Utilizing Genomics to Characterize the Common Oat Gene Pool-The Story of More Than a Century of Polish Breeding.

This study was undertaken to investigate the diversity and population structure of 487 oat accessions, including breeding lines from the ongoing programs of the three largest Polish breeding companies, along with modern and historical Polish and foreign cultivars. The analysis was based on 7411 DArTseq-derived SNPs distributed among three sub-genomes (A, C, and D). The heterogeneity of the studied material was very low, as only cultivars and advanced breeding lines were examined. Principal component analysis (PCA), principal coordinate analysis (PCoA), and cluster and STRUCTURE analyses found congruent results, which show that most of the examined cultivars and materials from Polish breeding programs formed major gene pools, that only some accessions derived from Strzelce Plant Breeding, and that foreign cultivars were outside of the main group. During the 120 year oat breeding process, only 67 alleles from the old gene pool were lost and replaced by 67 new alleles. The obtained results indicate that no erosion of genetic diversity was observed within the Polish native oat gene pool. Moreover, current oat breeding programs have introduced 673 new alleles into the gene pool relative to historical cultivars. The analysis also showed that most of the changes in relation to historical cultivars occurred within the A sub-genome with emphasis on chromosome 6A. The targeted changes were the rarest in the C sub-genome. This study showed that Polish oat breeding based mainly on traditional breeding methods-although focused on improving traits typical to this crop, i.e., enhancing the grain yield and quality and improving adaptability-did not significantly narrow the oat gene pool and in fact produced cultivars that are not only competitive in the European market but are also reservoirs of new alleles that were not found in the analyzed foreign materials.

Discovery and Chromosomal Location a Highly Effective Oat Crown Rust Resistance Gene Pc50-5.

Crown rust, caused by Puccinia coronata f. sp. avenae, is one of the most destructive fungal diseases of oat worldwide. Growing disease-resistant oat cultivars is the preferred method of preventing the spread of rust and potential epidemics. The object of the study was Pc50-5, a race-specific seedling crown rust resistant gene, highly effective at all growth stages, selected from the differential line Pc50 (Avena sterilis L. CW 486-1 × Pendek). A comparison of crown rust reaction as well as an allelism test showed the distinctiveness of Pc50-5, whereas the proportions of phenotypes in segregating populations derived from a cross with two crown rust-susceptible Polish oat cultivars, Kasztan × Pc50-5 and Bingo × Pc50-5, confirmed monogenic inheritance of the gene, indicating its usefulness in oat breeding programs. Effective gene introgression depends on reliable gene identification in the early stages of plant development; thus, the aim of the study was to develop molecular markers that are tightly linked to Pc50-5. Segregating populations of Kasztan × Pc50-5 were genotyped using DArTseq technology based on next-generation Illumina short-read sequencing. Markers associated with Pc50-5 were located on chromosome 6A of the current version of the oat reference genome (Avena sativa OT3098 v2, PepsiCo) in the region between 434,234,214 and 440,149,046 bp and subsequently converted to PCR-based SCAR (sequence-characterized amplified region) markers. Furthermore, 5426978_SCAR and 24031809_SCAR co-segregated with the Pc50-5 resistance allele and were mapped to the partial linkage group at 0.6 and 4.0 cM, respectively. The co-dominant 58163643_SCAR marker was the best diagnostic and it was located closest to Pc50-5 at 0.1 cM. The newly discovered, very strong monogenic crown rust resistance may be useful for oat improvement. DArTseq sequences converted into specific PCR markers will be a valuable tool for marker-assisted selection in breeding programs.

Characteristics of Resistance to Puccinia coronata f. sp. avenae in Avena fatua.

Crown rust, caused by Puccinia coronata f. sp. avenae, is the most widespread and harmful fungal disease of oat. The best defense against the pathogen is use of cultivars with genetic resistance, which is effective, economic, and an environmentally friendly alternative to chemical control. However, the continuous evolution of the pathogen can rapidly overcome major gene resistance, creating an urgent need to identify new sources. Wild oat accessions have already proven to be valuable donors of many resistance genes, but the weed species Avena fatua remains underexploited. Its abundance across multiple environments and the frequent occurrence of herbicide-resistant populations demonstrate its ready ability to adapt to biotic and abiotic stresses; yet, surprisingly, there are no extensive studies which describe crown rust resistance occurrence in gene bank stocks of A. fatua. In this study, 204 accessions of A. fatua maintained in the collections of the United States Department of Agriculture (USDA) and Polish National Centre for Plant Genetic Resources were evaluated at the seedling stage for crown rust reaction using host-pathogen tests with five highly diverse and virulent races of P. coronata. Of tested genotypes, 85% showed a heterogeneous infection pattern, while 61% were susceptible or moderately susceptible to all races. Of the 79 resistant A. fatua accessions, seedling resistance to at least two P. coronata isolates was recognized within 19 accessions, with 13 displaying a homogeneously resistant phenotype to one or two races. Accessions showing multiple single seedling resistance to three or four isolates were observed. Based on the seedling reaction to isolates used in the study, 18 infection profiles (IP) were determined. Using UPGMA clustering, resistant accessions were divided into six main clusters encompassing samples with similar IPs. Twelve of 18 patterns allowed us to postulate the likely presence of novel crown rust resistance genes, whose origin was predominantly from Kenya or Egypt. Future work will clarify the genetic basis of the resistances observed here, as well as confirm their potential utility in breeding resistant oat cultivars.

Resistance to Puccinia coronata f. sp. avenae in Avena magna, A. murphyi, and A. insularis.

Wild oat tetraploids of the section Pachycarpa have already been proven to be a rich source of useful genes but have largely been unexploited for Puccinia coronata resistance. In this study, accessions of Avena magna, A. murphyi, and A. insularis gathered from European and North American gene banks were evaluated at the seedling stage for crown rust reaction using the host-pathogen test and six highly diverse and virulent P. coronata isolates. Of the 92 Avena accessions analyzed, 58.7% were resistant to at least one crown rust race. In all, 37% of the tested accessions reacted nonuniformly, which indicated their heterogeneity. The highest level of resistance was observed in three of the accessions, one of which was verified by flow cytometry as being hexaploid and two of which were verified as being tetraploids. The infection profiles of 19 accessions corresponded to resistance determined by the genes Pc14, Pc39, Pc40, Pc48, Pc50, Pc54, Pc55, Pc61, Pc67, Pc68, Pc97, Pc101, or Pc104. The patterns of infection of the remaining resistant A. magna and A. murphyi accessions allowed us to postulate the presence of potentially novel crown rust resistance genes.

Avena sterilis L. Genotypes as a Potential Source of Resistance to Oat Powdery Mildew.

The aim of the present study was to identify Avena sterilis genotypes demonstrating a high level of resistance against oat powdery mildew, using host-pathogen tests. The study was conducted on 350 A. sterilis genotypes from different parts of the world. Six single-spore isolates of Blumeria graminis (DC.) f. sp. avenae, which demonstrated different levels of virulence to control lines and cultivars, were used in host-pathogen screening tests. To confirm the resistant response of selected genotypes, 13 other isolates were used. Reactions to the isolates were grouped into three classes: resistant, intermediate, and susceptible. Susceptible cultivars Sam and Fuchs were used as controls to estimate the degree of infection. The results of the screening test showed that 10 genotypes were classified as resistant. The second test based on 13 other isolates revealed that only four of the 10 genotypes were a valuable source of resistance against powdery mildew. The identified genotypes may be used in oat breeding programs to increase the level of resistance against powdery mildew. First, however, further studies aimed at identifying whether this resistance is conditioned by a single gene or combinations of different genes are required.