Molecular mapping of crown rust resistance genes is important to effectively utilize these genes and improve breeding efficiency through marker-assisted selection. Pc45 is a major race-specific crown rust resistance gene initially identified in the wild hexaploid oat Avenasterilis in the early 1970s. This gene was transferred to cultivated oat (Avena sativa) and has been used as a differential for identification of crown rust races since 1974. Previous research identified an association between virulence to Pc45 and PcKM, a crown rust resistance gene in the varieties 9Kame9 and 9Morton9. This study was undertaken to reveal the relationship between Pc45 and PcKM. Pc45 was studied in the crosses 9AC Morgan9/Pc45 and 9Kasztan9/Pc45, where Pc45 is the differential line carrying Pc45. F₂ progenies and F_2:3 families of both populations were inoculated with the crown rust isolate CR258 (race NTGG) and single gene segregation ratios were observed. SNP markers for PcKM were tested on these populations and linkage maps were generated. In addition, 17 newly developed SNP markers identified from genotyping-by-sequencing (GBS) data were mapped in these two populations, plus another three populations segregating for Pc45 or PcKM. Pc45 and PcKM mapped to the same location of Mrg08 (chromosome 12D) of the oat chromosome-anchored consensus map. These results strongly suggest that Pc45 and PcKM are the same resistance gene, but allelism (i.e. functionally different alleles of the same gene) or tight linkage (i.e. two tightly linked genes) cannot be ruled out based on the present data.

Key message: Six new PCR-based markers for thePc39crown rust resistance gene inAvena sativaL. were developed.Pc39was mapped to Mrg11 of the oat consensus map using BLASTn analysis. The aim of this study was the identification of molecular markers for thePc39gene in cultivated oat (Avena sativaL.).Pc39is a major race-specific crown rust resistance gene originally found in an Israeli accession of the wild hexaploidAvena sterilis. The effectiveness of this gene in Europe has decreased in recent years, but is still relatively high and breeding programs would benefit from the availability of molecular markers to aid in its mapping and deployment. The complexity of the oat genome poses a significant obstacle to genetic research. No oat rust resistance genes have yet been cloned, and even the number of relevant molecular markers is very limited. Here, genotyping of a segregating population derived from a cross ‘Celer’ (Pc39)/STH9210 (susceptible) was conducted using RAPD- and SRAP-PCR-based methods, as well as microarray-based DArT™ and next-generation sequencing DArTseq™ techniques. Markers associated withPc39were placed on the hexaploid oat consensus linkage group Mrg11 at 3.7–6.7 cM. Six new PCR-based markers were developed to allow identification of the resistantPc39allele. These tightly linked markers will be useful in marker-assisted selection, with the closest, SCAR_3456624, being within 0.37 cM ofPc39. The newly developed markers could find applications in the fine mapping or positional cloning of this gene. Moreover, easy-to-use PCR-based markers linked toPc39could facilitate the utilization of this gene in oat breeding programs, especially as a component of crown rust resistance gene pyramids.

© TÜBİTAK doi:10.3906/bot-1403-10 Comparative analysis of hexaploid Avena species using REMAP and ISSR method

Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health ^1,2 . Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues ³ . Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales ⁴ . In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oat lines, along with an atlas of gene expression across 6 tissues of different developmental stages in 23 of these lines. We construct an atlas of gene-expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory upregulation of the remaining homeologues, but this process is constrained by subgenome divergence. Chromosomal rearrangements have substantially affected recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semi-dwarf mutant has risen to prominence in Australian elite varieties. The oat pangenome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.

The appropriate selection of various traits in valuable plants is very important for modern plant breeding. Effective resistance to fungal diseases, such as powdery mildew, is an example of such a trait in oats. Marker-assisted selection is an important tool that reduces the time and cost of selection. The aims of the present study were the identification of dominant DArTseq markers associated with a new resistance gene, annotated as Pm11 and derived from Avena sterilis genotype CN113536, and the subsequent conversion of these markers into a PCR-based assay. Among the obtained 30,620 silicoDArT markers, 202 markers were highly associated with resistance in the analysed population. Of these, 71 were selected for potential conversion: 42 specific to resistant and 29 to susceptible individuals. Finally, 40 silicoDArT markers were suitable for primer design. From this pool, five markers, 3 for resistant and 2 for susceptible plants, were selected for product amplification in the expected groups. The developed method, based on 2 selection markers, provides certain identification of resistant and susceptible homozygotes. Also, the use of these markers allowed the determination of heterozygotes in the analysed population. Selected silicoDArT markers were also used for chromosomal localization of new resistance genes. Five out of 71 segregating silicoDArT markers for the Pm11 gene were found on the available consensus genetic map of oat. Five markers were placed on linkage groups corresponding to Mrg12 on the Avena sativa consensus map.