Genome-wide association study identifies novel genomic regions associated with yield-related traits in cassava (Manihot esculenta Crantz)

Cassava ( Manihot esculenta Crantz) is a vital calorie source in the tropics due to its adaptation to marginal agroecological conditions. Cassava’s dual role as a food security and industrial crop has stimulated extensive research into increasing yield. Genetic gain can be accelerated through investment in marker discovery and identification of genetic loci controlling important traits for use in breeding programs. Using the Diversity Array Technology genotyping-by-sequencing (DArTseq) platform, a population of 94 cassava accessions, comprising local landraces from Ghana and exotic lines from the International Institute of Tropical Agriculture (IITA), was genotyped with more than 30,000 SNP markers. A genome-wide association study (GWAS) was carried out for five yield-related traits, namely number of storage roots (NSR), mean storage root weight (MRW), root weight per plant (RW), harvest index (HI), and dry matter content (DMC) to survey the genome for the putative loci associated with these traits. A total of 55 significant marker-trait associations were detected, and haplotype analysis showed that favorable alleles at each locus had stronger genetic effects on yield-related traits, leading to the prediction of candidate genes. The identification of Manes.07G112000 (TPL-binding domain protein) and Manes.02G156800 (F-box domain) as candidate genes associated with MRW and DMC, respectively, highlights their potential roles in jasmonate signaling pathways. This connection suggests the existence of a defense-growth trade-off influencing yield traits in cassava. These findings lay a valuable foundation for the development of molecular markers to assist in breeding programs aimed at enhancing yield potential and overall productivity in cassava cultivars.