Inactivation of an aminoaldehyde dehydrogenase is responsible for fragrance in rice

Exogenous application of abscisic acid enhanced 2-acetyl-1-pyrroline biosynthesis, accumulation, and antioxidant activities in aromatic rice

BACKGROUND

Abscisic acid (ABA) is a crucial endogenous hormone in plants, regulating a myriad of processes integral to plant growth and development. However, there has been no reported impact on the production of aromatic rice following the application of exogenous ABA. Aromatic rice not only possesses intense aroma but also boasts higher nutritional value. 2-Acetyl-1-pyrroline (2-AP) is the primary compound responsible for the distinctive aroma of aromatic rice. A two-year field experiment was conducted to explore the impact of exogenous ABA application on the biosynthesis and accumulation of 2-AP, as well as the physiological characteristics, yield, and quality of aromatic rice varieties.

RESULTS

The two aromatic rice varieties, Meixiangzhan-2 (MXZ2) and Nanjingxiangzhan (NJXZ), underwent five applications of 20 mg/L abscisic acid (ABA) from the breakthrough stage, whereas the control group (CK) received deionized water sprays.The results indicated that the application of exogenous ABA significantly boosted the 2-AP content by 20.7%, primarily by enhancing the levels of its precursors and the activities of enzymes involved in 2-AP biosynthesis. Exogenous ABA also upregulated the transcription levels of ProDH, P5CS2, OAT, and DAO4 while downregulating BADH2 transcription. Furthermore, exogenous ABA strengthened the antioxidant activites (superoxide dismutase, peroxidase, and catalase) of aromatic rice, although it led to increased malondialdehyde content and slight decreases in yield and quality. Notably, compared with superior grains, exogenous ABA application had a more pronounced effect on enhancing the aroma of inferior grains in aromatic rice with fewer negative effects.

CONCLUSIONS

The exogenous application of ABA from the breakthrough stage notably elevated the biosynthesis and accumulation of 2-AP in aromatic rice production. This was achieved by augmenting the content of its precursors and the activities of related synthetic enzymes, along with an enhancement in antioxidant activities. However, the impact on the yield and quality of aromatic rice remained relatively modest.

Enhancement of cold tolerance in tea plants (Camellia sinensis) by glycine betaine accumulation through CsBADH overexpression

Cold stress significantly limits the growth and yield of tea plants (Camellia sinensis (L.) O. Kuntze), particularly in northern China, may lead to huge economic losses. Glycine betaine (GB), an osmotic regulator, is widely applied in crop resistance to abiotic stress. This study investigates the role of GB and its biosynthetic enzyme CsBADH in enhancing cold tolerance in tea plants. Two cultivars, 'Shuchazao' (cold-resistant) and 'Baiye 1' (cold-sensitive), were subjected to low temperature stress (0 °C). GB accumulation was measured, revealing that 'Shuchazao' exhibited 1.4-fold higher GB levels than 'Baiye 1', suggesting a link between higher GB accumulation and cold tolerance. Exogenous GB treatment improved cold resistance, especially in the cold-sensitive cultivar 'Baiye 1'. The CsBADH gene, a key enzyme in GB biosynthesis, was cloned and expressed in Escherichia coli, confirming its activity. Transgenic Arabidopsis thaliana, Nicotiana tabacum, and C. sinensis plants overexpressing CsBADH showed increased GB levels (1.5- to 2.4-fold), proline content, peroxidase (POD) activities, and enhanced cold tolerance, while silencing CsBADH decreased GB accumulation and cold resistance. These findings demonstrate that CsBADH plays a critical role in cold stress response by promoting GB accumulation, offering potential strategies for improving the resilience of tea and other leaf crops to cold stress.

Genome-wide association analysis reveals regulatory genes for the metabolite synthesis of 2-acetyl-1-pyrroline in aromatic coconut (Cocos nucifera L.)

Coconut (Cocos nucifera L.) is a key tropical economic tree valued for its fruit flavor, particularly 2-acetyl-1-pyrroline (2AP), a vital aroma metabolite. To enhance high-aromatic coconut breeding efforts, it is essential to deeply understand the hereditary factors governing the production of 2AP. In this study, a genome-wide association analysis identifies 32 loci that exhibit significant associations with 2AP content based on single nucleotide polymorphism (SNP) variations from 168 aromatic coconut germplasm resources. Transcriptome analysis then pinpoints 22 candidate genes near significant loci involved in 2AP metabolism. Proteins encoded by these genes are involved in amino acid metabolism, glycolysis, and secondary metabolism. Among these, Asparagine synthetase coding gene ASN1, Gamma-glutamylcysteine synthetase coding gene GSH1, and UbiA prenyltransferase coding gene UBIA are enriched in the linkage region constructed by significant locus Chr04_61490504. In particular, the SNP mutation of CnASN1 leads to amino acid changes in the functional region of the coding protein, potentially resulting in differences in 2AP content among haplotype populations. Identifying variations in related candidate genes, particularly the gene CnASN1, provides molecular markers closely associated with 2AP synthesis for coconut breeding and offers further insights into the metabolic mechanisms of 2AP.

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.

Characterization of a Drought-Induced Betaine Aldehyde Dehydrogenase Gene SgBADH from Suaeda glauca

Betaine aldehyde dehydrogenases (BADHs) are key enzymes in the biosynthesis of glycine betaine, which is an important organic osmolyte that maintains cell structure and improves plant tolerance to abiotic stresses, especially in halotolerant plants. Improving the drought tolerance of crops will greatly increase their yield. In this study, a novel BADH gene named SgBADH from Suaeda glauca was induced by drought stress or abscisic acid. To explore the biological function of SgBADH, the SgBADH gene was transformed into Arabidopsis. Then, we found SgBADH-overexpressing Arabidopsis seedlings showed enhanced tolerance to drought stress. SgBADH transgenic Arabidopsis seedlings also had longer roots compared with controls under drought stress, while SgBADH-overexpressing Arabidopsis exhibited increased glycine betaine accumulation and decreased malondialdehyde (MDA) under drought stress. Our results suggest that SgBADH might be a positive regulator in plants during the response to drought.

Application of Silicon Influencing Grain Yield and Some Grain Quality Features in Thai Fragrant Rice

Silicon (Si) is a beneficial nutrient that has been shown to increase rice productivity and grain quality. Fragrant rice occupies the high end of the rice market with prices at twice to more than three times those of non-fragrant rice. Thus, this study evaluated the effects of increasing Si on the yield and quality of fragrant rice. Also measured were the content of proline and the expression of the genes associated with 2AP synthesis and Si transport. The fragrant rice varieties were found to differ markedly in the effect of Si on their quality, as measured by the grain 2AP concentration, while there were only slight differences in their yield response to Si. The varieties with low 2AP when the Si supply is limited are represented by either PTT1 or BNM4 with only slight increases in 2AP when Si was increased. Si affects the gene expression levels of the genes associated with 2AP synthesis, and the accumulation of 2AP in fragrant rice mainly occurred through the upregulation of Badh2, DAO, OAT, ProDH, and P5CS genes. The findings suggest that Si is a potential micronutrient that can be utilized for improving 2AP and grain yield in further aromatic rice breeding programs.

