Functional Bph14 from Rathu Heenati promotes resistance to BPH at the early seedling stage of rice (Oryza sativa L.) as revealed by QTL-seq.

KEY MESSAGE: A QTL associated with BPH resistance at the early seedling stage was identified on chromosome 3. Functional Bph14 in Rathu Heenati was associated with BPH resistance at the early seedling stage. Brown planthopper (BPH; Nilaparvata lugens Stål) is considered the most important rice pest in many Asian countries. Several BPH resistance genes have previously been identified. However, there are few reports of genes specific for BPH resistance at the early seedling stage, a crucial stage for direct-seeding cultivation. In this study, we performed a QTL-seq analysis using two bulks (20 F2 lines in each bulk) of the F2 population (n = 300) derived from a cross of Rathu Heenati (RH) × HCS-1 to identify QTL/genes associated with BPH resistance at the early seedling stage. An important QTL was identified on chromosome 3 and Bph14 was identified as a potential candidate gene based on the differences in gene expression and sequence variation when compared with the two parents. All plants in the resistant bulks possessed the functional Bph14 from RH and all plants in the susceptible bulk and HCS-1 contained a large deletion (2703 bp) in Bph14. The functional Bph14 gene of RH appears to be important for BPH resistance at the early seedling stage of rice and could be used in conjunction with other BPH resistance genes in rice breeding programs that confer resistance to BPH at the early and later growth stages.

Rice height QTLs in KDML105 chromosome segment substitution lines.

Rice is an important crop that is consumed by approximately half of the world's population on a regular basis. Plant height is an important characteristic with shorter rice often having higher lodging resistance and better soil nutrient utilization allowing for lower fertilizer use. We used a Chromosome Segment Substitution Line (CSSL) population generated by introgressing segments of CT9993 and IR62266 into KDML 105. We identified height QTLs on chromosomes 1 and 4. We performed whole genome sequencing of the parental lines and found that IR62266 has the deletion in Gibberellin 20-oxidase 2 corresponding to the semi-dwarf 1 locus. However, short height on chromosome 1 came from CT9993 with no mutation in Gibberellin 20-oxidase 2, or any known height genes. The height QTL on chromosome 4 contains mutations in Peroxisome biogenesis protein 6, which has been linked to a reduced growth phenotype in A. thaliana, making this a good candidate height gene.

De novo chromosome-level assembly of the Centella asiatica genome.

Centella asiatica is a herbaceous, perennial species indigenous to India and Southeast Asia. C. asiatica possesses several medicinal properties: anti-aging, anti-inflammatory, wound healing and memory enhancing. The lack of available genomics resources significantly impedes the improvement of C. asiatica varieties through molecular breeding. Here, we combined the 10× Genomics linked-read technology and the long-range HiC technique to obtain the genome assembly. The final assembly contained nine pseudomolecules, corresponding to the haploid chromosome number in C. asiatica. These nine chromosomes covered 402,536,584 bases or 93.6% of the 430-Mb assembly. Comparative genomics analyses based on single-copy orthologous genes showed that C. asiatica and the common ancestor of Coriandrum sativum (coriander) and Daucus carota (carrot) diverged about 48 million years ago. This assembly provides a valuable reference genome for future molecular studies, varietal development through marker-assisted breeding and comparative genomics studies in C. asiatica.

QTL-seq reveals genomic regions associated with spikelet fertility in response to a high temperature in rice (Oryza sativa L.).

KEY MESSAGE: The QTL-seq approach was used to identify QTLs for spikelet fertility under heat stress in rice. QTLs were detected on chromosomes 1, 2 and 3. Rice is a staple food of more than half of the global population. Rice production is increasingly affected by extreme environmental fluctuations caused by climate change. Increasing temperatures that exceed the optimum temperature adversely affect rice growth and development, especially during reproductive stages. Heat stress during the reproductive stages has a large effect on spikelet fertility; hence, the yield decreases. To sustain rice yields under increasing temperatures, the development of rice varieties for heat tolerance is necessary. In this study, we applied the QTL-seq approach to rapidly identify QTLs for spikelet fertility under heat stress (air temperature of 40-45 °C) based on two DNA pools, each consisting of 25 individual plants that exhibited a heat-tolerant or heat-sensitive phenotype from an F2 population of a cross between M9962 (heat tolerant) and Sinlek (heat sensitive). Three QTLs, qSF1, qSF2 and qSF3, were detected on chromosomes 1, 2 and 3, respectively, according to the highest contrasting SNP index between the two bulks. The QTLs identified in this study were found to overlap or were linked to QTLs previously identified in other crosses using conventional QTL mapping. A few highly abundant and anther-specific genes that contain nonsynonymous variants were identified within the QTLs and were proposed to be potential candidate genes. These genes could be targets in rice breeding programs for heat tolerance.

