Expression analysis of candidate structural genes involved in starch biosynthetic pathway of Indonesian cassava (Manihot esculenta) storage roots

Cassava storage roots contribute most to a wide range of starch-based applications for food, feed, medicine, cosmetics, biopolymers, and biofuels. Cassava cultivars differ in the proportions of amylose and amylopectin starch components, which are regulated molecularly by a set of genes encoding starch biosynthetic enzymes. We performed a relative expression analysis of nine candidate genes encoding cassava starch enzymes, namely sucrose synthase (SuSy), granule bound starch synthase (GBSS1, GBSS2), starch synthase (SS), starch branching enzyme (SBE2-1, SBE2-2, SBE3), debranching enzyme (DBE), and glucan water dikinase (GWD). As a reference gene, zinc finger protein (ZnF), was included in the study. Total RNAs were extracted from nine-month-old storage roots of five Indonesian cassava cultivars representing higher-starch cultivars (Adira-4, Kristal Merah, Menti, Revita RV-1) and a low-starch cultivar (Singkong Tali). In addition, we analyzed amylose contents from storage roots of the cultivars. Among those cultivars, Kristal Merah starches contained high amylose contents (27.53%) and three cultivars (Adira 4, Menti, and Revita RV-1) contained the average amylose (22–25%). Results showed that GBSS1 was relatively expressed in all cultivars, suggesting an accumulation of amylose in starch granules. Relative expressions of SS were observed abundantly in Kristal Merah and Singkong Tali, indicating that the first step of amylopectin biosynthesis occurred. However, low levels of DBE expression in Kristal Merah may limit debranching of poly-glucans or pre-amylopectin molecules during amylopectin synthesis. Singkong Tali showed the most abundant expressions of GWD, which encodes a hydrolytic enzyme for amylopectin breakdown. This may explain the low levels of starch in Singkong Tali. The current findings will add to existing knowledge of molecular regulation, specifically causal genes, involved in differential starch accumulation between cassava varieties/cultivars.