A down-regulated epi-allele of the genomes uncoupled 4 gene generates a xantha marker trait in rice

Abstract

A γ-ray-induced xantha trait is epigenetically controlled by the genomes uncoupled 4 gene with enhanced promoter segment methylation and down-regulated expression in rice. For easy testing and to increase varietal purity, a xantha mutation (xnt), which turns plants yellow and makes them visually distinguishable from normal green rice, has been generated and bred into male sterile lines for hybrid rice production. The xnt locus was previously fine mapped to a ~100-kb interval on chromosome 11, but its identity was unknown. In this study, xnt was further narrowed down to a 57-kb fragment carrying eight opening reading frames (ORFs). All eight ORFs had identical genomic sequences and all but ORF2 (g enomes uncoupled 4, OsGUN4) had similar transcript abundance in the xantha mutant Huangyu B (HYB) and its parental variety Longtefu B (LTB). The expression of OsGUN4, however, was significantly reduced in HYB compared with LTB in terms of both transcript abundance (0.2% that of LTB) and expressed protein level (barely detectable in HYB but greater than the heat shock protein reference in LTB). Therefore, OsGUN4 was identified as the candidate gene underlying the xantha trait. The function of OsGUN4 in the xantha phenotype was confirmed by identification and characterization of new allelic OsGUN4 mutations. Comparative bisulfite genomic sequencing of OsGUN4 revealed increased methylation in a promoter region in the mutant, and the correlation between increased methylation and the xantha phenotype was further verified by demethylation treatment. In summary, we have identified an epi-allele of OsGUN4 as the causal gene of the xantha marker trait and revealed that enhanced methylation in its promoter down-regulated its expression in rice.

The xantha Marker Trait Is Associated with Altered Tetrapyrrole Biosynthesis and Deregulated Transcription of PhANGs in Rice

“…There were no reports describing GUN4 from other plant species until we revealed that an epi-allele of OsGUN4 is responsible for the xantha marker trait (Li et al, 2014). This previous study remains the only one involving a GUN4 from a crop plant.…”

“…Mutations to any of these genes may reduce or even eliminate chlorophyll biosynthesis, leading to leaf color changes (Liu et al, 2007, 2016; Yoo et al, 2009; Tian et al, 2013; Wang et al, 2014; Zhang et al, 2015; Yang et al, 2016). Through gene mapping and additional studies, the mutant gene responsible for the xantha marker trait of HYB was identified as a mutated OsGUN4 ( genomes uncoupled 4 ) (Chi et al, 2010; Li et al, 2014). …”

CLD1/SRL1 modulates leaf rolling by affecting cell wall formation, epidermis integrity and water homeostasis in rice

“…The results were consistent with a sharp reduction of SRL1 expression downstream of the third exon‐encoded region, indicating that DNA methylation in cld1 plays essential roles in the regulation of SRL1 expression. To further validate the correlation between the cld1 phenotype and SRL1 methylation, we treated cld1 seeds with 5‐aza‐2′‐deoxycytidine (5‐aza‐dC), an inhibitor of DNA methylation (Miura et al ., ; Li et al ., ). All the cld1 seedlings from untreated seeds showed the leaf‐rolling phenotype, whereas 63.1% of cld1 seedlings from 5‐aza‐dC‐treated seeds exhibited a flat leaf phenotype (Figure g).…”

The Birth of a Black Rice Gene and Its Local Spread by Introgression

“…Epialleles have been reported in several plant species, including maize (Brink, 1956;Banks et al, 1988;Das and Messing, 1994;Hollick and Chandler, 2001) and rice (Miura et al, 2009(Miura et al, , 2010Wang et al, 2010;Zhang et al, 2012;Li et al, 2014). The phenotypes of these epialleles are affected by DNA methylation status and/or histone modification resulting in the alteration of gene expression.…”