Deficiency in the amino aldehyde dehydrogenase encoded by GmAMADH2, the homologue of rice Os2AP, enhances 2-acetyl-1-pyrroline biosynthesis in soybeans (Glycine max L.)

Breeding exceptionally fragrant soybeans for soy milk with strong aroma

Knockout of the soybean (Glycine max) betaine aldehyde dehydrogenase genes GmBADH1 and GmBADH2 using CRISPR/Cas12i3 enhances the aroma of soybeans. Soy milk made from the gmbadh1/2 double mutant seeds exhibits a much stronger aroma, which consumers prefer; this mutant has potential for enhancing quality in soy-based products.

CsCuAO1 Associated with CsAMADH1 Confers Drought Tolerance by Modulating GABA Levels in Tea Plants

Our previous study showed that COPPER-CONTAINING AMINE OXIDASE (CuAO) and AMINOALDEHYDE DEHYDROGENASE (AMADH) could regulate the accumulation of γ-aminobutyric acid (GABA) in tea through the polyamine degradation pathway. However, their biological function in drought tolerance has not been determined. In this study, Camellia sinensis (Cs) CsCuAO1 associated with CsAMADH1 conferred drought tolerance, which modulated GABA levels in tea plants. The results showed that exogenous GABA spraying effectively alleviated the drought-induced physical damage. Arabidopsis lines overexpressing CsCuAO1 and CsAMADH1 exhibited enhanced resistance to drought, which promoted the synthesis of GABA and putrescine by stimulating reactive oxygen species' scavenging capacity and stomatal movement. However, the suppression of CsCuAO1 or CsAMADH1 in tea plants resulted in increased sensitivity to drought treatment. Moreover, co-overexpressing plants increased GABA accumulation both in an Agrobacterium-mediated Nicotiana benthamiana transient assay and transgenic Arabidopsis plants. In addition, a GABA transporter gene, CsGAT1, was identified, whose expression was strongly correlated with GABA accumulation levels in different tissues under drought stress. Taken together, CsCuAO1 and CsAMADH1 were involved in the response to drought stress through a dynamic GABA-putrescine balance. Our data will contribute to the characterization of GABA's biological functions in response to environmental stresses in plants.

CRISPR/Cas9 gene editing technology: a precise and efficient tool for crop quality improvement

MAIN CONCLUSION

This review provides a direction for crop quality improvement and ideas for further research on the application of CRISPR/Cas9 gene editing technology for crop improvement. Various important crops, such as wheat, rice, soybean and tomato, are among the main sources of food and energy for humans. Breeders have long attempted to improve crop yield and quality through traditional breeding methods such as crossbreeding. However, crop breeding progress has been slow due to the limitations of traditional breeding methods. In recent years, clustered regularly spaced short palindromic repeat (CRISPR)/Cas9 gene editing technology has been continuously developed. And with the refinement of crop genome data, CRISPR/Cas9 technology has enabled significant breakthroughs in editing specific genes of crops due to its accuracy and efficiency. Precise editing of certain key genes in crops by means of CRISPR/Cas9 technology has improved crop quality and yield and has become a popular strategy for many breeders to focus on and adopt. In this paper, the present status and achievements of CRISPR/Cas9 gene technology as applied to the improvement of quality in several crops are reviewed. In addition, the shortcomings, challenges and development prospects of CRISPR/Cas9 gene editing technology are discussed.

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.

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.

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.

A SNP of betaine aldehyde dehydrogenase (BADH) enhances an aroma (2-acetyl-1-pyrroline) in sponge gourd (Luffa cylindrica) and ridge gourd (Luffa acutangula)

Luffa is a genus of tropical and subtropical vines belonging to the Cucurbitaceae family. Sponge gourd (Luffa cylindrica) and ridge gourd (Luffa acutangula) are two important species of the genus Luffa and are good sources of human nutrition and herbal medicines. As a vegetable, aromatic luffa is more preferred by consumers than nonaromatic luffa. While the aroma trait is present in the sponge gourd, the trait is not present in the ridge gourd. In this study, we identified Luffa cylindrica’s betaine aldehyde dehydrogenase (LcBADH) as a gene associated with aroma in the sponge gourd based on a de novo assembly of public transcriptome data. A single nucleotide polymorphism (SNP: A > G) was identified in exon 5 of LcBADH, causing an amino acid change from tyrosine to cysteine at position 163, which is important for the formation of the substrate binding pocket of the BADH enzyme. Based on the identified SNP, a TaqMan marker, named AroLuff, was developed and validated in 370 F₂ progenies of the sponge gourd. The marker genotypes were perfectly associated with the aroma phenotypes, and the segregation ratios supported Mendelian’s simple recessive inheritance. In addition, we demonstrated the use of the AroLuff marker in the introgression of LcBADH from the aromatic sponge gourd to the ridge gourd to improve aroma through interspecific hybridization. The marker proved to be useful in improving the aroma characteristics of both Luffa species.

