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

Abstract

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.

Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species

“…indica lines lost both genes’ function ( Figure 5 C). These percentages were slightly different from those reported previously [ 16 , 18 ], perhaps because this study used a smaller number of individuals for sequence comparison using SRA data, which requires sufficient read depth to identify the TE region compared to conventional PCR analysis [ 11 ]. Mutation points and haplotype occupancy differed between japonica and indica .…”

“…In rice, the awn is a conspicuous trait that is considered to have been influenced by domestication. To date, several genes have been identified for awn development in rice, including An-1/RAE1 [ 11 , 13 ], LABA1/An-2 [ 12 , 14 ], RAE2/GAD1/GLA [ 16 , 17 , 18 ], TOB1 [ 19 ], and GLA1 [ 20 ]; among these, An-1/RAE1 , LABA1/An-2 , and RAE2/GAD1/GLA appear to have been selected through Asian rice domestication [ 11 , 12 , 16 ]. To explore the novel loci for regulating awn development and to clarify the conservation of RAE1 and RAE2 gene function among the AA genome rice group, we examined 11 sets of CSSL by comparing genotypes and awn phenotypes.…”

“…The long awn of wild progenitors was eliminated through rice domestication. Several major genes associated with awn development have been identified, including An-1/RAE1 [ 11 , 13 ], LABA1/An-2 [ 12 , 14 ], DL and OsETT2 [ 15 ], and RAE2/GAD1/GLA [ 16 , 17 , 18 ]. Genes suppressing awn formation have also been identified, including the YABBY transcription factor, TOB1 [ 19 ], and GLA1, which encodes the mitogen-activated protein kinase phosphatase [ 20 ].…”

A peptide pair coordinates regular ovule initiation patterns with seed number and fruit size

“…One of the underlying causal mutation inactivates an EPFL2 -orthologue, OsEPFL1, which also affects grain length and grain number, giving rise to more compact panicles with more seeds 48–50 . Although the underlying mechanism in rice is not yet understood, it highlights a role of EPFL2 -genes as evolutionary conserved integrators of ovule initiation patterns, seed number, seed size and floral organ development 51 .…”

Bulked QTL-Seq identified a major QTL for the awnless trait in spring wheat cultivars in Qinghai, China

“…Most studies have focused on B1, B2 and Hd. B1 is located on chromosome arms 5AL [3,5,12,13] a candidate gene of the B1 locus, encodes C2H2 zinc finger protein and has been isolated in wheat [14][15][16]. The promoter variations of B1 are closely associated with awn development in awnless and awned individuals [14].…”