Accession numbers: Accession numbers for sequence data generated in this study are ERP004444 (GBS reads) and ERP004445 (exome capture reads).Keywords: Hordeum bulbosum, crop wild relatives, introgression line, genotyping-by-sequencing, exome capture, next-generation sequencing. SummaryCrop wild relatives (CWR) provide an important source of allelic diversity for any given crop plant species for counteracting the erosion of genetic diversity caused by domestication and elite breeding bottlenecks. Hordeum bulbosum L. is representing the secondary gene pool of the genus Hordeum. It has been used as a source of genetic introgressions for improving elite barley germplasm (Hordeum vulgare L.). However, genetic introgressions from H. bulbosum have yet not been broadly applied, due to a lack of suitable molecular tools for locating, characterizing, and decreasing by recombination and marker-assisted backcrossing the size of introgressed segments. We applied next-generation sequencing (NGS) based strategies for unlocking genetic diversity of three diploid introgression lines of cultivated barley containing chromosomal segments of its close relative H. bulbosum. Firstly, exome capture-based (re)-sequencing revealed large numbers of single nucleotide polymorphisms (SNPs) enabling the precise allocation of H. bulbosum introgressions. This SNP resource was further exploited by designing a custom multiplex SNP genotyping assay. Secondly, twoenzyme-based genotyping-by-sequencing (GBS) was employed to allocate the introgressed H. bulbosum segments and to genotype a mapping population. Both methods provided fast and reliable detection and mapping of the introgressed segments and enabled the identification of recombinant plants. Thus, the utilization of H. bulbosum as a resource of natural genetic diversity in barley crop improvement will be greatly facilitated by these tools in the future.

Hordeum bulbosum L., a wild relative of barley (Hordeum vulgare L.), has been considered as a valuable source of genetic diversity for barley improvement. Since the 1990s, a considerable number of barley/H. bulbosum introgression lines (IL)s has been generated, with segments introgressed from H. bulbosum harboring a diverse set of desirable traits. However, the efficient utilization of these ILs has been hampered, largely due to the lack of suitable molecular tools for their genetic characterization and highly reduced interspecific recombination frequencies in the region of the introgression. In the present study, we utilized genotyping-by-sequencing for the detailed molecular characterization of 145 ILs. Genotypic information allows the genetic diversity within the set of ILs to be determined and a strategy was outlined to tackle the obstacle of reduced recombination frequencies. Furthermore, we compiled exome capture re-sequencing information of barley and H. bulbosum and designed an integrated barley/H. bulbosum sequence resource with polymorphism information on interspecific and intraspecific sequence variations of both species. The integrated sequence will be valuable for marker development in barley/H. bulbosum ILs derived from any barley and H. bulbosum donors. This study provides the tools for the widespread utilization of barley/H. bulbosum ILs in applied barley breeding and academic research.

Hordeum bulbosum L., a wild grass and close relative of cultivated barley (Hordeum vulgare L.), gained importance in plant breeding as inducer of haploid plants in crosses with barley and also as a genetic resource for introgression of disease resistance/ tolerance genes into cultivated barley. Genetic mapping of genes introgressed from H. bulbosum is a prerequisite for their efficient utilization in barley breeding, but often hindered due to repressed recombination. The mechanism underlying the reduced frequency or lack of meiotic recombination between H. bulbosum and H. vulgare chromatin in introgressed segments is not understood. It may be explained by lack of genome collinearity or other structural differences between both genomes. In the present study, two F 1 mapping populations of H. bulbosum were analyzed by genotyping-by-sequencing (GBS) and four dense H. bulbosum genetic maps containing 1449, 996, 720, and 943 SNP markers, respectively, revealed overall a high degree of collinearity for all seven homeologous linkage groups of H. vulgare and H. bulbosum. The patterns of distribution of recombination along chromosomes differed between barley and H. bulbosum, indicating organizational differences between both genomes.

Key message We mapped the Rym14Hb resistance locus to barley yellow mosaic disease in a 2Mbp interval. The co-segregating markers will be instrumental for marker-assisted selection in barley breeding. Abstract Barley yellow mosaic disease is caused by Barley yellow mosaic virus and Barley mild mosaic virus and leads to severe yield losses in barley (Hordeum vulgare) in Central Europe and East-Asia. Several resistance loci are used in barley breeding. However, cases of resistance-breaking viral strains are known, raising concerns about the durability of those genes. Rym14Hb is a dominant major resistance gene on chromosome 6HS, originating from barley’s secondary genepool wild relative Hordeum bulbosum. As such, the resistance mechanism may represent a case of non-host resistance, which could enhance its durability. A susceptible barley variety and a resistant H. bulbosum introgression line were crossed to produce a large F2 mapping population (n = 7500), to compensate for a ten-fold reduction in recombination rate compared to intraspecific barley crosses. After high-throughput genotyping, the Rym14Hb locus was assigned to a 2Mbp telomeric interval on chromosome 6HS. The co-segregating markers developed in this study can be used for marker-assisted introgression of this locus into barley elite germplasm with a minimum of linkage drag.

The mechanisms of aluminum (Al) resistance in wheat and rye involve the release of citrate and malate anions from the root apices. Many of the genes controlling these processes have been identified and their responses to Al treatment described in detail. This study investigated how the major Al resistance traits of wheat and rye are transferred to triticale (x Tritosecale Wittmack) which is a hybrid between wheat and rye. We generated octoploid and hexaploid triticale lines and compared them with the parental lines for their relative resistance to Al, organic anion efflux and expression of some of the genes encoding the transporters involved. We report that the strong Al resistance of rye was incompletely transferred to octoploid and hexaploid triticale. The wheat and rye parents contributed to the Al-resistance of octoploid triticale but the phenotypes were not additive. The Al resistance genes of hexaploid wheat, TaALMT1, and TaMATE1B, were more successfully expressed in octoploid triticale than the Al resistance genes in rye tested, ScALMT1 and ScFRDL2. This study demonstrates that an important stress-tolerance trait derived from hexaploid wheat was expressed in octoploid triticale. Since most commercial triticale lines are largely hexaploid types it would be beneficial to develop techniques to generate genetically-stable octoploid triticale material. This would enable other useful traits that are present in hexaploid but not tetraploid wheat, to be transferred to triticale.