Molecular characterization and genetic diversity of the starch branching enzyme (SBE) gene from Amaranthus: the evolutionary origin of grain amaranths

Abstract

Full-length genomic DNA clones encoding starch branching enzymes (SBEs) from three cultivated grain amaranths were isolated and characterized. A sequence analysis showed that the SBE genes from Amaranthus caudatus, A. cruentus, and A. hypochondriacus, viz. SBE-ca, SBE-cr, and SBE-hy, respectively, contained the same exon and intron structure and consisted of 961 amino acids with molecular weights of approximately 108.4 kDa. The lengths of the genes were 7,446 (SBE-ca), 7,453 (SBE-cr), and 7,443 bp (SBE-hy), and they are highly homologous. We also tested, for the first time, the potential use of SBE from diverse genetic sources to answer long-standing questions on the origin of grain amaranths. The maximum parsimony tree based on the SBE sequence data suggests that A. hybridus is the progenitor wild species of grain amaranths. The results could be summarized as follows: (1) the A. hybridus species comprise all grain amaranths, which can then be divided into two subgroups; (2) A. caudatus and A. hypochondriacus and/or A. caudatus and A. quitensis appear to be closely related to each other; (3) A. powellii was the most distantly related to the other five species in the A. hybridus complex. These results indicate that A. hybridus is the ancestor species in at least two separate domestication events, lending support to the theory of three separate, rather than one, domestication events involving A. hybridus as the common ancestor. A new approach to investigating the genetic diversity in Amaranthus using the nuclear gene SBE provided useful information on the evolutionary origin of three cultivated species.