Breeding oat for resistance to the crown rust pathogen Puccinia coronata f. sp. avenae: achievements and prospects

Crown rust, caused by Puccinia coronata f. sp. avenae (Pca), is a significant impediment to global oat production. Some 98 alleles at 92 loci conferring resistance to Pca in Avena have been designated; however, allelic relationships and chromosomal locations of many of these are unknown. Long-term monitoring of Pca in Australia, North America and elsewhere has shown that it is highly variable even in the absence of sexual recombination, likely due to large pathogen populations that cycle between wild oat communities and oat crops. Efforts to develop cultivars with genetic resistance to Pca began in the 1950s. Based almost solely on all all-stage resistance, this has had temporary benefits but very limited success. The inability to eradicate wild oats, and their common occurrence in many oat growing regions, means that future strategies to control Pca must be based on the assumption of a large and variable prevailing pathogen population with high evolutionary potential, even if cultivars with durable resistance are deployed and grown widely. The presence of minor gene, additive APR to Pca in hexaploid oat germplasm opens the possibility of pyramiding several such genes to give high levels of resistance. The recent availability of reference genomes for diploid and hexaploid oat will undoubtedly accelerate efforts to discover, characterise and develop high throughput diagnostic markers to introgress and pyramid resistance to Pca in high yielding adapted oat germplasm.Financial support from Judith and David Coffey and family, the Grains Research and Development Corporation (GRDC: DAS00133, UOS1707-003RTX, UOS2104-001RTX) and the University of Sydney is gratefully acknowledged. Some of the unpublished research reported on was undertaken as part of a long running program on national cereal rust surveillance, conducted at the University of Sydney since 1921. EP is funded by Spanish Ministry of Science and Innovation [PID2019-104518RB-100], (AEI/FEDER, UE) and regional government through the AGR-253 group, the European Regional and Social Development Funds.Peer reviewe

A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

Hexaploid oat ( L., 2 = 6 = 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 ( 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

Population Genomics Related to Adaptation in Elite Oat Germplasm

Six hundred thirty five oat ( L.) lines and 4561 single-nucleotide polymorphism (SNP) loci were used to evaluate population structure, linkage disequilibrium (LD), and genotype–phenotype 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 = 1 to 20 model-based analyses suggested a structured population. However, the PC and = 2 model-based analyses supported clustering of lines on spring oat vs. southern United States origin, accounting for 16% of genetic variation ( < 0.0001). Single-locus -statistic () 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 = 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

SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species

A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources

Peduncle breaking resistance: a potential selection criterion to improve lodging tolerance in Oat

Breeding for tolerance to lodging is an objective, but also a challenge, in oat (Avena sativa L.) breeding programs. A widely adopted method to assess breeding lines for tolerance to lodging is based on visual scoring of plant standability (1 = standing upright; 9 = completely lodged). The lack of sufficient lodging pressure due to weather or growing conditions often renders the visual scoring method ineffective. We present an alternative approach that allows selection for tolerance to stem lodging by screening for peduncle strength in the absence of lodging pressure. This approach also provides objective selection of lodging tolerance using a quantitatively measurable plant trait rather than subjective scoring of the lodged plants. Stem structural and mechanical properties of six oat cultivars with varying levels of lodging tolerance were tested at field experiments over 3 site-years under three nitrogen rates. Results suggested peduncle breaking resistance (PBR), measured below the panicle, as a potential selection criterion for stem strength and therefore lodging tolerance. Significant genetic variation among oat cultivars (p  0.73, p ≤ 0.05). This suggests that PBR provides a good estimation of the whole culm strength. Phenotyping of PBR can be easily integrated into breeding programs because of the ease of sampling and rapid measurement.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

