Molecular genetics and phenotypic assessment of foxtail millet (Setaria italica (L.) P. Beauv.) landraces revealed remarkable variability of morpho-physiological, yield, and yield‐related traits

Foxtail millet (Setaria italica (L.) P. Beauv.) is highly valued for nutritional traits, stress tolerance and sustainability in resource-poor dryland agriculture. However, the low productivity of this crop in semi-arid regions of Southern India, is further threatened by climate stress. Landraces are valuable genetic resources, regionally adapted in form of novel alleles that are responsible for cope up the adverse conditions used by local farmers. In recent years, there is an erosion of genetic diversity. We have hypothesized that plant genetic resources collected from the semi-arid climatic zone would serve as a source of novel alleles for the development of climate resilience foxtail millet lines with enhanced yield. Keeping in view, there is an urgent need for conservation of genetic resources. To explore the genetic diversity, to identify superior genotypes and novel alleles, we collected a heterogeneous mixture of foxtail millet landraces from farmer fields. In an extensive multi-year study, we developed twenty genetically fixed foxtail millet landraces by single seed descent method. These landraces characterized along with four released cultivars with agro-morphological, physiological, yield and yield-related traits assessed genetic diversity and population structure. The landraces showed significant diversity in all the studied traits. We identified landraces S3G5, Red, Black and S1C1 that showed outstanding grain yield with earlier flowering, and maturity as compared to released cultivars. Diversity analysis using 67 simple sequence repeat microsatellite and other markers detected 127 alleles including 11 rare alleles, averaging 1.89 alleles per locus, expected heterozygosity of 0.26 and an average polymorphism information content of 0.23, collectively indicating a moderate genetic diversity in the landrace populations. Euclidean Ward’s clustering, based on the molecular markers, principal coordinate analysis and structure analysis concordantly distinguished the genotypes into two to three sub-populations. A significant phenotypic and genotypic diversity observed in the landraces indicates a diverse gene pool that can be utilized for sustainable foxtail millet crop improvement

Farklı evrimsel basamaklarda yer alan bitki sınıflarında gamma aminobütirik asidin (GABA) çeşitli özelliklerinin incelenmesi

GABA (gamma aminobütirik asit) proteinlerin yapısına katılmayan bir amino asit olup tüm prokaryotik ve ökaryotik organizmalarda bulunmaktadır (Shelp et al., 1999; Kinnersley and Turano, 2000). GABA, fizyolojisi çok iyi belirlenmiş Arabidopsis, tütün ve domates gibi bitkilerde araştırılmış olmasına rağmen bitki sınıflarında evrimsel bir karşılaştırması yapılmamıştır. Çalışmamızda doğadan toplanan farklı bitki cinslerinde, bir alg ve liken cinsinde GABA (gamma aminobütirik asit) yolunda yer alan iki enzimin aktiviteleri ve GABA miktarı belirlenmiştir. Elde edilen veriler doğrultusunda farklı bitki türleri, bir alg ve liken cinsi GABA özelliklerine göre karşılaştırılmıştır

Genome-wide identification, phylogenetic analysis, and functional prediction of histone deacetylase genes in Spinacia oleracea L

