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

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 <i>OsWRKY21</i> (LOC_Os01g60640). Interestingly, further haplotype analysis showed that C/T difference only existed in the <i>indica</i> group but not in the <i>japonica</i> group, resulting in significant differences in plant height among the different <i>indica</i> rice varieties. <i>OsWRKY21</i> was expressed in embryo, radicle, shoots, leaves, and stems. Most notably, overexpressing <i>OsWRKY21</i> 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 (<i>GA20ox2</i>, <i>GA2ox6,</i> and <i>YABY1</i>) and cell wall biosynthesis (<i>CesA4</i>, <i>7,</i> and <i>9</i>) and regulation (<i>MYB103L</i>). These data suggest the essential role of <i>OsWRKY21</i> in regulation of internode elongation and plant height in rice.