Browsing by Author "Daniel Fonceka"

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Genome‐wide association studies reveal novel loci for resistance to groundnut rosette disease in the African core groundnut collection
(Theoretical and Applied Genetics, 2023-03-10) Esther Achola; Peter Wasswa; Daniel Fonceka; Josh Paul Clevenger; Prasad Bajaj; Peggy Ozias‐Akins; Jean‐François Rami; Carl Michael Deom; David A. Hoisington; Richard Edema; Damaris Achieng Odeny; David Kalule Okello
Key message We identified markers associated with GRD resistance after screening an Africa-wide core collection across three seasons in Uganda Abstract 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.
Multi-locus genome-wide association studies reveal genomic regions and putative candidate genes associated with leaf spot diseases in African groundnut (Arachis hypogaea L.) germplasm
(2023-01-05) Richard Oteng-Frimpong; Benjamin Karikari; Emmanuel Kofi Sie; Yussif Baba Kassim; Doris Kanvenaa Puozaa; Masawudu Abdul Rasheed; Daniel Fonceka; David Kallule Okello; Maria Balota; Mark Burow; Peggy Ozias-Akins
Early leaf spot (ELS) and late leaf spot (LLS) diseases are the two most destructive groundnut diseases in Ghana resulting in ≤ 70% yield losses which is controlled largely by chemical method. To develop leaf spot resistant varieties, the present study was undertaken to identify single nucleotide polymorphism (SNP) markers and putative candidate genes underlying both ELS and LLS. In this study, six multi-locus models of genome-wide association study were conducted with the best linear unbiased predictor obtained from 294 African groundnut germplasm screened for ELS and LLS as well as image-based indices of leaf spot diseases severity in 2020 and 2021 and 8,772 high-quality SNPs from a 48 K SNP array Axiom platform. Ninety-seven SNPs associated with ELS, LLS and five image-based indices across the chromosomes in the 2 two sub-genomes. From these, twenty-nine unique SNPs were detected by at least two models for one or more traits across 16 chromosomes with explained phenotypic variation ranging from 0.01 - 62.76%, with exception of chromosome (Chr) 08 (Chr08), Chr10, Chr11, and Chr19. Seventeen potential candidate genes were predicted at ± 300 kbp of the stable/prominent SNP positions (12 and 5, down- and upstream, respectively). The results from this study provide a basis for understanding the genetic architecture of ELS and LLS diseases in African groundnut germplasm, and the associated SNPs and predicted candidate genes would be valuable for breeding leaf spot diseases resistant varieties upon further validation.
Quantitative Trait Analysis Shows the Potential for Alleles from the Wild Species Arachis batizocoi and A. duranensis to Improve Groundnut Disease Resistance and Yield in East Africa
(Agronomy, 2022-09-16) Danielle A. Essandoh; Thomas Odong; David K. Okello; Daniel Fonceka; Joël Nguepjop; Aissatou Sambou; Carolina Ballén-Taborda; Carolina Chavarro; David J. Bertioli; Soraya C. M. Leal-Bertioli
Diseases are the most important factors reducing groundnut yields worldwide. In East Africa, late leaf spot (LLS) and groundnut rosette disease (GRD) are the most destructive diseases of groundnut. Limited resistance is available in pure pedigree cultivated groundnut lines and novel sources of resistance are required to produce resistant new varieties. In this work, 376 interspecific lines from 3 different populations derived from crosses with the wild species A. duranensis, A. ipaënsis, A. batizocoi and A. valida were phenotyped for 2 seasons and across 2 locations, Serere and Nakabango, in Uganda. Several genotypes showed a higher yield, a larger seed, an earlier flowering, and similar resistance to the local cultivar checks. Genotypic data was used to construct a linkage map for the AB-QTL population involving the cross between Fleur11 and [A. batizocoi x A. duranensis]4x. This linkage map, together with the phenotypic data was used to identify quantitative trait loci controlling disease resistance. These lines will be useful in combining good agronomic traits and stacking disease resistance to improve the groundnut crop in sub-Saharan Africa.