Evolutionary Analysis of GH3 Genes in Six Oryza Species/Subspecies and Their Expression under Salinity Stress in Oryza sativa ssp. japonica.

Weilong Kong,Hua Zhong,Ziyun Gong,Mayank Gautam,Xiaoxiao Deng,Chang Liu,Yangsheng Li,Gangqing Zhao,Yue Zhang

doi:10.3390/plants8020030

Abstract

Glycoside Hydrolase 3 (GH3), a member of the Auxin-responsive gene family, is involved in plant growth, the plant developmental process, and various stress responses. The GH3 gene family has been well-studied in Arabidopsis thaliana and Zea mays. However, the evolution of the GH3 gene family in Oryza species remains unknown and the function of the GH3 gene family in Oryza sativa is not well-documented. Here, a systematic analysis was performed in six Oryza species/subspecies, including four wild rice species and two cultivated rice subspecies. A total of 13, 13, 13, 13, 12, and 12 members were identified in O. sativa ssp. japonica, O. sativa ssp. indica, Oryza rufipogon, Oryza nivara, Oryza punctata, and Oryza glumaepatula, respectively. Gene duplication events, structural features, conserved motifs, a phylogenetic analysis, chromosome locations, and Ka/Ks ratios of this important family were found to be strictly conservative across these six Oryza species/subspecies, suggesting that the expansion of the GH3 gene family in Oryza species might be attributed to duplication events, and this expansion could occur in the common ancestor of Oryza species, even in common ancestor of rice tribe (Oryzeae) (23.07~31.01 Mya). The RNA-seq results of different tissues displayed that OsGH3 genes had significantly different expression profiles. Remarkably, the qRT-PCR result after NaCl treatment indicated that the majority of OsGH3 genes play important roles in salinity stress, especially OsGH3-2 and OsGH3-8. This study provides important insights into the evolution of the GH3 gene family in Oryza species and will assist with further investigation of OsGH3 genes’ functions under salinity stress.

Highlights

Auxin is crucial for various aspects of plant growth and development, including signaling transport, plant metabolism, apical dominance, and shoot elongation [1,2]
Based on the homologous sequence cluster result with Arabidopsis and O. sativa ssp. japonica, all Glycoside Hydrolase 3 (GH3) genes were grouped into two groups (Table 1 and Figure 1): group1 and group2
In O. sativa ssp. indica, O. rufipogon, and O. nivara, four members of GH3s belonged to group1, and nine members of GH3s belonged to group2

Summary

Introduction

Auxin is crucial for various aspects of plant growth and development, including signaling transport, plant metabolism, apical dominance, and shoot elongation [1,2]. Auxin-regulated genes include different Auxin-responsive families, such as. Auxin/Indole-3-Acetic Acid genes (AUX/IAAs act as repressors), Auxin Response Factor genes (ARFs act as transcription activators), Small Auxin Up RNA genes (SAURs regulate the auxin-signaling pathway), and Gretchen Hagen 3 genes (GH3s) [3,4]. GH3 genes have been categorized into three groups (I–III) based on sequence similarity and substrate specificities [5,9]. In Arabidopsis, GH3 proteins from group I, with JA and/or SA-amido synthetase activity, use JA or SA as a substrate. GH3 proteins from group II, with IAA-amido synthetase activity, have Auxin-inducible expression profiles [5,9]. AtGH3-12/PBS3, an acyladenylase family member, is the best-studied class III protein.

Methods

Results

Conclusion