Assessing the Barley Genome Zipper and Genomic Resources for Breeding Purposes

Abstract

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.

A Cluster of Nucleotide‐Binding Site–Leucine‐Rich Repeat Genes Resides in a Barley Powdery Mildew Resistance Quantitative Trait Loci on 7HL

“…Some positions of Morex WGS contigs were not in agreement with the genotypes of our lines. Differences in collinearity between several genetic maps and the POPSEQ reference have been already described (Cantalapiedra et al, 2015;Silvar et al, 2015). These incongruences are important for fine mapping purposes.…”

Collinearity Analysis and High-Density Genetic Mapping of the Wheat Powdery Mildew Resistance Gene Pm40 in PI 672538

“…Therefore, it is difficult to directly use the data from the wheat Genome Zipper in our research, like a previous report regarding the positional isolation of powdery mildew QTLs in barley [ 57 ]. Successful fine mapping of quantitative trait loci by using the synteny-based or zipper-based markers combined with primarily genome zipper and population sequencing analysis has been reported [ 58 , 59 ]. Based on previous research, 97 gene were identified according to our synteny analysis with EST-STS markers.…”

QTL for Water Use Related Traits in Juvenile Barley

“…The whole set of genotypes was analysed with the Infinium 9 k iSelect Chip (Illumina, San Diego, CA, USA). For mapping, a recent consensus map of single nucleotide polymorphism (SNP) markers by Silvar, et al [40] was used. After filtering for >5% minor allele frequency (MAF), <10% missing values and <5% heterozygous markers, 4438 SNP markers were used to construct a HapMap and to calculate a kinship of Roger's distances [74] in the open, web-based platform Galaxy [75][76][77].…”

“…Genotypic data can be generated applying e.g., next generation sequencing (NGS) [34,35], high throughput array technologies like the Infinium iSelect assay by Illumina [36], the Axiom technology by Affymetrix [37] or genotyping by sequencing (GBS) [38,39], resulting in high density genetic maps, e.g., published by Silvar, et al [40]. Quantitative trait loci (QTL) for water use related traits under drought stress treatment in barley were identified e.g., by Varshney, et al [41] for biomass on barley chromosome 3H, by Teulat, et al [42] and Honsdorf, et al [13] for WC on chromosomes 1H, 6H and 7H and by Diab, et al [43] and Chen, et al [44] for WUE on chromosomes 3H, 5H, 6H and 7H.…”