KEGG pathway analysis of differentially expressed transcripts identified more than 300 pathways that were common to both the genotypes. Top eight pathways identified in both genotypes along with important genes in each category are presented below (number of genes in parentheses). In VS16, these included metabolic processes (352), secondary metabolite biosynthesis (178), biosynthesis of antibiotics (100), ribosome (78), microbial metabolism in diverse environments (62), biosynthesis of amino acids (59), purine metabolism (43), and carbon metabolism (40) (Table 2 ; Supplementary Table S3). In AP13 these pathways included metabolic processes (344), secondary metabolite biosynthesis (183), biosynthesis of antibiotics (75), microbial metabolism in diverse environments (62), biosynthesis of amino acids (47), carbon metabolism (40), photosynthesis (33), and oxidative phosphorylation (32) (Table 2 ; Supplementary Table S3). Though several significant pathways were identified in this study, we have focused more on bioenergy affiliated genes such as those associated with photosynthesis pathways, C4 photosynthesis, photorespiration, and phenylpropanoid pathways that contribute to biomass production.
Number of genes identified from respective KEGG pathways in lowland AP13 and upland VS16 genotypes of switchgrass
C4 photosynthesis-related enzymes
Switchgrass (Panicum virgatum L.) is an important, warm season, C4 perennial grass. Switchgrass was selected as a dedicated feedstock for the production of biofuels by the US Department of Energy (DOE). Although it is native to North America, it is grown in South America, Europe and Asia (Parrish et al. 2012). Based on plant morphology and adaptation area, switchgrass has been classified into two distinct ecotypes, lowland and upland (Moser and Vogel 1995; Porter 1966). The lowland ecotypes are mainly adapted to flood plains of the southern USA and characterized by tall and coarse stems, long-wide leaves, high biomass potential, and relatively tolerant to pests and disease (Sanderson et al. 1996). The upland ecotypes are mainly adapted in the dry and cool habitats in the northern USA. Plants of this ecotype have short and narrow stems and leaves, usually less productive, and are more susceptible to damage by pests and disease (Sanderson et al. 1996). Conversely, upland ecotypes are more drought and cold tolerant than lowland ecotypes. Improvement of both ecotypes is very important to meet the one billion dry ton biomass production target of the DOE by 2030 (US DOE 2011). Identification of ecotype-specific genes associated with inherent biotic and abiotic tolerance, and understanding their role and expression pattern can greatly aid in switchgrass crop improvement.
Previous reports suggested that several TFs play a vital role in regulating the gene expression in plant stress responses and some are discussed here. The down-regulation of WRKY family transcription factors resulted in increased lignin content in cell walls that enhanced the biomass content in Medicago sativa (Gallego-Giraldo et al. 2015). WRKY-mediated transcriptional regulation in flooding tolerance has been reported in switchgrass (Barney et al. 2009). Transgenic switchgrass lines that overexpress the MYB4 TF showed higher lignocellulosic content (Shen et al. 2013). Here, we identified bHLH, MYB, WRKY, NAM, AP2 domain-containing, BWDNA-binding domain-containing, heat shock factor (HSF), NAC, MADS box, and Aintegumenta (Ant) families of TFs that had suggested roles in regulating lingocellulosic content in lateral meristems of switchgrass (Li et al. 2013). Recently, higher expression of WRKY and NAC genes independently involved in pathogen responses, and senescing of flag leaves of switchgrass have been reported (Serba et al. 2015). Majority of the TFs identified in this study overlapped with the abiotic stress-responsive TFs that have been reported in rice (Todaka et al. 2012).
AgriGo analysis of significantly enriched genes from RNA-Seq analysis of two switchgrass ecotypes: a AP13 and b VS16
Plant introductions (PIs) had been shown to increase the genetic variability for seed yield in soybean populations. The objectives of this study were to evaluate (a) genetic gain for seed yield in the cycle 1 (C1), cycle 2 (C2), and cycle 3 (C3) of AP10 to AP14 and (b) the mean seed yield and genetic variability in C1, C2, C3, and cycle 4 (C4) of the five populations. There was a significant linear increase in seed yield in all populations across the three cycles. The gain in selection for seed yield was 153 kg ha-1 cycle-1 for AP14, 80 for AP13, 85 for AP12, 54 for AP11, and 66 for AP10. Although AP14 was reported to have the lowest genetic variability in the cycle 0 population, it exhibited the greatest genetic gain per cycle during the three cycles of selection. The highest yielding line in each cycle was also from AP14. The results indicated that PIs did not enhance the response to recurrent selection for seed yield compared with populations developed from only high-yielding cultivars and experimental lines;When genetic variances for the five populations were compared in each of the four cycles of selection, the genetic variance estimates for AP14 were lower than that of AP11 and AP13 in C1 and C4, but were not different from that of the other populations in C2 and C3. The results indicated that the use of PIs did not provide greater variability for seed yield when recurrent selection was conducted for multiple cycles.
Authors: DARYA KONSTANTINOVNA CHERNYSHUK, LUBOV YEGOROVNA IVACHENKO, HÜLYA DOĞAN, GHULAM RAZA, MUHAMMAD AMJAD ALI, KIRILL SERGEYEVICH GOLOKHVAST, MUHAMMAD AMJAD NAWAZ
Abstract: In this study, the mechanism of the biochemical adaptation of wild soybean to the experimentally modeled effects of cadmium sulfate and copper sulfate in approximately double permissible concentration was investigated. The extracted concentrations of cadmium and copper in the experimental soil were determined by inversion voltammetry – 1.46 and 48.25 mg/kg, respectively. Growing soybeans in soil with the addition of copper and cadmium sulfates led to an increase in the concentration of malonic dialdehyde in soybean seeds relative to control by 62% and 38%, respectively, which confirmed the strengthening of oxidative processes. There was also an increase in the specific activity of peroxidase by 198% under the action of copper sulfate and 122% under the action of cadmium sulfate. Copper in the studied concentration was more toxic than cadmium. Acid phosphatase showed stable specific activity under the action of the studied metals. PAGE revealed multiple forms that were absent from the control: under the action of copper sulfate-AP7, AP12; cadmium sulfate-AP12. Dihydroquercetin treatment of soybean seeds before sowing in soil contaminated with copper and cadmium sulfates led to a decrease in the level of malonic dialdehyde by 20% and 11%, respectively, and a decrease in the specific activity of peroxidase by an average of 12%. There was a decrease in specific activity and the appearance of new multiple forms of acid phosphatase: under the action of copper sulfate by 18%, AP13; cadmium sulfate – 25%, AP2 and AP13. Thus, we suggest that flavonoids may take part in the adaptation of plants to the effects of copper and cadmium.
Dihydroquercetin increases the adaptive potential of wild soybean against copper sulfate and cadmium sulfate toxicity
Keywords: Glycine soja Sieb. & Zucc., acid phosphatase, biochemical adaptation, flavonoids, heavy metals, oxidative stress, peroxidase