelled primers and high-throughput capillary electrophoresis separation with high resolution. In order to characterize selected ITC accessions in more detail, we analyzed their ITS sequences and studied phylogenetic relationships within the Musaceae family. To date, we have genotyped more than 280 diploid and more than 300 triploid accessions including edible bananas and their putative parents, as well as wild Musa accessions, which have been described for the first time. This work provided new and important information on the accessions held at ITC and identified mislabeled and putative duplicated accessions

On linearized gravity in the Randall-Sundrum scenario

In the literature about the Randall-Sundrum scenario one finds on one hand that there exist (small) corrections to Newton's law of gravity on the brane, and on another that the exact (and henceforth linearized) Einstein equations can be recovered on the brane. The explanation for these seemingly contradictory results is that the behaviour of the bulk far from the brane is different in both models. We show that explicitely in this paper.Comment: 12 pages, plain TeX, no figure

Characterisation of wild musa accessions recently introduced to the International Gene Bank

Bananas and plantains (Musa spp.) are one of the most important world trade commodities and are a staple food for millions of people in countries of the humid tropics. The production of bananas is, however, threatened by the rapid spread of various diseases and adverse environmental conditions. The Musa genetic diversity, which is of paramount importance for breeding of resistant cultivars, needs to be preserved and better characterised. The world's largest banana and plantain collection is managed by the Bioversity International Transit Centre (ITC) in Belgium and contains more than 1500 accessions maintained in vitro. The collection is being continuously expanded by new accessions representing various edible cultivars, improved materials and wild species from different parts of the world. Recently new germplasm was collected in Indonesia and successively introduced into the international Musa gene bank. The aim of this work was to characterise the genotype of these accessions in order to shed light on their genome structure and to confirm their taxonomic classification. A total of 21 wild Musa accessions were analysed and their nuclear genome size and the genomic distribution of ribosomal RNA genes were determined, showing a high degree of variability in both characters. Genotyping with a set of 19 microsatellite markers identified Musa species that are closely related to the studied accessions and provided data to aid in their classification. Sequence analysis of their internal transcribed spacers ITS1 and ITS2 suggested that some of the accessions are of interspecific hybrid origin and/or represent backcross progenies of interspecific hybrids

The genome of cowpea (Vigna unguiculata [L.] Walp.)

[EN] Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. An assembly of the single-haplotype inbred genome of cowpea IT97K-499-35 was developed by exploiting the synergies between single-molecule real-time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination-poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high-recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS-LRR and the SAUR-like auxin superfamilies compared with other warm-season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presentedS

Numerical study of chemical reaction effects in magnetohydrodynamic Oldroyd B oblique stagnation flow with a non-Fourier heat flux model

Reactive magnetohydrodynamic (MHD) flows arise in many areas of nuclear reactor transport. Working fluids in such systems may be either Newtonian or non-Newtonian. Motivated by these applications, in the current study, a mathematical model is developed for electrically-conducting viscoelastic oblique flow impinging on stretching wall under transverse magnetic field. A non-Fourier Cattaneo-Christov model is employed to simulate thermal relaxation effects which cannot be simulated with the classical Fourier heat conduction approach. The Oldroyd-B non-Newtonian model is employed which allows relaxation and retardation effects to be included. A convective boundary condition is imposed at the wall invoking Biot number effects. The fluid is assumed to be chemically reactive and both homogeneous-heterogeneous reactions are studied. The conservation equations for mass, momentum, energy and species (concentration) are altered with applicable similarity variables and the emerging strongly coupled, nonlinear non-dimensional boundary value problem is solved with robust well-tested Runge-Kutta-Fehlberg numerical quadrature and a shooting technique with tolerance level of 10−4. Validation with the Adomian decomposition method (ADM) is included. The influence of selected thermal (Biot number, Prandtl number), viscoelastic hydrodynamic (Deborah relaxation number), Schmidt number, magnetic parameter and chemical reaction parameters, on velocity, temperature and concentration distributions are plotted for fixed values of geometric (stretching rate, obliqueness) and thermal relaxation parameter. Wall heat transfer rate (local heat flux) and wall species transfer rate (local mass flux) are also computed and it is observed that local mass flux increases with strength of heterogeneous reactions whereas it decreases with strength of homogeneous reactions. The results provide interesting insights into certain nuclear reactor transport phenomena and furthermore a benchmark for more general CFD simulations

The giant diploid faba genome unlocks variation in a global protein crop

Publisher Copyright: © 2023, The Author(s).Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.Peer reviewe