De Novo Next Generation Sequencing of Plant Genomes

The genome sequencing of all major food and bioenergy crops is of critical importance in the race to improve crop production to meet the future food and energy security needs of the world. Next generation sequencing technologies have brought about great improvements in sequencing throughput and cost, but do not yet allow for de novo sequencing of large repetitive genomes as found in most crop plants. We present a strategy that combines cutting edge next generation sequencing with “old school” genomics resources and allows rapid cost-effective sequencing of plant genomes.     

An efficient method for clonal propagation and in vitro establishment of softwood shoots from epicormic buds of teak (Tectona grandis L.)

Softwood shoots were produced from 40 cm long stem segments placed horizontally in flat trays containing sterilized sand under natural light or shade conditions for subsequent rooting and micropropagation studies in teak (Tectona grandis L.). Higher number of shoots (6.17) per log was produced under natural light as compared to shade conditions. Forcing was also better in natural light as compared to shade in terms of shoot length, number of nodes or leaves. For rooting, 2–4 cm long softwood shoots were excised and treated with either indole-3-butyric acid (IBA) or α-naphthyl acetic acid (NAA) at 0, 1000, 2000 or 3000 μmol·L^–1 each or with combinations (1000 + 1000, 2000 + 2000 or 3000 + 3000 μmol·L^–1) and then placed in flat trays containing autoclaved sand at 25 ± 2ºC in 16 h photoperiod at 35 µmol·m^–2·s^–1. After 28 days, softwood cuttings treated with IBA + NAA (3000 + 3000 μmol·L–1) had highest rooting percentage (89.3%) with 5.5 mean roots. Shoot apex and nodal explants of softwood cuttings were pretreated with 0.1% (w/v) ascorbic acid, boric acid, activated charcoal, citric acid, glutamine or polyvinylpolypyrollidone (PVP) for 24 h to remove phenolic compounds before surface disinfestation. Glutamine (Gl) and PVP were equally effective resulting in 60% establishment of shoot apices on MS medium supplemented with 10 μmol·L–1 6-benzylaminopurine (BAP) + 5 μmol·L–1 NAA. Using shoot apices, highest (42.80) number of multiple shoots with 54.33 mm shoot length were obtained on MS + BAP (8.8 μmol·L–1) + IBA (2 μmol·L–1) after 45 days. Shoots were successfully rooted and acclimatized to greenhouse     

Testing of rye-specific markers located on 1RS chromosome and distribution of 1AL.RS and 1BL.RS translocations in Turkish wheat (Triticumaestivum L., T.durum Desf.) varieties and landraces

Rye (Secale cereale L.) is a valuable source for alien chromosome translocations in wheat breeding, due to its capability to grow and sustain under harsh environmental conditions. Wheat germplasm with 1AL.1RS and 1BL.1RS wheat-rye chromosome translocations have been used worldwide by breeders. Determining 1AL.1RS and 1BL.1RS translocations in wheat is therefore of important practical value for wheat improvement. In this study, nine rye-specific markers detecting the rye chromosome 1RS in wheat background were evaluated. The markers PAWS5/S6, SCM9 and O-SEC5′-A/O-SEC3′-R amplified specific bands associated with 1AL.1RS and 1BL.1RS translocations. These three markers therefore provide a quick and reliable tool to identify and to discriminate these two wheat-rye translocations in wheat background. Six out of nine rye specific markers were subsequently used to determine the frequency of these translocations in commonly grown bread and durum wheat cultivars from Turkey. One hundred seven wheat cultivars and landraces were molecularly screened. Among them, only 4% (‘Seri-82’, ‘Yıldız-98’, ‘Tahirova’, and ‘Osmaniyem’) harbor the 1BL.1RS translocation whereas the 1AL.1RS translocation was not found. The information provided here will contribute to the creation of new Turkish wheat populations with a larger genetic diversity necessary for future requirements.     

Prediction of poppy thebaine alkaloid concentration using UAS remote sensing

Precision Agriculture - Alkaloid concentration, which represents the quality of industrial poppy, needs to be estimated in a spatially explicit manner to predict the value of crop prior to...     

Chemical constituents of Kigelia pinnata twigs and their GLUT4 translocation modulatory effect in skeletal muscle cells

Phytochemical investigation of the ethanolic extract of twigs of Kigelia pinnata DC. afforded one new iridoid 7-hydroxy eucommiol (1), and nine known compounds (2-10). The structure of compounds was elucidated by extensive spectroscopic methods, including 1D, 2D NMR experiments and MS analysis. All these compounds were evaluated for GLUT4 translocation modulatory effect in skeletal muscle cells. Four of the tested compounds 1, 5, 6 and 7 showed significant stimulation of GLUT4 translocation to cell surface in skeletal muscle cells without any adverse effect on cell viability. Effect of these four compounds was concentration-dependent and comparable to standard drug rosiglitazone. These findings indicate that constituents of K. pinnata may provide leads for the therapeutics for insulin resistance and diabetes.     

