Anik Dutta


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Dutta

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Anik

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0000-0003-1196-6305

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Publications 1 - 2 of 2
  • Genome-wide association study for septoria tritici blotch resistance reveals the occurrence and distribution of Stb6 in a historic Swiss landrace collection
    Item type: Journal Article
    Dutta, Anik; Croll, Daniel; McDonald, Bruce; et al. (2021)
    Euphytica
    Septoria tritici blotch (STB), caused by the fungus Zymoseptoria tritici, is a major constraint in global wheat production. The lack of genetic diversity in modern elite wheat cultivars largely hinders the improvement of STB resistance. Wheat landraces are reservoirs of untapped genetic diversity, which can be exploited to find novel STB resistance genes or alleles. Here, we characterized 188 Swiss wheat landraces for resistance to STB using four Swiss Z. tritici isolates. We used a genome-wide association study (GWAS) to identify genetic variants associated with the amount of lesion and pycnidia production by the fungus. The majority of the landraces were highly resistant for both traits to the isolate 1E4, indicating a gene-for-gene relationship, while higher phenotypic variability was observed against other isolates. GWAS detected a significant SNP on chromosome 3A that was associated with both traits in the isolate 1E4. The resistance response against 1E4 was likely controlled by the Stb6 gene. Sanger sequencing revealed that the majority of these ~ 100-year-old landraces carry the Stb6 resistance allele. This indicates the importance of this gene in Switzerland during the early 1900s for disease control in the field. Our study demonstrates the importance of characterizing historic landrace collections for STB resistance to provide valuable information on resistance variability and contributing alleles. This will help breeders in the future to make decisions on integrating such germplasms in STB resistance breeding.
  • Principles of Niche Adaptation in a Major Fungal Pathogen of Wheat
    Item type: Doctoral Thesis
    Dutta, Anik (2021)
    The enormous genetic diversity in plant pathogens facilitates rapid evolution and adaptation to diverse hosts and climatic conditions. Pathogen life-history trade-offs are suggested to maintain genetic diversity and create evolutionary constraints that prevent selection from driving multiple life-history traits towards maximization. Less is known about trade-offs in agroecosystems and how they can be engineered to impede pathogen evolution and delay the breakdown of host resistance. Additionally, the diversity of resistance genes in host genetic materials from gene banks is largely unknown for various diseases. In this PhD thesis, we screened a century-old historic collection of wheat landraces (n=188) from the Swiss Gene Bank for resistance to Septoria tritici blotch (STB) disease caused by the fungus Zymoseptoria tritici. A known major gene (Stb6) on wheat chromosome 3A was found to be associated with resistance to pathogen damage and reproduction in the Z. tritici isolate 1E4. Most of the landraces carrying a single resistant allele suggested the early selection of wheat plants showing field resistance to STB and germplasm exchanges for Swiss wheat breeding in the early 1990s. Next, we investigated how the relationship between virulence and reproduction, and the degree of host specialization influence pathogen evolution at the phenotypic level. We obtained largescale phenotypic data from a greenhouse assay on pathogenicity traits from a combination of 12 genetically distinct wheat hosts and 145 Z. tritici isolates. The isolates were sampled from Australia, Israel, Switzerland, and the USA. A positive correlation between virulence and reproduction indicated the possibility of increased transmission that may accelerate pathogen evolution given monocropping based agriculture. However, we found that isolates with high host specificity were on average less virulent, whereas isolates with a broader host range for virulence were generally less fecund. These costs might decelerate the evolution of super pathogen strains and maintain genetic diversity in life-history traits. Pathogens must encounter climatic variation, survive outside the host during off-seasons and resist application of agrochemicals. Yet, how pathogens adapt to abiotic environments and maintain pathogenicity on different hosts remains poorly understood. The third chapter established a correlational landscape between pathogen traits measured on and off the host. The strong positive genetic correlations driven by numerous pleiotropic loci between virulence and reproduction might indicate convergent evolution that facilitates rapid host adaptation. Importantly, genetic tradeoffs between host and survival traits may play an important role in determining the pathogen’s evolutionary potential. Isolates with high fungicide resistance showed a genetic constraint in their ability to cause damage to certain hosts. By leveraging information on genetic trade-offs, innovative disease management strategies can be designed to exploit evolutionary weaknesses of pathogens. The extensive heritable variation in life-history traits under different environments in Z. tritici is likely to be governed by numerous genes. The fourth chapter aimed at systematically uncovering these genes by performing large-scale genome-wide association mapping (GWAS) based on genetic datasets created from 19 Z. tritici genomes and a K-mer approach. The comprehensive GWAS analysis discovered numerous genes that might play an essential role in niche adaptation in Z. tritici. We showed that increasing the number of reference genomes resulted in an increased number of genes detected by GWAS. Moreover, the K-mer GWAS proved to be a powerful approach in discovering several novel and previously identified genes (e.g., Avr3D1 or CYP51). We highlighted the need to move beyond the realm of single reference to more innovative GWAS approaches to unravel the gene repertoire underpinning trait variation. Overall, this PhD thesis demonstrates the importance of investigating life-history trade-offs at the population and genetic level to better understand pathogen evolutionary trajectories and implement novel GWAS methods to pinpoint genetic determinants driving microbial niche adaptation.
Publications 1 - 2 of 2