Effects of paclobutrazol seed priming on seedling quality, photosynthesis, and physiological characteristics of fragrant rice

BACKGROUND

Paclobutrazol is widely used in the agricultural field. This study investigated the effects of seed priming with different concentrations of paclobutrazol on seedling quality, 2-acetyl-1-pyrroline (2-AP, a key aroma component of fragrant rice) biosynthesis, and related physiological and biochemical indicators in fragrant rice seedlings.

RESULTS

The experiment is being conducted at the College of Agriculture, South China Agricultural University. In the experiment, three concentrations of paclobutrazol (Pac 1: 20 mg·L-1; Pac 2: 40 mg·L-1; Pac 3: 80 mg·L-1) were used to initiate the treatment of fragrant rice seeds, while water treatment was used as a control (CK). The results showed that compared with CK, paclobutrazol treatment reduced plant height, increased stem diameter, and increased fresh and dry weight of aromatic rice seedlings. Moreover, paclobutrazol treatment also increased the seedlings' photosynthetic pigment content and net photosynthetic rate.

CONCLUSIONS

This study demonstrates that paclobutrazol primarily increases the content of proline by reducing the content of glutamate and down-regulating the expression of P5CS2, thereby promoting the conversion of proline to the aromatic substance 2-AP. Under the appropriate concentration of paclobutrazol (40 mg·L-1~80 mg·L-1), the seedling quality, stress resistance, and aroma of fragrant rice can be improved.

Transcription Factor OsbZIP60-like Regulating OsP5CS1 Gene and 2-Acetyl-1-pyrroline (2-AP) Biosynthesis in Aromatic Rice

The most important volatile in determining the aroma of fragrant rice is 2-Acetyl-1-pyrroline (2-AP); however, the transcriptional regulation mechanism of 2-AP biosynthesis in fragrant rice is still unclear. In this study, Osp5cs1 knockout mutant lines and OsP5CS1 over-expression lines were constructed by the genetic transformation of the Indica rice cultivar, i.e., 'Zhonghua11', which knocks out OsBADH2 to produce fragrance in aromatic rice. The OsP5CS1 gene was also identified as a key gene in the 2-AP biosynthesis pathway of aromatic rice. The OsP5CS1 promoter was used as bait, and the OsbZIP60-like transcription factor was screened by yeast one-hybrid assays. The OsbZIP60-like transcription factor specifically bound to the OsP5CS1 gene. The dual luciferase reporting system found that the OsbZIP60-like transcription factor promoted the transcriptional activation of OsP5CS1. Compared with the wild type, OsP5CS1 gene expression was significantly down-regulated in the Osbzip60-like mutant and resulted in a substantial reduction in 2-AP biosynthesis. Moreover, the OsP5CS1 gene expression was significantly up-regulated in OsbZIP60-like over-expressed plants, and the 2-AP concentrations were also increased, whereas the Osbzip60-like mutants were found to be sensitive to Zn deficiency. Overall, the OsbZIP60-like transcription factor promoted the 2-AP accumulation. This study provides a theoretical basis for the transcriptional regulation mechanism of 2-AP biosynthesis and explores the function of the OsbZIP transcription factor in fragrant rice.

Impact and mitigation of lead, cadmium and micro/nano plastics in fragrant rice

Heavy metals (HMs) and micro(nano)plastics (MNPs), represent a significant risk to global food supply as well as a potential risk to humankind. Over 50% of the worldwide population eat rice every day, and rice aroma is a significant qualitative trait that is highly valued by consumers and fetches premium prices in the global market. Despite the huge commercial importance of fragrant rice, limited studies were directed to investigate the influence of HMs and MNPs on yield related traits and 2-Acetyl-1-pyrroline (2-AP) compound, mainly responsible for aroma production in fragrant rice. In this review, we found that the interaction of HMs and MNPs in fragrant rice is complex and accumulation of HMs and MNPs was higher in root as compared to the grains. Nutrients and phytohormones mediated mitigation of HMs and MNPs were most effective sustainable strategies. In addition, monitoring the checkpoints of 2-AP biosynthesis and its interaction with HMs and MNPs is challenging. Finally, we explained the potential challenges that fragrant rice faces considering the continuous rise in environmental pollutants and discussed the future avenues of research to improve fragrant rice's yield and qualitative traits.

Zinc Oxide Nanoparticles Foliar Application Effectively Enhanced Zinc and Aroma Content in Rice (Oryza sativa L.) Grains

The search for an effective zinc fertilizer and its application method to effectively increase zinc content and enhance aroma in rice grains is a crucial objective. In this study, a 2-year field plot experiment was conducted to investigate the influence of ZnO NPs foliar spraying on rice quality, grain zinc and aroma content, along with exploring the physiological mechanisms underlying these effects. Our results demonstrated that the rice breakdown value and taste value of foliar spraying zinc oxide nanoparticles were improved by 31.0-41.7% and 8.2-13.0% compared with CK (control treatment involved spraying water), improving the tasting and steaming quality of rice. While Fe and Cu content in grains decreased for the application of zinc oxide nanoparticles, zinc oxide nanoparticles foliar spraying significantly increased the zinc content and accumulation of grains by 33.6-65.1% and 37.8-74.7%, respectively. Further analysis showed that the sprayed zinc oxide nanoparticles achieved effective enrichment of zinc in edible parts and increased the final bioavailability of Zn. In addition, foliar spraying of zinc oxide nanoparticles significantly increased activities of nitrate reductase and glutamine synthetase in leaves, which elevated nitrogen content in leaves and grains, and ultimately enhanced 2-acetyl-1-pyrroline (2-AP) content in grains at maturity by 6.1-21.4% compared to CK. Our findings indicated that zinc oxide nanoparticles can be practically applied as a foliar fertilizer at the gestation for quality improvement, zinc enrichment and aroma enhancement of rice grains.

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.

Dissecting the biochemical and molecular-genetic regulation of diverse metabolic pathways governing aroma formation in indigenous aromatic indica rice varieties

BACKGROUND

Aromatic rice is characterized by its distinct flavor and fragrance, imparted by more than 200 volatile organic compounds. The desirable trait of aroma relies on the type of the variety, with some varieties exhibiting considerably higher aroma content. This prompted us to undergo an exhaustive study of the aroma-associated biochemical pathways and expression of related genes, encoding the enzymes involved in those pathways in indigenous aromatic rice cultivars.

METHODS AND RESULTS

The higher aroma level in aromatic rice varieties was attributed to higher transcript levels of PDH, P5CS, OAT, ODC, DAO and TPI, but lower P5CDH and BADH2, as revealed by comparative expression profiling of genes in 11 aromatic and four non-aromatic varieties. Some of the high-aroma containing varieties exhibited lower expression of SPDS and SPMS genes, concomitant with higher PAO expression. Protein immunoblot analyses showed lesser BADH2 protein accumulation in the aromatic varieties. The involvement of shikimate pathway in aroma formation was justified by higher levels of shikimic and ferulic acids due to higher expression of SK1, SK2 and ARD genes. The aromatic varieties exhibited higher expression of LOX3 and HPL, with higher corresponding enzyme activity, accompanied with lower accumulation of lipid hydroperoxides and higher level of total terpenoids, signifying the role of oxylipin pathway and terpene-related volatiles in aroma formation. The pattern of transcript level and metabolite accumulation followed the same trend in both vegetative (seedling) and reproductive (seed) tissues. Sequence analyses revealed several mutations in the upstream region and different exons and introns of BADH2 in the examined aromatic varieties. The allele specific marker system acted as fingerprint to distinguish the selected aromatic rice varieties. The cleaved amplified polymorphic sequence marker established the absence of any mutation in the 14th exon of BADH2 in the aromatic varieties.

