Ploidy and genome composition of Musa germplasm at the International Institute of Tropical Agriculture (IITA)

Musa spp (bananas and plantains) constitute a hybrid-polyploid complex and are classified according to different genome compositions such as AA, BB, AB, AAA, AAB, ABB, AAAA, ABBB, AAAB and AABB. Knowledge of ploidy and exact genome compositions of the parental material is essential forMusa breeding. This study determined the ploidy levels and genome composition of the Musa germplasm collection, constituting over 300 accessions, at the International Institute of Tropical Agriculture in Nigeria and Uganda. Flow cytometric analysis of nuclear DNA content was used toestimate ploidy levels, while genome composition was ascertained with RAPD markers that are specific for the A and B genomes of Musa. It was determined that at least 8% of the plants in the germplasmcollection were miss-classified in terms of ploidy and/or genome composition. The cultivars 'Pisang awak', 'Foulah 4' and 'Nzizi', previously classified as triploids, were found to be tetraploids by flowcytometry and conventional root tip chromosome counts. Similarly, cultivars that were previously classified as diploids including ‘Too’, and ‘Toowoolee’ were found to be triploids in our analysis. Ploidy and genome classification in Musa was generally determined from morphological characteristics. While our study showed that such a system is not always reliable, it was interesting to find that none of the plantains in the germplasm collection were miss-classified with regards to both ploidy and genome composition

Slowly rotating voids in cosmology

We consider a spacetime consisting of an empty void separated from an almost Friedmann-Lema\^\i tre-Robertson-Walker (FLRW) dust universe by a spherically symmetric, slowly rotating shell which is comoving with the cosmic dust. We treat in a unified manner all types of the FLRW universes. The metric is expressed in terms of a constant characterizing the angular momentum of the shell, and parametrized by the comoving radius of the shell. Treating the rotation as a first order perturbation, we compute the dragging of inertial frames as well as the apparent motion of distant stars within the void. Finally, we discuss, in terms of in principle measurable quantities, 'Machian' features of the model.Comment: 21 pages, 5 figures, REVTex, accepted for publication in Class.Quant.Gravit

Gravity on de-Sitter 3-Brane, Induced Einstein-Hilbert Term and Massless Gravitons

We study the extensions of DGP model which are described by five-dimensional Einstein gravity coupled covariantly to 3-brane with induced gravity term and consider warped D=4 de Sitter background field solutions on the brane. The case with included D=5 AdS cosmological term is also considered. Following background field method we obtain the field equations described by the Lagrangean terms bilinear in gravitational field. In such a linear field approximation on curved dS background we calculate explicitly the five-dimensional massive terms as well as the mass-like ones on the brane. We investigate the eigenvalue problem of Schr\"{o}dinger-like equation in fifth dimension for graviton masses and discuss the existence of massless as well as massive graviton modes in the bulk and on the brane without and with induced gravity.Comment: LaTeX 26 pages, the version which appears in Class. Quant. Gra

Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides

Wild emmer wheat, Triticum turgidum ssp. dicoccoides is the wild relative of Triticum turgidum, the progenitor of durum and bread wheat, and maintains a rich allelic diversity among its wild populations. The lack of adequate genetic and genomic resources, however, restricts its exploitation in wheat improvement. Here, we report next-generation sequencing of the flow-sorted chromosome 5B of T. dicoccoides to shed light into its genome structure, function and organization by exploring the repetitive elements, protein-encoding genes and putative microRNA and tRNA coding sequences. Comparative analyses with its counterparts in modern and wild wheats suggest clues into the B-genome evolution. Syntenic relationships of chromosome 5B with the model grasses can facilitate further efforts for fine-mapping of traits of interest. Mapping of 5B sequences onto the root transcriptomes of two additional T. dicoccoides genotypes, with contrasting drought tolerances, revealed several thousands of single nucleotide polymorphisms, of which 584 shared polymorphisms on 228 transcripts were specific to the drought-tolerant genotype. To our knowledge, this study presents the largest genomics resource currently available for T. dicoccoides, which, we believe, will encourage the exploitation of its genetic and genomic potential for wheat improvement to meet the increasing demand to feed the world

A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A

Citation: Balcarkova, B., Frenkel, Z., Skopova, M., Abrouk, M., Kumar, A., Chao, S. M., . . . Valarik, M. (2017). A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A. Frontiers in Plant Science, 7, 14. https://doi.org/10.3389/fpls.2016.02063Bread wheat has a large and complex allohexaploid genome with low recombination level at chromosome centromeric and peri-centromeric regions. This significantly hampers ordering of markers, contigs of physical maps and sequence scaffolds and impedes obtaining of high-quality reference genome sequence. Here we report on the construction of high-density and high-resolution radiation hybrid (RH) map of chromosome 4A supported by high-density chromosome deletion map. A total of 119 endosperm-based RH lines of two RH panels and 15 chromosome deletion bin lines were genotyped with 90K iSelect single nucleotide polymorphism (SNP) array. A total of 2316 and 2695 markers were successfully mapped to the 4A RH and deletion maps, respectively. The chromosome deletion map was ordered in 19 bins and allowed precise identification of centromeric region and verification of the RH panel reliability. The 4A-specific RH map comprises 1080 mapping bins and spans 6550.9 cR with a resolution of 0.13 Mb/cR. Significantly higher mapping resolution in the centromeric region was observed as compared to recombination maps. Relatively even distribution of deletion frequency along the chromosome in the RH panel was observed and putative functional centromere was delimited within a region characterized by two SNP markers