Discovery of High-Confidence Single Nucleotide Polymorphisms from Large-Scale De Novo Analysis of Leaf Transcripts of Aegilops tauschii, A Wild Wheat Progenitor

Construction of high-resolution genetic maps is important for genetic and genomic research, as well as for molecular breeding. Single nucleotide polymorphisms (SNPs) are the,predominant class of genetic variation and can be used as molecular markers. Aegilops tauschii, the D-genome donor of common wheat, is considered a valuable genetic resource for wheat improvement. Our previous study implied that Ae. tauschii accessions can be genealogically divided into two major lineages. In this study, the transcriptome of two Ae. tauschii accessions from each lineage, lineage 1 (L1) and 2 (L2), was sequenced, yielding 9435 SNPs and 739 insertion/deletion polymorphisms (indels) after de novo assembly of the reads. Based on 36 contig sequences, 31 SNPs and six indels were validated on 20 diverse Ae. tauschii accessions. Because almost all of the SNP markers were polymorphic between L1 and L2, and the D-genome donor of common wheat is presumed to belong to L2, these markers are available for D-genome typing in crosses between common wheat varieties and L1-derived synthetic wheat. Due to the conserved synteny between wheat and barley chromosomes, the high-density expressed sequence tag barley map and the hypothetical gene order in barley can be applied to develop markers on target chromosomal regions in wheat

Study on a Quantization Condition and the Solvability of Schr\"{o}dinger-type Equations

In this thesis, we study a quantization condition in relation to the solvability of Schr\"{o}dinger equations. This quantization condition is called the SWKB (supersymmetric Wentzel-Kramers-Brillouin) quantization condition and has been known in the context of supersymmetric quantum mechanics for decades. The main contents of this thesis are recapitulated as follows: the foundation and the application of the SWKB quantization condition. The first half of this thesis aims to understand the fundamental implications of this condition based on extensive case studies. It turns out that the exactness of the SWKB quantization condition indicates the exact solvability of a system via the classical orthogonal polynomials. The SWKB quantization condition provides quantizations of energy, which we call the direct problem of the SWKB. We formulate the inverse problem of the SWKB: the problem of determining the superpotential from a given energy spectrum. The formulation successfully reconstructs all conventional shape-invariant potentials from the given energy spectra. We further construct novel solvable potentials, which are classical-orthogonal-polynomially quasi-exactly solvable, by this formulation. We further demonstrate several explicit solutions of the Schr\"{o}dinger equations with the classical-orthogonal-polynomially quasi-exactly solvable potentials, whose family is referred to as a harmonic oscillator with singularity functions in this thesis. In one case, the energy spectra become isospectral, with several additional eigenstates, to the ordinary harmonic oscillator for special choices of a parameter. By virtue of this, we formulate a systematic way of constructing infinitely many potentials that are strictly isospectral to the ordinary harmonic oscillator.Comment: 151 pages, Ph.D. thesi

Amplification profiles of the SSR markers in cultivars of hexaploid wheat and their relatives

Dissertação de Mestrado em Psicologia das Organizações e do Trabalho, apresentada à Faculdade de Psicologia e de Ciências da Educação da Universidade de CoimbraEsta investigação insere-se na linha de investigação ligada à abordagem dos stakeholders e teve como principal objectivo estudar as relações existentes entre os padrões discursivos adoptados pela gestão (o discurso financeiro e económico, o discurso da responsabilidade social da empresa e o discurso dos stakeholders) e a saliência atribuída aos quatro tipos de stakeholders considerados neste estudo (sócios/accionistas, clientes, colaboradores e comunidade). Procurámos, ainda, analisar se determinadas características organizacionais e dos gestores influenciavam os seus discursos, e investigámos a possibilidade de haver um efeito moderador do Ciclo de Vida das Organizações (CVO) na relação entre os discursos adoptados pelos gestores e a saliência atribuída aos diferentes stakeholders organizacionais. Neste sentido, foi utilizada uma amostra de 111 gestores, provenientes de 50 empresas de várias dimensões e sectores, maioritariamente da zona centro do país, que responderam a três questionários: Questionário da Gestão de Stakeholders (GS) de Carvalho (2007); Questionário das Preocupações e Prioridades da Gestão de Carvalho (2007); e, Questionário do Ciclo de Vida Organizacional (CVO) de Carvalho (2001). Os resultados encontrados sugerem que, apesar de se verificarem algumas relações significativas entre estas três variáveis em estudo, não se verificou, tal como previsto, que a variável CVO moderasse a relação entre os discursos dos gestores e a saliência dos stakeholders. As implicações teóricas e práticas destes resultados serão alvo de análise e de discussão.This research falls in the line of research related to the stakeholder approach and had a main objective to study the relationship between the predominant speech patterns adopted by management (the financial and economic discourse, the discourse of corporate social responsibility and the discourse of stakeholders) and the salience attributed to four types of stakeholders considered in this study (partners / shareholders, clients, employees and community). We also tried to test whether certain organizational and managerial characteristics influenced their speeches, and investigated the possibility of a moderating effect of the CVO in the relationship between the organizational discourses adopted by managers and the salience attributed to the different stakeholders. In this sense, we used a sample of 111 managers, from 50 companies of various sizes and sectors, mostly in the center of the country who responded to three questionnaires: Questionnaire Stakeholder Management (GS) (Carvalho, 2007); Questionnaire Concerns and Priorities of Management (Carvalho, 2007); and Questionnaire Organizational Life Cycle (CVO) (Carvalho, 2001). The results suggest that, despite showing some significant relationships between these three variables studied, the variable CVO did not moderate the relationship between discourses of managers and stakeholders’ salience, as expected. The theoretical and practical implications of these results will be subject to analysis and discussion

Harmonic Oscillator with a Step and Isospectrality

We investigate the one-dimensional Schr\"{o}dinger equation with a harmonic oscillator with a finite jump $a$ at the origin. The solution is constructed by employing the ordinary matching-of-wavefunctions technique. For the special choices of $a$, $a=4\ell$ ($\ell=1,2,\ldots$), the wavefunctions can be expressed by the Hermite polynomials. Moreover, we explore isospectral deformations of the potential via the Darboux transformation. In this context, infinitely many number of isospectral Hamiltonians to the ordinary harmonic oscillator are obtained.Comment: 17 pages, 8 figure

Next-generation survey sequencing and the molecular organization of wheat chromosome 6B.