Comparative Analysis and Development of a Flavor Fingerprint for Volatile Compounds of Vegetable Soybean Seeds Based on Headspace-Gas Chromatography-Ion Mobility Spectrometry

Evaluating the volatile compounds and characteristic fingerprints of the core cultivars of vegetable soybean would provide useful data for improving their aroma in the breeding programs. The present study used headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS) to evaluate the volatile compounds of vegetable soybean seeds at a specific growth stage. In total, 93 signal peaks were identified, 63 compounds qualitatively, with 14 volatile flavor compounds providing multiple signals. The 63 volatile compounds consisted of 15 esters, 15 aldehydes, 13 alcohols, 15 ketones, one acid, and four other compounds. The peak intensity of most of the volatile compounds varied greatly between the core cultivars. The alcohols and aldehydes determined the basic volatile flavor of the vegetable soybean seeds. Volatile flavors were determined by their respective esters, ketones, or other components. Characteristic fingerprints were found in some core vegetable soybean cultivars. Four cultivars (Xiangdou, ZHE1754, Zhexian 65018-33, and Qvxian No. 1) had pleasant aromas, because of their higher content of 2-acetyl-1-pyrroline (2-AP). A principal component analysis (PCA) was used to distinguish the samples based on the signal intensity of their volatile components. The results showed that the composition and concentration of volatile compounds differed greatly between the core cultivars, with the volatile flavor compounds of soybeans being determined by the ecotype of the cultivar, the direction of breeding selection, and their geographical origin. Characteristic fingerprints of the cultivars were established by HS-GC-IMS, enabling them to be used to describe and distinguish cultivars and their offspring in future breeding studies.

Creation of aromatic maize by CRISPR/Cas

Aroma is an important quality parameter for breeding in rice (Oryza sativa). For example, the aromatic rice varieties basmati and jasmine rice, with a popcorn-like scent, are popular worldwide and routinely command a price premium. 2-acetyl-1-pyrroline (2AP) is a key flavor compound among over 200 volatiles identified in fragrant rice. A naturally fragrant germplasm exists in multiple plant species besides rice, which all exhibit lower activity of BETAINE ALDEHYDE DEHYDROGENASE 2 (BADH2). However, no equivalent aromatic germplasm has been described in maize (Zea mays). Here, we characterized the two maize BADH2 homologs, ZmBADH2a and ZmBADH2b. We generated zmbadh2a and zmbadh2b single mutants and the zmbadh2a-zmbadh2b double mutant by CRISPR/Cas in four inbred lines. A popcorn-like scent was only noticeable in seeds from the double mutant, but not from either single mutant or in wild type. In agreement, we only detected 2AP in fresh kernels and dried mature seeds from the double mutant, which accumulated between 0.028 and 0.723 mg/kg 2AP. These results suggest that ZmBADH2a and ZmBADH2b redundantly participate in 2AP biosynthesis in maize, and represent the creation of the world's first aromatic maize by simultaneous genome editing of the two BADH2 genes.

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.

A deletion of the gene encoding amino aldehyde dehydrogenase enhances the "pandan-like" aroma of winter melon (Benincasa hispida) and is a functional marker for the development of the aroma

