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

Yanpei Zhang,Hongliang Zhang,Xingming Sun,Chao Chen,Ben Li,Yuntao Liang,Haifeng Guo,Yinghua Pan,Zhijian Xu,Xiaoyang Zhu,Jinjie Li,Zichao Li,Zhanying Zhang

doi:10.1111/pbi.13080

Abstract

SummaryRice (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 GAD1/RAE2, 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 (GLAVGL) 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.

Highlights

Rice (Oryza sativa L.), one of the earliest domesticated, primary food crops, feeds more than half of the world population (Khush, 1997)
near isogenic lines (NILs)-gla developed much shorter grains and more grains per panicle than NIL-GLA, but there was no significant difference in grain width (Figure 1c,d,h–j)
There was no significant difference in average cell number per unit area, cell length or cell width between NIL-GLA and NIL-gla, suggesting that cell number rather than cell size was mainly responsible for the longer grains in NIL-GLA (Figure 1f,g, k–m)

Summary

Introduction

Rice (Oryza sativa L.), one of the earliest domesticated, primary food crops, feeds more than half of the world population (Khush, 1997). Compared with its wild ancestors cultivated rice typically exhibits reduced seed shattering and dormancy, increased grain number per panicle, erect growth, closed panicles and no or short awns (Kovach et al, 2007; Sweeney and McCouch, 2007). All of these features that differ between wild rice and cultivars are known as domestication traits. Some domesticated genes are functionally characterized, such as seed shattering genes Sh4 (Li et al, 2006) and qSH1 (Konishi et al, 2006; Li et al, 2006), prog controlling straight growth (Jin et al, 2008; Tan et al, 2008), OsLG1 regulating closed panicles (Ishii et al, 2013; Zhu et al, 2013), grain size genes GW5/GSE5 (Duan et al, 2017; Liu et al, 2017), GS3 (Mao et al, 2010), OsLG3 (Yu et al, 2017) and OsLG3b (Yu et al, 2018), seed dormancy gene Sdr (Sugimoto et al, 2010), seed hull colour genes Bh4 (Zhu et al, 2011) and Rc (Sweeney et al, 2006), NOG1 increasing grain production (Huo et al, 2017) and awn development genes An-1 (Luo et al, 2013), An-2/LABA1 (Gu et al, 2015; Hua et al, 2015) and GAD1/RAE2 (BesshoUehara et al, 2016; Jin et al, 2016)

Results

Discussion

Conclusion