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

First author: Yanpei Zhang; Affiliations: China Agricultural University (中国农业大学): Beijing, China

Corresponding author: Zichao Li

Rice (Oryza sativa L.) cultivars harbor 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 (GLAva) 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 favorable allele for rice breeding.

水稻栽培种与野生稻具有不同的形态和生理性状，但驯化分子层面的机制还有待探索。本文研究显示芒和长的籽粒性状在近等基因系NIL‐GLA中是分别由GLA基因区的变异所控制的，该基因是GAD1/RAE2的一个新的等位基因，编码的蛋白属于EFPL家族。单倍型分析和转基因研究显示GLA基因启动子区的InDel1通过促进的GLA转录而增加籽粒长度。GLA基因编码区InDel3的缺失能够导致短芒或者无芒的表型。最小生成树和基因滲入区显示一个对于芒形成非常重要的基因An‐1会优先被驯化，并且An‐1突变成an‐1紧跟GLA和An‐2。随后，粳稻和籼稻群体之间发生了基因流。质量分析显示GLA导致了籽粒品质下降。在遗传改良过程中，籼稻芒少受到了选择，而粳稻中短籽、芒少与高品质一道受到了选择。本文的发现促进了我们对于水稻驯化的理解，并为水稻育种提供了一个优良的等位基因。

通讯：李自超  (http://cab.cau.edu.cn/art/2017/6/12/art_27217_141.html)

个人简介：1980-1984年，北京农业大学，学士；1990年，北京农业大学，硕士；1995-1996年，保加利亚遗传工程研究所，访问学者；2001年，中国农业大学，博士；2002–2003年，国际水稻研究所，合作研究；2010年，美国北卡州立大学，访问学者。

研究方向：主要利用旱稻DH、RIL和导入系群体及其种质资源通过连锁分析和GWAS相结合发掘根系、生理等抗旱相关性状的QTL或基因，利用基因组分析和RNA-Seq转录组分析技术研究了旱稻基因表达规律、旱稻抗旱的分子机制和旱生适应性进化；利用稻种核心种质培育的MCC-NAM群体和定向培育的产量性状、耐冷性状的近等基因系，通过连锁分析和GWAS相结合高效发掘和克隆水稻重要功能基因。

doi: https://doi.org/10.1111/pbi.13080

Journal: Plant Biotechnology Journal

Published date: January 21, 2019