AAC Jatharia Canada Western Red Spring Wheat

AAC Jatharia (BW483) is a hollow-stemmed, high protein, high yielding spring wheat (Triticum aestivum L.) for the longer season wheat growing areas of the Canadian Prairies. AAC Jatharia was the highest yielding line in the Central Bread Wheat Cooperative (CBWC) Registration Tests performed in eastern prairies in 2011, 2012, and 2013. Over two years of testing (2011-2012), AAC Jatharia had grain yield 2.5% higher than Unity, 11.6% higher than 5603HR, 7.8% higher than McKenzie, and 19.2% higher than CDC Teal across all locations. In 2013, AAC Jatharia yielded 6.3% higher than Unity across Manitoba and Saskatchewan locations. AAC Jatharia was resistant to leaf rust (Puccinia triticina Eriks.), and had intermediate resistance to stem rust (Puccinia graminis f. sp. tritici), stripe rust (Puccinia striiformis Westend), the leaf spot complex, and Fusarium head blight (FHB) (Fusarium graminearum) infection, with lower FHB index and deoxynivalenol (DON) content compared to Unity. AAC Jatharia was resistant to infestation of the orange wheat blossom midge (Sitodiplosis mosellana GĂŠhin) evaluated over two years (2012 and 2013). It had higher kernel weight and test weight compared to all check cultivars, whereas maturity was within the range of the check cultivars. AAC Jatharia is registered under the Canada Western Red Spring Wheat class for its premium quality attributes.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

AAC Warman Canada Western Red Spring wheat

AAC Warman is a high yielding Canada Western Red Spring (CWRS) wheat adapted to production in Western Canada. AAC Warman was 3% higher yielding than Unity, the highest yielding check in the Central Bread Wheat Cooperative registration trials (2014-2016). Within the same test, AAC Warman was 11% higher yielding than Carberry, a popular CWRS wheat variety across the Canadian prairies. AAC Warman matured 3 days earlier than Carberry and a day later than Unity, the earliest maturing check. AAC Warman was shorter than Unity and had better stem strength compared to Unity, however, the lodging score for AAC Warman was higher than the mean of the checks. Over three years of testing (2014-2016), the test weight and thousand kernel weight of AAC Warman was similar to Carberry. The grain protein content of AAC Warman was 0.3% lower than both Unity and Carberry. AAC Warman was rated moderately resistant to Fusarium head blight (Fusarium graminearum Schwabe), resistant to leaf rust (Puccinia triticina Erikss.) and stem rust (Puccinia graminis f. sp. tritici), but was moderately susceptible to stripe rust (Puccinia striiformis Westend) and common bunt [Tilletia caries (DC) Tul. C. Tul.]. It was rated moderately resistant to loose smut [Ustilago tritici (Pers.) Rostr.] and intermediate resistant to the leaf spot complex. AAC Warman was resistant to orange wheat blossom midge (Sitodiplosis mosellana GĂŠhin). Based on the milling and baking performance over three years (2014-2016) evaluated by the Grain Research Laboratory, Canadian Grain Commission, AAC Warman was registered under the CWRS class.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

AAC LeRoy Canada Western Red Spring wheat

AAC LeRoy (BW1049) is a hollow stemmed, awned, high-yielding Canada Western Red Spring (CWRS) wheat suited to the growing conditions in western Canada. AAC LeRoy was 10% higher yielding than Unity, the highest yielding check in the Central Bread Wheat Cooperative registration trials (2015–2017). Within the same test, AAC LeRoy was 13% higher yielding than Carberry, a popular CWRS wheat variety across the Canadian Prairies. AAC LeRoy matured 2 d earlier than Carberry and 1 d later than Unity, the earliest maturing check suited for eastern prairie growing conditions. AAC LeRoy was 6 cm shorter with better stem strength than Unity. The lodging score for AAC LeRoy was lower than the mean of the checks. The test weight of AAC LeRoy was similar to the mean of the checks. Over the 3 yr of testing (2015–2017), the 1000-kernel weight of AAC LeRoy was higher than all of the checks, with a grain protein content 0.6% units lower than Carberry. AAC LeRoy was rated as moderately resistant to Fusarium head blight (Fusarium graminearum Schwabe), leaf rust (Puccinia triticina Erikss.), stripe rust (Puccinia striiformis Westend.), and stem rust (Puccinia graminis Pers. f. sp. tritici Erikss. & E. Henn), including the Ug99 family of stem rusts. It also had a resistant reaction to loose smut [Ustilago tritici (Pers.) Rostr.] and an intermediately resistant reaction to common bunt [Tilletia caries (DC.) Tul. & C. Tul.]. AAC LeRoy was resistant to orange wheat blossom midge (Sitodiplosis mosellana Géhin). AAC LeRoy was registered under the CWRS market class.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author