Histone deacetylation process is controlled by histone deacetylases (HDAs), which catalyze removal of an acetyl group from the lysine residues of histone N-terminal tails. Although the HDAs are known to be involved in stress response and development in model plants, little is known about the roles of HDAs in crop species. Up to date, the HDAs in spinach (Spinacia oleracea L.) have not been identified and characterized. Here, we carried out genome-wide identification of HDA gene family in spinach, including physicochemical properties, subcellular localization prediction, phylogenetic analysis, conserved motifs, gene structure, Ka/Ks ratio, synteny analysis, functional prediction through cis-acting elements, and protein–protein interaction. Totally, six HDAs were identified from the spinach genome, and named SoSRT1, SoSRT2, SoHDA1, SoHDA2, SoHDA3, and SoHDA4. The phylogenetic tree showed that spinach HDAs were divided into four clades (Class I, Class II, RPD3-like, SIR2). RPD3/HDA1 family proteins and RPD3-like protein consisted of motif 1, Hist_deacetyl domain (PF00850), while two SIR2 class proteins included SIR2 domain (PF02146). Subcellular localization analysis indicated that the SoSRT and SoHDA proteins might localize in cytoskeleton, peroxisome, nucleus, and cytosol. SoSRT1 and SoSRT2 were located on chromosome 1, and the remaining four genes (HDA1-4) were distributed on chromosome 6. Ka/Ks ratio was lower than 1, suggesting that HDA genes might undergo purifying selection during evolution. Analysis of cis-acting elements revealed that the SoHDA genes participate in hormone regulation, light response, and abiotic stress response. New insights into the potential roles of histone deacetylases will be gained from this study in spinach, which is a cold-tolerant/heat-sensitive vegetable

Gamma-amino butyric acid, glutamate dehydrogenase and glutamate decarboxylase levels in phylogenetically divergent plants

WOS: 000313801600010Gamma-amino butyric acid (GABA) is a nonprotein amino acid found in a wide range of organisms including plants. Several studies have shown that GABA plays different roles in plant metabolism including carbon-nitrogen metabolism, energy balance, signaling and development. It has been suggested that the occurrence of GABA and the enzymes related to GABA biosynthesis in prokaryotes and eukaryotes may be important in evolution and diversification. However, studies of GABA biosynthesis and GABA levels in an evolutionary context are restricted to sequenced plant genomes. In this study we aimed to compare the activities of GDH and GAD enzymes and total nitrogen, and the contents of total soluble protein, succinate, glutamate, proline and GABA in plants from different phylogenetic levels including Ulva lactuca, Pseudevernia furfuracea, Nephrolepsis exaltata, Ginkgo biloba, Pinus pinea, Magnolia grandiflora, Nymphaea alba, Urtica dioica, Portulaca oleraceae, Malva sylvestris, Rosa canina, Lavandula stoechas, Washingtonia filifera, Avena barbata and Iris kaempferi. The activities of GAD and GDH enzymes differed according to the species and were not always parallel to GABA levels. The discrepancy in the contents of succinate and GABA between higher and primitive plants was also prominent. Glutamate levels were high with a few exceptions and proline contents were at similar low values as compared to other amino acids. Our results support the hypothesis that the GABA shunt plays a key role in carbon and nitrogen partitioning via linking amino acid metabolism and the tricarboxylic acid cycle which is essential for higher plant species.Ege University Research FoundationEge University [2009-FEN-020]The authors would like to thank Ege University Research Foundation for supporting this work (Grant Number 2009-FEN-020)

Salt and drought stress-mitigating approaches in sugar beet (Beta vulgaris L.) to improve its performance and yield

Main conclusion: Although sugar beet is a salt- and drought-tolerant crop, high salinity, and water deprivation significantly reduce its yield and growth. Several reports have demonstrated stress tolerance enhancement through stress-mitigating strategies including the exogenous application of osmolytes or metabolites, nanoparticles, seed treatments, breeding salt/drought-tolerant varieties. These approaches would assist in achieving sustainable yields despite global climatic changes. Abstract: Sugar beet (Beta vulgaris L.) is an economically vital crop for ~ 30% of world sugar production. They also provide essential raw materials for bioethanol, animal fodder, pulp, pectin, and functional food-related industries. Due to fewer irrigation water requirements and shorter regeneration time than sugarcane, beet cultivation is spreading to subtropical climates from temperate climates. However, beet varieties from different geographical locations display different stress tolerance levels. Although sugar beet can endure moderate exposure to various abiotic stresses, including high salinity and drought, prolonged exposure to salt and drought stress causes a significant decrease in crop yield and production. Hence, plant biologists and agronomists have devised several strategies to mitigate the stress-induced damage to sugar beet cultivation. Recently, several studies substantiated that the exogenous application of osmolytes or metabolite substances can help plants overcome injuries induced by salt or drought stress. Furthermore, these compounds likely elicit different physio-biochemical impacts, including improving nutrient/ionic homeostasis, photosynthetic efficiency, strengthening defense response, and water status improvement under various abiotic stress conditions. In the current review, we compiled different stress-mitigating agricultural strategies, prospects, and future experiments that can secure sustainable yields for sugar beets despite high saline or drought conditions