Genome-wide association mapping of virulence gene in rice blast fungus Magnaporthe oryzae using a genotyping by sequencing approach.

Magnaporthe oryzae is a fungal pathogen causing blast disease in many plant species. In this study, seventy three isolates of M. oryzae collected from rice (Oryza sativa) in 1996-2014 were genotyped using a genotyping-by-sequencing approach to detect genetic variation. An association study was performed to identify single nucleotide polymorphisms (SNPs) associated with virulence genes using 831 selected SNP and infection phenotypes on local and improved rice varieties. Population structure analysis revealed eight subpopulations. The division into eight groups was not related to the degree of virulence. Association mapping showed five SNPs associated with fungal virulence on chromosome 1, 2, 3, 4 and 7. The SNP on chromosome 1 was associated with virulence against RD6-Pi7 and IRBL7-M which might be linked to the previously reported AvrPi7.

Global metabolite profiles of rice brown planthopper-resistant traits reveal potential secondary metabolites for both constitutive and inducible defenses.

INTRODUCTION: Brown planthopper (BPH) is a phloem feeding insect that causes annual disease outbreaks, called hopper burn in many countries throughout Asia, resulting in severe damage to rice production. Currently, mechanistic understanding of BPH resistance in rice plant is limited, which has caused slow progression on developing effective rice varieties as well as effective farming practices against BPH infestation. OBJECTIVE: To reveal rice metabolic responses during 8 days of BPH attack, this study examined polar metabolome extracts of BPH-susceptible (KD) and its BPH-resistant isogenic line (IL308) rice leaves. METHODS: Ultra high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QToF-MS) was combined with multi-block PCA to analyze potential metabolites in response to BPH attack. RESULTS: This multivariate statistical model revealed different metabolic response patterns between the BPH-susceptible and BPH-resistant varieties during BPH infestation. The metabolite responses of the resistant IL308 variety occurred on Day 1, which was significantly earlier than those of the susceptible KD variety which showed an induced response by Days 4 and 8. BPH infestation caused metabolic perturbations in purine, phenylpropanoid, flavonoid, and terpenoid pathways. While found in both susceptible and resistant rice varieties, schaftoside (1.8 fold), iso-schaftoside (1.7 fold), rhoifolin (3.4 fold) and apigenin 6-C-α-L-arabinoside-8-C-ß-L-arabinoside levels (1.6 fold) were significantly increased in the resistant variety by Day 1 post-infestation. 20-hydroxyecdysone acetate (2.5 fold) and dicaffeoylquinic acid (4.7 fold) levels were considerably higher in the resistant rice variety than those in the susceptible variety, both before and after infestation, suggesting that these secondary metabolites play important roles in inducible and constitutive defenses against the BPH infestation. CONCLUSIONS: These potential secondary metabolites will be useful as metabolite markers and/or bioactive compounds for effective and durable approaches to address the BPH problem.

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.

KEY MESSAGE: 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.

Accelerating haploid induction rate and haploid validation through marker-assisted selection for qhir1 and qhir8 in maize.

Doubled haploid (DH) technology becomes more routinely applied in maize hybrid breeding. However, some issues in haploid induction and identification persist, requiring resolution to optimize DH production. Our objective was to implement simultaneous marker-assisted selection (MAS) for qhir1 (MTL/ZmPLA1/NLD) and qhir8 (ZmDMP) using TaqMan assay in F2 generation of four BHI306-derived tropical × temperate inducer families. We also aimed to assess their haploid induction rate (HIR) in the F3 generation as a phenotypic response to MAS. We highlighted remarkable increases in HIR of each inducer family. Genotypes carrying qhir1 and qhir8 exhibited 1 - 3-fold higher haploid frequency than those carrying only qhir1. Additionally, the qhir1 marker was employed for verifying putative haploid seedlings at 7 days after planting. Flow cytometric analysis served as the gold standard test to assess the accuracy of the R1-nj and the qhir1 marker. The qhir1 marker showed high accuracy and may be integrated in multiple haploid identifications at early seedling stage succeeding pre-haploid sorting via R1-nj marker.

