Browsing by Author "Kassim, Yussif Baba"

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    High-Throughput Plant Phenotyping (HTPP) in Resource-Constrained Research Programs: A Working Example in Ghana
    Kassim, Yussif Baba; Oteng-Frimpong, Richard; Puozaa, Doris Kanvenaa; Sie, Emmanuel Kofi; Abdul Rasheed, Masawudu; Abdul Rashid, Issah; Danquah, Agyemang; Akogo, Darlington A.; Rhoads, James; Hoisington, David; Burow, Mark D.; Balota, Maria (MDPI, 2022-11-04)
    In this paper, we present a procedure for implementing field-based high-throughput plant phenotyping (HTPP) that can be used in resource-constrained research programs. The procedure relies on opensource tools with the only expensive item being one-off purchase of a drone. It includes acquiring images of the field of interest, stitching the images to get the entire field in one image, calculating and extracting the vegetation indices of the individual plots, and analyzing the extracted indices according to the experimental design. Two populations of groundnut genotypes with different maturities were evaluated for their reaction to early and late leaf spot (ELS, LLS) diseases under field conditions in 2020 and 2021. Each population was made up of 12 genotypes in 2020 and 18 genotypes in 2021. Evaluation of the genotypes was done in four locations in each year. We observed a strong correlation between the vegetation indices and the area under the disease progress curve (AUDPC) for ELS and LLS. However, the strength and direction of the correlation depended upon the time of disease onset, level of tolerance among the genotypes and the physiological traits the vegetation indices were associated with. In 2020, when the disease was observed to have set in late in medium duration population, at the beginning of the seed stage (R5), normalized green-red difference index (NGRDI) and variable atmospheric resistance index (VARI) derived at the beginning pod stage (R3) had a positive relationship with the AUDPC for ELS, and LLS. On the other hand, NGRDI and VARI derived from images taken at R5, and physiological maturity (R7) had negative relationships with AUDPC for ELS, and LLS. In 2021, when the disease was observed to have set in early (at R3) also in medium duration population, a negative relationship was observed between NGRDI and VARI and AUDPC for ELS and LLS, respectively. We found consistently negative relationships of NGRDI and VARI with AUDPC for ELS and LLS, respectively, within the short duration population in both years. Canopy cover (CaC), green area (GA), and greener area (GGA) only showed negative relationships with AUDPC for ELS and LLS when the disease caused yellowing and defoliation. The rankings of some genotypes changed for NGRDI, VARI, CaC, GA, GGA, and crop senescence index (CSI) when lesions caused by the infections of ELS and LLS became severe, although that did not affect groupings of genotypes when analyzed with principal component analysis. Notwithstanding, genotypes that consistently performed well across various reproductive stages with respect to the vegetation indices constituted the top performers when ELS, LLS, haulm, and pod yields were jointly considered.
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    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
    Oteng-Frimpong, Richard; Karikari, Benjamin; Sie, Emmanuel Kofi; Kassim, Yussif Baba; Puozaa, Doris Kanvenaa; Rasheed, Masawudu Abdul; Fonceka, Daniel; Okello, David Kallule; Balota, Maria; Burow, Mark; Ozias-Akins, Peggy (Frontiers, 2023-01-05)
    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.
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    RGB-image method enables indirect selection for leaf spot resistance and yield estimation in a groundnut breeding program in Western Africa
    Sie, Emmanuel Kofi; Oteng-Frimpong, Richard; Kassim, Yussif Baba; Puozaa, Doris Kanvenaa; Adjebeng-Danquah, Joseph; Masawudu, Abdul Rasheed; Ofori, Kwadwo; Danquah, Agyemang; Cazenave, Alexandre Brice; Hoisington, David; Rhoads, James; Balota, Maria (Frontiers, 2022-08-04)
    Early Leaf Spot (ELS) caused by the fungus Passalora arachidicola and Late Leaf Spot (LLS) also caused by the fungus Nothopassalora personata, are the two major groundnut (Arachis hypogaea L.) destructive diseases in Ghana. Accurate phenotyping and genotyping to develop groundnut genotypes resistant to Leaf Spot Diseases (LSD) and to increase groundnut production is critically important in Western Africa. Two experiments were conducted at the Council for Scientific and Industrial Research-Savanna Agricultural Research Institute located in Nyankpala, Ghana to explore the effectiveness of using RGB-image method as a high-throughput phenotyping tool to assess groundnut LSD and to estimate yield components. Replicated plots arranged in a rectangular alpha lattice design were conducted during the 2020 growing season using a set of 60 genotypes as the training population and 192 genotypes for validation. Indirect selection models were developed using Red-Green-Blue (RGB) color space indices. Data was collected on conventional LSD ratings, RGB imaging, pod weight per plant and number of pods per plant. Data was analyzed using a mixed linear model with R statistical software version 4.0.2. The results showed differences among the genotypes for the traits evaluated. The RGB-image method traits exhibited comparable or better broad sense heritability to the conventionally measured traits. Significant correlation existed between the RGB-image method traits and the conventionally measured traits. Genotypes 73-33, Gha-GAF 1723, Zam-ICGV-SM 07599, and Oug-ICGV 90099 were among the most resistant genotypes to ELS and LLS, and they represent suitable sources of resistance to LSD for the groundnut breeding programs in Western Africa.