scholarly journals High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement

2021 ◽  
Author(s):  
Zhiying Ma ◽  
Yan Zhang ◽  
Liqiang Wu ◽  
Guiyin Zhang ◽  
Zhengwen Sun ◽  
...  
Keyword(s):  
Textile Industry ◽  
Large Scale ◽  
Natural Fiber ◽  
Agronomic Traits ◽  
Fiber Quality ◽  
Crop Improvement ◽  
Structural Variations ◽  
High Quality ◽  
Species Formation

AbstractCotton produces natural fiber for the textile industry. The genetic effects of genomic structural variations underlying agronomic traits remain unclear. Here, we generate two high-quality genomes of Gossypium hirsutum cv. NDM8 and Gossypium barbadense acc. Pima90, and identify large-scale structural variations in the two species and 1,081 G. hirsutum accessions. The density of structural variations is higher in the D-subgenome than in the A-subgenome, indicating that the D-subgenome undergoes stronger selection during species formation and variety development. Many structural variations in genes and/or regulatory regions potentially influencing agronomic traits were discovered. Of 446 significantly associated structural variations, those for fiber quality and Verticillium wilt resistance are located mainly in the D-subgenome and those for yield mainly in the A-subgenome. Our research provides insight into the role of structural variations in genotype-to-phenotype relationships and their potential utility in crop improvement.

scholarly journals High-quality rice RNA-seq-based co-expression network for predicting gene function and regulation

2017 ◽  
Author(s):  
Hua Yu ◽  
Bingke Jiao ◽  
Chengzhi Liang
Keyword(s):  
Large Scale ◽  
Network Inference ◽  
Agronomic Traits ◽  
Enrichment Analysis ◽  
Circular Rna ◽  
Rna Seq ◽  
Sequencing Data ◽  
High Quality ◽  
Crop Species ◽  
Functional Link

AbstractInferring the genome-scale gene co-expression network is important for understanding genetic architecture underlying the complex and various biological phenotypes. The recent availability of large-scale RNA-seq sequencing-data provides great potential for co-expression network inference. In this study, for the first time, we presented a novel heterogeneous ensemble pipeline integrating three frequently used inference methods, to build a high-quality RNA-seq-based Gene Co-expression Network (GCN) in rice, an important monocot species. The quality of the network obtained by our proposed method was first evaluated and verified with the curated positive and negative gene functional link datasets, which obviously outperformed each single method. Secondly, the powerful capability of this network for associating unknown genes with biological functions and agronomic traits was showed by enrichment analysis and case studies. Particularly, we demonstrated the potential applications of our proposed method to predict the biological roles of long non-coding RNA (lncRNA) and circular RNA (circRNA) genes. Our results provided a valuable data source for selecting candidate genes to further experimental validation during rice genetics research and breeding. To enhance identification of novel genes regulating important biological processes and agronomic traits in rice and other crop species, we released the source code of constructing high-quality RNA-seq-based GCN and rice RNA-seq-based GCN, which can be freely downloaded online at https://github.com/czllab/NetMiner.

scholarly journals Mapping Collected Memory: An Exploration of Memory-Based Navigation in Amman, Jordan

2014 ◽  
Vol 3 ◽  
pp. 138-159
Author(s):  
Regina Mamou
Keyword(s):  
Large Scale ◽  
Subjective Experience ◽  
High Quality ◽  
Large Format ◽  
Changing Environment ◽  
Still Images ◽  
Specific Location ◽  
The City

The purpose of this research is to explore navigational and image-making methods in a context where maps and formal address systems have been minimally consulted in recent years. This investigation is approached by way of a research-based art project on subjective cartography, which was carried out from 2009 to 2010 during a Fulbright fellowship to Amman, Jordan. The project examines the mutability of a specific location as well as its relationship between obsolescence in cartographic resources and the photographic medium. By reaching out to Ammani residents for informal tours of the city, selected guides were asked to narrate their experiences of navigating the city by memory and then directed to point out key landmarks during this process. Later, these tours were re-memorized and landmarks were photographed as a representation of the afterimage to capture high-quality still images through the use of a large-format photographic device. These afterimages are not intended to serve as documents or memorials of Amman but rather as ruminations on the faculties of memory in an ever-changing environment. This subjective experience, or the observation of a city’s minutiae amid wayfinding, poses a series of inquiries, vis-à-vis memory-based navigation and the role of still images, as an alternative to the panoptic view of a map. The result is a meditative project considering the plasticity of an urban entity, presented as a composition of written material and large-scale photographs, fragments of the city that when viewed as a series come together as a constellation of a subjective whole. 