Stress combination: When two negatives may become antagonistic,synergistic or additive for plants?

Plants in their natural environment are constantly subjected to various abiotic and biotic stressors and, therefore, have developed several defense mechanisms to maintain fitness. Stress responses are intricate and require various physiological, biochemical, and cellular changes in plants. The reaction mechanisms in plants subjected to drought, salinity, or heat stress alone have been explained in numerous studies. However, the field conditions are significantly different from the controlled lab...     

Structure, diversity, and regeneration potential of Monotheca buxifolia (Falc.) A. DC. dominated forests of Lower Dir District, Pakistan

This study reports on the multivariate analysis of the vegetation of Hindukush Range in Pakistan, concentrating on the structure and regeneration potential of Monotheca buxifolia and associated tree species. Twenty stands at different locations in the Dir District of the Hindukush Range in Pakistan were chosen for the study. A point centered quarter method for trees and 5m × 5m size quadrats were used for the sampling of understorey vegetation, including shrubs, seedlings, and saplings, respectively. The underlying group structure in vegetation was exposed by an agglomerative clustering technique, while major trends were disclosed by DCA ordination. Size class structure and regeneration potential of M. buxifolia and associated tree species were also examined, which reflects the future trend of species and, consequently, the forests where they dominate. The relationships between environmental factors and vegetation were investigated.     

Inoculant rhizobia suppressed root-knot disease,and enhanced plant productivity and nutrient uptake of some field-grown food legumes

The potential effect of rhizobial inoculation on root knot nematodes in chickpea, mungbean and pigeonpea were studied under field condition. The seed treatment with respective rhizobium strains increased the nodulation, leghemoglobin content, bacteriod population, plant growth, yield and nitrogen uptake of three three food legumes compared to the plants without the rhizobium treatment. The nematode (1500?juveniles/kg soil) incited oval galls on the roots of the three legumes, and suppressed plant growth and yield. The galling, egg mass production and soil population of the nematode was greater on the plants without the rhizobium treatment. The pure culture and culture filtrate of the rhizobium strains suppressed the egg hatching and induced mortality to the juveniles of M. incognita over control. The nematode infection reduced the nodulation, bacteroid population and leghemoglobin contents of the nodules and NPK uptake by the plants. Hence, the rhizobia treatment shall be integrated to common agronomic practice of food legume cultivation so as to enhance crop productivity and to protect roots from nematode attack.     

一株二甲基二硫醚降解菌的筛选、鉴定与降解性能

为了能够得到高效降解二甲基二硫醚（Dimethyl disulfide,DMDS）的菌种资源,降低其残留在环境中带来的不利影响,从苏州某废弃农药厂附近的土壤中分离、纯化出一株能够降解DMDS的细菌,并对该细菌进行分子生物学和生理生化鉴定,研究其在不同的初始浓度、转速、pH、温度及外加碳氮源条件下的降解性能。结果表明：将分离纯化得到的DMDS降解菌命名为SZT-1,经过表型分析及16S rDNA基因序列同源性比对鉴定,该菌株序列与芽孢杆菌属（Bacillus Cohn）有98%以上的同源性。SZT-1菌株可以在以DMDS为唯一碳源的无机盐培养基中生长,56 h后进入生长稳定期。经摇床接种培养和一级动力学分析,接种SZT-1可以有效提高DMDS的降解速率,使其半衰期由346.5 h缩短至86.6 h;通过单因素环境条件分析,该菌株在DMDS初始浓度为250mg·L^-1,转速为130 r·min^-1,pH为5,温度为30℃,外加碳源为淀粉,外加氮源为蛋白胨时,对DMDS的降解效果最佳,降解率达50%。试验首次提出了SZT-1对DMDS具有一定的降解效果,在进行相关技术完善后,有望用于治理土壤、地下水中DMDS带来的危害。     

An efficient method for clonal propagation and in vitro establishment of softwood shoots from epicormic buds of teak （Tectona grandis L.）

Softwood shoots were produced from 40 cm long stem segments placed horizontally in flat trays containing sterilized sand under natural light or shade conditions for subsequent rooting and micropropagation studies in teak(Tectona grandis L.) . Higher number of shoots(6.17) per log was produced under natural light as compared to shade conditions. Forcing was also better in natural light as compared to shade in terms of shoot length,number of nodes or leaves. For rooting,2-4 cm long softwood shoots were excise...