Securing Diversity for Food Security: The Case of Conservation and Use of Rice Genetic Resources

Producing enough food, fiber, and fuel, in this case, the second most important global crop called rice, remains a continuing challenge as global population increases and various production constraints ensue. Plant breeding scientists prefer using elite rice lines but also infuse new genetic resources into the parental genepool for desirable traits, such as resistance to pests and diseases, good flavor, and high nutritional quality on top of high-yielding potential. Prior research studies reveal the importance of germplasm resources including wild rice relatives as excellent sources of desirable traits in new crop breeds. Advances in molecular and genomics approaches (QTLs, GWAS, OMICs technologies) have identified and transferred genes, genomes, loci among other important genetic materials that are sought for. As knowledge builds up with these biotechniques, more rice genetic resources can be characterized at the molecular and systems levels for further utility in breeding better cultivars. Information generated from innovative approaches must be documented and processed as germplasm characterization data and must remain accessible at genebanks that exist centrally to conserve biodiversity. Development of germplasm information should be a collaborative effort of scientists who share similar interests in exploiting the valuable and novel genes within germplasm resources that are essential for crop improvement

Comparative Metabolome Profile between Tobacco and Soybean Grown under Water-Stressed Conditions

Understanding how plants respond to water deficit is important in order to develop crops tolerant to drought. In this study, we compare two large metabolomics datasets where we employed a nontargeted metabolomics approach to elucidate metabolic pathways perturbed by progressive dehydration in tobacco and soybean plants. The two datasets were created using the same strategy to create water deficit conditions and an identical metabolomics pipeline. Comparisons between the two datasets therefore reveal common responses between the two species, responses specific to one of the species, responses that occur in both root and leaf tissues, and responses that are specific to one tissue. Stomatal closure is the immediate response of the plant and this did not coincide with accumulation of abscisic acid. A total of 116 and 140 metabolites were observed in tobacco leaves and roots, respectively, while 241 and 207 were observed in soybean leaves and roots, respectively. Accumulation of metabolites is significantly correlated with the extent of dehydration in both species. Among the metabolites that show increases that are restricted to just one plant, 4-hydroxy-2-oxoglutaric acid (KHG) in tobacco roots and coumestrol in soybean roots show the highest tissue-specific accumulation. The comparisons of these two large nontargeted metabolomics datasets provide novel information and suggest that KHG will be a useful marker for drought stress for some members of Solanaceae and coumestrol for some legume species

Comparative Metabolome Profile between Tobacco and Soybean Grown under Water-Stressed Conditions

Understanding how plants respond to water deficit is important in order to develop crops tolerant to drought. In this study, we compare two large metabolomics datasets where we employed a nontargeted metabolomics approach to elucidate metabolic pathways perturbed by progressive dehydration in tobacco and soybean plants. The two datasets were created using the same strategy to create water deficit conditions and an identical metabolomics pipeline. Comparisons between the two datasets therefore reveal common responses between the two species, responses specific to one of the species, responses that occur in both root and leaf tissues, and responses that are specific to one tissue. Stomatal closure is the immediate response of the plant and this did not coincide with accumulation of abscisic acid. A total of 116 and 140 metabolites were observed in tobacco leaves and roots, respectively, while 241 and 207 were observed in soybean leaves and roots, respectively. Accumulation of metabolites is significantly correlated with the extent of dehydration in both species. Among the metabolites that show increases that are restricted to just one plant, 4-hydroxy-2-oxoglutaric acid (KHG) in tobacco roots and coumestrol in soybean roots show the highest tissue-specific accumulation. The comparisons of these two large nontargeted metabolomics datasets provide novel information and suggest that KHG will be a useful marker for drought stress for some members of Solanaceae and coumestrol for some legume species

Effect of Spectral Quality of Monochromatic LED Lights on the Growth of Artichoke Seedlings

