DArTseq SNP-based genetic diversity and population structure of spider plant (Cleome gynandra L.) accession populations from Zimbabwe

Understanding the genetic diversity and structure of the spider plant (Cleome gynandra L.) is essential for its potential improvement and conservation, although limited research has been reported in this area. In the present study, we characterized a set of 43 spider plant accessions collected from three agroecological zones (AEZ) in Zimbabwe, categorized by varying rainfall levels: high, moderate, and low. A total of 5,607 single nucleotide polymorphism (SNP) markers were identified using Diversity Array Technology sequencing (DArTseq), which facilitated the analysis of the population structure and genetic diversity of the spider plant. The SNP markers exhibited an average polymorphic information content (PIC) of 0.28, indicating highly informativeness. Population structure analysis, conducted through admixture and principal component analysis, consistently revealed three gene pools among the spider plant accessions, with average observed (Ho) and expected heterozygosity (He) values of 0.20 and 0.21, respectively. The mean Ho was found to be 0.15, while the He was 0.18 for the agroecological zone-based sub-populations. Notably, the structure-based clustering did not align with the AEZ. Analysis of molecular variance based on structure clustering indicated that 49% of the variation observed within samples, with an average genetic distance of 0.398, and 38% of the variance was among populations, reflecting high genetic differentiation (PhiPT = 0.38). The three gene pools and individual accession variation enhance our understanding of the genetic diversity in the 43 spider plant accessions from Zimbabwe and provide critical information for breeding initiatives, further genetic applications, and the conservation of these valuable genetic resources.