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NAERINGSPH-Nærings-phd

Oat breeding in the era of genomics: resistance to Fusarium (OatGen)

Alternative title: Havreforedling i genomikkens æra: Fusariumresistens (OatGen)

Awarded: NOK 1.8 mill.

The OatGen project is a collaboration between Graminor AS, NMBU (degree-giving institution) and NOFIMA. The project focuses on developing a more efficient oat breeding program through the implementation of new genetic tools, with the focus on Fusarium disease. OatGen has three Working Packages; (WP1) identify the best method to develop a training population for genomic selection Oats; (WP2) identify specific DNA regions that are associated with Fusarium resistance for implementation of DNA marker assisted selection breeding in oat breeding program; (WP3) evaluate and implement genomic selection in the Norwegian oat breeding program. The Industrial PhD student (Espen Sannes Sørensen) was approved and enrolled in the PhD study program at NMBU on 11 May 2018. PhD research and education plans have also been approved by NMBU. PhD these will be submitted to NMBU the 3rd of November 2023 and expect to defend during December 2023 as earliest. In this project, we utilized an Oat Breeding Panel (OBP) comprised of 1255 oat lines, encompassing Nordic breeding lines, market cultivars, and a core collection featuring older and exotic material. From this pool, we applied statistical models from WP1 to carefully curate a representative population consisting of 541 lines. This selected group served as the primary training population for genomic predictions and association mapping in WP2 and WP3. A paper detailing our work was published in the "Plant Breeding Journal" in autumn 2022. The population chosen from WP1 underwent genotyping in 2018, and we conducted phenotypic assessments for Fusarium resistance in the years 2020, 2021, and 2022. These Fusarium field experiments were carried out at the Vollebekk testing field (NMBU, ÅS) and the Staur testing field (Stange, Hedmark). In these experiments, we introduced Fusarium-infected oat seeds into the fields and controlled environmental conditions using irrigation systems to induce high infection pressure. NMBU provided the inoculum and maintaining the field trials in Ås. The seed samples from the trials were analysed for deoxynivalenol (DON) levels using enzyme-linked immunosorbent assay (ELISA) method and analysed for germination percentage at Graminor using “The International seed testing association” (ISTA) protocols. The analysis was completed in December 2022. Three separate breeding populations of 250 lines each have also been tested in field trials and has been genotyped by an external provider (TraitGenetics, Germany) in 2021 and 2022. A three-months stay from February to May 2022 with Dr. Jose Crossa at the International Maize and Wheat Improvement Centre” (CIMMYT) was done to increase knowledge and expertise in implementation and development of genomic prediction models. This stay was essential for the execution of WP3. The seed samples obtained from the trials underwent analysis for deoxynivalenol (DON) levels using the enzyme-linked immunosorbent assay (ELISA) method. Additionally, germination percentages were assessed at Graminor, following the protocols established by "The International Seed Testing Association" (ISTA). These comprehensive analyses were successfully completed in December 2022. In parallel, three distinct breeding populations, each comprising 250 lines, were subjected to field trials and subsequently genotyped by an external provider, TraitGenetics in Germany, during the years 2021 and 2022. To enhance our expertise and implementation of genomic prediction models, a three-month research visit took place from February to May 2022. This involved collaboration with Dr. Jose Crossa at the International Maize and Wheat Improvement Centre (CIMMYT). This invaluable experience was instrumental in facilitating the successful execution of WP3. The genotypic and phenotypic data collected were instrumental in conducting a series of statistical analyses throughout 2023 in the context of WP2 and WP3. In the spring, an association mapping study was carried out, successfully pinpointing 15 distinct regions associated with Fusarium resistance (WP2). These findings have been compiled into a paper currently under review by the "Plant Breeding Journal," with an anticipated publication date in the autumn of 2023. Furthermore, the same dataset was employed for genomic prediction with regards to DON levels and germination percentage (WP3). This analysis provided a robust assessment of breeding materials. The results of this work will be presented in a manuscript, and it is expected to be submitted for publication no earlier than December 2023.

• Insight into optimization criteria for training populations for genomic prediction. • Development of a training population utilized for genomic selection in the our national oat breeding program. • Development of new breeding tools for increased breeding efficiency in oat. • Knowledge about important Fusarium resistance genes in oat. • Experience and knowledge with genomic prediction in oat and strategies for continuous improvement. • Improved sustainability in the oat breeding program. • Genotypic information on a large number of breeding lines, enabling new genetic studies in oat. • Possibility to establish genomic prediction models for more traits in oat. • Enabling the development of new varieties to increase revenue for the oat industry from farmer to miller.

Oat has a long history as a major cereal crop, and is still very important to the Nordic countries as the third most produced cereal after barley and wheat. The recent outbreak of Fusarium Head Blight in the Nordic countries has caused a problem in oat production causing major economic losses. Of the Fusarium species, F. graminearum poses the biggest problem in Norway particularly in warm and wet weather conditions. Fungicides have had limited effect on the disease and they are costly and have a major negative effect on the environment. Therefore, resistance breeding is the most effective way to avoid negative damage. Graminor has the national responsibility to develop adaptable oat varieties with improved resistant to Fusarium disease. This will increase the company’s market competitiveness and market share of Graminor’s oat varieties in Norway and Nordic region. Graminor has invested heavily the last years in several research projects to effectively develop Fusarium-resistant oat varieties. The completed (2014-2017) innovation project ‘RESIFUS’ (GRAMINOR – IPN pr. # 233908) has made major groundwork in methodology and resistance research, so that resistance breeding can continue. OatGen will capitalize on the finding of RESIFU project to implement new genomics-based tools (i.e. Genomic Selection) in our national oat breeding. At OatGen project, and in collaboration with NMBU and NOFIMA, we will develop and study the genetic variation for fusarium resistance trait in the oat breeding panel to estimate the genomic breeding value (GEBV) for the application of genomic selection in the oat breeding program. Early and accurate estimation of GEBV can save time, and increase the genetic gain per year. The results will lead to a more efficient oat breeding that corresponds to the market’s need of new varieties with better resistance to fusarium disease, and increase competitiveness of Graminor as a leading Nordic plant breeding company.

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NAERINGSPH-Nærings-phd