A novel integrated method for large-scale detection, identification, and quantification of widely targeted metabolites: application in the study of rice metabolomics.

Plant metabolites are important to world food security in terms of maintaining sustainable yield and providing food with enriched phytonutrients. Here we report comprehensive profiling of 840 metabolites and a further metabolic genome-wide association study based on ∼6.4 million SNPs obtained from 529 diverse accessions of Oryza sativa. We identified hundreds of common variants influencing numerous secondary metabolites with large effects at high resolution. We observed substantial heterogeneity in the natural variation of metabolites and their underlying genetic architectures among different subspecies of rice. Data mining identified 36 candidate genes modulating levels of metabolites that are of potential physiological and nutritional importance. As a proof of concept, we functionally identified or annotated five candidate genes influencing metabolic traits. Our study provides insights into the genetic and biochemical bases of rice metabolome variation and can be used as a powerful complementary tool to classical phenotypic trait mapping for rice improvement.

Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism.

Epidemiological studies suggested that the low incidence of certain chronic diseases in rice-consuming regions of the world might be associated with the antioxidant compound contents of rice. The molecules with antioxidant activity contained in rice include phenolic acids, flavonoids, anthocyanins, proanthocyanidins, tocopherols, tocotrienols, γ-oryzanol, and phytic acid. This review provides information on the contents of these compounds in rice using a food composition database built from compiling data from 316 papers. The database provides access to information that would have otherwise remained hidden in the literature. For example, among the four types of rice ranked by color, black rice varieties emerged as those exhibiting the highest antioxidant activities, followed by purple, red, and brown rice varieties. Furthermore, insoluble compounds appear to constitute the major fraction of phenolic acids and proanthocyanidins in rice, but not of flavonoids and anthocyanins. It is clear that to maximize the intake of antioxidant compounds, rice should be preferentially consumed in the form of bran or as whole grain. With respect to breeding, japonica rice varieties were found to be richer in antioxidant compounds compared with indica rice varieties. Overall, rice grain fractions appear to be rich sources of antioxidant compounds. However, on a whole grain basis and with the exception of γ-oryzanol and anthocyanins, the contents of antioxidants in other cereals appear to be higher than those in rice.

/pdf/rice-antioxidants-phenolic-acids-flavonoids-anthocyanins-1ybtlk419j.pdf

Rice antioxidants: phenolic acids, flavonoids, anthocyanins, proanthocyanidins, tocopherols, tocotrienols, γ-oryzanol, and phytic acid

Background: The domestication of Asian rice (Oryza sativa) was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers. Methodology/Principal Findings: In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV) consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations. Conclusions/Significance: Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species.

/pdf/genomic-diversity-and-introgression-in-o-sativa-reveal-the-1u27acr71w.pdf

Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome.

Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variation in eukaryotic genomes. SNPs may be functionally responsible for specific traits or phenotypes, or they may be informative for tracing the evolutionary history of a species or the pedigree of a variety. As genetic markers, SNPs are rapidly replacing simple sequence repeats (SSRs) because they are more abundant, stable, amenable to automation, efficient, and increasingly cost-effective. The integration of high throughput SNP genotyping capability promises to accelerate genetic gain in a breeding program, but also imposes a series of economic, organizational and technical hurdles. To begin to address these challenges, SNP-based resources are being developed and made publicly available for broad application in rice research. These resources include large SNP datasets, tools for identifying informative SNPs for targeted applications, and a suite of custom-designed SNP assays for use in marker-assisted and genomic selection, association and QTL mapping, positional cloning, pedigree analysis, variety identification and seed purity testing. SNP resources also make it possible for breeders to more efficiently evaluate and utilize the wealth of natural variation that exists in both wild and cultivated germplasm with the aim of improving the productivity and sustainability of agriculture.

/pdf/development-of-genome-wide-snp-assays-for-rice-256mz3kd9h.pdf

Development of genome-wide SNP assays for rice

A valuable core collection that is a subset of a whole germplasm collection should capture most of the variation present in the whole collection, while allowing for more efficient evaluation and management due to smaller size. The United States Department of Agriculture (USDA) rice (Oryza sativa L.) core subset (RCS), assembled by stratified random sampling, consists of 1790 entries from 114 countries and represents approximately 10% of the 18412 accessions in the rice whole collection (RWC). Data for this study were obtained from the USDA germplasm system at www.ars-grin.gov for the RWC and from an evaluation conducted in 2002 for the RCS. Comparative analysis for frequency distributions of 14 descriptors demonstrated that the RCS was highly correlated with the RWC (r = 0.94, P 0.9, indicating that the RCS was highly representative of the RWC. Correlation coefficients for the other six descriptors were lower (0.65-0.88), but still significant.

