Metabolomics and genomics combine to unravel the pathway for the presence of fragrance in rice

Progresses in biosynthesis pathway, regulation mechanism and potential application of 2-acetyl-1-pyrroline in fragrant rice

The formation of rice aroma is a complex process that is influenced by genetic and environmental factors. More than 500 fragrance compounds have been documented in fragrant rice, among which 2-AP dominates the aroma of rice. This paper introduced the identification of OsBadh2 in the biosynthesis of 2-AP in rice. Then, non-enzymatic and enzymatic pathways of the 2-AP biosynthesis have been comprehensively investigated. In detail, 2-AP biosynthesis-associated enzyme, such as OsBADH2, OsP5CS, OsGAD, OsGAPDH, OsProDH, OsOAT, OsODC and OsDAO, have been summarized, while MG and fatty acids are also implicated in modulating the biosynthesis of 2-AP by providing the acetyl groups. Moreover, extensive collections of traditional fragrant rice varieties have been collated, together with the OsBadh2 haplotypes of 312 fragrant rice germplasm in China. And finally, genetic engineering of OsBadh2 and other genes in the 2-AP biosynthesis to develop fragrant rice are discussed.

Metabolome and Transcriptome Unveil the Correlated Metabolites and Transcripts with 2-acetyl-1-pyrroline in Fragrant Rice

Fragrance is a valuable trait in rice varieties, with its aroma significantly influencing consumer preference. In this study, we conducted comprehensive metabolome and transcriptome analyses to elucidate the genetic and biochemical basis of fragrance in the Shangsixiangnuo (SSXN) variety, a fragrant indica rice cultivated in Guangxi, China. Through sensory evaluation and genetic analysis, we confirmed SSXN as strongly fragrant, with an 806 bp deletion in the BADH2 gene associated with fragrance production. In the metabolome analysis, a total of 238, 233, 105 and 60 metabolic compounds exhibited significant changes at the seedling (S), reproductive (R), filling (F), and maturation (M) stages, respectively. We identified four compounds that exhibited significant changes in SSXN across all four development stages. Our analyses revealed a significant upregulation of 2-acetyl-1-pyrroline (2AP), the well-studied aromatic compound, in SSXN compared to the non-fragrant variety. Additionally, correlation analysis identified several metabolites strongly associated with 2AP, including ethanone, 1-(1H-pyrrol-2-yl)-, 1H-pyrrole, and pyrrole. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) analysis highlighted the magenta and yellow modules as particularly enriched in aroma-related metabolites, providing insights into the complex aromatic compounds underlying the fragrance of rice. In the transcriptome analysis, a total of 5582, 5506, 4965, and 4599 differential expressed genes (DEGs) were identified across the four developmental stages, with a notable enrichment of the common pathway amino sugar and nucleotide sugar metabolism in all stages. In our correlation analysis between metabolome and transcriptome data, the top three connected metabolites, phenol-, 3-amino-, and 2AP, along with ethanone, 1-(1H-pyrrol-2-yl)-, exhibited strong associations with transcripts, highlighting their potential roles in fragrance biosynthesis. Additionally, the downregulated expression of the P4H4 gene, encoding a procollagen-proline dioxygenase that specifically targets proline, in SSXN suggests its involvement in proline metabolism and potentially in aroma formation pathways. Overall, our study provides comprehensive insights into the genetic and biochemical mechanisms underlying fragrance production in rice, laying the foundation for further research aimed at enhancing fragrance quality in rice breeding programs.

Biosynthesis of 2-Acetyl-1-pyrroline in Fragrant Rice: Recent Insights into Agro-management, Environmental Factors, and Functional Genomics

Rice is a staple food for more than half of the world's population, and rice fragrance is a key quality attribute which is highly desired by consumers and attracts premium prices in the international market. There are around 200 volatile compounds involved in rice fragrance, but 2-acetyl-1-pyrroline (2-AP) has been considered a master regulator of aroma in fragrant rice. Consequently, efforts were made to increase the 2-AP contents in the grain by managing agronomical practices or by using modern functional genomic tools, which successfully converted nonfragrant cultivars to fragrant rice. Furthermore, environmental factors were also reported to influence the 2-AP contents. However, a comprehensive analysis of 2-AP biosynthesis in response to agro-management practices, environmental factors, and the application of functional genomic tools for fragrant rice production was missing. In this Review, we summarize how micro/macronutrients, cultivation practices, amino acid precursors, growth regulators, and environmental factors, such as drought, salinity, light, and temperature, influence the 2-AP biosynthesis to modulate the aroma of fragrant rice. Furthermore, we also summarized the successful conversion of nonfragrant rice cultivars to fragrant rice using modern gene editing tools, such as RNAi, TALENS, and CRISPR-Cas9. Finally, we discussed and highlighted the future perspective and challenges related to the aroma of fragrant rice.

