Molecular characterization and expression analysis of a gene encoding an isoamylase-type starch debranching enzyme 3 (ISA3) in grain amaranths

A cDNA clone from amaranth perisperm that encodes an isoamylase (ISA)-type starch debranching enzyme 3 was isolated and analyzed for the first time. The cDNA consisted of 2,715 bp with a single open reading frame of 2,346 bp, encoding a protein of 781 amino acid residues. The deduced amino acid sequence of CrISA3 shared 63–71 % identity with those of other plant ISA3s. We also investigated the genetic diversity of ISA3 in three species of grain amaranth. A comparison of their ISA3 coding sequences revealed an extremely high level of conservation and only 11 single nucleotide polymorphisms were detected. The expression of the CrISA3 gene in amaranth developmental seeds and several tissues was investigated by qRT-PCR analysis. The results showed that CrISA3 was rapidly expressed at the early stage during seed maturation. It was also expressed in non-storage tissues (leaf, petiole, stem, and root) as well as in storage tissue. This observation demonstrates that CrISA3 may play an important role in perisperm starch accumulation at the early developmental stages. In addition, our results indicate that CrISA3 plays important roles in the synthesis of storage and transitory starches. The characterization of the CrISA3 gene will contribute to further studies on starch biosynthesis in Amaranthus.