The gene conferring a "pandan-like" aroma of winter melon was identified. The sequence variation (804-bp deletion) found in the gene was used as the target for functional marker development. Winter melon (Benincasa hispida), a member of the Cucurbitaceae family, is a commonly consumed vegetable in Asian countries that is popular for its nutritional and medicinal value. A "pandan-like" aroma, which is economically important in crops including rice and soybean, is rarely found in most commercial varieties of winter melon, but is present in some landraces. This aroma is a value-added potential trait in breeding winter melon with a higher economic value. In this study, we confirmed that the aroma of winter melon is due to the potent volatile compound 2-acetyl-1-pyrroline (2AP) as previously identified in other plants. Based on an analysis of public transcriptome data, BhAMADH encoding an aminoaldehyde dehydrogenase (AMADH) was identified as a candidate gene conferring aroma of winter melon. A sequence comparison of BhAMADH between the aromatic and non-aromatic accessions revealed an 804-bp deletion encompassing exons 11-13 in the aromatic accession. The deletion caused several premature stop codons and could result in a truncated protein with a length of only 208 amino acids compared with 503 amino acids in the normal protein. A functional marker was successfully developed based on the 804-bp deletion and validated in 237 F₂ progenies. A perfect association of the marker genotypes and aroma phenotypes indicates that BhAMADH is the major gene conferring the aroma. The recently developed functional marker could be efficiently used in breeding programs for the aroma trait in winter melon.

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

Since it was first characterised in 1983, 2-acetyl-1-pyrroline (2AP) has been considered to be the most important aroma compound in rice. In this study, we show four other amine heterocycles: 6-methyl, 5-oxo-2,3,4,5-tetrahydropyridine (6M5OTP), 2-acetylpyrrole, pyrrole and 1-pyrroline, that correlate strongly with the production of 2AP, and are present in consistent proportions in a set of elite aromatic rice varieties from South East Asia and Australia as well as in a collection of recombinant inbred lines (RILs) derived from indica Jasmine-type varieties, Australian long grain varieties (temperate japonica) and Basmati-type rice (Grp V). These compounds were detected through untargeted metabolite profiling by two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOF-MS), and their identity were confirmed by comparison with authentic standards analysed using gas chromatography mass spectrometry (GC-MS) and High Resolution GC × GC-TOF-MS (GC × GC HRT-4D). Genome-wide association analysis indicates that all compounds co-localised with a single quantitative trait locus (QTL) that harbours the FGR gene responsible for the production of GABA. Together, these data provide new insights into the production of 2AP, and evidence for understanding the pathway leading to the accumulation of aroma in fragrant rice.

Evaluation of 2-acetyl-1-pyrroline in foods, with an emphasis on rice flavour

The popcorn-like aroma compound 2-acetyl-1-pyrroline (2-AP) is a key contributor to the desirable aroma of fragrant rice and is also important in the aroma of other foods, such as pandan leaf, popcorn and Mediterranean sausage. It can be formed enzymatically in the rice grain as it grows and is also formed, as part of the Maillard reaction, when rice is heated. This review examines the formation of 2-AP in rice and other foods, particularly its formation during cooking, focusing on the importance of the Maillard reaction between reducing sugar breakdown products and 1-pyrroline derived from the amino acids proline and ornithine. The synthesis of 2-AP is discussed alongside the attempts that have been made to stabilise this relatively unstable compound. The analysis of 2-AP by instrumental techniques, particularly gas chromatography-mass spectrometry and gas chromatography-olfactometry, alongside the use of sensory studies, is also discussed.

Identification of aroma volatiles and understanding 2-acetyl-1-pyrroline biosynthetic mechanism in aromatic mung bean (Vigna radiata (L.) Wilczek)

Mung bean having high food value and easily digestible proteins, is one of the socioeconomically important crop of India. Among the varied cultivars, Sona mung is having aroma and hence popularly cultivated in the pockets of Ganga river basin at Bhutnir char village of Malda District in the West Bengal state. In the present study, aroma volatiles with special reference to 2-acetyl-1-pyrroline (2AP) were analyzed using HS-SPME-GCMS from Sona mung bean and compared with non-scented mung bean (PHULE M-9339). 26 volatiles in seeds of Sona mung and 20 in non-scented mung bean were identified, in which 3,7-dimethyl-6-octenal, (2E)-2-decen-1-ol, 2-ethyl-1-dodecanol and 3,5,5-trimethyl-2-cyclohexene-1-one are first time reported. 0.19 ± 0.001 ppm 2AP was recorded in Sona mung seeds whereas it was not detected in non-scented mung bean. PCA analysis indicated that 2AP, octanal, 1 pentanol, decanal, phenylmethanol and 2-nonen-1-ol were the major contributors in the aroma of Sona mung bean. The significantly higher level proline, methylglyoxal and lower level of BADH2 transcript were detected in Sona mung than non-scented mung, suggesting similar 2AP biosynthesis mechanism in Sona mung bean as reported in scented rice, sorghum and soybean.