Metabolite Profiling of Wheat Response to Cultivar Improvement and Nitrogen Fertilizer

Both genetic improvement and the application of N fertilizer increase the quality and yields of wheat. However, the molecular kinetics that underlies the differences between them are not well understood. In this study, we performed a non-targeted metabolomic analysis on wheat cultivars from different release years to comprehensively investigate the metabolic differences between cultivar and N treatments. The results revealed that the plant height and tiller number steadily decreased with increased ears numbers, whereas the grain number and weight increased with genetic improvement. Following the addition of N fertilizer, the panicle numbers and grain weights increased in an old cultivar, whereas the panicle number and grain number per panicle increased in a modern cultivar. For the 1950s to 2010s cultivar, the yield increases due to genetic improvements ranged from -1.9% to 96.7%, whereas that of N application ranged from 19.1% to 81.6%. Based on the untargeted metabolomics approach, the findings demonstrated that genetic improvements induced 1.4 to 7.4 times more metabolic alterations than N fertilizer supply. After the addition of N, 69.6%, 29.4%, and 33.3% of the differential metabolites were upregulated in the 1950s, 1980s, and 2010s cultivars, respectively. The results of metabolic pathway analysis of the identified differential metabolites via genetic improvement indicated enrichment in 1-2 KEGG pathways, whereas the application of N fertilizer enriched 2-4 pathways. Our results provide new insights into the molecular mechanisms of wheat quality and grain yield developments.

A comparative HS-SPME/GC-MS-based metabolomics approach for discriminating selected japonica rice varieties from different regions of China in raw and cooked form

Japonica rice is widely planted in different regions of China. Rice of different geographical origins may have substantially different economic values. In this study, An untargeted metabolomics based approach using headspace solid-phase microextraction coupled to gas chromatography-mass spectrometry (HS-SPME/GC-MS) was applied to distinguish 27 japonica rice varieties originated from South, Northern and Northeastern China in raw and cooked form, respectively. Orthogonal partial least-squares discriminant analysis (OPLS-DA) models exhibited good geographic discrimination. Sixteen and twenty-two volatiles were selected as the discriminant markers in raw and cooked rice, respectively. However, only hexanal, 3,5-octadien-2-one and 2-butyl-2-octenal were selected both in raw and cooked rice. Markers in raw rice mainly involved in terpenes, lipoxygenases, indole, and shikimate and benzoic acid pathways. Markers in cooked rice were mainly derived from lipid oxidation. The results provided a deeper understanding of volatiles variation of rice in China from different geographic origins.

Determination of 2-Acetyl-1-pyrroline via a Color-Change Reaction Using Chromium Hexacarbonyl

At present, there is no colorimetric method for the quantitation of the aroma compound 2-acetyl-1-pyrroline (2AP). A novel colorimetric method was developed for the determination of 2AP content using chromium hexacarbonyl (Cr(CO)₆) as a reagent. The reaction of synthetic 2AP with chromium hexacarbonyl reagent solution in the presence of light produced a green product with an absorption maximum (λ_max) at 623 nm. GC–MS was used to confirm the color-change reaction, which showed the loss of 2AP after the addition of Cr(CO)₆. This novel method enables facile and cost-effective determination of 2AP in fragrant rice. A comparative analysis of fragrant and nonfragrant rice grain extracts showed that no color-change reaction occurred with the nonfragrant rice sample. A limit of detection (LOD) of 2.00 mg L⁻¹ was determined by method validation with an effective linear concentration ranging from 5.00 to 60.00 mg L⁻¹ of 2AP. The results obtained using the developed colorimetric method were consistent with those obtained by automated static headspace gas chromatography with nitrogen-phosphorus detection (SHS-GC–NPD).

