Phenotypic and genotypic characterization of awns in elite U.S. rice breeding germplasm

Abstract Awns are needle or bristle-like structures that grow at the tip of the lemma in rice grains. In cultivated rice, awnless material is preferred for agricultural and processing practices. Most cultivated rice produces no awns or very short awns, however, the causal genetic factors responsible for the loss of awns in cultivated rice remain largely unknown. Most studies conducted to investigate the genetic factors responsible for awn formation focused on plant material derived from crosses between awnless and wild awned parents. In this study, genetic analysis of awns was carried out using a breeding population developed from U.S. elite conventional and Provisia™ awnless parents. Before the use of indica germplasm and the Provisia™ technology, awns were not typically observed in the elite U.S. breeding material, where tropical japonica is predominant. We hypothesized that the presence of awns in populations derived from crosses with Provisia™ material was due to its indica background. We mapped a 1557 Kb awn-related region on chromosome 3 that appears to be a major source of awn formation when Provisia™ material (indica-type) is used for crossing with U.S. elite varieties. Two single nucleotide polymorphism (SNP) markers, SNP261 and SNP1251 explained 26% and 28% of the phenotypic variation in awn formation and elongation. Contingency analysis of F2, F2:3, and F3:4 generations showed that the awnless, short-awned, and low percentage of awns per panicle phenotype is explained by the presence of japonica alleles. When used together, these markers help differentiate awnless material.