Thirty-three years of 2-acetyl-1-pyrroline, a principal basmati aroma compound in scented rice (Oryza sativa L.): a status review

Rice is the staple food of around 3 billion people, most of them in Asia which accounts for 90% of global rice consumption. Aromatic rices have been preferred over non-aromatic rice for hundreds of years. They have a premium value in national as well as international market owing to their unique aroma and quality. Many researchers were involved in identifying the compound responsible for the pleasant aroma in aromatic rice in the 20th century. However, due to its unstable nature, 2-acetyl-1-pyrroline (2AP) was discovered very late, in 1982. Buttery and co-workers found 2AP to be the principal compound imparting the pleasant aroma to basmati and other scented rice varieties. Since then, 2AP has been identified in all fragrant rice (Oryza sativa L.) varieties and a wide range of plants, animals, fungi, bacteria and various food products. The present article reviews in detail biochemical and genetic aspects of 2AP in living systems. The site of synthesis, site of storage and stability in plant systems in vivo is of interest. This compound requires more research on stability to facilitate use as a food additive. © 2016 Society of Chemical Industry.

De novo transcriptome assembly and identification of the gene conferring a "pandan-like" aroma in coconut (Cocos nucifera L.)

Thailand's aromatic coconut (Cocos nucifera L.) is a special type of green dwarf coconut, the liquid endosperm of which is characterized by a pleasant "pandan-like" aroma due to the presence of 2-acetyl-1-pyrroline (2AP). The aim of this study was to perform a de novo assembly of transriptome from C. nucifera endosperm and to identify the gene responsible for 2AP biosynthesis. CnAMADH2 was identified as an ortholog of the rice aromatic gene and a G-to-C substitution found in exon 14 was associated with 2AP content in the aromatic green dwarf coconut accessions. The base substitution caused an amino-acid change, alanine-to-proline, at position 442 (P442A). The presence of P at this position might alter the steric conformation at the loop region and subsequently result in an unstabilized dimer conformation that could lower AMADH enzyme activity. Among AMADH/BADH protein sequences in different plant species, the P442A mutation was found exclusively in aromatic coconut. The PCR marker developed based on this sequence variation can perfectly detect the aromatic and non-aromatic alleles of the gene. This study confirms the hypothesis that plants may share a mechanism of 2AP biosynthesis. This is the first identification of the gene associated with 2AP biosynthesis in a tree plant.

A single base substitution in BADH/AMADH is responsible for fragrance in cucumber (Cucumis sativus L.), and development of SNAP markers for the fragrance

Sequence analysis revealed that an SNP (A1855G) in CsBADH of cucumber accession PK2011T202 causes amino acid change in a highly conserved motif, Y163C. Gene mapping showed association between the SNP and the fragrance. Pandan-like fragrance is a value-added trait in several food crops such as rice, vegetable soybean and sorghum. The fragrance is caused by the volatile chemical 2-acetyl-1-pyrroline (2AP). Mutation(s) in betaine aldehyde dehydrogenase 2 (BADH2; also known as aminoaldehyde dehydrogenase 2) gene causes defective BADH2 and results in biosynthesis of 2AP. Recently, cucumber cultivars possessing pandan-like fragrance were discovered in Thailand. In this study, we report an association between CsBADH and the fragrance in cucumber accession "PK2011T202". Gene expression analysis of CsBADH in leaves of PK2011T202 and "301176" (non-fragrant) at various growth stages revealed that CsBADH was expressed in both accessions. Sequence comparison of CsBADH showed that PK2011T202 possesses a single base substitution (A1855G) in exon 5 which causes an amino acid change in a highly conserved motif of BADH, Y163C. Single nucleotide-amplified polymorphism markers were developed to detect the SNP polymorphism between the wild-type and fragrance alleles. Since CsBADH is located on chromosome 1, quantitative trait locus (QTL) mapping was conducted for this chromosome using an F2 and a backcross populations developed from the cross between PK2011T202 and 301176. QTL analysis in both populations showed that the major QTL for fragrance, qFgr, was co-localized with the CsBADH. We concluded that the defect function of CsBADH is responsible for fragrance in cucumber PK2011T202.

