Natural alleles of GLA for grain length and awn development were differently domesticated in rice subspecies japonica and indica

Summary Rice ( Oryza sativa L.) cultivars harbour morphological and physiological traits different from those of wild rice ( O. rufipogon Griff.), but the molecular mechanisms underlying domestication remain controversial. Here, we show that awn and long grain traits in the near‐isogenic NIL ‐ GLA are separately controlled by variations within the GLA ( Grain Length and Awn Development ) gene, a new allele of GAD 1 / RAE 2 , which encodes one member of the EFPL (epidermal patterning factor‐like protein) family. Haplotype analyses and transgenic studies revealed that InDel1 (variation for grain length, VGL ) in the promoter region of GLA ( GLA VGL ) increases grain length by promoting transcription of GLA . Absence of InDel3 (variation for awn formation, VA ) in the coding region ( CDS ) of GLA ( GLA va ) results in short awn or no awn phenotypes. Analyses of minimum spanning trees and introgression regions demonstrated that An‐1 , an important gene for awn formation, was preferentially domesticated and its mutation to an‐1 was followed by GLA and An‐2 . Gene flow then occurred between the evolved japonica and indica populations. Quality analysis showed that GLA causes poor grain quality. During genetic improvement, awnlessness was selected in ssp. indica , whereas short–grained and awnless phenotypes with good quality were selected in japonica . Our findings facilitate an understanding of rice domestication and provide a favourable allele for rice breeding.