Microsatellites and a single-nucleotide polymorphism differentiate apparentamylose classes in an extended pedigree of US rice germ plasm

Abstract

The Waxy gene (Wx) encodes the granule-bound starch synthase responsible for the synthesis of amylose in rice (Oryza sativa). Recently, a polymorphic microsatellite sequence closely linked to the Wx gene was reported. To determine whether polymorphism in this sequence correlates with variation in apparent amylose content, we tested an extended pedigree of 92 current and historically important long-, medium- and short-grain US rice cultivars representing the efforts of many breeders over more than 80 years. Seven Wx microsatellite alleles were identified which together explained 82.9% of the variation in apparent amylose content of the 89 non-glutinous rice cultivars tested. Similar results were also obtained with 101 progenyof a cross between low- and intermediate-amylose breeding lines. An additional, unique microsatelliteallele, (CT)16, was detected in one glutinous cultivar,CI 5309. However, the other glutinous cultivars,Calmochi 101 and Tatsumi mochi, were in the (CT)17 class along with three other cultivars that contained15–16.5% amylose.