Functional and expression analyses of two kinds of betaine aldehyde dehydrogenases in a glycinebetaine-hyperaccumulating graminaceous halophyte, Leymus chinensis

Glycinebetaine (GB) is an important compatible solute for salinity tolerance in many plants. In this study, we analyzed the enzymatic activity and the expression level of betaine aldehyde dehydrogenase (BADH), an important enzyme that catalyzes the last step in the GB synthesis in Leymus chinensis, a GB-hyperaccumulating graminaceous halophyte, and compared with those of barley, a graminaceous glycophyte. We have isolated cDNAs for two BADH genes, LcBADH1 and LcBADH2. LcBADH1 has a putative peroxisomal signal peptide (PTS1) at its C-terminus, while LcBADH2 does not have any typical signal peptide. Using immunofluorescent labeling, we showed that BADH proteins were localized to the cytosol and dot-shaped organelles in the mesophyll and bundle sheath cells of L.chinensis leaves. The affinity of recombinant LcBADH2 for betaine aldehyde was comparable to other plant BADHs, whereas recombinant LcBADH1 showed extremely low affinity for betaine aldehyde, indicating that LcBADH2 plays a major role in GB synthesis in L. chinensis. In addition, the recombinant LcBADH2 protein was tolerant to NaCl whereas LcBADH1 wasn't. The kinetics, subcellular and tissue localization of BADH proteins were comparable between L. chinensis and barley. The activity and expression level of BADH proteins were higher in L. chinensis compared with barley under both normal and salinized conditions, which may be related to the significant difference in the amount of GB accumulation between two plants.

RNAi-directed downregulation of betaine aldehyde dehydrogenase 1 (OsBADH1) results in decreased stress tolerance and increased oxidative markers without affecting glycine betaine biosynthesis in rice (Oryza sativa)

As an important osmoprotectant, glycine betaine (GB) plays an essential role in resistance to abiotic stress in a variety of organisms, including rice (Oryza sativa L.). However, GB content is too low to be detectable in rice, although rice genome possesses several orthologs coding for betaine aldehyde dehydrogenase (BADH) involved in plant GB biosynthesis. Rice BADH1 (OsBADH1) has been shown to be targeted to peroxisome and its overexpression resulted in increased GB biosynthesis and tolerance to abiotic stress. In this study, we demonstrated a pivotal role of OsBADH1 in stress tolerance without altering GB biosynthesis capacity, using the RNA interference (RNAi) technique. OsBADH1 was ubiquitously expressed in different organs, including roots, stems, leaves and flowers. Transgenic rice lines downregulating OsBADH1 exhibited remarkably reduced tolerance to NaCl, drought and cold stresses. The decrease of stress tolerance occurring in the OsBADH1-RNAi repression lines was associated with an elevated level of malondialdehyde content and hydrogen peroxidation. No GB accumulation was detected in transgene-positive and transgene-negative lines derived from heterozygous transgenic T0 plants. Moreover, transgenic OsBADH1-RNAi repression lines showed significantly reduced seed set and yield. In conclusion, the downregulation of OsBADH1, even though not causing any change of GB content, was accounted for the reduction of ability to dehydrogenate the accumulating metabolism-derived aldehydes and subsequently resulted in decreased stress tolerance and crop productivity. These results suggest that OsBADH1 possesses an enzyme activity to catalyze other aldehydes in addition to betaine aldehyde (the precursor of GB) and thus alleviate their toxic effects under abiotic stresses.

Genetic polymorphisms in Japanese fragrant landraces and novel fragrant allele domesticated in northern Japan

Rice fragrance is an important characteristic for Southeast Asian consumers, and fragrant landraces from Japan were first recorded in the 17th century. Principal component analysis clearly showed that Japanese fragrant landraces were genetically different from non-Japanese fragrant landraces. Japanese fragrant landraces were composed of six clades, none of which carried the most common fragrance mutation, an 8-bp deletion in exon 7 of Badh2. Fragrant landraces comprised two major groups carrying different Badh2 mutations. One group carried a known SNP at exon13 and the other a SNP at the exon1-intron1 junction as splicing donor site. The latter was considered to be a potential splicing mutant group as a novel allele at Badh2. Heterozygosity (He) scores in the two fragrant groups were not significantly different from non-fragrant landraces and modern cultivars. However, lower He scores were found around the Badh2 locus in the two groups. The potential splicing mutant group showed a more extended haplotype than the E13 SNP group. A likely causal factor responsible for loss of function is a novel splicing mutation allele that may have been generated quite recently. The fragrance allele has dispersed as a result of out-crossing under local environmental conditions.

