Browsing by Subject "Lupinus"

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    Anthracnose in white lupin : genetic diversity, virulence and host resistance
    (2022) Alkemade, Joris A.; Vögele, Ralf
    White lupin (Lupinus albus L.) is a grain legume that is known for its high protein content, nutritional quality, efficient nitrogen fixation and unique ability to form specialized cluster roots that support phosphorus uptake. Despite a severe production decline at the end of the past century, white lupin has seen a recent revival to sustain the demand for plant-based protein and reduce Europe’s dependency on imported soybean. A major problem in (white) lupin cultivation is anthracnose disease, caused by the globally dispersed, seed- and air-borne fungal pathogen Colletotrichum lupini. This PhD thesis aims to provide insights on how to sustainably control anthracnose disease in white lupin in order to support its re-introduction into European cultivation systems. It describes (i) the genetic diversity, phylogeography and virulence of C. lupini, (ii) the development of a high-throughput phenotyping protocol to reliably screen white lupin germplasm, (iii) a genome-wide association study identifying resistance candidate genes and (iv) the exploration of effective seed treatments to reduce the primary pathogen inoculum. Multi-locus phylogeny and morphological characterization of 39 C. lupini isolates showed that diversity is greater than previously reported, distinguishing a total of six genetic groups and ten distinct morphotypes. Highest diversity was found across the South American Andes, indicating it to be the center of origin of C. lupini. Results reveal that the current pandemic is caused by strains belonging to genetic group II, which are spread globally, and are genetically and morphologically uniform. Group II isolates were shown to be highly aggressive on tested white and Andean lupin accessions. Isolates belonging to the other five genetic groups were mostly found locally and showed distinct virulence patterns on both white and Andean lupin accessions. Despite its uniformity, it was shown that two highly virulent group II isolates from Chile could overcome resistance of elite white lupin breeding material, stressing the need to implement phytosanitary protocols for international seed transports. A reliable high-throughput phenotyping tool was developed to identify anthracnose resistance in white lupin germplasm and study pathogen-host interactions. Phenotyping under controlled conditions, performing stem wound inoculation on seedlings, showed to be applicable for high-throughput and its disease scores strongly correlated with two-year Swiss field disease assessments (r = 0.95) and yield (r = -0.64). Phenotyping a diverse set of 40 white lupin accessions revealed eight accessions with improved resistance to anthracnose, which can be incorporated into white lupin breeding programs. A genome-wide association study (GWAS) was done to dissect the genetic architecture for anthracnose resistance in white lupin. White lupin genotypes, collected from the center of domestication and traditional cultivation regions, were screened for anthracnose resistance and characterized through genotyping-by-sequencing (GBS). GWAS revealed two significant SNPs associated with anthracnose resistance on gene Lalb_Chr05_g0216161, encoding a RING zinc-finger E3 ubiquitin ligase potentially involved in plant immunity. Further validation experiments are now required to confirm involvement in plant resistance. Population analysis showed a remarkably fast linkage disequilibrium (LD) decay, weak population structure and grouping of commercial varieties with landraces, corresponding to the slow domestication history and scarce breeding efforts in white lupin. A total of eleven different seed treatments was tested in field trials in Switzerland between 2018 and 2021 to identify treatments that reduce C. lupini infection levels in white lupin. Treatments consisted of hot water, steam, electron, long term storage, vinegar, plant extracts and biological control agents (BCAs). The BCAs were tested under controlled conditions for potential antagonistic activity against C. lupini during white lupin infection prior to field trials. Results showed that long term storage and vinegar treatments can successfully reduce disease incidence and increase yield to levels similar to those observed for certified seeds. In order to sustainably and effectively control anthracnose disease in white lupin, an integrative approach, including modern breeding efforts, disease prevention strategies and mixed cropping systems, is recommended. Further research is required to increase our understanding on white lupin-C. lupini interaction and to identify genetic regions involved in resistance or virulence, respectively, which could greatly support white lupin breeding. This thesis provides the basis to further explore C. lupini population dynamics, virulence and host-speciation, white lupin resistance mechanisms and sustainable ways to control anthracnose disease in order to further facilitate successful white lupin cultivation.