Production of aromatic three-line hybrid rice using novel alleles of BADH2

Aroma is a key grain quality trait that directly influences the market price of rice globally. Loss of function of betaine aldehyde dehydrogenase 2 (OsBADH2) affects the biosynthesis of 2-acetyl-1-pyrroline (2-AP), which is responsible for aroma in fragrant rice. The current study was aimed at creating new alleles of BADH2 using CRISPR/Cas9 gene editing technology under the genetic background of the japonica Ningjing 1 (NJ1) and indica Huang Huazhan (HHZ) varieties. Sensory evaluation and analysis using headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) showed that the grains of the four homozygous T₁ lines with new alleles of BADH2 (nj1-cr ^BADH2 -1, nj1-cr ^BADH2 -2, hhz-cr ^BADH2 -1 and hhz-cr ^BADH2 -2) produced moderate fragrance and had significantly increased 2-AP content compared with wild-types. Moreover, there were no significant differences in the amylose content and gelatinization temperature among the four lines with new alleles of BADH2 to the wild-types. Thereafter, we crossed the HHZ background new alleles of BADH2 with CMS line Taonong 1A (TN1A) to produce a three-line hybrid variety B-Tao-You-Xiangzhan (BTYXZ) with increased grain aroma. The 2-AP content in grains of the improved BTYXZ-1 and BTYXZ-2 reached at 26.16 and 18.74 μg/kg, and the gel consistency of BTYXZ-1 and BTYXZ-2 increased significantly by 9.1% and 6.5%, respectively, compared with the wild-type Tao-You-Xiangzhan (TYXZ). However, the γ-aminobutyric acid (GABA) content in the improved three-line hybrid rice BTYXZ-1 (5.6 mg/100 g) and BTYXZ-2 (10.7 mg/100 g) was significantly lower than that of the TYXZ. These results demonstrated that CRISPR/Cas9 gene editing technology could be successfully utilized in improving aroma in non-fragrant japonica and indica varieties. In addition, the newly developed BADH2 alleles provided important genetic resources for grain aroma improvement in three-line hybrid rice.

Metabolomics and genomics in natural products research: complementary tools for targeting new chemical entities

Covering: 2010 to 2021Organisms in nature have evolved into proficient synthetic chemists, utilizing specialized enzymatic machinery to biosynthesize an inspiring diversity of secondary metabolites. Often serving to boost competitive advantage for their producers, these secondary metabolites have widespread human impacts as antibiotics, anti-inflammatories, and antifungal drugs. The natural products discovery field has begun a shift away from traditional activity-guided approaches and is beginning to take advantage of increasingly available metabolomics and genomics datasets to explore undiscovered chemical space. Major strides have been made and now enable -omics-informed prioritization of chemical structures for discovery, including the prospect of confidently linking metabolites to their biosynthetic pathways. Over the last decade, more integrated strategies now provide researchers with pipelines for simultaneous identification of expressed secondary metabolites and their biosynthetic machinery. However, continuous collaboration by the natural products community will be required to optimize strategies for effective evaluation of natural product biosynthetic gene clusters to accelerate discovery efforts. Here, we provide an evaluative guide to scientific literature as it relates to studying natural product biosynthesis using genomics, metabolomics, and their integrated datasets. Particular emphasis is placed on the unique insights that can be gained from large-scale integrated strategies, and we provide source organism-specific considerations to evaluate the gaps in our current knowledge.

Metabolomics and complementary techniques to investigate the plant phytochemical cosmos

Covering: up to 2021Plants and their associated microbial communities are known to produce millions of metabolites, a majority of which are still not characterized and are speculated to possess novel bioactive properties. In addition to their role in plant physiology, these metabolites are also relevant as existing and next-generation medicine candidates. Elucidation of the plant metabolite diversity is thus valuable for the successful exploitation of natural resources for humankind. Herein, we present a comprehensive review on recent metabolomics approaches to illuminate molecular networks in plants, including chemical isolation and enzymatic production as well as the modern metabolomics approaches such as stable isotope labeling, ultrahigh-resolution mass spectrometry, metabolome imaging (spatial metabolomics), single-cell analysis, cheminformatics, and computational mass spectrometry. Mass spectrometry-based strategies to characterize plant metabolomes through metabolite identification and annotation are described in detail. We also highlight the use of phytochemical genomics to mine genes associated with specialized metabolites' biosynthesis. Understanding the metabolic diversity through biotechnological advances is fundamental to elucidate the functions of the plant-derived specialized metabolome.

Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management

Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.