Indoor farming is becoming a popular alternative approach in food production to meet the demand of a growing world population. Under this production system, artificial light provides the main source of illumination in sustaining plant growth and development. The use of light-emitting diodes (LEDs) is a popular source of artificial light for indoor farms due to its narrow light spectra, modular design and energy efficiency. This study purposely assessed the effect of monochromatic LED light quality on the growth of three varieties of artichoke seedlings compared to greenhouse condition. Spectral quality assessment showed that photosynthetic photon flux density (PPFD) was highest under red LED light, but only a third of the total PPFD under natural light. Seedlings grown under red light showed 60–100% more shoot dry weight and were 67–115% taller than seedlings grown in the greenhouse. However, seedlings under blue or white light conditions showed 67–76% less in biomass compared to greenhouse-grown seedlings. Overall, plant response of seedlings under red light condition was much better compared to greenhouse-grown seedlings emphasizing the importance of red light spectral quality in plant growth and development

Understanding Water-Stress Responses in Soybean Using Hydroponics System—A Systems Biology Perspective

This article discusses using a system of reduced complexity like hydroponics to identify the potential candidates for water-stress tolerance by plants

The evolution of WRKY transcription factors

BACKGROUND: The availability of increasing numbers of sequenced genomes has necessitated a re-evaluation of the evolution of the WRKY transcription factor family. Modern day plants descended from a charophyte green alga that colonized the land between 430 and 470 million years ago. The first charophyte genome sequence from Klebsormidium flaccidum filled a gap in the available genome sequences in the plant kingdom between unicellular green algae that typically have 1-3 WRKY genes and mosses that contain 30-40. WRKY genes have been previously found in non-plant species but their occurrence has been difficult to explain. RESULTS: Only two WRKY genes are present in the Klebsormidium flaccidum genome and the presence of a Group IIb gene was unexpected because it had previously been thought that Group IIb WRKY genes first appeared in mosses. We found WRKY transcription factor genes outside of the plant lineage in some diplomonads, social amoebae, fungi incertae sedis, and amoebozoa. This patchy distribution suggests that lateral gene transfer is responsible. These lateral gene transfer events appear to pre-date the formation of the WRKY groups in flowering plants. Flowering plants contain proteins with domains typical for both resistance (R) proteins and WRKY transcription factors. R protein-WRKY genes have evolved numerous times in flowering plants, each type being restricted to specific flowering plant lineages. These chimeric proteins contain not only novel combinations of protein domains but also novel combinations and numbers of WRKY domains. Once formed, R protein WRKY genes may combine different components of signalling pathways that may either create new diversity in signalling or accelerate signalling by short circuiting signalling pathways. CONCLUSIONS: We propose that the evolution of WRKY transcription factors includes early lateral gene transfers to non-plant organisms and the occurrence of algal WRKY genes that have no counterparts in flowering plants. We propose two alternative hypotheses of WRKY gene evolution: The “Group I Hypothesis” sees all WRKY genes evolving from Group I C-terminal WRKY domains. The alternative “IIa + b Separate Hypothesis” sees Groups IIa and IIb evolving directly from a single domain algal gene separate from the Group I-derived lineage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-015-0456-y) contains supplementary material, which is available to authorized users

Phenotypic Diversity of Farmers’ Traditional Rice Varieties in the Philippines

Traditional rice varieties maintained and cultivated by farmers are likely sources of germplasm for breeding new rice varieties. They possess traits potentially adaptable to a wide range of abiotic and biotic stresses. Characterization of these germplasms is essential in rice breeding and provides valued information on developing new rice cultivars. In this study, 307 traditional rice varieties newly conserved at the PhilRice genebank were characterized to assess their phenotypic diversity using 57 morphological traits. Using the standardized Shannon-Weaver diversity index, phenotypic diversity indices averaged at 0.73 and 0.45 for quantitative and qualitative traits, respectively. Correlation analyses among agro-morphological traits showed a high positive correlation in some traits such as culm number and panicle number, flag leaf width and leaf blade width, grain width and caryopsis width. Cluster analysis separated the different varieties into various groups. Principal component analysis (PCA) showed that seven independent principal components accounted for 74.95% of the total variation. Component loadings for each principal component showed morphological characters, such as culm number, panicle number and caryopsis ratio that were among the phenotypic traits contributing positive projections in three principal components that explained 48% of variation. Analyses of results showed high diversity in major traits assessed in farmers’ rice varieties. Based on plant height and maturity, 11 accessions could be potential donor parents in a rice breeding program. Future collection trips and characterization studies would further enrich diversity, in particular traits low in diversity, such as anthocyanin coloration, awn presence, awn color, culm habit, panicle type and panicle branching

