Rice ERECT LEAF 1 acts in an alternative brassinosteroid signaling pathway independent of the receptor kinase OsBRI1

Genomic regions and candidate genes selected during the breeding of rice in Vietnam

Vietnam harnesses a rich diversity of rice landraces adapted to a range of conditions, which constitute a largely untapped source of diversity for the continuous improvement of cultivars. We previously identified a strong population structure in Vietnamese rice, which is captured in five Indica and four Japonica subpopulations, including an outlying Indica‐5 group. Here, we leveraged that strong differentiation and 672 native rice genomes to identify genomic regions and genes putatively selected during the breeding of rice in Vietnam. We identified significant distorted patterns in allele frequency (XP‐CLR) and population differentiation scores (F_ST) resulting from differential selective pressures between native subpopulations, and later annotated them with QTLs previously identified by GWAS in the same panel. We particularly focussed on the outlying Indica‐5 subpopulation because of its likely novelty and differential evolution, where we annotated 52 selected regions, which represented 8.1% of the rice genome. We annotated the 4576 genes in these regions and selected 65 candidate genes as promising breeding targets, several of which harboured alleles with nonsynonymous substitutions. Our results highlight genomic differences between traditional Vietnamese landraces, which are likely the product of adaption to multiple environmental conditions and regional culinary preferences in a very diverse country. We also verified the applicability of this genome scanning approach to identify potential regions harbouring novel loci and alleles to breed a new generation of sustainable and resilient rice.

PtBRI1.2 promotes shoot growth and wood formation through a brassinosteroid-mediated PtBZR1-PtWNDs module in poplar

Brassinosteroid-insensitive-1 (BRI1) plays important roles in various signalling pathways controlling plant growth and development. However, the regulatory mechanism of BRI1 in brassinosteroid (BR)-mediated signalling for shoot growth and wood formation in woody plants is largely unknown. In this study, PtBRI1.2, a brassinosteroid-insensitive-1 gene, was overexpressed in poplar. Shoot growth and wood formation of transgenic plants were examined and the regulatory genes involved were verified. PtBRI1.2 was localized to the plasma membrane, with a predominant expression in leaves. Ectopic expression of PtBRI1.2 in Arabidopsis bri1-201 and bri1-5 mutants rescued their retarded-growth phenotype. Overexpression of PtBRI1.2 in poplar promoted shoot growth and wood formation in transgenic plants. Further studies revealed that overexpression of PtBRI1.2 promoted the accumulation of PtBZR1 (BRASSINAZOLE RESISTANT1) in the nucleus, which subsequently activated PtWNDs (WOOD-ASSOCIATED NAC DOMAIN transcription factors) to up-regulate expression of secondary cell wall biosynthesis genes involved in wood formation. Our results suggest that PtBRI1.2 plays a crucial role in regulating shoot growth and wood formation by activating BR signalling.

ERECT LEAF1 suppresses jasmonic acid response in rice by decreasing OsWRKY4 stability

ERECT LEAF 1 (ELF1), which was identified as a component of brassinosteroid signaling in rice, is involved in brassinosteroid-mediated suppression of jasmonic acid response. Here, by conducting yeast two-hybrid assay and in vitro ubiquitination experiments, we demonstrate that ELF1 interacts with the OsWRKY4 transcription factor, a positive regulator of defense responses to rice sheath blight. ELF1 decreased the stability of OsWRKY4, whereas exogenous jasmonic acid treatment suppressed this effect of ELF1, resulting in OsWRKY4 accumulation in rice plants. In wild-type rice, OsWRKY4 expression was up-regulated by jasmonic acid treatment but down-regulated by brassinosteroid treatment, suggesting that jasmonic acid-induced OsWRKY4 accumulation was caused by a combination of increased production and suppressed degradation. The expression levels of the OsWRKY4 target genes, PR1b and PR5, seemed to be correlated with the OsWRKY4 level. These results suggest that ELF1 indirectly controls the expression of PR1b and PR5 genes by regulating the OsWRKY4 protein level, and support a hypothesis that brassinosteroid and jasmonic acid cooperate to maintain the balance between growth and defense responses. We conclude that ELF1 participates in the antagonistic interaction between these two phytohormones by suppressing the jasmonic acid response through the down-regulation of OsWRKY4 protein level in rice.