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Six hundred thirty five oat (Avena sativa L.) lines and 4561 single-nucleotide polymorphism (SNP) loci were used to evaluate population structure, linkage disequilibrium (LD), and genotypephenotype association with heading date. The first five principal components (PCs) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 25 PCs nor the cross-validation errors from K = 1 to 20 model-based analyses suggested a structured population. However, the PC and K = 2 model-based analyses supported clustering of lines on spring oat vs. southern United States origin, accounting for 16% of genetic variation (p < 0.0001). Single-locus F-statistic (F ST ) in the highest 1% of the distribution suggested linkage groups that may be differentiated between the two population subgroups. Population structure and kinship-corrected LD of r 2 = 0.10 was observed at an average pairwise distance of 0.44 cM (0.71 and 2.64 cM within spring and southern oat, respectively). On most linkage groups LD decay was slower within southern lines than within the spring lines. A notable exception was found on linkage group Mrg28, where LD decay was substantially slower in the spring subpopulation. It is speculated that this may be caused by a heterogeneous translocation event on this chromosome. Association with heading date was most consistent across location-years on linkage groups Mrg02, Mrg12, Mrg13, and Mrg24. Core Ideas• An oat association-mapping panel contributed by active breeding programs worldwide.• Characterized population structure and found subdivisions related to adaptation• Characterized genome-wide and chromosomespecific linkage disequilibrium• Performed association-mapping and post hoc modeling of heading date• Found several consistently associated QTL

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Fusarium head blight (FHB), caused by Fusarium graminearum Schwabe, is a serious disease problem on durum wheat (Triticum turgidum L. var. durum) in the USA. To date, the resistance to FHB available in hexaploid wheat (T. aestivum L.) sources has not been transferred successfully to tetraploid durum. In the 1980s, USDA geneticist L.R. Joppa produced a set of disomic lines [LDN(DIC)] derived from wild emmer (T. turgidum L. var. dicoccoides). Each line had a different pair of chromosomes from T. dicoccoides substituted for the corresponding ‘Langdon’ durum chromosomes. The purpose of this study was to determine if any of the LDN(DIC) lines showed useful levels of resistance to FHB. We tested these lines for FHB response by inoculation with F. graminearum in the greenhouse. Inoculation was accomplished via the single spikelet method, in which a droplet of conidiospore suspension is placed into one spikelet per spike followed by mist–high humidity for 3 d to establish infection. After 21 d, spikes were scored for extent of FHB symptoms and the average disease severity of the lines compared. A low disease severity score in this test indicated the presence of resistance to FHB in that line. Each test was replicated and the tests were done five times. In each test, some lines differed significantly. One line, LDN(DIC‐3A), was consistently less susceptible and another line, LDN(DIC‐2A), was consistently more susceptible than the parent Langdon durum, which itself showed an intermediate FHB reaction. Several other LDN(DIC) lines showed a trend either for increased or reduced susceptibility to FHB. Since each line differs by a single chromosome pair, the results suggest that genes affecting FHB resistance are present on several different T. dicoccoides or Langdon durum chromosomes.

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Traditionally, the oat crop (Avena sativa) has been neglected in a number of respects, cultivated in cropping areas not optimal for wheat, barley or maize. In recent years the interest in oats has increased, particularly because of its dietary benefits and therapeutic potential for human health. The uniqueness and advantages of naked oats over other popular cereals, due to its potentially valuable nutritional composition, have been well studied and reported, opening new market “niches” for oats. Despite the well‐documented benefits, the status of the oat crop is still fragile, due to many reasons. The area cultivated for the oat crop is much less compared with other cereals, and therefore commercial efforts in oat breeding are less. Oat groat yield is lower than other cereals such as wheat and the nutritious uniqueness has not been reflected in agreeable market prices. The same price still exists for both naked and conventional/covered oats in the world grain market. The absence of visible market competitiveness, and some of the oat biological drawbacks, including low grain yield, keeps the oat crop as a lower profitability minor crop. This review is intended to analyse and summarise main achievements and challenges in oat genetics, agronomy and phytopathology to find possible ways of oat improvement and future perspectives for oat breeding.

Oat crown rust, caused by Puccinia coronata f. sp. avenae, is a major constraint to oat (Avena sativa L.) production in many parts of the world. In this first comprehensive multienvironment genomewide association map of oat crown rust, we used 2972 singlenucleotide polymorphisms (SNPs) genotyped on 631 oat lines for association mapping of quantitative trait loci (QTL). Seedling reaction to crown rust in these lines was assessed as infection type (IT) with each of 10 crown rust isolates. Adult plant reaction was assessed in the field in a total of 10 location-years as percentage severity (SV) and as infection reaction (IR) in a 0-to-1 scale. Overall, 29 SNPs on 12 linkage groups were predictive of crown rust reaction in at least one experiment at a genome-wide level of statistical significance. The QTL identified here include those in regions previously shown to be linked with seedling resistance genes Pc48, Pc58a, Pc68, Pc71, Pc91, and PcKM and also with adult-plant resistance and adaptation-related QTL. In addition, QTL on linkage groups Mrg03, Mrg08, and Mrg23 were identified in regions not previously associated with crown rust resistance. Evaluation of marker genotypes in a set of crown rust differential lines supported Pc91 as the identity of QPc.CORE.18.3. The SNPs with rare alleles associated with lower disease scores may be suitable for use in marker-assisted selection of oat lines for crown rust resistance.

Many core collections have been developed from large collections of crop germplasm, but most of these have not been characterized, particularly using molecular techniques, for germplasm management and utilization. We have attempted to characterize a structured sample representing a world collection of 11,622 cultivated hexaploid oat accessions in the hope of understanding the genetic structure of the world collection. The amplified fragment length polymorphism (AFLP) technique was applied to screen 670 accessions representing 79 countries and one group of uncertain origin. For each accession, 170 AFLP polymorphic bands detected by five AFLP primer pairs were scored. Analyses of the AFLP data showed the effectiveness of the stratified sampling applied in capturing country-wise AFLP variation. The frequencies of polymorphic bands ranged from 0.11 to 0.99, with an average of 0.72. The majority (89.9%) of the AFLP variation resided within accessions of each country, and only 6.2% of the AFLP differences existed among accessions of major geographic regions. Accessions from the Mediterranean region were the most distinct, while those from Russia and the USA were the most diverse. The two distinct groups that were observed were separated largely on the basis of common oat and red oat. Red oat was genetically more diverse than its common and hull-less counterparts, and hull-less oat was more related to common oat than red oat. Landrace and non-landrace accessions displayed similar AFLP variation patterns. These patterns are significant for understanding the domestication of cultivated oat and are useful in classifying the intraspecific diversity of oat germplasm, developing specific core subsets of the oat collection, and exploring new sources of genes for oat improvement.