Genome-Wide Association Study of Root Quality Traits in Cassava (Manihot esculenta Crantz)

Cassava (Manihot esculenta Crantz) is a major staple crop globally, valued for its storage roots, which serve as a key source of food, feed, and industrial products such as starch and flour. Consequently, root quality traits are central to the cassava value chain. This study aimed to identify genomic regions associated with five important root quality traits: dry matter content (DMC), total carotenoid content (TCC), beta-carotene content (BCC), hydrogen cyanide content (HCN), and water absorption during boiling for 20 and 30 min (WAB_20min, WAB_30min). A panel of 300 cassava accessions was phenotyped for these traits and genotyped using genotyping-by-sequencing (GBS: 30,046 SNPs) and DArTag (2526 SNPs) platforms for genome-wide association analysis. Correlation analysis revealed generally low to moderate relationships among traits, except for a strong positive association between TCC and BCC, and between the WAB measurements, indicating relative independence among most root quality traits. Under the GBS platform, 10 significant SNPs were detected for each of HCN and BCC, 4 for TCC, and 2 for each of DMC and WAB_20min. Under the DArTag platform, 9 significant SNPs were identified for HCN, 5 for TCC, 5 for BCC, 1 for DMC, and 1 for WAB_20min. Across both marker platforms, no significant SNP was detected for WAB_30min. Overall, these findings provide insights into the genetic architecture of cassava root quality traits and highlight the potential of integrating genomic tools to enhance selection efficiency in cassava breeding programs.