CONCLUSION

The present work clearly highlighted the biochemical and molecular-genetic mechanism of differential aroma levels which could be attributed to differential regulation of metabolites and genes, belonging to 2-acetyl-1-pyrroline, shikimate, oxylipin and terpenoid metabolic pathways in the indigenous aromatic rice varieties.

Trans-Zeatin induce regulation the biosynthesis of 2-acetyl-1-pyrroline in fragrant rice (Oryza sativa L.) seedlings

BACKGROUND

In plants, cytokinin is activated into trans-zeatin to fight abiotic stresses. However, the mechanism of the effect of trans-zeatin on 2-acetyl-1-pyrroline (2-AP) biosynthesis in fragrant rice has yet to be studied. The present study was conducted to explore the effects of exogenous trans-zeatin on enzymes activities, genes expression, and precursors involved in 2-AP biosynthesis and 2-AP contents as well as the seedling quality of a fragrant rice cultivar viz., Meixiangzhan2. Four concentrations of trans-zeatin solutions at 20, 40, and 80 μmol L^- 1 (ZT1, ZT2, and ZT3) were sprayed onto rice seedlings.

RESULTS

Compared to the control, trans-zeatin treatments showed significantly higher 2-AP contents of fragrant rice seedlings. Increased plant height and stem width were observed due to trans-zeatin treatments. The trans-zeatin application increased 1-pyrroline, methylglyoxal, proline, and P5C contents, enhanced P5CS and OAT activities, and reduced glutamic acid contents. In addition, expressions of ProDH, P5CS2, and DAO4 were comparatively higher under trans-zeatin treatments than CK in fragrant rice seedlings.

CONCLUSIONS

Overall, up-regulation of P5C, 1-pyrroline, and proline and down-regulation of glutamic acid under appropriate trans-zeatin concentrations (20 and 40 μmol L^- 1) resulted in enhanced 2-AP biosynthesis in fragrant rice seedlings and 20-40 μmol L^- 1 was considered as the suggested concentrations of trans-zeatin application in fragrant rice seedling.

CRISPR-Cas9-mediated editing of BADH2 gene triggered fragrance revolution in rice

Fragrance is one of the most important quality traits for breeding in rice. The natural aroma substance 2-acetyl-1-pyrroline (2-AP) is a key fragrance compound among over 200 volatiles identified in fragrant rice. In addition to rice, there are other plant species that contain a germplasm that naturally produces a fragrant aroma. These other plant species all have lower activity levels of the enzyme BETAINE ALDEHYDE DEHYDROGENASE 2 (BADH2). Therefore, improving fragrance efficiency has been a focus of intensive research. Recent studies have engineered BADH2 gene, which is responsible for fragrance trait in non-fragrant cultivars of rice, using CRISPR-Cas9. Although engineering rice BADH2 can be useful for upregulating 2-AP, there are still a lot of restrictions on how it can be applied in practice. In this review article, we discuss the recent developments in BADH2 editing and propose potential future strategies to effectively target BADH2 for transcriptional regulation, with the goal of producing a better fragrance.

Combined Metabolomic and Quantitative RT-PCR Analyses Revealed the Synthetic Differences of 2-Acetyl-1-pyrroline in Aromatic and Non-Aromatic Vegetable Soybeans

Aroma is an important economic trait of vegetable soybeans, which greatly influences their market value. The 2-acetyl-1-pyrroline (2AP) is considered as an important substance affecting the aroma of plants. Although the 2AP synthesis pathway has been resolved, the differences of the 2AP synthesis in the aromatic and non-aromatic vegetable soybeans are unknown. In this study, a broad targeted metabolome analysis including measurement of metabolites levels and gene expression levels was performed to reveal pathways of aroma formation in the two developmental stages of vegetable soybean grains [35 (S5) and 40 (S6) days after anthesis] of the 'Zhexian No. 8' (ZX8, non-aromatic) and ZK1754 (aromatic). The results showed that the differentially accumulated metabolites (DAMs) of the two varieties can be classified into nine main categories including flavonoids, lipids, amino acids and derivatives, saccharides and alcohols, organic acids, nucleotides and derivatives, phenolic acids, alkaloids and vitamin, which mainly contributed to their phenotypic differences. Furthermore, in combination with the 2AP synthesis pathway, the differences of amino acids and derivatives were mainly involved in the 2AP synthesis. Furthermore, 2AP precursors' analysis revealed that the accumulation of 2AP mainly occurred from 1-pyrroline-5-carboxylate (P5C), not 4-aminobutyraldehyde (GABald). The quantitative RT-PCR showed that the associated synthetic genes were 1-pyrroline-5-carboxylate dehydrogenase (P5CDH), ∆¹-pyrroline-5-carboxylate synthetase (P5CS), proline dehydrogenase (PRODH) and pyrroline-5-carboxylate reductase (P5CR), which further verified the synthetic pathway of 2AP. Furthermore, the betaine aldehyde dehydrogenase 2 (GmBADH2) mutant was not only vital for the occurrence of 2AP, but also for the synthesis of 4-aminobutyric acid (GABA) in vegetable soybean. Therefore, the differences of 2AP accumulation in aromatic and non-aromatic vegetable soybeans have been revealed, and it also provides an important theoretical basis for aromatic vegetable soybean breeding.

Insights of Improved Aroma under Additional Nitrogen Application at Booting Stage in Fragrant Rice

Plant mineral nutrition substantially affects the growth, yield and quality of rice, whereas nitrogen (N) application contributes significantly in this regard. Undoubtedly, N application improves rice aroma biosynthesis; however, the molecular mechanism underlying the regulation of grain 2-acetyl-1-pyrroline (2-AP) biosynthesis in the presence of nitrogen application at the booting stage has remained largely unexplored. The present study examined the effects of three N levels, i.e., 0 g per pot (N0), 0.43 g per pot (N1) and 0.86 g per pot (N2) on intermediates, enzymes and genes involved in 2-AP biosynthesis, as well as on the yield of two fragrant rice cultivars viz, Meixiangzhan2 and Xiangyaxiangzhan. N was additionally applied at the booting stage. The results depicted that the levels of precursor, such as proline, and the activity of enzymes involved in 2-AP biosynthesis, such as Δ1-pyrroline-5-carboxylate synthetase (P5CS) and diamine oxidase (DAO), and P5CS1 gene expression were comparatively higher under N1 than N0 in both fragrant rice cultivars. Moreover, the N2 treatment increased the grain panicle-1, filled grain percentage and grain yield of both rice cultivars, while the grain yield of Meixiangzhan2 and Xiangyaxiangzhan was increased by 15.87% and 12.09%, respectively, under N2 compared to N1 treatment. Hence, 0.43 g per pot of N showed positive performances in yield and aroma accumulation in fragrant rice and should be further employed in the practice and production for better cultivation in the rice market.

