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.

Mutations in OsDET1, OsCOP10, and OsDDB1 confer embryonic lethality and alter flavonoid accumulation in Rice (Oryza sativa L.) seed.

Morphological and biochemical changes accompanying embryogenesis and seed development are crucial for plant survival and crop productivity. Here, we identified a novel yellowish-pericarp embryo lethal (yel) mutant of the japonica rice cultivar Sindongjin (Oryza sativa L.), namely, yel-sdj. Seeds of the yel-sdj mutant showed a yellowish pericarp and black embryo, and were embryonic lethal. Compared with wild-type seeds, the yel-sdj mutant seeds exhibited significantly reduced grain size, grain weight, and embryo weight, and a remarkably lower rate of embryo retention in kernels subjected to milling. However, the volume of air space between embryo and endosperm, density of embryo, and total phenolic content (TPC) and antioxidant activity of mature grains were significantly higher in the yel-sdj mutant than in the wild type. Genetic analysis and mapping revealed that the yel-sdj mutant was non-allelic to the oscop1 null mutants yel-hc, yel-cc, and yel-sk, and its phenotype was controlled by a single recessive gene, LOC_Os01g01484, an ortholog of Arabidopsis thaliana DE-ETIOLATED 1 (DET1). The yel-sdj mutant carried a 7 bp deletion in the second exon of OsDET1. Seeds of the osdet1 knockout mutant, generated via CRISPR/Cas9-based gene editing, displayed the yel mutant phenotype. Consistent with the fact that OsDET1 interacts with CONSTITUTIVE PHOTOMORPHOGENIC 10 (OsCOP10) and UV-DAMAGED DNA BINDING PROTEIN 1 (OsDDB1) to form the COP10-DET1-DDB1 (CDD), seeds of oscop10 and osddb1 knockout mutants also showed the yel phenotype. These findings will enhance our understanding of the functional roles of OsDET1 and the CDD complex in embryogenesis and flavonoid biosynthesis in rice seeds.

Quantitation of 2-acetyl-1-pyrroline in aseptic-packaged cooked fragrant rice by HS-SPME/GC-MS.

Aseptic-packaged cooked rice (APCR) is a rice-based food product with a rapidly increasing market size, and APCR made of fragrant rice (FR) has recently appeared on the market. The fragrance of FR is produced by a combination of odoriferous compounds, among which 2-acetyl-1-pyrroline (2AP) has been identified as the most important contributor to overall aroma. This study describes the development of a method to quantify 2AP in FR-based APCR using headspace solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC-MS). The recovery of 2AP spiked into APCR was lower than 10%, which suggests significant matrix effects and inappropriateness of external standard-based calibration. For standard addition calibration method, up to 1,000 ng of 2AP were spiked into APCR containing 0% to 100% FR. Subsequent regression analyses of recovered peak area (Y) as a function of the amount of 2AP spiked (X) yielded highly linear calibration curves (R 2 > 0.9917) with consistent slopes (RSD = 2.7%), regardless of FR composition. Y-intercepts, however, which represent the amount of 2AP in APCR without spiking, increased linearly (R 2 = 0.9898) in proportion to the composition of FR in the APCR. The amount of 2AP in APCR, determined by extrapolating the standard addition calibration curves, also increased linearly (R 2 = 0.9963) as a function of FR composition. Practicality of developed method was tested by monitoring 2AP contents in APCR under realistic storage conditions, which successfully demonstrated 38% and 60% 2AP reductions in APCR of 20% FR after 1 and 2 months of storage at 25°C, respectively. The present study demonstrates that a standard addition method, whereby up to 1,000 ng of 2AP standard is spiked into 4 g of APCR containing 5%-100% FR in a 20-mL headspace vial followed by SPME/GC-MS, may serve as an effective means of quantitating 2AP in fragrant rice-based APCR.

Effects of milling on aromatics, lipophilic phytonutrients, and fatty acids in unprocessed white rice of scented rice 'Cheonjihyang-1-se'.

To understand effects of milling, scented rice 'Cheonjihyang-1-se' was milled from 10 to 140 s and changes in volatiles, phytonutrients, and fatty acids were evaluated. Among 43 identified odor-active compounds, four volatiles, including hexan-3-one, exhibited decreases of up to 78%, while four others including (E)-non-2-enal, increased following milling. Levels of 2-acetyl-1-pyrroline, the most distinctive popcorn-flavoring compound in scented rice, were not affected by the degree of milling (DM). Partial least squares discriminant analyses of volatiles were able to differentiate white rice according to the DM. Benzene and 2-pentylfuran showed the highest variable importance in projection scores, which could be applied in estimating the DM of rice. Milling significantly decreased tocopherols, tocotrienols, squalene, phytosterols contents and oleic acid composition, while palmitic acid composition was increased. These results suggest milling-dependent variations in phytonutrient levels and lipid composition, as well as changes in aroma and subsequent market quality, in 'Cheonjihyang-1-se' rice.