Gene discovery and functional marker development for fragrance in sorghum (Sorghum bicolor (L.) Moench)

Sequence analysis and genetic mapping revealed that a 1,444 bp deletion causes a premature stop codon in SbBADH2 of sorghum IS19912. The non-function of SbBADH2 is responsible for fragrance in sorghum IS19912. 2-acetyl-1-pyrroline (2AP) is a potent volatile compound causing fragrance in several plants and foods. Seeds of some varieties of rice, sorghum and soybean possess fragrance. The genes responsible for fragrance in rice and soybean are orthologs that correspond to betaine aldehyde dehydrogenase 2 (BADH2). Genotypes harboring fragrance in rice and soybean contain a premature stop codon in BADH2 which impairs the synthesis of full length functional BADH2 protein leading to the accumulation of 2AP. In this study, we reported an association between the BADH2 gene and fragrance in sorghum. An F2 population of 187 plants developed from a cross between KU630 (non-fragrant) and IS19912 (fragrant) was used. Leaves of F2 and F3 progenies were evaluated for fragrance by organoleptic test, while seeds of F2 plants were analyzed for 2AP. The tests consistently showed that the fragrance is controlled by a single recessive gene. Gene expression analysis of SbBADH1 and SbBADH2 in leaves of KU630 and IS19912 at various stages revealed that SbBADH1 and SbBADH2 were expressed in both accessions. Sequence comparison between KU630 and IS19912 revealed a continuous 1,444 bp deletion encompassing exon 12 to 15 of SbBADH2 in IS19912 which introduces a frameshift mutation and thus causes a premature stop codon. An indel marker was developed to detect polymorphism in SbBADH2. Bulk segregant and QTL analyses confirmed the association between SbBADH2 and fragrance.

Plant ALDH10 family: identifying critical residues for substrate specificity and trapping a thiohemiacetal intermediate

Plant ALDH10 family members are aminoaldehyde dehydrogenases (AMADHs), which oxidize ω-aminoaldehydes to the corresponding acids. They have been linked to polyamine catabolism, osmoprotection, secondary metabolism (fragrance), and carnitine biosynthesis. Plants commonly contain two AMADH isoenzymes. We previously studied the substrate specificity of two AMADH isoforms from peas (PsAMADHs). Here, two isoenzymes from tomato (Solanum lycopersicum), SlAMADHs, and three AMADHs from maize (Zea mays), ZmAMADHs, were kinetically investigated to obtain further clues to the catalytic mechanism and the substrate specificity. We also solved the high resolution crystal structures of SlAMADH1 and ZmAMADH1a because these enzymes stand out from the others regarding their activity. From the structural and kinetic analysis, we can state that five residues at positions 163, 288, 289, 444, and 454 (PsAMADHs numbering) can, directly or not, significantly modulate AMADH substrate specificity. In the SlAMADH1 structure, a PEG aldehyde derived from the precipitant forms a thiohemiacetal intermediate, never observed so far. Its absence in the SlAMADH1-E260A structure suggests that Glu-260 can activate the catalytic cysteine as a nucleophile. We show that the five AMADHs studied here are capable of oxidizing 3-dimethylsulfoniopropionaldehyde to the cryo- and osmoprotectant 3-dimethylsulfoniopropionate. For the first time, we also show that 3-acetamidopropionaldehyde, the third aminoaldehyde besides 3-aminopropionaldehyde and 4-aminobutyraldehyde, is generally oxidized by AMADHs, meaning that these enzymes are unique in metabolizing and detoxifying aldehyde products of polyamine degradation to nontoxic amino acids. Finally, gene expression profiles in maize indicate that AMADHs might be important for controlling ω-aminoaldehyde levels during early stages of the seed development.