Identification of volatile organic compounds related to the eating quality of cooked japonica rice

Eating quality (EQ) of rice has a complex nature composed of physicochemical properties. Nevertheless, breeding programs evaluating EQ through sensory test or taste-evaluation instruments have been laborious, time-consuming and inefficient. EQ is affected by both taste and aroma. However, in actual breeding programs, aroma of cooked rice has been considered the least due to lack of information. Here we identified a total of 41 volatile compounds potentially affecting the EQ of non-aromatic, cooked japonica rice, identified by GC-MS, sensory panel test, and Toyo taste-meter analyses. Partial least squares discriminant analysis demonstrated an outstanding classification effect of the identified volatile compounds on eating-quality discrimination. Several volatile compounds related to lipid oxidation and fatty acid degradation were identified to affect the EQ in japonica rice. Of them, 1-octen-3-ol, 1-ethyl-3,5-dimethylbenzene, 2,6,11-trimethyldodecane, 3-ethyloctane, 2,7,10-trimethyldodecane, methyl salicylate, 2-octanone, and heptanal were selected as important compounds. The discriminant model for the classification of the quality of cultivars was robust and accurate, an r-squared value was 0.91, a q squared value was 0.85, and an accuracy was 1.0. Overall, the results of this study characterize EQ of rice cultivars based on volatile compounds, suggesting the application of metabolite profiling data for rice breeding of high eating quality.

Foliar application of procyanidins enhanced the biosynthesis of 2-acetyl-1-pyrroline in aromatic rice (Oryza sativa L.)

BACKGROUND

Procyanidins is a polyphenolic compound with multiple properties. However, the application of exogenous procyanidins in crops has not been reported. Aromatic rice is a high-quality rice with a special aroma and popular with consumers. The 2-acetyl-1-pyrroline (2-AP) is a key compound of aromatic rice aroma. In the current study, aromatic rice plants were sprayed with procyanidins solutions at 0.25 (Pr0.25), 0.50 (Pr0.50), 1.00 (Pr1.00), 2.00 (Pr2.00) g L^-1, respectively and treatment sprayed with distilled water was taken as control (CK). The effects of exogenous procyanidins on growth and 2-AP biosynthesis of aromatic rice plants were explored.

RESULTS

Compared with CK, Pr1.00 and Pr2.00 treatments significantly increased 2-AP content by 16.67% and 37.68%, respectively. Higher proline, 1-pyrroline-5-carboxylic acid (P5C), 1-pyrroline, methylglyoxal contents, and lower γ- aminobutyric acid (GABA) content were recorded in Pr1.00 and Pr2.00 treatments than CK. Compared with CK, Pr1.00 and Pr2.00 treatments significantly improved the activities of P5CS and OAT and diminished the activity of BADH. Furthermore, compared with CK, Pr1.00 and Pr2.00 treatments significantly up-regulated the transcript levels of P5CS2, P5CR, OAT, DAO4 and down-regulated the transcript levels of BADH2. Exogenous procyanidins had no substantial effects on plant height, stem diameter, fresh weight, and dry weight of aromatic rice plants.

CONCLUSIONS

In conclusion, our findings reported the increment of 2-AP content in aromatic rice under exogenous procyanidins. Our results indicated that the application of exogenous procyanidins enhanced 2-AP biosynthesis by improving proline biosynthesis and inhibiting GABA formation.

CsCuAOs and CsAMADH1 Are Required for Putrescine-Derived γ-Aminobutyric Acid Accumulation in Tea

Polyamines are a potential source of γ-aminobutyric acid (GABA) in plants under abiotic stress. However, studies on GABA enrichment in tea mostly focus on the GABA shunt, while the correlation between polyamine degradation and GABA formation in tea is largely unknown. In this study, tea plants responded to exogenous putrescine, resulting in a significant increase in GABA content, while the glutamate level did not change. At the same time, five copper-containing amine oxidase (CuAO) and eight aminoaldehyde dehydrogenase (AMADH) genes involved in the putrescine-derived GABA pathway were identified from the Tea Plant Information Archive. Expression analysis indicated that CsCuAO1, CsCuAO3 as well as CsAMADH1 were induced to play an important function in response to exogenous putrescine. Thus, the three genes were cloned and the catalytic efficiency of soluble recombinant proteins was determined. CsCuAOs and CsAMADH1 exhibited indispensable functions in the GABA production from putrescine in vitro. Subcellular localization assays indicated that CsAMADH1 was localized in plastid, while both CsCuAO1 and CsCuAO3 were localized in peroxisome. In addition, the synergistic effects of CsCuAOs and CsAMADH1 were investigated by a transient co-expression system in Nicotiana benthamiana. Our data suggest that these three genes regulate the accumulation of GABA in tea by participating in the polyamine degradation pathway and improve the content of GABA in tea to a certain extent. The results will greatly contribute to the production of GABA tea.

Molecular profiling of BADH2 locus reveals distinct functional allelic polymorphism associated with fragrance variation in Indian aromatic rice germplasm

Allelic variability of the aroma gene, betaine aldehyde dehydrogenase 2 (BADH2) was studied in a random subset of indigenous aromatic rice germplasm along with a few exotic aromatic accessions. Use of functional markers of four badh2 alleles identified that the test panel possessed only two alleles, badh2-E7 and badh2-p-5'UTR. Two other alleles, badh2.2 and badh2-E4-5.2 were absent. Based on the alleles present, four functional polymorphisms (FP) were detected, namely FP1 to FP4. 188 genotypes possessed FP1 having both the badh2-p-5'UTR and badh2-E7 (71.8%) alleles. The badh2 allele with FP1 is named badh2-E7-p. 39 genotypes (14.9%) possessed only the badh2-p-5'UTR allele (FP3), while three genotypes were found to carry only the badh2-E7 allele (FP2). We also found that 32 genotypes (12.2%) did not have any of the target aroma alleles tested in this study (FP4). Interestingly, for badh2-p-5'UTR marker, the expected 198 bp amplicon for the non-aromatic allele could not be detected among any of the genotypes tested. Instead, an amplicon of 456 bp length appeared with 100% presence in the non-aromatic checks. Notwithstanding, the 456 bp allele also showed a 16% presence among the aromatic lines. This article forms the first report of this allele, named badh2-p1, among aromatic rice. Quantification of 2-Acetyl-1-Pyrroline (2AP) content and sensory evaluation among the test genotypes showed that those with FP1 are highly aromatic than the genotypes carrying other types of FPs. But, a few strongly aromatic lines showed lower 2AP content. The BADH2 characterization carried out in this study is suggestive of identifying the additional gene(s)/ allele(s) governing aroma among the Indian fragrant rice.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01181-9.