コムギのゲノム配列の概要解読に成功 -コムギの新品種開発の加速化に期待-. 京都大学プレスリリース. 2014-07-24.Common wheat (Triticum aestivum L.) is one of the most important cereals in the world. To improve wheat quality and productivity, the genomic sequence of wheat must be determined. The large genome size (∼17 Gb/1 C) and the hexaploid status of wheat have hampered the genome sequencing of wheat. However, flow sorting of individual chromosomes has allowed us to purify and separately shotgun-sequence a pair of telocentric chromosomes. Here, we describe a result from the survey sequencing of wheat chromosome 6B (914 Mb/1 C) using massively parallel 454 pyrosequencing. From the 4.94 and 5.51 Gb shotgun sequence data from the two chromosome arms of 6BS and 6BL, 235 and 273 Mb sequences were assembled to cover ∼55.6 and 54.9% of the total genomic regions, respectively. Repetitive sequences composed 77 and 86% of the assembled sequences on 6BS and 6BL, respectively. Within the assembled sequences, we predicted a total of 4798 non-repetitive gene loci with the evidence of expression from the wheat transcriptome data. The numbers and chromosomal distribution patterns of the genes for tRNAs and microRNAs in wheat 6B were investigated, and the results suggested a significant involvement of DNA transposon diffusion in the evolution of these non-protein-coding RNA genes. A comparative analysis of the genomic sequences of wheat 6B and monocot plants clearly indicated the evolutionary conservation of gene contents

Wheat-barley hybridization – the last forty years

Abstract Several useful alien gene transfers have been reported from related species into wheat (Triticum aestivum), but very few publications have dealt with the development of wheat/barley (Hordeum vulgare) introgression lines. An overview is given here of wheat 9 barley hybridization over the last forty years, including the development of wheat 9 barley hybrids, and of addition and translocation lines with various barley cultivars. A short summary is also given of the wheat 9 barley hybrids produced with other Hordeum species. The meiotic pairing behaviour of wheat 9 barley hybrids is presented, with special regard to the detection of wheat– barley homoeologous pairing using the molecular cytogenetic technique GISH. The effect of in vitro multiplication on the genome composition of intergeneric hybrids is discussed, and the production and characterization of the latest wheat/barley translocation lines are presented. An overview of the agronomical traits (b-glucan content, earliness, salt tolerance, sprouting resistance, etc.) of the newly developed introgression lines is given. The exploitation and possible use of wheat/barley introgression lines for the most up-to-date molecular genetic studies (transcriptome analysis, sequencing of flow-sorted chromosomes) are also discussed

Dual Role of Irrigation Schemes for NERICA Diffusion in the Central Highlands in Kenya: Sources of Supplemental Water and Technology Information

This paper considers the possibility of the diffusion of NERICA, new upland rice varieties, in the Kenya’s central highlands, where few farmers have ever grown upland rice, particularly focusing on the role of irrigation schemes. The data we use were collected from 160 member farmers of 4 irrigation schemes and 80 non-member farmers living in the same command area of the irrigation through our own survey conducted in March 2012 at the beginning of the long rain season of 2012. We find that among the member farmers those who have more irrigation taps tend to adopt NERICA, implying that water availability from irrigation is an important factor that encourages farmers to grow NERICA. As for the knowledge about upland rice, we find that those who have heard about upland rice and/or have seen rice growing on upland are more willing to purchase or receive NERICA seed. If we compare farmers belonging to an irrigation scheme and farmers not belonging to any irrigation scheme, the former have better knowledge about upland rice. Thus, the irrigation schemes have a role of information dissemination among members, which may reduce the risk of the failure of new crop.この論文は、陸稲を栽培したことのある農民のほとんどいないケニア中央高地における陸稲新品種のネリカの普及の可能性について、灌漑組織の役割に焦点をあてて検討する。使用するデータは、4 つの灌漑組織に属する160 名の農民とその灌漑の受益地に居住するが灌漑組織には所属しない80 名を対象に、2012 年大雨期の始まる2012 年3 月に著者らが自ら実施した調査により収集した。分析の結果、灌漑組織に属する農民の中では灌漑用水栓を多く持つ農家ほど、ネリカの採用に積極的であることが判明した。これは灌漑水が十分に利用できることがネリカの導入に重要な役割を果たすことを意味する。また、陸稲に関する知識については、陸稲のことを聞いたことがある農家、および実際に畑で育っているのを見たことがある農家の方が、ネリカを採用する傾向があることもわかった。そこで、灌漑組織に属する農民と属さない農民を比べると、前者の方が陸稲に関する知識が豊富である。つまり、灌漑組織は、所属するメンバー間で情報の交換が盛んであり、新しい作物を栽培することに対するリスクを軽減する役割を持っている。departmental bulletin pape