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Genomic prediction of zinc-biofortification potential in rice gene bank accessions.

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A genomic prediction model successfully predicted grain Zn concentrations in 3000 gene bank accessions and this was verified experimentally with selected potential donors having high on-farm grain-Zn in Madagascar. Increasing zinc (Zn) concentrations in edible parts of food crops, an approach termed Zn-biofortification, is a global breeding objective to alleviate micro-nutrient malnutrition. In particular, infants in countries like Madagascar are at risk of Zn deficiency because their dominant food source, rice, contains insufficient Zn. Biofortified rice varieties with increased grain Zn concentrations would offer a solution and our objective is to explore the genotypic variation present among rice gene bank accessions and to possibly identify underlying genetic factors through genomic prediction and genome-wide association studies (GWAS). A training set of 253 rice accessions was grown at two field sites in Madagascar to determine grain Zn concentrations and grain yield. A multi-locus GWAS analysis identified eight loci. Among these, QTN_11.3 had the largest effect and a rare allele increased grain Zn concentrations by 15%. A genomic prediction model was developed from the above training set to predict Zn concentrations of 3000 sequenced rice accessions. Predicted concentrations ranged from 17.1 to 40.2 ppm with a prediction accuracy of 0.51. An independent confirmation with 61 gene bank seed samples provided high correlations (r = 0.74) between measured and predicted values. Accessions from the aus sub-species had the highest predicted grain Zn concentrations and these were confirmed in additional field experiments, with one potential donor having more than twice the grain Zn compared to a local check variety. We conclude utilizing donors from the aus sub-species and employing genomic selection during the breeding process is the most promising approach to raise grain Zn concentrations in rice.

SUBMITTER: Rakotondramanana M

PROVIDER: S-EPMC9271118 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND: Rice is the primary source of food for billions of people in developing countries, yet the commonly consumed polished grain contains insufficient levels of the key micronutrients iron (Fe), zinc (Zn) and Vitamin A to meet daily dietary requirements. Experts estimate that a rice-based diet should contain 14.5 µg g(-1) Fe in endosperm, the main constituent of polished grain, but breeding programs have failed to achieve even half of that value. Transgenic efforts to increase the Fe concentration of rice endosperm include expression of ferritin genes, nicotianamine synthase genes (NAS) or ferritin in conjunction with NAS genes, with results ranging from two-fold increases via single-gene approaches to six-fold increases via multi-gene approaches, yet no approach has reported 14.5 µg g(-1) Fe in endosperm. METHODOLOGY/PRINCIPAL FINDINGS: Three populations of rice were generated to constitutively overexpress OsNAS1, OsNAS2 or OsNAS3, respectively. Nicotianamine, Fe and Zn concentrations were significantly increased in unpolished grain of all three of the overexpression populations, relative to controls, with the highest concentrations in the OsNAS2 and OsNAS3 overexpression populations. Selected lines from each population had at least 10 µg g(-1) Fe in polished grain and two OsNAS2 overexpression lines had 14 and 19 µg g(-1) Fe in polished grain, representing up to four-fold increases in Fe concentration. Two-fold increases of Zn concentration were also observed in the OsNAS2 population. Synchrotron X-ray fluorescence spectroscopy demonstrated that OsNAS2 overexpression leads to significant enrichment of Fe and Zn in phosphorus-free regions of rice endosperm. CONCLUSIONS: The OsNAS genes, particularly OsNAS2, show enormous potential for Fe and Zn biofortification of rice endosperm. The results demonstrate that rice cultivars overexpressing single rice OsNAS genes could provide a sustainable and genetically simple solution to Fe and Zn deficiency disorders affecting billions of people throughout the world.

Project description:BackgroundIdentification of the allelopathy-interrelated metabolites from the allelopathic rice rhizosphere is crucial to understand the allelopathic mechanism of rice, which in turn can promote its applications to farming. In this study, the metabolites from the rhizosphere soil of five different rice lines, including allelopathic rice accession PI312777 (PI) and non-allelopathic rice accession Lemont (Le) as well as their genetic derivatives (e.g., phenylalanine ammonia-lyase (PAL) gene overexpression transgenic lines of PI and Le, namely, PO and LO respectively, and PAL RNA interference line of PI, namely, PR) were identified and comparatively analyzed to explore the positive compounds that are involved in the process of rice allelopathy.ResultsThe results showed that 21 non-polar compounds and 21 polar compounds differed in content in the rhizosphere soil of PI and Le, which include several volatile fatty acids and long-chain fatty acids. The relative contents of fatty acids also differed between PAL overexpressing or RNA interference (RNAi)-silenced line and their wild-type respectively. Acetic acid content also differed among groups, i.e., it is higher in the high allelopathic potential rice. Further analysis showed that different metabolites from the ADS8 resin-extracted phase were more abundant than that those from the ADS21 resin-extracted phase, suggesting that the allelochemicals in root exudates of allelopathic rice are mainly non-polar substances. KEGG annotation of these differential metabolites revealed that these compounds were related to nutrient metabolism, secondary metabolite synthesis, signaling substance synthesis, and toxin degradation.ConclusionsRice allelochemicals deposited in the ADS8 resin-extracted phase were more abundant than those in the ADS21 resin-extracted phase. Allelochemicals in root exudates of allelopathic rice are mainly non-polar substances, and long-chain fatty acids are considered as allelopathy interrelated metabolites.

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Genomic prediction of zinc-biofortification potential in rice gene bank accessions.

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