RNA Sequence Analysis of Cassava Varieties with High-Starch Content Using De Novo Assembly

Abstract

Cassava (Manihot esculenta Crantz) is an important raw material of cassava starch and biological energy worldwide. Among the key traits for crop improvement, elite cassava varieties with high starch content represent a major research target. However, the high genetic heterozygosity of cassava limits its conventional breeding. Identification of novel molecular markers associated with starch biosynthesis facilitates the creation of elite cassava varieties via marker-associated breeding. To increase the number of markers with higher efficiency and stabilization, the transcriptomic profiles of root starch synthesis that were derived from high- and low-starch cassava varieties [Radiation Selection 01 (RS01) and South of China 124 (SC124)] were monitored. More than 292 million reads were deduced by RNA sequencing, which were assembled into 45,007 unigenes. Additionally, 46,925 and 32,421 unigenes from RS01 and SC124, respectively, could be annotated into the Non-redundant protein database, Nucleotide database, Swiss-Prot protein sequence database, Kyoto Encyclopedia of Genes and Genomes, Clusters of Orthologous Groups of proteins database (COG), and Gene Ontology (GO) following their assembly. In the different classification systems of COG and GO, 23,172 and 21,835 unigenes had specific protein functions in RS01 and SC124, respectively. In the statistical classification of function in the differential genes in GO, the involved biological processes included metabolic pathways (ko01100), biosynthesis of secondary metabolites (ko01110), ribosome (ko03010), and RNA transportation (ko03013), among others. Several markers and genes associated with high starch traits were developed. These results provide a feasible and effective framework to improve approaches of cassava starch biosynthesis with the intent of creating high-quality cassava species with novel features.