A Sequence Variation in GmBADH2 Enhances Soybean Aroma and Is a Functional Marker for Improving Soybean Flavor

The vegetable soybean (Glycine max L. Merr.) plant is commonly consumed in Southeast Asian countries because of its nutritional value and desirable taste. A "pandan-like" aroma is an important value-added quality trait that is rarely found in commercial vegetable soybean varieties. In this study, three novel aromatic soybean cultivars with a fragrant volatile compound were isolated. We confirmed that the aroma of these cultivars is due to the potent volatile compound 2-acetyl-1-pyrroline (2AP) that was previously identified in soybean. A sequence comparison of GmBADH1/2 (encoding an aminoaldehyde dehydrogenase) between aromatic and non-aromatic soybean varieties revealed a mutation with 10 SNPs and an 11-nucleotide deletion in exon 1 of GmBADH2 in Quxian No. 1 and Xiangdou. Additionally, a 2-bp deletion was detected in exon 10 of GmBADH2 in ZK1754. The mutations resulted in a frame shift and the introduction of premature stop codons. Moreover, genetic analyses indicated that the aromatic trait in these three varieties was inherited according to a single recessive gene model. These results suggested that a mutated GmBADH2 may be responsible for the aroma of these three aromatic soybean cultivars. The expression and function of GmBADH2 in aromatic soybean seeds were confirmed by qRT-PCR and CRISPR/Cas9. A functional marker developed on the basis of the mutated GmBADH2 sequence in Quxian No. 1 and Xiangdou was validated in an F2 population. A perfect association between the marker genotypes and aroma phenotypes implied that GmBADH2 is a major aroma-conferring gene. The results of this study are potentially useful for an in-depth analysis of the molecular basis of 2-AP formation in soybean and the marker-assisted breeding of aromatic vegetable soybean cultivars.

Genome Editing Technology and Its Application to Metabolic Engineering in Rice

Genome editing technology can be used for gene engineering in many organisms. A target metabolite can be fortified by the knockout and modification of target genes encoding enzymes involved in catabolic and biosynthesis pathways, respectively, via genome editing technology. Genome editing is also applied to genes encoding proteins other than enzymes, such as chaperones and transporters. There are many reports of such metabolic engineering using genome editing technology in rice. Genome editing is used not only for site-directed mutagenesis such as the substitution of a single base in a target gene but also for random mutagenesis at a targeted region. The latter enables the creation of novel genetic alleles in a target gene. Recently, genome editing technology has been applied to random mutagenesis in a targeted gene and its promoter region in rice, enabling the screening of plants with a desirable trait from these mutants. Moreover, the expression level of a target gene can be artificially regulated by a combination of genome editing tools such as catalytically inactivated Cas protein with transcription activator or repressor. This approach could be useful for metabolic engineering, although expression cassettes for inactivated Cas fused to a transcriptional activator or repressor should be stably transformed into the rice genome. Thus, the rapid development of genome editing technology has been expanding the scope of molecular breeding including metabolic engineering. In this paper, we review the current status of genome editing technology and its application to metabolic engineering in rice.

Co-functioning of 2AP precursor amino acids enhances 2-acetyl-1-pyrroline under salt stress in aromatic rice (Oryza sativa L.) cultivars

Aromatic rice (Oryza sativa) fetches a premium price due to the pleasant aroma. The major aroma compound 2-acetyl-1-pyrroline (2AP) has been found to be enhanced under stress. This condition can be considered to study the genes, precursors, enzymes, and metabolites involved in elevated levels of 2AP biosynthesis. In the present study, 100 mM salt treatment was given to two aromatic rice cultivars Ambemohar-157 (A-157) and Basmati-370 (B-370) at the vegetative stage (VS₃). After salt treatment, in the leaves, 2AP contents were elevated by 2.2 and 1.8 fold in A-157 and B-370, respectively. Under these elevated 2AP conditions, the precursor amino acids (glutamate, putrescine, ornithine, and proline), their related genes, enzymes, and metabolites (methylglyoxal and γ-aminobutyric acid (GABA) related to 2AP biosynthesis were analyzed. In addition, agronomic characters were also studied. It was observed that the proline content was enhanced in both the cultivars by 29% (A-157) and 40% (B-370) as compared to control. The Δ¹-pyrroline-5-carboxylate synthetase (P5CS) enzyme activity was increased in salt-treated plants leaf tissue by 31% (A-157) and 40% (B-370) compared to control. The P5CS gene expression was enhanced by A-157 (1.8 fold) and B-370 (2.2 fold) compared to control, putrescine content in A-157 and B-370 decreased by 2.5 and 2.7 fold respectively as compared to control. The ornithine decarboxylase (ODC) activity was enhanced in A-157 (12%) and B-370 (35%) over control. Further, ODC gene expression was enhanced in both the cultivars A-157 (1.5 fold) and B-370 (1.3 fold). The diamino oxidase (DAO) enzyme activity was increased by 28% (A-157) and 35% (B-370) respectively over control. The GABA content marginally increased over control in both the cultivars namely, A-157 (1.9%) and B-370 (9.5%). The methylglyoxal levels were enhanced by 1.4 fold in A-157 and 1.6 fold in B-370. Interestingly, the enhancement in 2AP in the vegetative stage also helped to accumulate it in mature grains (twofold in A-157 and 1.5 fold in B-370) without test weight penalty. The study indicated that the ornithine and proline together along with methylglyoxal contribute towards the enhancement of 2AP under salt stress.

Proline, a multifaceted signalling molecule in plant responses to abiotic stress: understanding the physiological mechanisms

Abiotic stresses have a detrimental impact on plant growth and productivity and are a major threat to sustainable crop production in rapidly changing environments. Proline, an important amino acid, plays an important role in maintaining the metabolism and growth of plants under abiotic stress conditions. Many insights indicate a positive relationship between proline accumulation and tolerance of plants to various abiotic stresses. Because of its metal chelator properties, it acts as a molecular chaperone, an antioxidative defence molecule that scavenges reactive oxygen species (ROS), as well as having signalling behaviour to activate specific gene functions that are crucial for plant recovery from stresses. It also acts as an osmoprotectant, a potential source to acquire nitrogen as well as carbon, and plays a significant role in the flowering and development of plants. Overproduction of proline in plant cells contributes to maintaining cellular homeostasis, water uptake, osmotic adjustment and redox balance to restore the cell structures and mitigate oxidative damage. Many reports reveal that transgenic plants, particularly those overexpressing genes tailored for proline accumulation, exhibit better adaptation to abiotic stresses. Therefore, this review aims to provide a comprehensive update on proline biosynthesis and accumulation in plants and its putative regulatory roles in mediating plant defence against abiotic stresses. Additionally, the current and future directions in research concerning manipulation of proline to induce gene functions that appear promising in genetics and genomics approaches to improve plant adaptive responses under changing climate conditions are also highlighted.

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.

Multi-omics analysis reveals the genetic basis of rice fragrance mediated by betaine aldehyde dehydrogenase 2

INTRODUCTION

Fragrance is an important economic and quality trait in rice. The trait is controlled by the recessive gene betaine aldehyde dehydrogenase 2 (BADH2) via the production of 2-acetyl-1-pyrroline (2AP).

OBJECTIVES

Variation in BADH2 was evaluated at the population, genetic, transcriptional, and metabolic levels to obtain insights into fragrance regulation in rice.