Consumer Acceptance of Brown and White Rice Varieties

Rice is consumed as a staple food by more than half of the world's population. Due to a higher fibre and micronutrient content, brown rice is more nutritious than white rice, but the consumption of brown rice is significantly lower than that of white rice, primarily due to sensory attributes. Therefore, the present research aimed to identify the sensory attributes which drive liking of Australian-grown brown and white rice varieties. Participants (n = 139) tasted and scored (9-point hedonic scale) their liking (i.e., overall liking, aroma, colour and texture) of brown and white rice types of Jasmine (Kyeema), Low GI (Doongara), and Medium grain rice (Amaroo). In addition, participants scored aroma, colour, hardness, fluffiness, stickiness, and chewiness, on Just About Right Scales. A within-subjects crossover design with randomised order (William's Latin Square design) was used with six repeated samples for liking and Just About Right scales. Penalty analyses were applied to determine the relative influence of perception of sensory attributes on consumer liking of the rice varieties. Across all varieties, white rice was liked more than brown rice due to the texture and colour, and Jasmine rice was preferred over Low GI and Medium Grain. Rice texture (hardness and chewiness) was the most important sensory attribute among all rice varieties and aroma was important for driving of liking between white rice varieties.

Promoting Human Nutrition and Health through Plant Metabolomics: Current Status and Challenges

Simple Summary

This review summarizes the status, applications, and challenges of plant metabolomics in the context of crop breeding, food quality and safety, and human nutrition and health. It also highlights the importance of plant metabolomics in elucidating biochemical and genetic bases of traits associated with nutritive and healthy beneficial foods and other plant products to secure food supply, to ensure food quality, to protect humans from malnutrition and other diseases. Meanwhile, this review calls for comprehensive collaborations to accelerate relevant researches and applications in the context of human nutrition and health.

Abstract

Plant metabolomics plays important roles in both basic and applied studies regarding all aspects of plant development and stress responses. With the improvement of living standards, people need high quality and safe food supplies. Thus, understanding the pathways involved in the biosynthesis of nutritionally and healthily associated metabolites in plants and the responses to plant-derived biohazards in humans is of equal importance to meet people’s needs. For each, metabolomics has a vital role to play, which is discussed in detail in this review. In addition, the core elements of plant metabolomics are highlighted, researches on metabolomics-based crop improvement for nutrition and safety are summarized, metabolomics studies on plant natural products including traditional Chinese medicine (TCM) for health promotion are briefly presented. Challenges are discussed and future perspectives of metabolomics as one of the most important tools to promote human nutrition and health are proposed.

Untargeted and Targeted Metabolomic Profiling of Australian Indigenous Fruits

Selected Australian native fruits such as Davidson's plum, finger lime and native pepperberry have been reported to demonstrate potent antioxidant activity. However, comprehensive metabolite profiling of these fruits is limited, therefore the compounds responsible are unknown, and further, the compounds of nutritional value in these native fruits are yet to be described. In this study, untargeted and targeted metabolomics were conducted using the three fruits, together with assays to determine their antioxidant activities. The results demonstrate that targeted free and hydrolysed protein amino acids exhibited high amounts of essential amino acids. Similarly, important minerals like potassium were detected in the fruit samples. In antioxidant activity, Davidson's plum reported the highest activity in ferric reducing power (FRAP), finger lime in antioxidant capacity (ABTS), and native pepperberry in free radical scavenging (DPPH) and phosphomolybdenum assay. The compounds responsible for the antioxidant activity were tentatively identified using untargeted GC×GC-TOFMS and UHPLC-QqQ-TOF-MS/MS metabolomics. A clear discrimination into three clusters of fruits was observed using principal component analysis (PCA) and partial least squares (PLS) analysis. The correlation study identified a number of compounds that provide the antioxidant activities. GC×GC-TOFMS detected potent aroma compounds of limonene, furfural, and 1-R-α-pinene. Based on the untargeted and targeted metabolomics, and antioxidant assays, the nutritional potential of these Australian bush fruits is considerable and supports these indigenous fruits in the nutraceutical industry as well as functional ingredients for the food industry, with such outcomes benefiting Indigenous Australian communities.

