Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley

Dissecting the Complex Genome of Crested Wheatgrass by Chromosome Flow Sorting

Wheatgrass (Agropyron sp.) is a potential source of beneficial traits for wheat improvement. Among them, crested wheatgrass [A. cristatum (L.) Gaertn.] comprises a complex of diploid, tetraploid, and hexaploid forms with the basic genome P, with some accessions carrying supernumerary B chromosomes (Bs). In this work, we applied flow cytometry to dissect the complex genome of crested wheatgrass into individual chromosomes to facilitate its analysis. Flow karyotypes obtained after the analysis of 4',6-diamidino-2-phenylindole (DAPI)-stained mitotic chromosomes of diploid and tetraploid accessions consisted of three peaks, each corresponding to a group of two or three chromosomes. To improve the resolution, bivariate flow karyotyping after fluorescent labeling of chromosomes with fluorescein isothiocyanate (FITC)-conjugated probe (GAA) microsatellite was applied and allowed discrimination and sorting of P genome chromosomes from wheat-crested wheatgrass addition lines. Chromosomes 1P-6P and seven telomeric chromosomes could be sorted at purities ranging from 81.7 to 98.2% in disomics and from 44.8 to 87.3% in telosomics. Chromosome 7P was sorted at purities reaching 50.0 and 39.5% in diploid and tetraploid crested wheatgrass, respectively. In addition to the whole complement chromosomes (A), Bs could be easily discriminated and sorted from a diploid accession at 95.4% purity. The sorted chromosomes will streamline genome analysis of crested wheatgrass, facilitating gene cloning and development of molecular tools to support alien introgression into wheat.

Assessing the Barley Genome Zipper and Genomic Resources for Breeding Purposes

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.