Candidate genes affecting stomatal density in rice (Oryza sativa L.) identified by genome-wide association.

Stomata regulate photosynthesis and water loss. They have been an active subject of research for centuries, but our knowledge of the genetic components that regulate stomatal development in crops remains very limited in comparison to the model plant Arabidopsis thaliana. Leaf stomatal density was found to vary by over 2.5-fold across a panel of 235 rice accessions. Using GWAS, we successfully identified five different QTLs associated with stomatal density on chromosomes 2, 3, 9, and 12. Forty-two genes were identified within the haplotype blocks corresponding to these QTLs. Of these, nine genes contained haplotypes that were associated with different stomatal densities. These include a gene encoding a trehalose-6-phosphate synthase, an enzyme that has previously been associated with altered stomatal density in Arabidopsis, and genes encoding a B-BOX zinc finger family protein, a leucine-rich repeat family protein, and the 40 S ribosomal protein S3a, none of which have previously been linked to stomatal traits. We investigated further and show that a closely related B-BOX protein regulates stomatal development in Arabidopsis. The results of this study provide information on genetic associations with stomatal density in rice. The QTLs and candidate genes may be useful in future breeding programs for low or high stomatal density and, consequently, improved photosynthetic capacity, water use efficiency, or drought tolerance.

Promotion of seed germination and early plant growth by KNO3 and light spectra in Ocimum tenuiflorum using a plant factory.

The plant factory with artificial light (PFAL) is a novel cultivation system of agriculture technology for crop production under controlled-environment conditions. However, there are a number of issues relating to low quality of seed germination and seedling vigor that lead to decreased crop yields. The present study investigates the optimal KNO3 concentration for seed germination, and the influence of different light spectra on early plant growth in holy basil (Ocimum tenuiflorum) under a PFAL system. Experiment 1 investigated the effects of KNO3 concentration (0, 0.2, 0.4 and 0.6%) on germination of seeds primed for 24 h under white Light emitting diodes (LED). Results show that sowing holy basil seeds in 0.4% KNO3 enhanced seed germination percentage (GP) and germination index (GI), while decreasing mean germination time (MGT). Experiment 2 investigated the effect of four light spectra on seed germination and early plant growth by sowing with 0 and 0.4% KNO3 and germinating for 15 days continuously under different monochromatic light settings: white, red, green and blue in PFAL. It was found that the green spectrum positively affected shoot and root length, and also decreased shortened MGT at 0 and 0.4% KNO3 when compared with other light treatments. Additionally, pre-cultivated seedlings under the green spectrum showed significant improvement in the early plant growth for all holy basil varieties at 15 days after transplanting by promoting stem length, stem diameter, plant width, fresh weights of shoot and root, and dry weights of shoot and root. These findings could be useful in developing seed priming and light treatments to enhance seed germination and seedling quality of holy basil resulting in increased crop production under PFAL.

Identification of broad-spectrum resistance QTLs against rice blast fungus and their application in different rice genetic backgrounds.

Rice blast disease is found worldwide leading to economic losses. Use of resistance gene is effective to improve rice resistance variety. Therefore, to deploy genomic regions harbouring resistance genes, a population of 587 F2:6 recombinant inbred lines (RILs) was developed from a cross between Jao Hom Nin, a Thai black rice variety with broad-spectrum resistance to blast disease, and Kao Dawk Mali 105, a susceptible Thai jasmine variety. The RILs were challenged with 17 blast isolates collected from Thailand and Laos PDR. Quantitative trait locus analysis identified genomic regions associated with broad-spectrum quantitative resistance (qBSRLs) and racespecific quantitative resistance (qRSRLs). Two qBSRLs were detected on chromosomes 1 and 11, and two qRSRLs were detected on chromosomes 8 and 12. The two qBSRLs were introgressed into two new genetic backgrounds through marker-assisted selection (MAS). Twelve breeding lines were tested for their spectra of resistance against 35 blast isolates. The results indicated that both qBSRLs were effective in new genetic backgrounds. The flanking markers and qBSRLs identified in the large mapping population showed high selection accuracy and effectiveness, suggesting the routine deployment of MAS technique in rice breeding programmes.

