Czech J. Genet. Plant Breed., X:X | DOI: 10.17221/121/2025-CJGPB

Genetic diversity assessment of hydrogen cyanide, total carotenoid content, and dry matter content in biofortified cassava using trait-linked SNP markersOriginal Paper

Bismark Anokye1,4*, Peter Amoah ORCID...2, Bardee Wrojay Potter3, Abdoul-Razak Oumarou Mahamane ORCID...5, Theophilus Adu-Gyamfi ORCID...6, Levitikos Dembure2, Nezif Abajebal Abadura2, Bunmi Olasanmi7, Elizabeth Parkes1*
1 International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
2 Departement of Crop Production and Landscape Management, University of Ebonyi State, Abakaliki, Nigeria
3 Pan African University Life and Earth Sciences Institute (including Health and Agriculture), Ibadan, Nigeria
4 Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
5 Department of Crop Sciences, North-West University (Mahikeng Campus), Mmabatho, South Africa
6 Department of Plant Science, University of Cambridge, Cambridge, UK
7 Department of Agronomy, University of Ibadan, Ibadan, Nigeria

Assessing of genetic diversity is essential for identifying useful alleles for crop improvement. This study evaluated genetic diversity among two cassava breeding populations for total carotenoid content (TCC), dry matter content (DMC), and hydrogen cyanide (HCN) concentration using trait-linked single nucleotide polymorphism (SNP) markers. A total of 360 genotypes were analysed, including 261 from the IITA breeding programme (Population 1), 23 progenitor lines, and 76 from the University of Ibadan Cassava (UIC) breeding programme (Population 2). Minor allele frequency (MAF), gene diversity (GD), observed heterozygosity (He), and polymorphic information content (PIC) were computed. Principal component analysis (PCA) and hierarchical clustering were performed to examine genetic variation and population structure. Call rates were high (96–100%). MAF ranged from 0.00 to 0.50, with mean values of 0.28, 0.28, and 0.29 for Population 1, Population 2, and progenitors, respectively. GD averaged 0.36, 0.36, and 0.35 across these groups. Observed heterozygosity was 0.42, 0.41, and 0.43, while PIC values averaged 0.29, 0.27, and 0.27 for Population 1, Population 2, and progenitors, respectively. PCA and clustering analyses grouped the genotypes into three clusters containing 257, 88, and 15 genotypes. The first two principal components explained 39.1% of the total genetic variation. The results indicate substantial genetic diversity among the studied genotypes, suggesting strong potential for allele pyramiding and highlighting the informativeness of the SNP markers used.

Keywords: biofortification; cassava; dry matter content; genetic diversity; hydrogen cyanide; SNP markers; total carotenoid

Received: December 3, 2025; Revised: February 24, 2026; Accepted: March 5, 2026; Prepublished online: March 23, 2026 

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