Characterization and expression analysis of the starch synthase gene family in grain amaranth (Amaranthus cruentus L.).

Characterization and expression analysis of the starch synthase gene family was performed from grain amaranth. Extensive searches for sequence data for amaranth starch synthase genes were done in the literature and in GenBank, and identified four genes encoding GBSSI, SSSI, SSSII, and SBE. Alignment of predicted amino acid sequences showed that there were low levels of sequence identity among these four genes (10.6-34.5%). There was higher homology in the C-terminal region and lower homology in the N-terminal region of the amaranth starch synthases. Starch synthases in plants can be classified into six groups, and phylogenetic analyses showed that the starch synthases from amaranth were in four of these groups; GBSSs, SSSIs, SSSIIs, and SBEs of dicot plants. Interestingly, all amaranth starch synthases were sister to the subgroup consisting of the rest of the dicot plants, clustering more closely with dicots than with monocots. Analysis of the expression patterns of starch synthase genes in storage and non-storage tissues of amaranth revealed two types of expression patterns; (1) GBSSI was rapidly expressed at the middle or mid-late stages of seed development; and (2) SSSI, SSSII and SBE genes were expressed constitutively during seed maturation. These four genes were expressed in non-storage tissues as well as in storage tissue, suggesting that non-storage and storage tissues of amaranth share a common mechanism for expression of starch synthase genes. This summary of the basic characteristics of starch synthase genes will contribute further studies on amaranth starch.