Abstract
WRKY gene family is widespread in plants, which is of significance in determining plant development and stress response. Although WRKY transcription factors have been widely characterized in many plants, a genome-wide analysis of the WRKY gene family is still lacking in Oryza rufipogon. In this study, we identified 101 O. rufipogon WRKY (OrWRKY) transcription factors, which were further classified into eight subgroups. Phylogenetic analysis showed that OrWRKY transcription factors were supported by highly conserved motifs and gene structures. Chromosomal distribution of OrWRKYs indicated that most genes were dispersed on all twelve chromosomes, especially enriched on Chromosome 1. Syntenic analysis revealed that 69 (68.3%) genes were derived from either segmental (49) or tandem duplication events (20), suggesting a essential role of segmental duplications. We characterized a total of 39 orthologous gene pairs between O. sativa ssp. japonica WRKY (OsjWRKY) and OrWRKY. We then performed quantitative real-time polymerase chain reaction (qPCR) experiments to validate tissue-specific and differential expression of the OrWRKYs. We also investigated corresponsive expression of the OrWRKYs in response to salt stresses in leaves and roots. This study gains a new insight on the evolution of the OrWRKYs and will help further functional characterization of candidate genes towards wild rice germplasm exploration for rice genetic improvement.
Highlights
Among the genus Oryza comprising 23 species and nine recognized genome types (Vaughan et al, 2003), common wild rice, Oryza rufipogon Griff., is, besides the assumed annual wild progenitor Oryza nivara, another presumed perennial wild progenitor of Asian cultivated rice, Oryza sativa (Oka, 1988; Khush, 1997; Cheng et al, 2003; Fuller et al, 2010; Huang X. et al, 2012), which feeds half of the human population in the world
The proteins of all candidate O. rufipogon WRKY (OrWRKY) and OsiWRKY genes were aligned against the Oryza sativa ssp. japonica WRKY (OsjWRKY) proteins via BLASTP program with E value 1e−13 and named the OrWRKY and OsiWRKY genes according to their homology to O. sativa ssp. japonica cv
We totally detected 101 non-redundant deduced OrWRKY gene members, which were further named as OrWRKY1 to OrWRKY121 according to names of their OsjWRKY orthologs (Supplementary Table S2)
Summary
Among the genus Oryza comprising 23 species and nine recognized genome types (Vaughan et al, 2003), common wild rice, Oryza rufipogon Griff., is, besides the assumed annual wild progenitor Oryza nivara, another presumed perennial wild progenitor of Asian cultivated rice, Oryza sativa (Oka, 1988; Khush, 1997; Cheng et al, 2003; Fuller et al, 2010; Huang X. et al, 2012), which feeds half of the human population in the world. As a result of the domestication under intensive human cultivation, O. sativa has undergone considerable phenotypic and physiological changes, leading to an extensive loss of genetic diversity through successive bottlenecks and artificial selection for WRKY Analysis in Wild Rice agronomic traits compared to its wild progenitors (Kovach et al, 2007; Xu et al, 2012). As a promising donor for genetic improvement of cultivated rice, many of alien genes associated with morphological traits, quality traits, abiotic stress- and disease resistance-related traits have successfully been introduced through introgression lines from O. rufipogon, which has helped expand the rice gene pool important to the generation of environmentally resilient and high-yielding varieties (Brar and Ramos, 2008). Transcription factors play an essential role in this process by binding to specific DNA regions (Singh et al, 2002)
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