Phosphorylation of bip130 by OsMPK1 regulates abscisic acid-induced antioxidant defense in rice

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.

Phosphorylation of OsABA2 at Ser197 by OsMPK1 regulates abscisic acid biosynthesis in rice

The mitogen-activated protein kinase OsMPK1 is involved in abscisic acid (ABA) biosynthesis in rice (Oryza sativa L.). However, the underlying molecular mechanisms of OsMPK1 in regulating ABA biosynthesis are poorly understood. Here, by using yeast two-hybrid assay and firefly luciferase complementary imaging assay, we show that OsMPK1 physically interact with a short-chain dehydrogenase protein OsABA2. However, OsMPK5, a homolog of OsMPK1, does not interact with OsABA2. Further, OsMPK1 can phosphorylate OsABA2^S197 in vitro. Phosphorylation at the position of OsABA2^S197 does not affect its subcellular localization, but enhances the stability of OsABA2 protein. We also found that OsABA2 has feedback regulation on OsMPK1 kinase activity. Further research reveals that OsMPK1 and OsABA2 coordinately regulate the biosynthesis of ABA, and phosphorylation of OsABA2 at Ser197 by OsMPK1 plays a crucial role in regulating the biosynthesis of ABA. Finally, genetic analysis showed that OsABA2 can enhance the sensitivity of rice to ABA and the tolerance of rice to drought and salt stress.

Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam

BACKGROUND

Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns.

RESULTS

We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width.

CONCLUSIONS

We showed how the rice diversity within Vietnam relates to the wider Asian rice diversity by using a number of approaches to provide a clear picture of the novel diversity present within Vietnam, mainly around the Indica-5 subpopulation. Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of low input sustainable and climate resilient rice.

Subcellular Localization of Rice Acyl-CoA-Binding Proteins ACBP4 and ACBP5 Supports Their Non-redundant Roles in Lipid Metabolism

Acyl-CoA-binding proteins (ACBPs), conserved at the acyl-CoA-binding domain, can bind acyl-CoA esters as well as transport them intracellularly. Six ACBPs co-exist in each model plant, dicot Arabidopsis thaliana (thale cress) and monocot Oryza sativa (rice). Although Arabidopsis ACBPs have been studied extensively, less is known about the rice ACBPs. OsACBP4 is highly induced by salt treatment, but down-regulated following pathogen infection, while OsACBP5 is up-regulated by both wounding and pathogen treatment. Their differential expression patterns under various stress treatments suggest that they may possess non-redundant functions. When expressed from the CaMV35S promoter, OsACBP4 and OsACBP5 were subcellularly localized to different endoplasmic reticulum (ER) domains in transgenic Arabidopsis. As these plants were not stress-treated, it remains to be determined if OsACBP subcellular localization would change following treatment. Given that the subcellular localization of proteins may not be reliable if not expressed in the native plant, this study addresses OsACBP4:GFP and OsACBP5:DsRED expression from their native promoters to verify their subcellular localization in transgenic rice. The results indicated that OsACBP4:GFP was targeted to the plasma membrane besides the ER, while OsACBP5:DsRED was localized at the apoplast, in contrast to their only localization at the ER in transgenic Arabidopsis. Differences in tagged-protein localization in transgenic Arabidopsis and rice imply that protein subcellular localization studies are best investigated in the native plant. Likely, initial targeting to the ER in a non-native plant could not be followed up properly to the final destination(s) unless it occurred in the native plant. Also, monocot (rice) protein targeting may not be optimally processed in a transgenic dicot (Arabidopsis), perhaps arising from the different processing systems for routing between them. Furthermore, changes in the subcellular localization of OsACBP4:GFP and OsACBP5:DsRED were not detectable following salt and pathogen treatment, respectively. These results suggest that OsACBP4 is likely involved in the intracellular shuttling of acyl-CoA esters and/or other lipids between the plasma membrane and the ER, while OsACBP5 appears to participate in the extracellular transport of acyl-CoA esters and/or other lipids, suggesting that they are non-redundant proteins in lipid trafficking.