Methodology to establish a composite collection: case study in lentil

2006 ◽  
Vol 4 (1) ◽  
pp. 2-12 ◽  
Author(s):  
Bonnie J Furman
Keyword(s):  
Genetic Diversity ◽  
Large Scale ◽  
Dna Analysis ◽  
Agronomic Traits ◽  
Agricultural Research ◽  
Crop Improvement ◽  
Hierarchical Cluster ◽  
Wild Relatives ◽  
Crop Species ◽  
Cluster Analyses

The International Center for Agricultural Research in the Dry Areas (ICARDA) is participating in a large-scale programme, Subprogram 1 of the Consultative Group on International Agricultural Research (CGIAR) Generation Challenge Program, that aims to explore the genetic diversity of the global germplasm collections held by the CGIAR research centres. This project will identify a ‘composite collection’ of germplasm for individual crops, representing the range of diversity of each crop species and its wild relatives, and characterize each composite set using anonymous molecular markers, mainly simple sequence repeats (SSRs). The overall goal of this project is to study diversity across given genera and identify genes for resistance to biotic and abiotic stresses that can be used in crop improvement programmes. ICARDA was responsible for creating the composite collection for lentil. ICARDA has the global mandate for lentil and houses the largest global collection of this crop with 10,509 accessions. From this collection, a global composite collection of 1000 lentil accessions was established with the aim to represent genetic diversity and the agro-climatological range of lentil. Accessions for the composite collection were compiled from landraces, wild relatives, and elite germplasm and cultivars. The methodology presented here combined classical hierarchical cluster analyses using agronomic traits and two-step cluster analyses using agro-climatological data linked to the geographical coordinates of the accessions' collection sites. Genotyping for 30 SSR loci will be carried out for all 1000 accessions. Plants grown for DNA analysis will be harvested and progeny will be evaluated under field conditions at ICARDA.

The role of molybdenum in Co-Mo/MgO for large-scale production of high quality carbon nanotubes

2010 ◽  
Vol 493 (1-2) ◽  
pp. 539-543 ◽  
Author(s):  
Wei-Ming Yeoh ◽  
Kim-Yang Lee ◽  
Siang-Piao Chai ◽  
Keat-Teong Lee ◽  
Abdul Rahman Mohamed
Keyword(s):  
Carbon Nanotubes ◽  
Large Scale ◽  
Scale Production ◽  
High Quality ◽  
Large Scale Production

scholarly journals Classification of grain amaranths using chromosome-level genome assembly of ramdana, A. hypochondriacus

2020 ◽  
Author(s):  
Saptarathi Deb ◽  
Suvratha J ◽  
Samathmika Ravi ◽  
Raksha Rao K ◽  
Saurabh Whadgar ◽  
...  
Keyword(s):  
Reference Genome ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Draft Genome ◽  
Local Environment ◽  
High Quality ◽  
Low Coverage ◽  
High Quality Genome ◽  
Chromosome Level

ABSTRACTIn the age of genomics-based crop improvement, a high-quality genome of a local landrace adapted to the local environmental conditions is critically important. Grain amaranths produce highly nutritional grains with a multitude of desirable properties including C4 photosynthesis highly sought-after in other crops. For improving the agronomic traits of grain amaranth and for the transfer of desirable traits to dicot crops, a reference genome of a local landrace is necessary. Towards this end, our lab had initiated sequencing the genome of Amaranthus (A.) hypochondriacus (A.hyp_K_white) and had reported a draft genome in 2014. We selected this landrace because it is well adapted for cultivation in India during the last century and is currently a candidate for TILLING-based crop improvement. More recently, a high-quality chromosome-level assembly of A. hypochondriacus (PI558499, Plainsman) was reported. Here, we report a chromosome-level assembly of A.hyp_K_white (AhKP) using low-coverage PacBio reads, contigs from the reported draft genome of A.hyp_K_white, raw HiC data and reference genome of Plainsman. The placement of A.hyp_K_white on the phylogenetic tree of grain amaranths of known accessions clearly suggests that A.hyp_K_white is genetically distal from Plainsman and is most closely related to the accession PI619259 from Nepal (Ramdana). Furthermore, the classification of another accession, Suvarna, adapted to the local environment and selected for yield and other desirable traits, is clearly A. cruentus. A classification based on hundreds of thousands of SNPs validated taxonomy-based classification for a majority of the accessions providing the opportunity for reclassification of a few.

