High-resolution mapping of the barley Ryd3 locus controlling tolerance to BYDV

Lüpken, Thomas; Stein, Nils; Perović, Dragan; Habekuß, Antje; Serfling, Albrecht; Krämer, Ilona; Hähnel, Urs; Steuernagel, Burkhard; Scholz, Uwe; Ariyadasa, Ruvini; Martis, Mihaela; Mayer, Klaus; Niks, Rients E.; Collins, Nicholas C.; Friedt, Wolfgang; Ordon, Frank

doi:10.1007/s11032-013-9966-1

Cited by 9 publications

(10 citation statements)

References 56 publications

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“…The region appears to be homologous with one carrying markers for a major BYD tolerance locus identified in separate oat populations by Jin et al (1998) and Barbosa-Neto et al (2000) . Ryd3 is a major gene for BYD tolerance in barley which has been mapped to a genetic interval corresponding to a segment of rice chromosome Os02 ( Lüpken et al, 2013 ). Oat Mrg17 shares a large region of synteny with Os02 ( Chaffin et al, 2016 ), raising the possibility that the BYD tolerance QTN identified in the present study may be a Ryd3 orthologue.…”

Section: Discussionmentioning

confidence: 99%

Population Structure and Genotype–Phenotype Associations in a Collection of Oat Landraces and Historic Cultivars

et al. 2016

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Population structure and genetic architecture of phenotypic traits in oat (Avena sativa L.) remain relatively under-researched compared to other small grain species. This study explores the historic context of current elite germplasm, including phenotypic and genetic characterization, with a particular focus on identifying under-utilized areas. A diverse panel of cultivated oat accessions was assembled from the USDA National Small Grains Collection to represent a gene pool relatively unaffected by twentieth century breeding activity and unlikely to have been included in recent molecular studies. The panel was genotyped using an oat iSelect 6K beadchip SNP array. The final dataset included 759 unique individuals and 2,715 polymorphic markers. Some population structure was apparent, with the first three principal components accounting for 38.8% of variation and 73% of individuals belonging to one of three clusters. One cluster with high genetic distinctness appears to have been largely overlooked in twentieth century breeding. Classification and phenotype data provided by the Germplasm Resources Information Network were evaluated for their relationship to population structure. Of the structuring variables evaluated, improvement status (cultivar or landrace) was relatively unimportant, indicating that landraces and cultivars included in the panel were all sampled from a similar underlying population. Instead, lemma color and region of origin showed the strongest explanatory power. An exploratory association mapping study of the panel using a subset of 2,588 mapped markers generated novel indications of genomic regions associated with awn frequency, kernels per spikelet, lemma color, and panicle type. Further results supported previous findings of loci associated with barley yellow dwarf virus tolerance, crown rust (caused by Puccinia coronata f. sp. avenae) resistance, days to anthesis, and growth habit (winter/spring). In addition, two novel loci were identified for crown rust resistance.

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Section: Discussionmentioning

confidence: 99%

Population Structure and Genotype–Phenotype Associations in a Collection of Oat Landraces and Historic Cultivars

et al. 2016

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“…Between two and six contigs were identified by sequence comparison for the seven barley loci. Those loci derived from mapping populations with higher resolution permitted the definition of tiling paths holding a lower number of FPCs (data not shown) as long as the target loci are not allocated to centromeric regions (Lüpken et al, 2014). Identified contigs were employed to make a shallow approximation to the lately anchored physical map of barley and the established MTP containing 66,772 overlapping clones (Ariyadasa et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

“…However, in the breeding context, the use of this information remains mostly unexploited. Only few reports in the last years have been partly focused on the application of the barley GZ for marker saturation of genetic intervals containing interesting traits, such as spike density, resistance to powdery mildew, barley yellow and mild mosaic virus, or barley yellow dwarf disease (Shahinnia et al, 2012; Silvar et al, 2013; Ordon and Perovic, 2013; Yang et al, 2013; Lüpken et al, 2013, 2014). In barley breeding, there is an urgent need for tools mostly directed to the quick and efficient identification of sets of molecular markers that are closely linked to the traits of interest.…”

