ORCID Profile
0000-0001-9145-3571
Current Organisations
International Rice Research Institute
,
University of Nottingham
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Publisher: Cold Spring Harbor Laboratory
Date: 22-04-2019
DOI: 10.1101/615278
Abstract: Understanding the factors that influence the outcome of crop interactions with microbes is key to managing crop diseases and improving yield. While the composition, structure and functional profile of crop microbial communities are shaped by complex interactions between the host, microbes and the environment, the relative contribution of each of these factors is mostly unknown. Here, we profiled the community composition of bacteria across leaves of 3,024 rice ( Oryza sativa ) accessions from field trials in China and the Philippines using metagenomics. Despite significant differences in ersity between environments, the structure and metabolic profiles of the microbiome appear to be conserved, suggesting that microbiomes converge onto core functions. Furthermore, co-occurrence analysis identified microbial hubs that regulate the network structure of the microbiome. We identified rice genomic regions controlling the abundance of these hubs, enriched for processes involved in stress responses and carbohydrate metabolism. We functionally validated the importance of these processes, finding that abundance of hub taxa was different in rice mutants with altered cellulose and salicylate accumulation, two major metabolites at the host-microbe interactions interface. By identifying key host genomic regions, host traits and hub microbes that govern microbiome composition, our study opens the door to designing future cropping systems.
Publisher: Springer Science and Business Media LLC
Date: 28-10-2015
DOI: 10.1038/SREP15183
Abstract: Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs. Here we demonstrate the requirement of multiple intra-QTL genes for the full impact of QTL qDTY 12.1 on rice yield under drought. Multiple evidences are presented for the need of the transcription factor ‘no apical meristem’ ( OsNAM 12.1 ) and its co-localized target genes of separate GO categories for qDTY 12.1 function, raising a regulon-like model of genetic architecture. The molecular underpinnings of qDTY 12.1 support its effectiveness in further improving a drought tolerant genotype and for its validity in multiple genotypes/ecosystems/environments. Resolving the combinatorial value of OsNAM 12.1 with in idual intra-QTL genes notwithstanding, identification and analyses of qDTY 12.1 has fast-tracked rice improvement towards food security.
Publisher: Springer Science and Business Media LLC
Date: 25-01-2016
DOI: 10.1038/SREP19792
Abstract: More than two billion people are micronutrient deficient. Polished grains of popular rice varieties have concentration of approximately 2 μg g −1 iron (Fe) and 16 μg g −1 zinc (Zn). The HarvestPlus breeding programs for biofortified rice target 13 μg g −1 Fe and 28 μg g −1 Zn to reach approximately 30% of the estimated average requirement (EAR). Reports on engineering Fe content in rice have shown an increase up to 18 μg g −1 in glasshouse settings in contrast, under field conditions, 4 μg g −1 was the highest reported concentration. Here, we report on selected transgenic events, field evaluated in two countries, showing 15 μg g −1 Fe and 45.7 μg g −1 Zn in polished grain. Rigorous selection was applied to 1,689 IR64 transgenic events for insert cleanliness and, trait and agronomic performances. Event NASFer-274 containing rice nicotianamine synthase ( OsNAS2 ) and soybean ferritin ( SferH-1 ) genes showed a single locus insertion without a yield penalty or altered grain quality. Endosperm Fe and Zn enrichment was visualized by X-ray fluorescence imaging. The Caco-2 cell assay indicated that Fe is bioavailable. No harmful heavy metals were detected in the grain. The trait remained stable in different genotype backgrounds.
Publisher: Oxford University Press (OUP)
Date: 12-2012
DOI: 10.1093/JXB/ERS313
Abstract: Numerous transgenes have been reported to increase rice drought resistance, mostly in small-scale experiments under vegetative-stage drought stress, but few studies have included grain yield or field evaluations. Different definitions of drought resistance are currently in use for field-based and laboratory evaluations of transgenics, the former emphasizing plant responses that may not be linked to yield under drought. Although those fundamental studies use efficient protocols to uncover and validate gene functions, screening conditions differ greatly from field drought environments where the onset of drought stress symptoms is slow (2-3 weeks). Simplified screening methods, including severely stressed survival studies, are therefore not likely to identify transgenic events with better yield performance under drought in the target environment. As biosafety regulations are becoming established to allow field trials in some rice-producing countries, there is a need to develop relevant screening procedures that scale from preliminary event selection to greenhouse and field trials. Multilocation testing in a range of drought environments may reveal that different transgenes are necessary for different types of drought-prone field conditions. We describe here a pipeline to improve the selection efficiency and reproducibility of results across drought treatments and test the potential of transgenic rice for the development of drought-resistant material for agricultural purposes.
Publisher: Springer Science and Business Media LLC
Date: 24-08-2015
Abstract: Global socioeconomic developments create strong incentives for farmers to shift from transplanted to direct-seeded rice (DSR) as a means of intensification and economization(1). Rice production must increase to ensure food security(2) and the bulk of this increase will have to be achieved through intensification of cultivation, because expansion of cultivated areas is reaching sustainable limits(3). Anaerobic germination tolerance, which enables uniform germination and seedling establishment under submergence(4), is a key trait for the development of tropical DSR varieties(5,6). Here, we identify a trehalose-6-phosphate phosphatase gene, OsTPP7, as the genetic determinant in qAG-9-2, a major quantitative trait locus (QTL) for anaerobic germination tolerance(7). OsTPP7 is involved in trehalose-6-phosphate (T6P) metabolism, central to an energy sensor that determines anabolism or catabolism depending on local sucrose availability(8,9). OsTPP7 activity may increase sink strength in proliferating heterotrophic tissues by indicating low sugar availability through increased T6P turnover, thus enhancing starch mobilization to drive growth kinetics of the germinating embryo and elongating coleoptile, which consequently enhances anaerobic germination tolerance.
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Inez Slamet-Loedin.