Metabolite database for root, tuber, and banana crops to facilitate modern breeding in understudied crops

Roots, tubers, and bananas (RTB) are vital staples for food security in the world's poorest nations. A major constraint to current RTB breeding programmes is limited knowledge on the available diversity due to lack of efficient germplasm characterization and structure. In recent years large-scale efforts have begun to elucidate the genetic and phenotypic diversity of germplasm collections and populations and, yet, biochemical measurements have often been overlooked despite metabolite composition being directly associated with agronomic and consumer traits. Here we present a compound database and concentration range for metabolites detected in the major RTB crops: banana (Musa spp.), cassava (Manihot esculenta), potato (Solanum tuberosum), sweet potato (Ipomoea batatas), and yam (Dioscorea spp.), following metabolomics-based diversity screening of global collections held within the CGIAR institutes. The dataset including 711 chemical features provides a valuable resource regarding the comparative biochemical composition of each RTB crop and highlights the potential diversity available for incorporation into crop improvement programmes. Particularly, the tropical crops cassava, sweet potato and banana displayed more complex compositional metabolite profiles with representations of up to 22 chemical classes (unknowns excluded) than that of potato, for which only metabolites from 10 chemical classes were detected. Additionally, over 20% of biochemical signatures remained unidentified for every crop analyzed. Integration of metabolomics with the on-going genomic and phenotypic studies will enhance 'omics-wide associations of molecular signatures with agronomic and consumer traits via easily quantifiable biochemical markers to aid gene discovery and functional characterization.

Evaluation of Whole-Genome Sequence, Genetic Diversity, and Agronomic Traits of Basmati Rice (Oryza sativa L.)

Basmati is considered a unique varietal group of rice (Oryza sativa L.) because of its aroma and superior grain quality. Previous genetic analyses of rice showed that most of the Basmati varieties are classified into the aromatic group. Despite various efforts, genomic relationship of Basmati rice with other varietal groups and genomic variation in Basmati rice are yet to be understood. In the present study, we resequenced the whole genome of three traditional Basmati varieties at a coverage of more than 25X using Illumina HiSeq2500 and mapped the obtained sequences to the reference genome sequences of Nipponbare (japonica rice), Kasalath (aus rice), and Zhenshan 97 (indica rice). Comparison of these sequences revealed common single nucleotide polymorphisms (SNPs) in the genic regions of three Basmati varieties. Analysis of these SNPs revealed that Basmati varieties showed fewer sequence variations compared with the aus group than with the japonica and indica groups. Gene ontology (GO) enrichment analysis indicated that SNPs were present in genes with various biological, molecular, and cellular functions. Additionally, functional annotation of the Basmati mutated gene cluster shared by Nipponbare, Kasalath, and Zhenshan 97 was found to be associated with the metabolic process involved in the cellular aromatic compound, suggesting that aroma is an important specific genomic feature of Basmati varieties. Furthermore, 30 traditional Basmati varieties were classified into three different groups, aromatic (22 varieties), aus (four varieties), and indica (four varieties), based on genome-wide SNPs. All 22 aromatic Basmati varieties harbored the fragrant-inducing Badh2 allele. We also performed comparative analysis of 13 key agronomic and grain quality traits of Basmati rice and other rice varieties. Three traits including length-to-width ratio of grain (L/W ratio), panicle length (PL), and amylose content (AC) showed significant (P < 0.05 and P < 0.01) differences between the aromatic and indica/aus groups. Comparative analysis of genome structure, based on genome sequence variation and GO analysis, revealed that the Basmati genome was derived mostly from the aus and japonica groups. Overall, whole-genome sequence data and genetic diversity information obtained in this study will serve as an important resource for molecular breeding and genetic analysis of Basmati varieties.

Occurrence of 2-Acetyl-1-pyrroline and Its Nonvolatile Precursors in Celtuce (Lactuca sativa L. var. augustana)

Lactuca sativa L. var. augustana has a basmati rice-like odor with a green note in the background. This typical odor is due to the release of 2-acetyl-1-pyrroline (2-AP) after heating, which is confirmed by volatile analysis. Recent metabolomic and genomic studies of different rice varieties highlighted that the presence of 2-AP was linked to the accumulation of γ-aminobutyraldehyde; genome-wide association studies also indicated that acyltransferases were involved. These results prompted us to analyze nonvolatile compound precursors in L. sativa L. var. augustana (celtuce) to search for compound derivatives with a 4,5-dioxohexan alkyl amine-like structure. Hypothetical synthetic compounds were prepared from a reductive amination between 4,5-dioxohexanal and glycine, alanine, aspartic acid, and glutamic acid to give 2-(2-acetylpyrrolidin-1-yl) alkanoic acid. We proved that 2-(2-acetylpyrrolidin-1-yl) propionic acid is present in L. sativa, which, when thermally treated, released 2-AP. Other 2-AP precursors occurring in this plant are discussed.