The influence of different light spectra on physiological responses, antioxidant capacity and chemical compositions in two holy basil cultivars.

Light-emitting diodes (LEDs) are an artificial light source used in indoor cultivation to influence plant growth, photosynthesis performance and secondary metabolite synthesis. Holy basil plants (Ocimum tenuiflorum) were cultivated under fully controlled environmental conditions with different red (R) and blue (B) light intensity ratios (3R:1B, 1R:1B and 1R:3B), along with combined green (G) LED (2R:1G:2B). The photosynthetic activities of both cultivars were maximal under 3R:1B. However, the highest fresh (FW) and dry (DW) weight values of green holy basil were recorded under 3R:1B and 2R:1G:2B, significantly higher than those under alternative light conditions. For red holy basil, the highest FW and DW were recorded under 1R:3B. Moreover, 2R:1G:2B treatment promoted pigment (chlorophyll and carotenoid) accumulation in green holy basil, while red holy basil was found to be rich in both pigments under 3R:1B. Antioxidant capacity was also influenced by light spectrum, resulting in greater total phenolic content (TPC) and DPPH accumulation in both cultivars under 1R:3B. The highest content of flavonoid in green holy basil was detected under 1R:1B; meanwhile, 1R:3B treatment significantly promoted flavonoid content in red holy basil. In addition, anthocyanin content increased in red holy basil under 1R:3B conditions. Gas chromatography coupled with mass spectrometry (GC-MS/MS) analysis of chemical composition showed higher proportional accumulation in Methyleugenol and Caryophyllene of two cultivars grown under all light spectrum ratios at two developmental stages. Overall, specific light spectrum ratios induced different chemical composition responses in each cultivar and at each developmental stage. These results suggest that 3R:1B was favorable for biomass accumulation and photosynthetic responses in green holy basil, while 1R:3B provided antioxidant accumulation. For red holy basil cultivation, 1R:3B provided optimal growing conditions, promoting improvements in plant biomass, and physiological and antioxidant capacities.

Physiological responses, yield and medicinal substance (andrographolide, AP1) accumulation of Andrographis paniculata (Burm. f) in response to plant density under controlled environmental conditions.

Agricultural practice in adjusting planting density and harvest date are important factors for plant development and crop improvement, reaching maximum yields and enhancing the production of secondary metabolites. However, it is unclear as to the optimal planting densities during mass production that encourage consistent, high yield secondary metabolite content. For this, controlled environment, crop production facilities such as plant factories with artificial lighting (PFAL) offer opportunity to enhance quality and stabilize production of herbal plants. This study assessed the effect of plant density and harvest date on physiological responses, yield and andrographolide (AP1) content in Andrographis paniculata (Andrographis) using hydroponic conditions in a PFAL system. Andrographis, harvested at vegetative stage (30 days after transplanting; 30 DAT) and initial stage of flowering (60 DAT) exhibited no significant differences in growth parameters or andrographolide accumulation according to planting densities. Harvest time at flowering stage (90 DAT) showed the highest photosynthetic rates at a planting density of 15 plants m-2. Highest yield, number of leaves, and Andrographolide (AP1) content (mg per gram of DW in m2) were achieved at a more moderate planting density (30 plants m-2). Finally, five out of seventeen indices of leaf reflectance reveal high correlation (r = 0.8 to 1.0 and r = -0.8 to -1.0, P<0.01) with AP1 content. These results suggest that a planting density of 30 plants m-2 and harvest time of 90 DAT provide optimal growing condition under the hydroponic PFAL system.

riceExplorer: Uncovering the Hidden Potential of a National Genomic Resource Against a Global Database.