METHODS

Whole-genome resequencing of the Korean World Rice Collection of 475 rice accessions, including 421 breeding lines and 54 wild accessions, was performed. Transcriptome analyses of a subset of 279 accessions, proteome analyses of 64 accessions, and volatile profiling of 421 breeding lines were also performed.

RESULTS

We identified over 3.1 million high-quality single nucleotide polymorphisms (SNPs) in Korean rice collection. Most SNPs were present in intergenic regions (79%), and 190,148 SNPs (6%) were located in the coding sequence, of which 53% were nonsynonymous. In total, 38 haplotypes were identified in the BADH2 coding region, including four novel haplotypes (one in cultivated and three in wild accessions). Tajima's D values suggested that BADH2 was under balancing selection in japonica rice. Furthermore, we identified 316 expression quantitative trait loci (eQTL), including 185 cis-eQTLs and 131 trans-eQTLs, involved in BADH2 regulation. A protein quantitative trait loci (pQTL) analysis revealed the presence of trans-pQTLs; 13 pQTLs were mapped 1 Mbp from the BADH2 region. Based on variable importance in projection (VIP) scores, 15 volatile compounds, including 2AP, discriminated haplotypes and were potential biomarkers for rice fragrance.

CONCLUSION

We generated a catalog of haplotypes based on a resequencing analysis of a large number of rice accessions. eQTLs and pQTLs associated with BADH2 gene expression and protein accumulation are likely involved in the regulation of 2AP variation in fragrant rice. These data improve our understanding of fragrance and provide valuable information for rice breeding.

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.

Transcriptomic Analysis Provides Insights into Foliar Zinc Application Induced Upregulation in 2-Acetyl-1-pyrroline and Related Transcriptional Regulatory Mechanism in Fragrant Rice

The involvement of zinc (Zn) in terms of aroma formation has been rarely investigated. This study shows that the regulation of 2-acetyl-1-pyrroline (2AP) biosynthesis was evaluated in two different rice cultivars under foliar Zn application. The results showed that the 2AP and Zn contents in leaves and grains were improved substantially under foliar Zn application. The 2AP content was positively related to the expression P5CS2 gene, contents of proline, 1-pyrroline, and Δ1-pyrroline-5-carboxylate (P5C), and the activity of pyrroline-5-carboxylate synthase (P5CS) under Zn application in fragrant rice. Multiple transcription factors (TFs) were differently expressed, such as bZIPs, NACs, and MYBs, to play a role under Zn treatments in fragrant rice, suggesting the crucial role of 46 differently expressed TFs in 2AP improvements in fragrant rice. Furthermore, this study showed that the optimal foliar Zn application at a concentration of 30 mg L^-1 could increase the 2AP content of aromatic rice and keep the yield stable or increase the yield. TFs were involved in regulating to promote the 2AP formation in aromatic rice under the foliar Zn application. However, the relationship between 2AP biosynthesis pathway genes and TFs in fragrant rice remains to be further studied.

Functional modification of HHCB: Strategy for obtaining environmentally friendly derivatives

Galaxolide (HHCB), one of the most widely used synthetic musks in personal care products (PCPs), has been recognized as an emerging contaminant with potential human health concerns. To overcome such adverse effects, a systematic molecular design, screening and performance evaluation approach was developed to generate functionally improved and environmentally friendly HHCB derivatives. Among the 90 designed HHCB derivatives, 15 were screened with improved functional properties (i.e., odor stability and intensity) and less environmental impacts (i.e., lower bio-toxicity, bio-accumulation ability, and mobility) using 3D-QSAR models and density functional theory methods. Their human health risks were then assessed by toxicokinetic analysis, which narrowed the candidates to four. Derivative 7, the designed molecule with the least dermal adsorption potential, was evaluated for its interaction with other PCPs additives (i.e., anti-photosensitivity materials and moisturizer) and such impacts on human health risks using molecular docking and molecular dynamic simulation. The environmental fate of Derivative 7 after transformation (i.e., photodegradation, biotransformation, and chlorination) was also discussed. Biotransformation and chlorination were recognized as optimum options for Derivative 7 mitigation. This study provided the theoretical basis for the design of functionally improved and environmentally friendly HHCB alternatives and advanced the understanding of their environmental behaviors and health risks.

Nitrogen sources affected the biosynthesis of 2-acetyl-1-pyrroline, cooked rice elongation and amylose content in rice

Many studies have been carried out on N sources effect on fragrant rice; however, their impact on rice grain quality is largely unclear. In this study, we evaluated the effects of different types of N sources on rice growth, yield, 2-acetyl-1-pyrroline (2AP), amylose and cooked rice elongation. Two indica rice cultivars, Basmati 385 (B385), Xiangyaxiangzhan (XYXZ) and two japonica cultivars, Yunjingyou (YJY), Daohuaxiang (DHX) were grown in experimental pots with six replications under four N sources: Potassium nitrate (KNO3), ammonium bicarbonate (NH4HCO3), urea (H2NCONH2) and sodium nitrate (NaNO3) in 2019 and 2020 early seasons. Our results showed that N dynamics regulated the number of panicles, 1000-grain weight, grain yield, 2-acetyl-1-pyrroline, amylose and cooked rice elongation across all the four treatments. The NH4HCO3 treatment significantly increased the number of panicles and grain yield across the four rice varieties compared with KNO3, H2NCONH2 and NaNO3 N sources in both 2019 and 2020 early season, The KNO3 treatment significantly showed higher 1000-grain weight in B-385, YJY, XYXZ and DHX compared to other N sources. Compared with other N sources treatment, the NH4HCO3 treatments significantly increased the 2AP contents in heading stage leaves, matured leaves and grains of B-385, YJY, XYXZ and DHX respectively. Cooked rice elongation percentage also showed significant difference in all treatments studied with KNO3 recorded the highest across the four varieties. Analysis of major enzymes and compounds such as P5C, P5CS, PDH, Pyrroline, proline and Methylglyoxal showed remarkable differences in each cultivar at heading and maturity stages with higher activity in NH4HCO3 and H2NCONH2 treatments. Similarly, in all treatments, we also observed significant increase in amylose content percentage, with NH4HCO3 having greater percentage of amylose.

Fragrance in Pandanus amaryllifoliusRoxb. Despite the Presence of a Betaine Aldehyde Dehydrogenase 2

Pandanus amaryllifolius Roxb. accumulates the highest concentration of the major basmati aroma volatile 2-acetyl-1-pyrroline (2AP) in the plant kingdom. The expression of 2AP is correlated with the presence of a nonfunctional betaine aldehyde dehydrogenase 2(BADH2) in aromatic rice and other plant species. In the present study, a full-length BADH2 sequence was reconstructed from the transcriptome data of leaf tissue from P. amaryllifolius seedlings. Based on this sequence, a 1509 bp coding sequence was defined that encoded a 54 kD PaBADH2 protein. This revealed the presence of a full-length BADH2 protein in P. amaryllifolius. Moreover, quantitative real-time PCR analysis, combined with BADH2 enzyme activity, confirmed the expression and functionality of the PaBADH2 protein. To understand the apparent structural variation, docking analysis was carried out in which protein showed a good affinity with both betaine aldehyde (BAD) and γ-aminobutyraldehyde (GAB-ald) as substrates. Overall, the analysis showed the presence of a functional BADH2, along with substantial 2AP synthesis (4.38 ppm). Therefore, we conclude that unlike all other plants studied to date, 2AP biosynthesis in P. amaryllifolius is not due to the inactivation of BADH2.

