Candidate gene identification and molecular marker development for the small granule starch trait in cassava (Manihot esculenta Crantz)

Abstract

Abstract Cassava ( Manihot esculenta ) is both a vital staple and industrial cash crop, with growing global demand for specialty starches. Small granule cassava starch is highly valued for industrial uses because its reduced size, high amylose content, and improved processing efficiency make it ideal for specific applications such as bioethanol production. The genetic basis for this trait in cassava is unknown, and no molecular tools are currently available to support breeding. Here, we combine in silico genomic analysis, phenotyping and independent genome-wide association study (GWAS) to identify candidate genomic regions and develop a robust molecular marker. Cassava genome exploration revealed nine α-glucan phosphorylase (PHS1/PHO1) genes, with six clustered in tandem duplication on chromosome 2. Whole-genome sequence analysis of 392 progenitors identified a key single nucleotide polymorphism (SNP) at Chr02:4,238,800 in the 5′ untranslated region (UTR) of Manes.02G052600 that strongly associated with the trait. We designed a Kompetitive Allele Specific PCR (KASP) assay targeting this SNP and validated it in a multi-parental population ( n = 962). The marker explained 48% of the phenotypic variation. This is the first molecular marker for cassava starch granule size, providing a cost-effective high-throughput tool for marker-assisted selection (MAS) to accelerate the development of specialty starch varieties.