Agricultural crop breeding programs, particularly at the national level, typically consist of a core panel of elite breeding cultivars alongside a number of local landrace varieties (or other endemic cultivars) that provide additional sources of phenotypic and genomic variation or contribute as experimental materials (e.g., in GWAS studies). Three issues commonly arise. First, focusing primarily on core development accessions may mean that the potential contributions of landraces or other secondary accessions may be overlooked. Second, elite cultivars may accumulate deleterious alleles away from nontarget loci due to the strong effects of artificial selection. Finally, a tendency to focus solely on SNP-based methods may cause incomplete or erroneous identification of functional variants. In practice, integration of local breeding programs with findings from global database projects may be challenging. First, local GWAS experiments may only indicate useful functional variants according to the diversity of the experimental panel, while other potentially useful loci-identifiable at a global level-may remain undiscovered. Second, large-scale experiments such as GWAS may prove prohibitively costly or logistically challenging for some agencies. Here, we present a fully automated bioinformatics pipeline (riceExplorer) that can easily integrate local breeding program sequence data with international database resources, without relying on any phenotypic experimental procedure. It identifies associated functional haplotypes that may prove more robust in determining the genotypic determinants of desirable crop phenotypes. In brief, riceExplorer evaluates a global crop database (IRRI 3000 Rice Genomes) to identify haplotypes that are associated with extreme phenotypic variation at the global level and recorded in the database. It then examines which potentially useful variants are present in the local crop panel, before distinguishing between those that are already incorporated into the elite breeding accessions and those only found among secondary varieties (e.g., landraces). Results highlight the effectiveness of our pipeline, identifying potentially useful functional haplotypes across the genome that are absent from elite cultivars and found among landraces and other secondary varieties in our breeding program. riceExplorer can automatically conduct a full genome analysis and produces annotated graphical output of chromosomal maps, potential global diversity sources, and summary tables.

Identification of Pathogenicity Loci in Magnaporthe oryzae Using GWAS with Neck Blast Phenotypic Data.

Magnaporthae oryzae (M. oryzae) is the most destructive disease of rice worldwide. In this study, one hundred and two isolates of M. oryzae were collected from rice (Oryzae sativa L.) from 2001 to 2017, and six rice varieties with resistance genes Pizt, Pish, Pik, Pib, and Pi2 were used in a genome-wide association study to identify pathogenicity loci in M. oryzae. Genome-wide association analysis was performed using 5338 single nucleotide polymorphism (SNPs) and phenotypic data of neck blast screening by TASSEL software together with haplotype block and SNP effect analysis. Twenty-seven significant SNPs were identified on chromosomes 1, 2, 3, 4, 5, 6, and 7. Many predicted genes (820 genes) were found in the target regions of six rice varieties. Most of these genes are described as putative uncharacterized proteins, however, some genes were reported related to virulence in M. oryzae. Moreover, this study revealed that R genes, Pik, Pish, and Pi2, were broad-spectrum resistant against neck blast disease caused by Thai blast isolate. Haplotype analysis revealed that the combination of the favorable alleles causing reduced virulence of isolates against IRBLz5-CA carrying Pi2 gene contributes 69% of the phenotypic variation in pathogenicity. The target regions and information are useful to develop marker-specific genes to classify blast fungal isolates and select appropriate resistance genes for rice cultivation and improvement.

Determination of traits responding to iron toxicity stress at different stages and genome-wide association analysis for iron toxicity tolerance in rice (Oryza sativa L.).

Rice is the staple food for more than half of the world's population. Iron toxicity limits rice production in several regions of the world. Breeding Fe-tolerant rice varieties is an excellent approach to address the problem of Fe toxicity. Rice responds differently to Fe toxicity at different stages. Most QTLs associated with Fe toxicity have been identified at the seedling stage, and there are very few studies on Fe toxicity across different stages. In this study, we investigated agro-morphological and physiological traits in response to Fe toxicity in a rice diversity panel at seedling, vegetative, and reproductive stages and applied GWAS to identify QTLs/genes associated with these traits. Among agro-morphological and physiological parameters, leaf bronzing score (LBS) is a key parameter for determining Fe toxicity response at all stages, and SDW could be a promising parameter at the seedling stage. A total of 29 QTLs were identified on ten chromosomes. Among them, three colocalized QTLs were identified on chromosome 5, 6, and 11. Several QTLs identified in this study overlapped with previously identified QTLs from bi-parental QTL mapping and association mapping. Two genes previously reported to be associated with iron homeostasis were identified, i.e., LOC_Os01g72370 (OsIRO2, OsbHLH056) and LOC_Os04g38570 (OsABCB14). In addition, based on gene-based haplotype analysis, LOC_Os05g16670 was identified as a candidate gene for the colocalized QTL on chromosome 5 and LOC_Os11g18320 was identified as a candidate gene for the colocalized QTL on chromosome 11. The QTLs and candidate genes identified in this study could be useful for rice breeding programs for Fe toxicity tolerance.

Photosynthetic Plasticity and Stomata Adjustment in Chromosome Segment Substitution Lines of Rice Cultivar KDML105 under Drought Stress.

