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      A genetic analysis of the resistance in barley to Soil-borne wheat mosaic virus

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          Abstract

          Soil-borne wheat mosaic virus (SBWMV), a ubiquitous pathogen commonly encountered in temperate regions of the Northern hemisphere, can damage a number of economically important cereal crops, notably wheat and barley. Given that the plasmodiophorid cercozoan Polymyxa graminis, which acts as the vector of SBWMV, can survive in the soil for many decades, the only feasible control measure is the deployment of resistant cultivars. Here, a quantitative trait locus (QTL) approach was taken to characterize the genetic basis of the SBWMV resistance exhibited by the barley cultivar Haruna Nijo. The analysis revealed that between 33% and 41% of the variation for the measure chosen to represent resistance was under the control of a gene(s) mapping to a region at the distal end of the short arm of chromosome 2H. In contrast to most of the genes known to encode resistance to soil-borne mosaic viruses, the allele specifying resistance was dominant over those present in a susceptible genotype.

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          A chromosome conformation capture ordered sequence of the barley genome

          Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
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            Development and implementation of high-throughput SNP genotyping in barley

            Background High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource. Results Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM. Conclusion The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.
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              TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

              Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.
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                Author and article information

                Journal
                Breed Sci
                Breed Sci
                jsbbs
                Breeding Science
                Japanese Society of Breeding
                1344-7610
                1347-3735
                December 2020
                28 November 2020
                : 70
                : 5
                : 617-622
                Affiliations
                [1 ] Tochigi Prefectural Agricultural Experiment Station , Utsunomiya, Tochigi 320-0002, Japan
                [2 ] Institute of Crop Science, National Agriculture and Food Research Organization (NARO) , Tsukuba, Ibaraki 305-8518, Japan
                [3 ] Graduate School of Horticulture, Chiba University , Matsudo, Chiba 271-8510, Japan
                Author notes
                [* ]Corresponding author (e-mail: takao@ 123456affrc.go.jp )

                Communicated by Nils Stein

                Article
                JST.JSTAGE/jsbbs/20071 20071
                10.1270/jsbbs.20071
                7878938
                33603558
                d97567c9-8efe-4983-a414-0768f0222062
                Copyright © 2020 by JAPANESE SOCIETY OF BREEDING

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 19 June 2020
                : 13 September 2020
                Categories
                Research Paper

                Animal agriculture
                furovirus,polymyxa graminis,gene mapping,dominant gene,doubled haploid
                Animal agriculture
                furovirus, polymyxa graminis, gene mapping, dominant gene, doubled haploid

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