Nitrogen application and different water regimes at booting stage improved yield and 2-acetyl-1-pyrroline (2AP) formation in fragrant rice

BACKGROUND

Water (W) and nitrogen (N) management generally cause regulations in the 2-acetyl-1-pyrroline (2AP) accumulation in fragrant rice; nevertheless, the feasibility of such management strategies at booting stage in improving 2AP accumulation has not been examined in details.

METHODS

Field experiments were conducted in the early season (March-July) and repeated in the late season (July-November) in 2013. The treatments were applied urea (90 kg ha^- 1), calcium super phosphate (90 kg ha^- 1) and potassium chloride (195 kg ha^- 1) as basal fertilizer, and urea (65 kg ha^- 1) at tillering stage. Three N levels i.e., 0 kg N ha^- 1 (N1), 30 kg N ha^- 1 (N2), and 60 kg N ha^- 1 (N3) and three water levels i.e., W1 treatment (well-watered treatment with water layer of 2-4 cm), W2 treatment (soil water potential was - 15 ± 5 kPa), and W3 treatment (soil water potential was - 25 ± 5 kPa) at booting stage was set up for three rice varieties i.e., Nongxiang 18, Yungengyou 14 and Basmati. The grain yield, head milled rice yield, 2AP contents and the biochemical parameters related to 2AP formation were investigated.

RESULTS

Result indicated that W and N dynamics regulated the grain yield, head milled rice yield, and 2AP contents in brown rice across three varieties. The N2 and N3 treatment significantly increased the 2AP contents in brown rice by 9.54% and 11.95%, and 8.88% and 32.54% in the early and the late season, respectively; improved grain yield and head milled rice yield. The W3 treatment improved grain yield, head milled rice yield and 2AP content. Significant W and N interaction effect on 2AP content in brown rice was detected, where the W3 N3 treatment showed the strongest interaction regarding improvement of 2AP contents in brown rice. The 2AP accumulation and its related biochemical parameters and their relationships in different plant tissues at different growth stages under W and N treatments had also been assessed. The 2AP content, P5C content and DAO activity during grain filling periods was highly related to the 2AP content in brown rice.

CONCLUSION

This study revealed that the 60 kg N ha^- 1 coupled with - 25 ± 5 kPa treatment showed the best positive effects on yield and aroma in fragrant rice, suggested that water and nitrogen management at booting stage can improve grain yield and fragrance in fragrant rice. However, further study to evaluate the metabolic and molecular basis of 2AP accumulation in fragrant rice is needed.

The Future of Digital Sequence Information for Plant Genetic Resources for Food and Agriculture

The recent debates on the legal status of "digital sequence information" (DSI) at the international level could have extensive consequences for the future of agriculture and food security. A large majority of recent advances in biology, medicine, or agriculture were achieved by sharing and mining of freely accessible sequencing data. It is most probably because of the tremendous success of modern genomics and advances of synthetic biology that concerns were raised about possible fair and equitable ways of sharing data. The DSI concept is relatively new, and all concerned parties agreed upon the need for a clear definition. For example, the extent to which DSI understanding is limited only to genetic sequence data has to be clarified. In this paper, I focus on a subset of DSI essential to humankind: the DSI originating from plant genetic resources for food and agriculture (PGRFA). Two international agreements shape the conservation and use of plant genetic resources: the Convention on Biodiversity and the International Treaty for Plant Genetic Resources for Food and Agriculture. In an attempt to mobilize DSI users and producers involved in research, breeding, and conservation, I describe here how the increasing amount of genomic data, information, and studies interact with the existing legal framework at the global level. Using possible scenarios, I will emphasize the complexity of the issues surrounding DSI for PGRFA and propose potential ways forward for developing an inclusive governance and fair use of these genetic resources.