Moisture sorption characteristics of seeds of five ornamental species

Genetic resources conservation of ornamental crops and their relatives is a challenging task because of limited available information. In seed genebanks, seed moisture content and temperature play an important role in stored seed longevity. In this study, the moisture sorption characteristics of four priority genera and one minor genus of the Ornamental Plant Germplasm Center were evaluated. Moisture sorption isotherms were conducted on seeds of Aster ptarmicoides, Impatiens walleriana, Lupinus texensis, Salvia splendens and Tagetes patula using seven different salt solutions with relative humidities (RH) ranging from 7 to 96%. Seeds were stored at 5, 15, 25 and 35oC until they achieved equilibrium with the ambient RH and the seed moisture contents (MC) were determined by the air-oven method. Constructed moisture sorption isotherm curves showed that seed MC increased with increasing RH in all temperature regimes. Rate of water loss in each species was studied on imbibed seeds stored in an ultra-dry RH-controlled cabinet set at 10% RH. Seed weight loss during desorption was continuously recorded until the seeds achieved equilibrium MC. The initial MC (in parentheses) of imbibed A. ptarmicoides (37%), I. walleriana (37%), L. texensis (13%), S. splendens (44%) and T. patula (26%) equilibrated during storage to 4, 3, 5, 4 and 4%, respectively. Weight loss during desorption accounted for 9 to 40% of the original seed weight until equilibrium was achieved during storage. Rapid weight loss occurred between 4-12 h of storage in the cabinet with weight loss ranging between 5-37%. This study showed that seed MC of five ornamental species is influenced by RH and temperature of the storage environment

Systems Biology Approach to Identify WRKY Transcription Factors Involved in the Response of Tobacco (Nicotiana Tabacum l.) to Water Conditions

The staggering growth in population with no expansion for arable land, provide enormous pressure to increase food production. However, food production is seriously hampered by abiotic stresses such as drought. To address this issue, crop tolerance to drought must be improved. In order to develop strategies to improve plant responses to water stress, one must understand the regulatory pathways involve in plant’s responses to water stress. One of the major components in the web of regulatory networks is transcription factors. In plants, one of the biggest families is the WRKY transcription factors. In this study, we would like to elucidate the role of WRKY transcription factors in plant responses to water stress. Using tobacco as our model plant, we analyzed the spatial and temporal transcriptome and metabolome profiles of tobacco plants subjected to water stress at different time points (20, 40, 60, 120 and 240 min). Transcriptome profile showed major transcription factor families such as ERF, WRKY, NAC, bHLH and MYB to be highly induced by water stress in both roots and leaves of tobacco. Downstream genes such as late embryogenesis abundant proteins (LEA), dehydrins, aquaporins, raffinose synthase and galactinol synthase where also highly induced. Gene expression profile showed that the gene products from the stress-inducible genes can be group as regulatory proteins and proteins involved in direct protection of the cell from stress. Metabolome profile showed accumulation of proteinogenic amino acids as well as compatible solutes such as proline, trehalose and raffinose. Expression profile of our target genes concurred with our metabolome profile. Promoter analyses of up-regulated WRKY and enzyme-coding genes provided an overview of cis-regulatory elements present in stress-inducible genes. In vivo and in planta analyses of promoter of stress-inducible genes showed responses of transformants to phytohormones and other abiotic stresses

Understanding water-stress responses in Soybean using Hydroponics system - A Systems Biology Perspective

The deleterious changes in environmental conditions such as water stress bring physiological and biochemical changes in plants, which results in crop loss. Thus, combating water stress is important for crop improvement to manage the needs of growing population. Utilization of hydroponics system in growing plants is questionable to some researchers, as it does not represent an actual field condition. However, trying to address a complex problem like water stress we have to utilize a simpler growing condition like the hydroponics system wherein every input given to the plants can be controlled. With the advent of high-throughput technologies, it is still challenging to address all levels of the genetic machinery whether a gene, protein, metabolite, and promoter. Thus, using a system of reduced complexity like hydroponics can certainly direct us towards the right candidates, if not completely help us to resolve the issue