Development and evaluation of a core subset of the USDA rice germplasm collection

Emerging evidence supports that cooked rice (Oryza sativa L.) contains metabolites with biomedical activities, yet little is known about the genetic diversity that is responsible for metabolite variation and differences in health traits. Metabolites from ten diverse varieties of cooked rice were detected using ultra performance liquid chromatography coupled to mass spectrometry. A total of 3,097 compounds were detected, of which 25% differed among the ten varieties. Multivariate analyses of the metabolite profiles showed that the chemical diversity among the varieties cluster according to their defined subspecies classifications: indica, japonica, and aus. Metabolite-specific genetic diversity in rice was investigated by analyzing a collection of single nucleotide polymorphisms (SNPs) in genes from biochemical pathways of nutritional importance. Two classes of bioactive compounds, phenolics and vitamin E, contained nonsynonymous SNPs and SNPs in the 5′ and 3′ untranslated regions for genes in their biosynthesis pathways. Total phenolics and tocopherol concentrations were determined to examine the effect of the genetic diversity among the ten varieties. Per gram of cooked rice, total phenolics ranged from 113.7 to 392.6 µg (gallic acid equivalents), and total tocopherols ranged between 7.2 and 20.9 µg. The variation in the cooked rice metabolome and quantities of bioactive components supports that the SNP-based genetic diversity influenced nutritional components in rice, and that this approach may guide rice improvement strategies for plant and human health.

/pdf/metabolomic-and-functional-genomic-analyses-reveal-varietal-4iqlavrjdo.pdf

Metabolomic and functional genomic analyses reveal varietal differences in bioactive compounds of cooked rice.

http://csu-cvmbs.colostate.edu/documents/erhs-forster-food-chemistry-eryan-lab.pdf

Rice varietal differences in bioactive bran components for inhibition of colorectal cancer cell growth

Whole grain rice is a rich source of fiber, nutrients, and phytochemicals that may promote gastrointestinal health, but such beneficial components are typically removed with the bran during polishing. Soluble feruloylated arabinoxylan oligosaccharides (FAXO) and polyphenols (RBPP) isolated from rice bran are hypothesized to have positive impacts on human gut microbiota through a prebiotic function. Using an in vitro human fecal fermentation bioassay, FAXO and RBPP treatments were assessed for short-chain fatty acids (SCFA) production patterns and by evaluating their impacts on the phylogentic composition of human gut microbiota by 16S rRNA gene sequencing. Fresh fecal samples collected from healthy adults (n = 10, 5 males, 5 females) were diluted with anaerobic medium. Each sample received five treatments: CTRL (no substrates), FOS (fructooligosaccharides), FAXO, RBPP, and MIX (FAXO with RBPP). Samples were incubated at 37 °C and an aliquot was withdrawn at 0, 4, 8, 12, and 24 h Results showed that SCFA production was significantly increased with FAXO and was comparable to fermentation with FOS, a well-established prebiotic. RBPP did not increase SCFA productions, and no significant differences in total SCFA production were observed between FAXO and MIX, indicating that RBPP does not modify FAXO fermentation. Changes in microbiota population were found in FAXO treatment, especially in Bacteroides, Prevotella, and Dorea populations, indicating that FAXO might modulate microbiota profiles. RBPP and MIX increased Faecalibacterium, specifically F. prausnitzii. Combined FAXO and RBPP fermentation increased abundance of butyrogenic bacteria, Coprococcus and Roseburia, suggesting some interactive activity. Results from this study support the potential for FAXO and RBPP from rice bran to promote colon health through a prebiotic function.

/pdf/in-vitro-fermentation-patterns-of-rice-bran-components-by-2r2x7via9w.pdf

In vitro Fermentation Patterns of Rice Bran Components by Human Gut Microbiota

Rice ( L.) end-use cooking quality is vital for producers and billions of consumers worldwide. Grain quality is a complex trait with interacting genetic and environmental factors. Deciphering the complex genetic architecture associated with grain quality provides essential information for improved breeding strategies to enhance desirable traits that are stable across variable climatic and environmental conditions. In this study, genome-wide association (GWA) analysis of three rice diversity panels, the USDA rice core subset (1364 accessions), the minicore (MC) (173 accessions after removing non-), and the high density rice array-MC (HDMC) (383 accessions), with simple sequence repeats, single nucleotide polymorphic markers, or both, revealed large- and small-effect loci associated with known genes and previously uncharacterized genomic regions. Clustering of the significant regions in the GWA results suggests that multiple grain quality traits are inherited together. The 11 novel candidate loci for grain quality traits and the seven candidates for grain chalk identified are involved in the starch biosynthesis pathway. This study highlights the intricate pleiotropic relationships that exist in complex genotype-phenotypic associations and gives a greater insight into effective breeding strategies for grain quality improvement.

Ming-Hsuan Chen

Papers

Development and evaluation of a core subset of the USDA rice germplasm collection

Metabolomic and functional genomic analyses reveal varietal differences in bioactive compounds of cooked rice.

Rice varietal differences in bioactive bran components for inhibition of colorectal cancer cell growth

In vitro Fermentation Patterns of Rice Bran Components by Human Gut Microbiota

Association Analysis of Three Diverse Rice (Oryza sativa L.) Germplasm Collections for Loci Regulating Grain Quality Traits.