Genetic diversity and population structure of Uganda cassava germplasm

Abstract

The genetic diversity and population structure were assessed in 155 Uganda cassava genotypes using 5,247 single nucleotide polymorphism (SNP) markers which had an average call rate of 96%. Polymorphic information content values of the markers ranged from 0.1 to 0.5 with an average of 0.4 which was considered to be moderately high. The Principal Component analysis (PCA) showed that the first two components captured ~ 24.2% of the genetic variation. The average genetic diversity was 0.3. The analysis of Molecular Variance (AMOVA) indicated that 66.02% and 33.98% of the total genetic variation occurred within accessions and between sub-populations, respectively. Five sub-populations were identified based on ADMIXTURE structure analysis (K = 5). Neighbor-joining tree and hierarchical clustering tree revealed the presence of three different groups which were primarily based on the source of the genotypes. The results suggested that there was considerable genetic variation among the cassava genotypes which is useful in cassava improvement and conservation efforts.