The Role of Sense of Direction and Other Factors During Navigation in a Large-Scale, Unconstrained Environment

2013 ◽  
Author(s):  
Elisabeth J. Ploran ◽  
Ericka Rovira ◽  
James C. Thompson ◽  
Raja Parasuraman
Keyword(s):  
Large Scale ◽  
Sense Of Direction

Making Movies and Community of Talent

2019 ◽  
Vol 10 (11) ◽  
pp. 1057-1064
Author(s):  
Katsuhiko Hirasawa ◽  
Keyword(s):  
Shop Floor ◽  
High Quality ◽  
Democratic Leadership ◽  
Staff Members

Staff members at a movie company Daiei, known for presumably the world’s best film technology, continued to produce movies for several months even after the company went bankrupt. It was because they desired to make outstanding films. A director can create a high-quality film by combining the skills and ideas of such staff. Akira Kurosawa named the group that could produce excellent works the “Community of Talents”. By using research on a community as a clue, this paper aims to highlight how the “Community of Talents” is organized. First I point out that a “Community of Talents” is formulated primarily by the labor of the staff based on Kumazawa’s “Community on the Shop Floor”. The paper subsequently refers to research by Heinrich Nicklish, a representative researcher on the study of community in Germany, in an attempt to verify that the community is a group of people established on functions. Lastly, the paper explores Guido Fisher’s research to reveal the role of democratic leadership centered on the director who transforms the objectified staff in the organization into an independently-minded presence and help them prove their abilities. The paper continues to emphasize the significance of leadership in the formation of the “Community of Talents”.

Magnetic Properties of xCeO2•(50 − x) PbO•50B2O3 Glasses and Glass Ceramics

2017 ◽  
Vol 13 (1) ◽  
pp. 4486-4494 ◽  
Author(s):  
G.El Damrawi ◽  
F. Gharghar
Keyword(s):  
Magnetic Properties ◽  
Large Scale ◽  
Glass Ceramics ◽  
Magnetic Behavior ◽  
Crystal Formation ◽  
Dual Roles ◽  
Effective Agent ◽  
Ordered Structures ◽  
Essential Change

Cerium oxide in borate glasses of composition xCeO2·(50 − x)PbO·50B2O3 plays an important role in changing both microstructure and magnetic behaviors of the system. The structural role of CeO2 as an effective agent for cluster and crystal formation in borate network is clearly evidenced by XRD technique. Both structure and size of well-formed cerium separated clusters have an effective influence on the structural properties. The cluster aggregations are documented to be found in different range ordered structures, intermediate and long range orders are the most structures in which cerium phases are involved. The nano-sized crystallized cerium species in lead borate phase are evidenced to have magnetic behavior.  The criteria of building new specific borate phase enriched with cerium as ferrimagnetism has been found to keep the magnetization in large scale even at extremely high temperature. Treating the glass thermally or exposing it to an effective dose of ionized radiation is evidenced to have an essential change in magnetic properties. Thermal heat treatment for some of investigated materials is observed to play dual roles in the glass matrix. It can not only enhance alignment processes of the magnetic moment but also increases the capacity of the crystallite species in the magnetic phases. On the other hand, reverse processes are remarked under the effect of irradiation. The magnetization was found to be lowered, since several types of the trap centers which are regarded as defective states can be produced by effect of ionized radiation. 

The Impact of Quantitative Easing on Emerging Markets – Literature Review

e-Finanse ◽  
2018 ◽  
Vol 14 (4) ◽  
pp. 67-76
Author(s):  
Piotr Bartkiewicz
Keyword(s):  
Emerging Markets ◽  
Large Scale ◽  
Empirical Literature ◽  
Quantitative Easing ◽  
Methodological Choices ◽  
The Subject ◽  
Methodological Approaches ◽  
The Impact ◽  
Sufficient Precision

AbstractThe article presents the results of the review of the empirical literature regarding the impact of quantitative easing (QE) on emerging markets (EMs). The subject is of interest to policymakers and researchers due to the increasingly larger role of EMs in the world economy and the large-scale capital flows occurring after 2009. The review is conducted in a systematic manner and takes into consideration different methodological choices, samples and measurement issues. The paper puts the summarized results in the context of transmission channels identified in the literature. There are few distinct methodological approaches present in the literature. While there is a consensus regarding the direction of the impact of QE on EMs, its size and durability have not yet been assessed with sufficient precision. In addition, there are clear gaps in the empirical findings, not least related to relative underrepresentation of the CEE region (in particular, Poland).

Sign in / Sign up

Export Citation Format

Share Document