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confidence: 99%

Assessing the Barley Genome Zipper and Genomic Resources for Breeding Purposes

et al. 2015

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The aim of this study was to estimate the accuracy and convergence of newly developed barley (Hordeum vulgare L.) genomic resources, primarily genome zipper (GZ) and population sequencing (POPSEQ), at the genome-wide level and to assess their usefulness in applied barley breeding by analyzing seven known loci. Comparison of barley GZ and POPSEQ maps to a newly developed consensus genetic map constructed with data from 13 individual linkage maps yielded an accuracy of 97.8% (GZ) and 99.3% (POPSEQ), respectively, regarding the chromosome assignment. The percentage of agreement in marker position indicates that on average only 3.7% GZ and 0.7% POPSEQ positions are not in accordance with their centimorgan coordinates in the consensus map. The fine-scale comparison involved seven genetic regions on chromosomes 1H, 2H, 4H, 6H, and 7H, harboring major genes and quantitative trait loci (QTL) for disease resistance. In total, 179 GZ loci were analyzed and 64 polymorphic markers were developed. Entirely, 89.1% of these were allocated within the targeted intervals and 84.2% followed the predicted order. Forty-four markers showed a match to a POPSEQ-anchored contig, the percentage of collinearity being 93.2%, on average. Forty-four markers allowed the identification of twenty-five fingerprinted contigs (FPCs) and a more clear delimitation of the physical regions containing the traits of interest. Our results demonstrate that an increase in marker density of barley maps by using new genomic data significantly improves the accuracy of GZ. In addition, the combination of different barley genomic resources can be considered as a powerful tool to accelerate barley breeding.

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“…However, using these marker systems, gene isolation was a laborious and time consuming effort. Advances in molecular marker technologies as well as the previous version of the barley genome sequence already facilitated an accelerated fine mapping of disease resistance genes (Lüpken et al, 2013, 2014; Yang et al, 2014). New Illumina SNP genotyping assays, namely 9K and 50K (Comadran et al, 2012; Bayer et al, 2017), together with GBS (Poland et al, 2012) opened a new way for a more efficient and faster marker saturation of target loci in barley.…”

Section: Discussionmentioning

confidence: 99%

“…The other extreme are hotspots of high recombination rates in telomeric regions (Bhakta et al, 2015). In case of the locus of Ryd3 , which is located in a centromeric region, the physical/genetic ratio has been estimated at 14–60 Mb/cM, while the genome-wide average is 4.4 Mb/cM (Lüpken et al, 2014). At the rym4/rym5 locus, the ratio of physical to genetic distances was in the range between 0.8 and 2.3 Mb cM and have increased to over 30 Mb cM, although the gene has been mapped on the telomeric region of chromosome 3H (Stein and Graner, 2005).…”

Section: Introductionmentioning

confidence: 99%

High Resolution Mapping of RphMBR1012 Conferring Resistance to Puccinia hordei in Barley (Hordeum vulgare L.)

et al. 2019

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Isolation of disease resistance genes in barley was hampered by the large genome size, but has become easy due to the availability of the reference genome sequence. During the last years, many genomic resources, e.g., the Illumina 9K iSelect, the 50K Infinium arrays, the Barley Genome Zipper, POPSEQ, and genotyping by sequencing (GBS), were developed that enable enhanced gene isolation in combination with the barley genome sequence. In the present study, we developed a fine map of the barley leaf rust resistance gene Rph MBR 1012 . 537 segmental homozygous recombinant inbred lines (RILs) derived from 4775 F 2 -plants were used to construct a high-resolution mapping population (HRMP). The Barley Genome Zipper, the 9K iSelect chip, the 50K Infinium chip and GBS were used to develop 56 molecular markers located in the target interval of 8 cM. This interval was narrowed down to about 0.07 cM corresponding to 0.44 Mb of the barley reference genome. Eleven low-confidence and 18 high-confidence genes were identified in this interval. Five of these are putative disease resistance genes and were subjected to allele-specific sequencing. In addition, comparison of the genetic map and the reference genome revealed an inversion of 1.34 Mb located distally to the resistance locus. In conclusion, the barley reference sequence and the respective gene annotation delivered detailed information about the physical size of the target interval, the genes located in the target interval and facilitated the efficient development of molecular markers for marker-assisted selection for Rph MBR1012.

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High-resolution mapping of the barley Ryd3 locus controlling tolerance to BYDV

Cited by 9 publications

References 56 publications

Population Structure and Genotype–Phenotype Associations in a Collection of Oat Landraces and Historic Cultivars

Population Structure and Genotype–Phenotype Associations in a Collection of Oat Landraces and Historic Cultivars

Assessing the Barley Genome Zipper and Genomic Resources for Breeding Purposes

High Resolution Mapping of RphMBR1012 Conferring Resistance to Puccinia hordei in Barley (Hordeum vulgare L.)

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