Hexaploid oat (Avena sativa L., 2n = 6x = 42) is a member of the Poaceae family and has a large genome (~12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice (Oryza sativa L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.

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

Developing new blueberry cultivars requires plant breeders to be aware of current and emerging needs throughout the supply chain, from producer to consumer. Because breeding perennial crop plants (such as blueberry) is time- and resource-intensive, understanding and targeting priority traits is critical to enhancing the efficiency of breeding programs. This study assesses blueberry industry breeding priorities for fruit and plant quality traits based on a survey conducted at commodity group meetings across nine U.S. states and in British Columbia (Canada) between Nov. 2016 and Mar. 2017. In general, industry responses signaled that the most important trait cluster was fruit quality including the firmness, flavor, and shelf life. Fruit quality traits affect price premiums received by producers; influence consumer’s preferences; and have the potential to increase the feasibility of mechanical harvesting, all critical to the economic viability of the industry. There were differences across regions in the relative importance assigned to traits for disease resistance, arthropod resistance, and tolerance to abiotic stresses. Our findings will be useful to researchers seeking solutions for challenges to the North American blueberry industry including development of new cultivars with improved traits using accelerated DNA-based selection strategies.

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.

Accessions of common wheat (Triticum aestivum L. subsp. aestivum) from the USDA-ARS National Small Grains Collection (NSGC) are a resource for wheat scientists worldwide. The

A new gene for Ug99 resistance from wheat landrace PI 374670 was detected on the long arm of chromosome 7A. Wheat landrace PI 374670 has seedling and field resistance to stem rust caused by Puccinia graminis f. sp tritici Eriks. & E. Henn (Pgt) race TTKSK. To elucidate the inheritance of resistance, 216 BC1F2 families, 192 double haploid (DH) lines, and 185 recombinant inbred lines (RILs) were developed by crossing PI 374670 and the susceptible line LMPG-6. The parents and progeny were evaluated for seedling resistance to Pgt races TTKSK, MCCFC, and TPMKC. The DH lines were tested in field stem rust nurseries in Kenya and Ethiopia. The DH lines were genotyped with the 90K wheat iSelect SNP genotyping platform. Goodness-of-fit tests indicated that a single dominant gene in PI 374670 conditioned seedling resistance to the three Pgt races. The seedling resistance locus mapped to the long arm of chromosome 7A and this result was verified in the RIL population screened with the flanking SNP markers using KASP assays. In the same region, a major QTL for field resistance was detected in a 7.7 cM interval and explained 34-54 and 29-36% of the variation in Kenya and Ethiopia, respectively. Results from tests with specific Pgt races and the csIH81 marker showed that the resistance was not due to Sr22. Thus, a new stem rust resistance gene or allele, either closely linked or allelic to Sr15, is responsible for the seedling and field resistance of PI 374670 to Ug99.

Anthracnose is a destructive disease of strawberry caused by several Colletotrichum species including C. acutatum, C. fragariae, and C. gloeosporioides. Identification of anthracnose resistant strawberry germplasm has commonly relied on inoculation of whole plants with isolates of these pathogens. In this study, whole plants and detached leaves from 81 germplasm lines were inoculated with a conidial suspension of isolates of C. acutatum, C. fragariae, and C. gloeosporioides, incubated in the dark at 30°C, 100% relative humidity, for 48 h, and assessed for disease severity based on symptoms on inoculated petioles and leaves. The correlation between the disease severity ratings of the whole plants rated 30 days after inoculation and detached leaves rated 5 days after inoculation was determined. Based on leaf symptoms and petiole lesions, the association between the whole plant leaf disease severity rating (DSR) and detached leaf DSR was positive (r = 0.70), and the association between the whole plant DSR and the detached leaf DSR was also positive (r = 0.66). Whole plant and detached leaf DSRs were used to assign each germplasm line to a resistance category, and a posthoc Tukey's test showed that the whole plant DSR means and the detached leaf DSR means for each resistance category differed significantly at p < 0.05. This research was used to develop a strawberry detached leaf assay which can reliably and quickly determine the degree of resistance of strawberry germplasm to anthracnose.

Developing oat cultivars with partial resistance to crown rust would be beneficial and cost-effective for disease management. Two recombinant inbred-line populations were generated by crossing the susceptible cultivar Provena with two partially resistant sources, CDC Boyer and breeding line 94197A1-9-2-2-2-5. A third mapping population was generated by crossing the partially resistant sources to validate the quantitative trait locus (QTL) results. The three populations were evaluated for crown rust severity in the field at Louisiana State University (LSU) in 2009 and 2010 and at the Cereal Disease Laboratory (CDL) in St. Paul, MN, in 2009, 2010, and 2011. An iSelect platform assay containing 5,744 oat single nucleotide polymorphisms was used to genotype the populations. From the 2009 CDL test, linkage analyses revealed two QTLs for partial resistance in the Provena/CDC Boyer population on chromosome 19A. One of the 19A QTLs was also detected in the 2009 LSU test. Another QTL was detected on chromosome 12D in the CDL 2009 test. In the Provena/94197A1-9-2-2-2-5 population, only one QTL was detected, on chromosome 13A, in the CDL 2011 test. The 13A QTL from the Provena/94197A1-9-2-2-2-5 population was validated in the CDC Boyer/94197A1-9-2-2-2-5 population in the CDL 2010 and 2011 tests. Comparative analysis of the significant marker sequences with the rice genome database revealed 15 candidate genes for disease resistance on chromosomes 4 and 6 of rice. These genes could be potential targets for cloning from the two resistant parents.