Genomic-Wide Association Markers and Candidate Genes for the High-Protein Trait in Storage Roots of Cassava (Manihot esculenta)

Cassava (<i>Manihot esculenta</i> Crantz) is a globally important staple crop. Although its leaves are rich in crude protein, the protein content in its storage roots is typically less than 2%, which limits its nutritional value. Exploring high-protein storage root genotypes from germplasm collections is essential to elucidate the mechanisms underlying protein allocation, yet this remains poorly understood. Here, we conducted a three-year field evaluation of protein content in storage roots of 261 lines derived from a hybrid population (SC205*18R). It was found that there were 21 lines with high protein content that was stably above 4%. A total of 22 significant associated loci of protein content in storage roots were identified through genome-wide association analysis, with their contribution rates ranging from 0.12 to 0.35. For instance, the haplotypes of SNP-6831776 and SNP-7090537 have a prominent contribution to the protein content in the storage roots and can be used as major-effect markers in breeding. Based on this, we found 82 candidate genes, 7 of which exhibited the strongest and most consistent associations with root protein accumulation. qRT-PCR validation demonstrated that six candidate genes were significantly upregulated in high-protein varieties. These resources and findings provide a crucial foundation for breeding for storage roots with high protein and enhancing the nutritional and economic value of cassava.