Barley Genome Organization, Mapping, and Synteny

Graner, Andreas; Kilian, Andrzej; Kleinhofs, A.

doi:10.1002/9780470958636.ch3

Cited by 7 publications

(5 citation statements)

References 161 publications

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“…Despite the difficulties resulting from the large size and complexity of the barley genome, relevant achievements in barley genomics have been accomplished during the last years. GZ, POPSEQ, and the resources established in the framework of the IBSC, including various high‐density marker maps, have accelerated the exploitation of this Triticeae crop (Graner et al, 2011; Feuillet et al, 2012). However, these resources need further validation to become beneficial for plant breeders, who demand tools that allow not only the expeditious improvement of molecular markers tightly linked to genes or QTL of interest but also the usefulness of these markers across different germplasm resources (Varshney et al, 2006; Kilian and Graner, 2012; Keilwagen et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

“…The major impediment for its full exploitation comes from the presence of a large and complex repeat‐rich genome of 5.1 Gb (Dolezel et al, 1998). Nevertheless, progress in barley genetics and genomics research has been continuously moving forward (Graner et al, 2011; Kumlehn and Stein, 2014).…”

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confidence: 99%

Assessing the Barley Genome Zipper and Genomic Resources for Breeding Purposes

et al. 2015

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“…Reducing the LOD threshold to 3.0 did not reduce the number of LGs identified. The entire map comprised just 496 cM (Supplemental Table 2), a length which is under half that determined from other biparental crosses (Graner et al 2011). The presence of gaps and the foreshortening of the map are assumed to reflect the relatively close relationship between the two parental cultivars.…”

Section: Linkage Mappingmentioning

confidence: 99%

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

et al. 2022

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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.

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“…The total production of barley in Western Canada is estimated at 10,416,300 tonnes in the 2020 ( Marta and Tricia, 2020 ). In the past, barley was used as human food but evolved mostly into a feed, and grain brewing ( Baik and Ullrich, 2008 ; Graner et al., 2010 ). Due to the high levels of beneficial components for the human diet, barley now used as a functional food improvement ( Dvořáková et al., 2008 ; Galli et al., 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure assessment of Western Canadian barley cooperative trials

et al. 2023

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Studying the population structure and genetic diversity of historical datasets is a proposed use for association analysis. This is particularly important when the dataset contains traits that are time-consuming or costly to measure. A set of 96 elite barley genotypes, developed from eight breeding programs of the Western Canadian Cooperative Trials were used in the current study. Genetic diversity, allelic variation, and linkage disequilibrium (LD) were investigated using 5063 high-quality SNP markers via the Illumina 9K Barley Infinium iSelect SNP assay. The distribution of SNPs markers across the barley genome ranged from 449 markers on chromosome 1H to 1111 markers on chromosome 5H. The average polymorphism information content (PIC) per locus was 0.275 and ranged from 0.094 to 0.375. Bayesian clustering in STRUCTURE and principal coordinate analysis revealed that the populations are differentiated primarily due to the different breeding program origins and ear-row type into five subpopulations. Analysis of molecular variance based on PhiPT values suggested that high values of genetic diversity were observed within populations and accounted for 90% of the total variance. Subpopulation 5 exhibited the most diversity with the highest values of the diversity indices, which represent the breeding program gene pool of AFC, AAFRD, AU, and BARI. With increasing genetic distance, the LD values, expressed as r2, declined to below the critical r2 = 0.18 after 3.91 cM, and the same pattern was observed on each chromosome. Our results identified an important pattern of genetic diversity among the Canadian barley panel that was proposed to be representative of target breeding programs and may have important implications for association mapping in the future. This highlight, that efforts to identify novel variability underlying this diversity may present practical breeding opportunities to develop new barley genotypes.

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Barley Genome Organization, Mapping, and Synteny

Cited by 7 publications

References 161 publications

Assessing the Barley Genome Zipper and Genomic Resources for Breeding Purposes

Assessing the Barley Genome Zipper and Genomic Resources for Breeding Purposes

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

Genetic diversity and population structure assessment of Western Canadian barley cooperative trials

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