Genome‑wide association studies reveal novel loci for resistance to groundnut rosette disease in the African core groundnut collection

Groundnut is cultivated in several African countries where it is a major source of food, feed and income. One of
the major constraints to groundnut production in Africa is groundnut rosette disease (GRD), which is caused by a complex
of three agents: groundnut rosette assistor luteovirus, groundnut rosette umbravirus and its satellite RNA. Despite several
years of breeding for GRD resistance, the genetics of the disease is not fully understood. The objective of the current study
was to use the African core collection to establish the level of genetic variation in their response to GRD, and to map genomic
regions responsible for the observed resistance. The African groundnut core genotypes were screened across two GRD hotspot
locations in Uganda (Nakabango and Serere) for 3 seasons. The Area Under Disease Progress Curve combined with 7523
high quality SNPs were analyzed to establish marker-trait associations (MTAs). Genome-Wide Association Studies based
on Enriched Compressed Mixed Linear Model detected 32 MTAs at Nakabango: 21 on chromosome A04, 10 on B04 and 1
on B08. Two of the significant markers were localised on the exons of a putative TIR-NBS-LRR disease resistance gene on
chromosome A04. Our results suggest the likely involvement of major genes in the resistance to GRD but will need to be
further validated with more comprehensive phenotypic and genotypic datasets. The markers identified in the current study
will be developed into routine assays and validated for future genomics-assisted selection for GRD resistance in groundnut.