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Sammanfattning

In sub‐Saharan Africa, cassava (Manihot esculenta Crantz) is a key food security crop, providing calories to over 800 million people. It grows well in poor soils and tolerates drought. However, its production is threatened by cassava mosaic disease (CMD), caused by African cassava mosaic virus (ACMV), which can devastate yields. While genetic loci associated with CMD resistance have been identified, the influence of epigenetic regulation on disease resilience remains largely unexplored. This thesis investigates the epigenetic basis for the variation in CMD responses between two farmer’s preferred African cassava cultivars: TMEB693 (tolerant) and TMEB117 (susceptible). In the study, we generated a reference genome of TMEB117 for the epigenetics study. This genome enabled a comparative genomic analysis that revealed a previously unknown ~9.7 Mbp repeat‐rich insertion on chromosome 12. This region is enriched with MUDR‐Mutator transposable elements and chromatin‐regulating genes (HDA14, SRT2), whose presence varied across 16 cassava landraces. Although not directly linked to CMD resistance, this hypervariable region may influence epigenetic plasticity and crop adaptation. Genome‐wide methylation analysis showed that TMEB117 undergoes overall hypomethylation upon infection, resembling the methylation profile of the tolerant genotype (TMEB693). These findings suggest that TMEB117 undergoes virus‐ induced epigenetic reprogramming, but the resulting reduced methylation level may be too low to confer effective tolerance to the virus. In contrast, the stable methylation profile of TMEB693 may reflect a defence state that is constitutively maintained. This study highlights the role of DNA methylation in CMD resistance and establishes a genomic and epigenetic framework for identifying candidate genes and regulatory factors linked to disease resilience. Such knowledge provides a foundation for integrating molecular markers into cassava breeding programs, enabling the development of cultivars with durable CMD resilience and contributing to strengthened food security across sub‐Saharan Africa.

Nyckelord

Cassava; genome assembly; hypervariable; cassava mosaic disease; DNA methylation; hypomethylation; resistant; tolerant

Publicerad i

Acta Universitatis Agriculturae Sueciae
2025, nummer: 2025:61
Utgivare: Swedish University of Agricultural Sciences

SLU författare

UKÄ forskningsämne

Botanik
Genetik och förädling inom lantbruksvetenskap

Publikationens identifierare

  • DOI: https://doi.org/10.54612/a.1g43ig22a9
  • ISBN: 978-91-8124-045-0
  • eISBN: 978-91-8124-091-7

Permanent länk till denna sida (URI)

https://res.slu.se/id/publ/142462