Control of awn length in rice breeding programs in Hokkaido

Abstract

Understanding genetic diversity among local populations may facilitate the development of new crop varieties and is a primary goal of the molecular evolution of genes. Awn length is a well-documented phenotype among domestication traits in rice (Oryza sativa L.), from long to short awns. Short awned or awnless varieties have been selected in rice breeding programs. Awnlessness is favored by rice farmers in the current agriculture system. Here, we identified the genetic basis of awn length during rice breeding programs in Hokkaido, Japan. We found variation in awn length ranging from 0.0 to 37.6 mm among a local population consisted of breeding lines. Genetic analysis of awn length identified that RAE1 and RAE2 on chromosomes 4 and 8, respectively, accounted for awn presence. These genes are well known to be significant during Asian rice domestication. Sequence variations in these genes may clarify the molecular evolution of the genes for awn length in rice breeding programs. Firstly, a loss-of-function allele in RAE1, rae1, was selected for short awn length. Then, alleles of RAE2, RAE2-H01 to RAE2-H04, were targeted for the selection of short awns or awnlessness. The selections of an awnlessness phenotype can diversify these alleles in the genes RAE1 and RAE2 exhibiting variation in awn length.