An effector- and genomics-assisted pipeline for necrotrophic pathogen resistance breeding in wheat

EfectaWheat is an ERA-CAPS project with partners from Great Britain, Germany, Denmark and Norway. The aim is to utilize genomics and new insight into the host-pathogen interactions of necrotrophic plant pathogens to enable a more effective resistance breeding against leaf blotch diseases in winter wheat. The pathogen populations of Septoria nodorum blotch (Parastagonospora nodorum), Septoria tritici blotch (Zymoseptoria tritici) and tan spot (Pyrenophora tritici-repentis) are being compared by collection and analysis of leaf samples from wheat fields across the four countries. Two MAGIC (Multi-parent Advanced Generation Inter-Cross) populations have been tested for resistance against these diseases in field trials in the four countries, and QTL analyses have beenperformed based on genotyping with SNP markers. The Norwegian part of the project has had a special focus on Septoria nodorum blotch, which is the most important leaf blotch disease on wheat in Norway. The Norwegian part of the project has given the following results: Leaf samples were collected from wheat fields across the main wheat growing areas of Norway during the 2015, 2016 and 2017 seasons and sent to Denmark for quantification of leaf blotch diseases. During the first year, samples were collected from 20 winter wheat fields, while for the latter two seasons samples were collected from both spring and winter wheat fields (20 spring wheat and 20 winter wheat samples per year) in order to enable comparisons of the two crops. The analyses of these samples confirmed that Parastastagonospora nodorum is the most common leaf blotch pathogen in Norway, in both spring and winter wheat. Some of the winter wheat samples were dominated by Zymoseptoria tritici or Pyrenophora tritici-repentis while in most cases only low infection levels of these pathogens were found in the spring wheat samples. The collected leaf samples were also used to establish a collection of single spore isolates of P. nodorum. A total of 165 Norwegian isolates were collected and compared with 9 international isolates. These were analysed with PCR markers for mating type and known effector genes as well as 20 SSR markers. Results show that all the three effector genes ToxA, Tox1 and Tox3 are common in the Norwegian pathogen population, and therefore need to be taken into account in the breeding of cultivars with improved resistance. Moreover, the analyses demonstrated that the Norwegian pathogen population has a high genetic diversity based on frequent sexual recombination combined with fast dispersal of new genotypes across the country aided by seed-transmission. Two MAGIC populations and one Norwegian association mapping panel of winter wheat lines were tested for Septoria nodorum blotch (SNB) resistance in field trials at Ås in 2016, 2017 and 2018 field seasons. QTL analyses have been done for all three mapping populations in all tested years. The results indicate a complex quantitative genetic control of SNB resistance with several QTL on different chromosomes involved. One common QTL on chromosome 2A was identified from QTL analysis of the UK MAGIC population in different years across two countries. This stable QTL might be caused by a novel host-pathogen interaction mechanism. Even though the genetic resistance mechanism to leaf blotch and glume blotch are different, we have found some evidence for overlapping mechanisms in field resistance. In addition, we have found some QTL after greenhouse infiltration and inoculation experiments that coincide with field resistance QTL. QTL mapping in the German MAGIC population show the same main picture with many QTL involved in field resistance. Here, we also found significant effects of the same 2A QTL as in the UK population. Further studies are being planned to follow-up this and other promising QTL from the two MAGIC populations. The association mapping has verified several of the QTL from the two MAGIC populations as well as identified some new ones. QTL that show consistent effects across years and different populations will be interesting to use in resistance breeding. An important applied output from the EfectaWheat consortium is the development of KASP markers that plant breeders can use as selection tools for developing new wheat cultivars with improved leaf blotch resistance. These will be published along with the association mapping study once the results have been validated. The project has financed a PhD student who is expected to complete her doctoral studies during the autumn of 2019.

Prosjektet har hatt følgende virkninger: - Styrket nasjonal kompetanse på bladflekksykdommer i hvete - Utdanning av en doktorgrad i plantepatologi og planteforedling - Molekylær innsikt i plante-patogen samspillet for hveteaksprikk - Kunnskap om patogenpopulasjonene og tilgjengelig resistens i aktuelt sortsmateriale - Nye verktøy til å foredle hvetesorter med bedre resistens mot hveteaksprikk og andre bladflekksykdommer. - Styrket internasjonalt samarbeid og koordinering av et nytt SusCrop ERA-NET prosjekt Forventet langsiktige effekt: - En mer bærekraftig europeisk hveteproduksjon basert på sorter med bedre resistens. Prosjektet har her bidratt med nødvendig kunnskap og utviklet verktøy til mer effektiv resistensforedling som hveteforedlere er interesserte i å ta i bruk.

EfectaWheat is a partnership of five complementary institutes from the UK (NIAB), Germany (LFL), Denmark (AARHUS), Norway (NMBU) and Australia (CCDM, self-funded), as well as a subcontract to the UK governmental agency, FERA. The partners form a multidisciplinary team focusing on the economically important wheat leaf spot group (LSG) of necrotrophic pathogens: Parastagonospora nodorum (Pn, cause of Septoria nodorum blotch; SNB), Zymoseptoria tritici (Zt, Septoria tritici blotch; STB) and Pyrenophora tritici-repentis (Ptr, tan spot; TS). High-resolution wheat genetic mapping populations (available at NIAB and LFL) and high-density genotyping will be combined with effector-based tools, pathogen re-sequencing approaches (CCDM), and expertise in pathogen diagnostics, virulence assessment (LFL, AARHUS, FERA), and field pathotesting across all partner countries (NMBU, NIAB, AARHUS, LFL). These combine to deliver a genomics- and effector-based pipeline for the genetic dissection of LSG host-pathogen interactions in Europe. Specifically, this project will: (1) Establish relative impact of LSG pathogens in target EU countries using molecular approaches. (2) Identify new TS and SNB effectors. (3) Determine the effector profile of Pn and Ptr isolates and the sensitivity of cultivars to effectors. (4) Screen TS, SNB and STB effectors against high-resolution wheat germplasm resources. (5) Resolve multiple LSG effector and field resistance QTLs at high-resolution. (6) Establish prevention and management strategies against multiple LSG pathogens. (7) Deliver tools (effectors and markers) for LSG resistance breeding to EU breeders and researchers. The unique positions of partners at the interface between crop research and translation ensure effective dissemination of project outputs to European agri-industry.