Nucleotide sequence variation associated with β-amylase deficiency in the sweet potato Ipomoea batatas (L.) Lam

Amy beta is a single gene that encodes beta-amylase, a starch-hydrolyzing enzyme that confers sweetness to sweet potato roots upon cooking. To clarify the genetic basis underlying beta-amylase null activity, we sequenced a highly conserved region of Amy beta, including the Amy beta active center, from normal and null cultivars. Comparison of the sequences revealed the presence of the In-Del sequences in null cultivars, which was thought to be a loss-of-function mutation causing a change from sweet to non-sweet. The In-Del frequency revealed using a multiple sequencing approach, and its association with P-amylase activity, showed that an inactive allele of Amy beta gene (Amy beta-I) exists. Aim expression analysis showed that Amy beta-I is transcribed normally, suggesting that translational control of beta-amylase activity occurs in null mutants. The insertion in Amy beta-I caused a sequence frameshift resulting in an amino acid substitution with the incorporation of a stop codon in Amy beta-I. The Amy beta-I amino acid Substitution and premature termination affect the Substrate binding and catalytic site of the enzyme, which may result in an inactive protein that is responsible for the beta-amylase inactivity in non-sweet cultivars. These findings are the basis of selection markers for non-sweetness in sweet potato breeding.