Urinary volatile metabolites of amygdala-kindled mice reveal novel biomarkers associated with temporal lobe epilepsy

Epilepsy is a chronic neurological disorder affecting mammals, including humans. Uncontrolled epilepsy is associated with poor quality of life, accidents, and sudden death. In particular, temporal lobe epilepsy (TLE) is the most common type of pharmacoresistant epilepsy, which easily gets out of control in human adults. The aim of this study was to profile urinary volatile organic compounds (VOCs) in a mouse model of TLE using solid-phase microextraction (SPME) gas chromatography mass spectrometry (GC-MS). Thirteen urinary VOCs exhibited differential abundance between epileptic and control mice, and the corresponding areas under the receiver operating characteristic (ROC) curve were greater than 0.8. Principal component analysis (PCA) based on these 13 VOCs separated epileptic from sham operated-mice, suggesting that all these 13 VOCs are epilepsy biomarkers. Promax rotation and dendrogram analysis concordantly separated the 13 VOCs into three groups. Stepwise linear discriminant analysis extracted methanethiol; disulfide, dimethyl; and 2-butanone as predictors. Based on known metabolic systems, the results suggest that TLE induced by amygdala stimulation could affect both endogenous metabolites and the gut flora. Future work will elucidate the physiological meaning of the VOCs as end-products of metabolic networks and assess the impact of the metabolic background involved in development of TLE.

The genetics and biosynthesis of 2-acetyl-1-pyrroline in fragrant rice

Rice (Oryza sativa L.) is a staple food for the majority of the world's population. Rice fragrance, aroma, or scent is not just a cooking quality, but also an eating quality of rice. Rice fragrance is a trait that is widely desired among rice consumers. Consequently, rice producers are sorting for rice cultivars with strong fragrance. High demand for fragrant rice cultivars has prompted rice breeders and researchers to investigate the genetics and the ways to improve fragrance in rice. It has been established by many researches that fgr gene on the chromosome 8 of rice controls its fragrance. As with other plants, rice contains BADH but because rice does not accumulate GB, a catalyst for BADH coding, BADH1 on chromosome 4 of rice and BADH2 on chromosome 8 of rice have been widely reported to be responsible for encoding BADH. badh2, a recessive allele of BADH2 has been confirmed to be responsible for fragrance in rice. badh2 and its alleles have been associated with the accumulation and synthesis of 2AP. Proline, ornithine, glutamate, methylglyoxal, Δ1-pyrroline-5-carboxylate synthetase and glyceraldehyde-3-phosphate dehydrogenase have all been identified as the precursors for the synthesis and accumulation of 2AP. By reviewing and summarising the main results of various researchers, we have been able to elucidate how various genes and metabolites influence 2AP accumulation in fragrant rice. It is our hope that this paper will be beneficial to researchers, who are working on the improvement of rice fragrance.

Comparative Rice Bran Metabolomics across Diverse Cultivars and Functional Rice Gene⁻Bran Metabolite Relationships

Rice (Oryza sativa L.) processing yields ~60 million metric tons of bran annually. Rice genes producing bran metabolites of nutritional and human health importance were assessed across 17 diverse cultivars from seven countries using non-targeted metabolomics, and resulted in 378–430 metabolites. Gambiaka cultivar had the highest number and Njavara had the lowest number of metabolites. The 71 rice bran compounds of significant variation by cultivar included 21 amino acids, seven carbohydrates, two metabolites from cofactors and vitamins, 33 lipids, six nucleotides, and two secondary metabolites. Tryptophan, α-ketoglutarate, γ-tocopherol/β-tocopherol, and γ-tocotrienol are examples of bran metabolites with extensive cultivar variation and genetic information. Thirty-four rice bran components that varied between cultivars linked to 535 putative biosynthetic genes using to the OryzaCyc 4.0, Plant Metabolic Network database. Rice genes responsible for bran composition with animal and human health importance is available for rice breeding programs to utilize in crop improvement.

Quality evaluation, fatty acid analysis and untargeted profiling of volatiles in Cambodian rice

This study provides the first investigation of the physical traits, pasting properties and volatile compounds of Cambodian rice cultivars, including traditional, improved, and improved traditional varieties, allowing for their differentiation as high and low quality rice. Analysis of the grain quality traits illustrates interesting features of traditional varieties and correlations between traits that assist with understanding texture. Untargeted profiling of volatile compounds shows that high quality fragrant varieties not only contain 2-acetyl-1-pyrroline but also several other compounds, including aldehydes, alcohols and 2-alkylfurans that contribute to overall aroma. Moreover, low odour threshold volatile compounds, which can be derived from the oxidation of unsaturated fatty acids, were more abundant in the fragrant varieties. The percentage area of both oleic and linoleic acid were found to be significantly different among the rice varieties tested. Such findings suggest that unsaturated fatty acids in milled rice contribute to rice fragrance, and thereby to overall quality.