Recent Development on Plant Aldehyde Dehydrogenase Enzymes and Their Functions in Plant Development and Stress Signaling

Abiotic and biotic stresses induce the formation of reactive oxygen species (ROS), which subsequently causes the excessive accumulation of aldehydes in cells. Stress-derived aldehydes are commonly designated as reactive electrophile species (RES) as a result of the presence of an electrophilic α, β-unsaturated carbonyl group. Aldehyde dehydrogenases (ALDHs) are NAD(P)⁺-dependent enzymes that metabolize a wide range of endogenous and exogenous aliphatic and aromatic aldehyde molecules by oxidizing them to their corresponding carboxylic acids. The ALDH enzymes are found in nearly all organisms, and plants contain fourteen ALDH protein families. In this review, we performed a critical analysis of the research reports over the last decade on plant ALDHs. Newly discovered roles for these enzymes in metabolism, signaling and development have been highlighted and discussed. We concluded with suggestions for future investigations to exploit the potential of these enzymes in biotechnology and to improve our current knowledge about these enzymes in gene signaling and plant development.

Comparison of the sensory properties of fragrant and non-fragrant rice (Oryza sativa), focusing on the role of the popcorn-like aroma compound 2-acetyl-1-pyrroline

2-Acetyl-1-pyrroline (2-AP) has been widely reported as a key contributor to the popcorn-like aroma of fragrant rice (Oryza sativa). To gain a greater understanding of its contribution to the aroma in both fragrant and non-fragrant rice, sensory profiling was conducted with a trained panel to examine the sensory properties of six boiled rice samples, three fragrant and three non-fragrant varieties. The intensity of the popcorn note as an orthonasal odour, a retronasal flavour and as an after-effect was significantly higher in fragrant rice than in non-fragrant rice. However, panellists could not differentiate these popcorn attributes between the three different fragrant rice varieties. 2-AP was extracted from the boiled rice samples by headspace solid-phase microextraction and quantified by gas chromatography-mass spectrometry. 2-AP was below the limits of quantitation in non-fragrant varieties; however, gas chromatography-olfactometry of samples indicated the presence of 2-AP in both raw fragrant and non-fragrant rice varieties.

Light and water treatment during the early grain filling stage regulates yield and aroma formation in aromatic rice

The effect of light and water on aromatic rice remain largely unclear. A pot experiment was conducted to investigate the influences of light-water treatments (CK: natural light and well-watered conditions, WS: natural light and water-stressed conditions, LL: low light and well-watered conditions, LL-WS: low light and water-stressed treatment) on yield and 2-acetyl-1-pyrroline (2AP) formation in aromatic rice. Compared with CK, the light-water treatments decreased grain yield (10.32–39.19%) due to reductions in the filled grain percentage and total dry weight, in the regulation of biomass distribution, and in the attributes of gas exchange and antioxidant response parameters. The 2AP content in grains increased in the LL treatment (5.08–16.32%) but decreased in the WS treatment compared with that in CK. The changes in 2AP were associated with changes in 2AP formation-related traits and element content. Low light and water stress led to yield declines in aromatic rice, but low light alleviated the decrease in 2AP content caused by water stress.

Characterization of Haplotype Diversity in the BADH2 Aroma Gene and Development of a KASP SNP Assay for Predicting Aroma in U.S. Rice

BACKGROUND

Aroma is an important grain quality trait in rice, controlled by mutations within the BADH2 gene. The trait is simply inherited, and its importance in variety development makes it a practical target for marker-assisted selection in applied breeding programs. The predominant functional mutation within BADH2, an 8-bp indel, can be reliably detected using a PCR-based assay, but the available assays and associated genotyping platforms are insufficient for large-scale applied molecular breeding applications and are not compatible with outsourcing genotyping services.

RESULTS

We first characterized SNP diversity across the BADH2 gene in a collection of 2932 rice varieties to determine the number of gene haplotypes in O. sativa. Using 297 gene-based SNPs, 11 haplotype groups were detected, and subsequently identified a minimal set of nine informative SNPs that uniquely identified the BADH2 haplotypes. These nine SNPs were developed into KASP assays and used to examine a panel of 369 U.S. rice accessions. The panel represented modern breeding germplasm and included all known aroma pedigree sources in U.S. rice. Six haplotypes were detected within the U.S. panel, of which two were found in majority (85%) of varieties. A representative set of 39 varieties from all haplotype groups was evaluated phenotypically to distinguish aromatic from non-aromatic lines.

CONCLUSION

One haplotype (Hap 6) was found to be perfectly associated with the aromatic phenotype. A single KASP SNP unique to Hap 6 was demonstrated to reliably differentiate aromatic from non-aromatic rice varieties across U.S. germplasm.

RNAi-mediated down regulation of BADH2 gene for expression of 2-acetyl-1-pyrroline in non-scented indica rice IR-64 (Oryza sativa L.)

2-acetyl-1-pyrroline (2AP) is a principal aroma compound in scented rice and a mutation in betaine aldehyde dehydrogenase 2 (OsBADH2) is responsible aroma in scented rice. The present study was aimed at inducing 2AP production in non-scented indica rice cultivar IR-64 by silencing OsBADH2 via RNAi technique. A vector pBSK was used for the construction of RNAi cassette and pRI101ON as a binary vector. Agrobacterium (GV3101)-mediated transformation was done using embryogenic calli of IR-64. The resultant transgenic lines showed up to 14-fold reduction in expression of OsBADH2 gene and 50% inhibition in enzyme activity. Gas chromatography (GC-MS) analyses showed a significant amount of 2AP production in RNAi callus, leaves, and seeds of IR-64. A total 39 volatile compounds were identified from the control and RNAi seeds of IR-64. Among them, octanal and 2-pentylfuron were found to be increased (30-40%) in RNAi seeds of IR-64. The content of precursors, proline, and methylglyoxal increased substantially, whereas GABA content reduced up to 25% in transgenic IR-64 lines. The study demonstrated that RNAi approach could be successfully used for imparting pleasant aroma character in non-scented indica rice cultivars.

Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice

Background

The circum-basmati group of cultivated Asian rice (Oryza sativa) contains many iconic varieties and is widespread in the Indian subcontinent. Despite its economic and cultural importance, a high-quality reference genome is currently lacking, and the group’s evolutionary history is not fully resolved. To address these gaps, we use long-read nanopore sequencing and assemble the genomes of two circum-basmati rice varieties.