Aldehyde dehydrogenase (ALDH) superfamily in plants: gene nomenclature and comparative genomics

In recent years, there has been a significant increase in the number of completely sequenced plant genomes. The comparison of fully sequenced genomes allows for identification of new gene family members, as well as comprehensive analysis of gene family evolution. The aldehyde dehydrogenase (ALDH) gene superfamily comprises a group of enzymes involved in the NAD(+)- or NADP(+)-dependent conversion of various aldehydes to their corresponding carboxylic acids. ALDH enzymes are involved in processing many aldehydes that serve as biogenic intermediates in a wide range of metabolic pathways. In addition, many of these enzymes function as 'aldehyde scavengers' by removing reactive aldehydes generated during the oxidative degradation of lipid membranes, also known as lipid peroxidation. Plants and animals share many ALDH families, and many genes are highly conserved between these two evolutionarily distinct groups. Conversely, both plants and animals also contain unique ALDH genes and families. Herein we carried out genome-wide identification of ALDH genes in a number of plant species-including Arabidopsis thaliana (thale crest), Chlamydomonas reinhardtii (unicellular algae), Oryza sativa (rice), Physcomitrella patens (moss), Vitis vinifera (grapevine) and Zea mays (maize). These data were then combined with previous analysis of Populus trichocarpa (poplar tree), Selaginella moellindorffii (gemmiferous spikemoss), Sorghum bicolor (sorghum) and Volvox carteri (colonial algae) for a comprehensive evolutionary comparison of the plant ALDH superfamily. As a result, newly identified genes can be more easily analyzed and gene names can be assigned according to current nomenclature guidelines; our goal is to clarify previously confusing and conflicting names and classifications that might confound results and prevent accurate comparisons between studies.

RNA silencing as a tool to uncover gene function and engineer novel traits in soybean

RNA silencing refers collectively to diverse RNA-mediated pathways of nucleotide-sequence-specific inhibition of gene expression. It has been used to analyze gene function and engineer novel traits in various organisms. Here, we review the application of RNA silencing in soybean. To produce soybean lines, in which a particular gene is stably silenced, researchers have frequently used a transgene that transcribes inverted repeats of a target gene segment. Suppression of gene expression in developing soybean embryos has been one of the main focuses of metabolic engineering using transgene-induced silencing. Plants that have enhanced resistance against diseases caused by viruses or cyst nematode have also been produced. Meanwhile, Agrobacterium rhizogenes-mediated transformation has been used to induce RNA silencing in roots, which enabled analysis of the roles of gene products in nodulation or disease resistance. RNA silencing has also been induced using viral vectors, which is particularly useful for gene function analysis. So far, three viral vectors for virus-induced gene silencing have been developed for soybean. One of the features of the soybean genome is the presence of a large number of duplicated genes. Potential use of RNA silencing technology in combination with forward genetic approaches for analyzing duplicated genes is discussed.

A SNP in GmBADH2 gene associates with fragrance in vegetable soybean variety "Kaori" and SNAP marker development for the fragrance

Fragrance in soybean is due to the presence of 2-acetyl-1-pyrroline (2AP). BADH2 gene coding for betaine aldehyde dehydrogenase has been identified as the candidate gene responsible for fragrance in rice (Oryza sativa L.). In this study, using the RIL population derived from fragrant soybean cultivar "Kaori" and non-fragrant soybean cultivar "Chiang Mai 60" (CM60), STS markers designed from BADH2 homolog were found associating with 2AP production. Genetic mapping demonstrated that QTL position of fragrance and 2AP production coincides with the position of GmBADH2 (Glycine max betaine aldehyde dehydrogenase 2). Sequence comparison of GmBADH2 between Kaori and non-fragrant soybeans revealed non-synonymous single-nucleotide polymorphism (SNP) in exon 10. Nucleotide substitution of G to A in the exon results in an amino acid change of glycine (GGC; G) to aspartic acid (GAC; D) in Kaori. The amino acid substitution changes the conserved EGCRLGPIVS motif of GmBADH2, which is essential for functional activity of GmBADH2 protein, to EGCRLDPIVS motif, suggesting that the SNP in GmBADH2 is responsible for the fragrance in Kaori. Five single nucleotide-amplified polymorphism (SNAP) markers which are PCR-based allele specific SNP markers were developed for fragrance based on the SNP in GmBADH2. Two markers specific to A allele produced a band in only Kaori, while three markers specific to G alleles produced a band in only CM60. The simple PCR-based allele specific SNAP markers developed in the present study are useful in marker-assisted breeding of fragrant soybean.