Genome-Wide Association Study in Rice Revealed a Novel Gene in Determining Plant Height and Stem Development, by Encoding a WRKY Transcription Factor.

Xiaoshuang Wei,Lingqiang Wang,Deying Xie,Guosheng Xie,Mingchong Yang,Jianguo Li,Tianli Chang,Lihua Hu,Jihong Wang,Dongxin Wang,Hailian Zhou

doi:10.3390/ijms22158192

Abstract

Semi-dwarfism is a main agronomic trait in crop breeding. In this study, we performed genome-wide association study (GWAS) and identified a new quantitative trait nucleotide (QTN) for rice shoot length. The peak QTN (C/T) was located in the first coding region of a group III WRKY transcription factor OsWRKY21 (LOC_Os01g60640). Interestingly, further haplotype analysis showed that C/T difference only existed in the indica group but not in the japonica group, resulting in significant differences in plant height among the different indica rice varieties. OsWRKY21 was expressed in embryo, radicle, shoots, leaves, and stems. Most notably, overexpressing OsWRKY21 resulted in the semi-dwarf phenotype, early heading date and short internodes compared to the wild type, while the knockout mutant plants by CRISPR/Cas9 technology yielded the opposite. The overexpressing lines exhibited the decreased length of the cells near sclerenchyma epidermis, accompanied with the lower levels of indole-3-acetic acid (IAA) and gibberellin 3 (GA3), but increased levels of the abscisic acid (ABA) and salicylic acid (SA) in the internodes at heading stage. Moreover, the semi-dwarf phenotype could be fully rescued by exogenous GA3 application at seedling stage. The RNA-seq and qRT-PCR analysis confirmed the differential expression levels of genes in development and the stress responses in rice, including GA metabolism (GA20ox2, GA2ox6, and YABY1) and cell wall biosynthesis (CesA4, 7, and 9) and regulation (MYB103L). These data suggest the essential role of OsWRKY21 in regulation of internode elongation and plant height in rice.

Highlights

Rice (Oryza sativa L.) is a major staple crop worldwide that feeds more than half of the global population [1]
To identify the quantitative trait nucleotide (QTN) associated with the rice shoot length, we collected the phenotypic data from the seedling of 469 accessions being cultivated under normal conditions in a growth chamber
To confirm whether the semi-dwarf phenotype of OsWRKY21-OE plants is caused by gibberellic acid (GA) deficiency, we investigated the response of OE plants to exogenous GA at seedling stage

Summary

Introduction

Rice (Oryza sativa L.) is a major staple crop worldwide that feeds more than half of the global population [1]. Semi-dwarfism is one of the most attractive traits in cereal crop breeding programs. Dwarf cultivars of many crop plants have been identified with enhanced lodging resistance, improved harvest index, and being responsive to fertilizer input [2]. The adoption of two well-known dwarf genes, semi-dwarf (sd1) in rice, and reduced height (Rht1) in wheat (Triticum aestivum), to create semi-dwarf varieties has significantly increased crop yields and initiated the “Green Revolution” [3]. Since the plant height is typically quantitatively inherited, the genetic mapping and subsequent gene cloning by quantitative trait loci (QTLs) and/or genome-wide association study (GWAS)

Methods

Results

Conclusion