Results

We generate two high-quality, chromosome-level reference genomes that represent the 12 chromosomes of Oryza. The assemblies show a contig N50 of 6.32 Mb and 10.53 Mb for Basmati 334 and Dom Sufid, respectively. Using our highly contiguous assemblies, we characterize structural variations segregating across circum-basmati genomes. We discover repeat expansions not observed in japonica—the rice group most closely related to circum-basmati—as well as the presence and absence variants of over 20 Mb, one of which is a circum-basmati-specific deletion of a gene regulating awn length. We further detect strong evidence of admixture between the circum-basmati and circum-aus groups. This gene flow has its greatest effect on chromosome 10, causing both structural variation and single-nucleotide polymorphism to deviate from genome-wide history. Lastly, population genomic analysis of 78 circum-basmati varieties shows three major geographically structured genetic groups: Bhutan/Nepal, India/Bangladesh/Myanmar, and Iran/Pakistan.

Conclusion

The availability of high-quality reference genomes allows functional and evolutionary genomic analyses providing genome-wide evidence for gene flow between circum-aus and circum-basmati, describes the nature of circum-basmati structural variation, and reveals the presence/absence variation in this important and iconic rice variety group.

Exogenous application of zinc (Zn) at the heading stage regulates 2-acetyl-1-pyrroline (2-AP) biosynthesis in different fragrant rice genotypes

Zinc (Zn) is an important microelement for rice and plays a key role in many physiological processes. This study assessed the physio-biochemical responses involved in biosynthesis of 2-acety-1-pyrroline (2-AP), which is a key compound in the aroma of fragrant rice, in four different fragrant rice varieties, i.e., Meixiangzhan-2, Xiangyaxiangzhan, Ruanhuayou-134, and Yunjingyou. Four concentrations (0, 0.50, 1.00 and 2.00 g L-1) of zinc chloride were applied to fragrant rice foliage at the heading stage and named CK, Zn1, Zn2 and Zn3, respectively. Our results showed that compared with CK, the Zn1, Zn2 and Zn3 treatments all significantly increased the 2-AP concentration in mature grains of the four fragrant rice genotypes. Furthermore, exogenous application of Zn not only enhanced the activities of enzymes, including proline dehydrogenase (PDH), △1-pyrroline-5-carboxylic acid synthetase (P5CS), and diamine oxidase (DAO), which are involved in 2-AP biosynthesis, but also improved the contents of the related precursors, such as Δ1-pyrroline, proline and pyrroline-5-carboxylic acid (P5C). In addition, compared to the CK treatment, the Zn2 treatment markedly increased the net photosynthetic rate of fragrant rice during the grain filling stage and increased the seed-setting rate, 1000-grain weight and grain yield in all fragrant rice genotypes. Foliar application of Zn also markedly increased the grain Zn content. In general, 1.00 g L-1 seemed to be the most suitable application concentration because the highest 2-AP content and grain weight were recorded with this treatment.

Application of γ-aminobutyric acid (GABA) and nitrogen regulates aroma biochemistry in fragrant rice

The 2-acetyl-1-pyrroline (2AP) is a key aroma compound in fragrant rice. The present study assessed the γ-aminobutyric acid (GABA) and nitrogen (N) application induced regulations in the biochemical basis of rice aroma formation. Four N levels, that is, 0, 0.87, 1.75, and 2.61 g/pot, and two GABA treatments, that is, 0 mg/L (GABA0) and 250 mg/L (GABA250), were applied to three fragrant rice cultivars, that is, Yuxiangyouzhan, Yungengyou 14, and Basmati-385. Results showed that GABA250 increased 2AP, Na, Mn, Zn, and Fe contents by 8.44%, 10.95%, 25.70%, 11.14%, and 43.30%, respectively, under N treatments across cultivars. The GABA250 further enhanced the activities of proline dehydrogenase (PDH), ornithine aminotransferase (OAT) (both at 15 days after heading (d AH), and diamine oxidase (DAO) (at maturity) by 20.36%, 11.24%, and 17.71%, respectively. Significant interaction between GABA and N for Mn, Zn, and Fe contents in grains, proline content in leaves, GABA content in leaves at 15 d AH and maturity stage (MS), Δ1-pyrroline-5-carboxylic acid (P5C) contents in leaves at 15 d AH, and Δ1-pyrroline-5-carboxylate synthase (P5CS), PDH, and OAT activities in leaves at MS was noted. Moreover, the 2AP contents in grains at MS showed a significant and positive correlation with the proline contents in the leaves at 15d AH. In conclusion, GABA250 enhanced the 2AP, Na, Mn, Zn, and Fe contents, as well as the enzyme activities involved in 2AP biosynthesis. Exogenous GABA and N application improved the 2AP contents and nutrient uptake in fragrant rice.

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.

Aroma profile of rice varieties by a novel SPME method able to maximize 2-acetyl-1-pyrroline and minimize hexanal extraction

The solid phase microextraction (SPME) has been the most used technique for the extraction of volatile compounds from rice because of its easy operation and solvent-free. The extraction parameters, sample mass and incubation temperature, were optimized through a central composite rotational design (CCRD), aiming at maximizing the extraction of 2-acetyl-1-pyrroline (2AP), the main compound responsible for the aroma in aromatic rice, and minimizing the generation of hexanal, a marker of lipid oxidation. Besides, the time of sample incubation and fiber exposure for the extraction of the volatile compounds from rice were determined. The optimized conditions for SPME were: 2.5 g of ground rice in a 20 mL vial, sample incubation at 80 °C for 60 min and exposure of the divinylbenzene/carboxene/polydimethylsiloxane (DVB/CAR/PDMS) fiber in the headspace for 10 min. The optimized method was sucessfuly applied to 12 varieties of rice and principal component analysis (PCA) was performed to observe similarities in their volatile profile. A total of 152 volatile compounds were identified among the different rice varieties. From these, 42 were identified in arborio rice, 47 in basmati brand A, 43 in basmati brand B, 55 in black rice, 63 in brown rice, 39 in jamine rice, 50 in parboiled brown rice, 43 in parboiled rice, 54 in red rice, 63 in sasanishiki rice, 46 in white rice and 70 in wild rice.

Fine Scale Genomic Signals of Admixture and Alien Introgression among Asian Rice Landraces

Modern rice cultivars are adapted to a range of environmental conditions and human preferences. At the root of this diversity is a marked genetic structure, owing to multiple foundation events. Admixture and recurrent introgression from wild sources have played upon this base to produce the myriad adaptations existing today. Genome-wide studies bring support to this idea, but understanding the history and nature of particular genetic adaptations requires the identification of specific patterns of genetic exchange. In this study, we explore the patterns of haplotype similarity along the genomes of a subset of rice cultivars available in the 3,000 Rice Genomes data set. We begin by establishing a custom method of classification based on a combination of dimensionality reduction and kernel density estimation. Through simulations, the behavior of this classifier is studied under scenarios of varying genetic divergence, admixture, and alien introgression. Finally, the method is applied to local haplotypes along the genome of a Core set of Asian Landraces. Taking the Japonica, Indica, and cAus groups as references, we find evidence of reciprocal introgressions covering 2.6% of reference genomes on average. Structured signals of introgression among reference accessions are discussed. We extend the analysis to elucidate the genetic structure of the group circum-Basmati: we delimit regions of Japonica, cAus, and Indica origin, as well as regions outlier to these groups (13% on average). Finally, the approach used highlights regions of partial to complete loss of structure that can be attributed to selective pressures during domestication.