Identification of two novel waxy alleles and development of their molecular markers in sorghum

High amylopectin grains of waxy sorghum have a high economic value in the food and bioenergy industries because of their increased starch digestibility and higher ethanol conversion rate compared with wild-type sorghum grains. Mutation in the granule-bound starch synthase (GBSS) gene contributes to the waxy phenotype. Two classes of waxy alleles, wx(a) and wx(b), have been characterized previously. In the present work, we identified two novel types of waxy mutations in the sorghum GBSS gene, designated as wx(c) and wx(d). The wx(c) allele has a G deletion at the 5' splicing site of the ninth intron, causing a shift of the 5' cleavage site; in turn, a reading frame shift occurred and resulted in an early translation termination. The wx(d) allele contained a mutation at the 3' splicing site of the 10th intron, which led to a splicing site shift and resulted in the deletion of five amino acids (GTGKK) in the predicted translation product. Furthermore, cleaved amplified polymorphic sequence (CAPS) markers were developed to detect the wx(c) and wx(d) alleles. With these markers, classification of waxy alleles was performed in nearly 100 sorghum accessions from our breeding program. Most waxy sorghum cultivars in China were either wx(a) or wx(c), implying that these two mutations are preferentially maintained during domestic selection in glutinous sorghum production.