The impact of increasing drought periods on crop yields as a result of global climate change is a major concern in modern agriculture. Thus, a greater understanding of crop physiological responses under drought stress can guide breeders to develop new cultivars with enhanced drought tolerance. In this study, selected chromosome segment substitution lines of KDML105 (KDML105-CSSL) were grown in the Plant Phenomics Center of Kasetsart University in Thailand under well-watered and drought-stressed conditions. Physiological traits were measured by observing gas exchange dynamics and using a high-throughput phenotyping platform. Furthermore, because of its impact on plant internal gas and water regulation, stomatal morphological trait variation was recorded. The results show that KDML105-CSS lines exhibited plasticity responses to enhance water-use efficiency which increased by 3.62%. Moreover, photosynthesis, stomatal conductance and transpiration decreased by approximately 40% and plant height was reduced by 17.69%. Stomatal density tended to decrease and was negatively correlated with stomatal size, and stomata on different sides of the leaves responded differently under drought stress. Under drought stress, top-performing KDML105-CSS lines with high net photosynthesis had shorter plant height and improved IWUE, as influenced by an increase in stomatal density on the upper leaf side and a decrease on the lower leaf side.

Induced Genetic Variations in Stomatal Density and Size of Rice Strongly Affects Water Use Efficiency and Responses to Drought Stresses.

Rice (Oryza sativa L.) is an important food crop relied upon by billions of people worldwide. However, with increasing pressure from climate change and rapid population growth, cultivation is very water-intensive. Therefore, it is critical to produce rice that is high-yielding and genetically more water-use efficient. Here, using the stabilized fast-neutron mutagenized population of Jao Hom Nin (JHN) - a popular purple rice cultivar - we microscopically examined hundreds of flag leaves to identify four stomatal model mutants with either high density (HD) or low density (LD) stomata, and small-sized (SS) or large-sized (LS) stomata. With similar genetic background and uniformity, the stomatal model mutants were used to understand the role of stomatal variants on physiological responses to abiotic stress. Our results show that SS and HD respond better to increasing CO2 concentration and HD has higher stomatal conductance (gs) compared to the other stomatal model mutants, although the effects on gas exchange or overall plant performance were small under greenhouse conditions. In addition, the results of our drought experiments suggest that LD and SS can better adapt to restricted water conditions, and LD showed higher water use efficiency (WUE) and biomass/plant than other stomatal model mutants under long-term restricted water treatment. Finally, our study suggests that reducing stomata density and size may play a promising role for further work on developing a climate-ready rice variety to adapt to drought and heat stress. We propose that low stomata density and small size have high potential as genetic donors for improving WUE in climate-ready rice.

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.

Physiological responses and variation in secondary metabolite content among Thai holy basil cultivars (Ocimum tenuiflorum L.) grown under controlled environmental conditions in a plant factory.

Holy basil (Ocimum Tenuiflorum L.) is a widely used herb containing several bioactive compounds of interest for the food and pharmaceutical industries. Plant factories using artificial lighting (PFAL) is a modern agricultural system that offers opportunity to improve crop production and stabilizes productivity in many herbal plants. However, little is known about the variation among holy basil varieties that can be cultivated and provide reasonable biomass and bioactive compounds in PFAL. We therefore evaluated 10 Thai accessions and two commercial cultivars in a PFAL (with hydroponic cultivation) to categorize cultivar characteristics by investigating physiological responses and secondary metabolite variation at plant flowering stage. Among Thai varieties, net photosynthetic rate (Pn) was significantly highest in varieties OC059 and OC081. The greatest growth and biomass measures were observed in OC064. Antioxidant capacity also varied, with the greatest accumulation of total phenolic compounds (TPC), flavonoids, and antioxidant activity by DPPH assay in OC064, and highest terpenoid content in OC194. The accumulation of major compounds confirmed by showing the highest levels of eugenol in OC057, OC063, OC194, and OC195 and methyl eugenol in OC072 and OC081. The highest α-humulene content was found in OC059. PCA based on physiological responses and secondary metabolites indicate that OC064 was clearly distinguished from other cultivars/accessions. These findings demonstrate variation across holy basil accessions for physiologic responses, antioxidant capacity, and secondary compounds in PFAL. These insights lead to identification of suitable varieties which is the most important step of developing an efficient method for producing high quality raw materials of Thai holy basil for supplying the foods and pharmaceutical industries.