Augmented Quantum Yield of a 2D Monolayer Photodetector by Surface Plasmon Coupling.

Monolayer (1L) transition metal dichalcogenides (TMDCs) are promising materials for nanoscale optoelectronic devices because of their direct band gap and wide absorption range (ultraviolet to infrared). However, 1L-TMDCs cannot be easily utilized for practical optoelectronic device applications (e.g., photodetectors, solar cells, and light-emitting diodes) because of their extremely low optical quantum yields (QYs). In this investigation, a high-gain 1L-MoS2 photodetector was successfully realized, based on the surface plasmon (SP) of the Ag nanowire (NW) network. Through systematic optical characterization of the hybrid structure consisting of a 1L-MoS2 and the Ag NW network, it was determined that a strong SP and strain relaxation effect influenced a greatly enhanced optical QY. The photoluminescence (PL) emission was drastically increased by a factor of 560, and the main peak was shifted to the neutral exciton of 1L-MoS2. Consequently, the overall photocurrent of the hybrid 1L-MoS2 photodetector was observed to be 250 times better than that of the pristine 1L-MoS2 photodetector. In addition, the photoresponsivity and photodetectivity of the hybrid photodetector were effectively improved by a factor of ∼1000. This study provides a new approach for realizing highly efficient optoelectronic devices based on TMDCs.

Role of the Growth Temperature in MoS2 Growth by Chemical Vapor Deposition.

In this paper, we discuss the effect of synthesis temperature on the lateral growth of MoS2 thin films in chemical vapor deposition. With increasing temperature, surface coverage with MoS2 triangular islands is significantly improved due to an increase in the density of nuclei and fully continuous MoS2 thin film is grown when the growth temperature reached 800 °C. The MoS2 triangular islands grown at the temperature from 650 to 750 °C are monolayer and highly crystalline, whereas the large-area continuous film grown at the temperature of 800 °C is composed of double-layer or overlapping MoS2 nanosheets. Our research provides that synthesis temperature is the key to growth large area and high quality single crystal MoS2 films.

Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era.

BACKGROUND: Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remains challenging, it is important to establish practical methods to manage them. A core collection, by definition, refers to a subset of the entire population that preserves the majority of genetic diversity, enhancing the efficiency of germplasm utilization. RESULTS: Here, we report whole-genome resequencing of the 137 rice mini core collection or Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in the Korean genebank of the Rural Development Administration (RDA). We implemented the Illumina HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8 depths using Nipponbare as a reference. Comparisons of the sequences with the reference genome yielded more than 15 million (M) single nucleotide polymorphisms (SNPs) and 1.3 M INDELs. Phylogenetic and population analyses using 2,046,529 high-quality SNPs successfully assigned rice accessions to the relevant rice subgroups, suggesting that these SNPs capture evolutionary signatures that have accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for four exemplary agronomic traits in the KRIC_CORE manifest the utility of KRICE_CORE; that is, identifying previously defined genes or novel genetic factors that potentially regulate important phenotypes. CONCLUSION: This study provides strong evidence that the size of KRICE_CORE is small but contains high genetic and functional diversity across the genome. Thus, our resequencing results will be useful for future breeding, as well as functional and evolutionary studies, in the post-genomic era.

Resequencing Reveals Different Domestication Rate for BADH1 and BADH2 in Rice (Oryza sativa).

BADH1 and BADH2 are two homologous genes, encoding betaine aldehyde dehydrogenase in rice. In the present study, we scanned BADHs sequences of 295 rice cultivars, and 10 wild rice accessions to determine the polymorphisms, gene functions and domestication of these two genes. A total of 16 alleles for BADH1 and 10 alleles for BADH2 were detected in transcribed region of cultivars and wild species. Association study showed that BADH1 has significant correlation with salt tolerance in rice during germination stage, the SNP (T/A) in exon 4 is highly correlated with salt tolerance index (STI) (P<10(-4)). While, BADH2 was only responsible for rice fragrance, of which two BADH2 alleles (8 bp deletion in exon 7 and C/T SNP in exon 13) explain 97% of aroma variation in our germplasm. Theses indicate that there are no overlapping functions between the two homologous genes. In addition, a large LD block was detected in BADH2 region, however, there was no large LD blocks in a 4-Mb region of BADH1. We found that BADH2 region only showed significant bias in Tajima's D value from the balance. Extended haplotype homozygosity study revealed fragrant accessions had a large LD block that extended around the mutation site (8 bp deletion in exon 7) of BADH2, while both of the BADH1 alleles (T/A in exon 4) did not show large extended LD block. All these results suggested that BADH2 was domesticated during rice evolution, while BADH1 was not selected by human beings.