Beyond the genetic code in leaf senescence

Leaf senescence is not only genetically programmed but also induced by exogenous stress to ensure completion of the plant life cycle, successful reproduction and environmental adaptability. Genetic reprogramming is a major aspect of leaf senescence, and the senescence signaling that follows is controlled by a complex regulatory network. Recent studies suggest that the activity of transcription factors together with epigenetic mechanisms ensures the robustness of this network, with the latter including chromatin remodeling, DNA modification, and RNA-mediated control of transcription factors and other senescence-associated genes. In this review, we provide an overview of the relevant epigenetic mechanisms and summarize recent findings of epigenetic regulators of plant leaf senescence involved in DNA methylation and histone modification along with the functions of small RNAs in this process © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.1

Day and Night Fluctuations in GABA Biosynthesis Contribute to Drought Responses in Nicotiana tabacum L

When synchronized with the light/dark cycle the circadian rhythm is termed a diurnal rhythm and this organizes an organism's daily life cycle in relation to the metabolic shifts during the day/night cycles. This is a complex task, particularly under stress conditions. Accurate maintenance of the diurnal rhythm becomes an issue under environmental extremes, such as drought due to the impairment of metabolism, redox balance, and structural integrity. In plants, the non-proteinogenic amino acid GABA accumulates to high levels in response to several stress factors but this is not always dependent on the activation of its biosynthesis. Here we propose a regulatory role to GABA during the diurnal rhythm in plants which is similar to its function in animals where it adjusts the circadian rhythm. Here we investigated whether GABA-biosynthesis was affected by drought stress during the diurnal cycle. For this, we took samples from leaves of N. tabacum plants subjected to PEG-mediated drought stress (-0.73 MPa) during the day and night cycle during a 24 hour period. Glutamate, GABA, and proline contents, along with GDH, GAD enzyme activities and transcript profiles were analyzed. Overall, we conclude that the oscillations in GABA biosynthesis during day and night cycle have an impact on drought stress responses which needs to be elucidated by further analysis.The authors thank to Prof. Steven Footitt for his critical reading and helpful contributions to the manuscript. This work was supported by grant-in-aid 14-FEN-045 from Ege University Research Foundation.Ege University Research Foundation [14-FEN-045

Salt and drought stress responses in cultivated beets (Beta vulgaris L.) and wild beet (Beta maritima L.)

Cultivated beets, including leaf beets, garden beets, fodder beets, and sugar beets, which belong to the species Beta vulgaris L., are economically important edible crops that have been originated from a halophytic wild ancestor, Beta maritima L. (sea beet or wild beet). Salt and drought are major abiotic stresses, which limit crop growth and production and have been most studied in beets compared to other environmental stresses. Characteristically, beets are salt- and drought-tolerant crops; however, prolonged and persistent exposure to salt and drought stress results in a significant drop in beet productivity and yield. Hence, to harness the best benefits of beet cultivation, knowledge of stress-coping strategies, and stress-tolerant beet varieties, are prerequisites. In the current review, we have summarized morpho-physiological, biochemical, and molecular responses of sugar beet, fodder beet, red beet, chard (B. vulgaris L.), and their ancestor, wild beet (B. maritima L.) under salt and drought stresses. We have also described the beet genes and noncoding RNAs previously reported for their roles in salt and drought response/tolerance. The plant biologists and breeders can potentiate the utilization of these resources as prospective targets for developing crops with abiotic stress tolerance