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

Abstract

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 (H_e), 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.