Two dominant genes in barley ( <i>Hordeum vulgare</i> L.) complementarily encode perfect resistance to <i>Japanese soil-borne wheat mosaic virus</i>

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

Japanese soil-borne wheat mosaic virus ( Furovirus) is a damaging pathogen of wheat and barley. This virus can survive in the soil for several decades, so the deployment of resistant cultivars represents the only practical control measure. Here, a genetic analysis has identified two regions of the barley genome—one on chromosome 2H and the other on chromosome 3H—as harboring gene(s) encoding resistance to this virus. The joint presence of both loci, termed Jmv1 and Jmv2, made the plants essentially immune, with resistance being dominant over susceptibility at each locus. Phylogenetic analysis showed that the virus is not closely related to the type Furovirus species Soil-borne wheat mosaic virus. There was a difference between the RNA1- and RNA2-based phylogenies of the virus species in Furovirus implying the independent segregation of the virus subgenomes.

Related collections

Most cited references 45

Record: found
Abstract: found
Article: found

Is Open Access

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)

Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.

0 comments Cited 16337 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

The Sequence Alignment/Map format and SAMtools

Heng Li, Bob Handsaker, Alec Wysoker … (2009)

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk

0 comments Cited 14288 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Aaron McKenna, Matthew Hanna, Eric R. Banks … (2010)

Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS--the 1000 Genome pilot alone includes nearly five terabases--make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.

0 comments Cited 5744 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Journal

Journal ID (nlm-ta): Breed Sci

Journal ID (iso-abbrev): Breed Sci

Journal ID (publisher-id): jsbbs

Title: Breeding Science

Publisher: Japanese Society of Breeding

ISSN (Print): 1344-7610

ISSN (Electronic): 1347-3735

Publication date (Print): December 2022

Publication date (Electronic): 13 December 2022

Volume: 72

Issue: 5

Pages: 372-382

Affiliations

[1 ] Tochigi Prefectural Agricultural Experiment Station , 1080 Kawaraya-cho, Utsunomiya, Tochigi 320-0002, Japan

[2 ] Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO) , Kan-non-dai, Tsukuba, Ibaraki 305-8518, Japan

[3 ] Institute of Crop Science, National Agriculture and Food Research Organization (NARO) , Kan-non-dai, Tsukuba, Ibaraki 305-8518, Japan

[4 ] Institute of Plant Science and Resources, Okayama University , 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan

[5 ] Graduate School of Horticulture, Chiba University , Matsudo, Chiba 271-8510, Japan

[6 ] Crop Research Institute, Shandong Academy of Agricultural Sciences (SAAS) , 202 Gongyebei Road, Licheng District, Ji’nan, 250100 Shandong, China

Author notes

[* ]Corresponding author (e-mail: takao_komatsuda@ 123456kzc.biglobe.ne.jp )

Communicated by Nils Stein

Article

Publisher ID: JST.JSTAGE/jsbbs/22046 Publisher-manuscript ID: 22046

DOI: 10.1270/jsbbs.22046

PMC ID: 9895801

PubMed ID: 36776442

SO-VID: db044029-038d-4f35-b689-e85c164ae18c

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution (BY) License (CC-BY 4.0: https://creativecommons.org/licenses/by/4.0/).

Two dominant genes in barley ( Hordeum vulgare L.) complementarily encode perfect resistance to Japanese soil-borne wheat mosaic virus

Read this article at

Abstract

Related collections

SDG 2: Zero Hunger

Most cited references 45

Trimmomatic: a flexible trimmer for Illumina sequence data

The Sequence Alignment/Map format and SAMtools

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Author and article information

Journal

Affiliations

Author notes

Article

History

Categories

Comments

Comment on this article

Similar content 438

Cited by 2

Most referenced authors 1,094