Browsing by Author "Liu, Yiming"

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    Antioxidant metabolism variation associated with alkali-salt tolerance in thirty switchgrass (Panicum virgatum) lines
    Hu, Guofu; Liu, Yiming; Duo, Tianqi; Zhao, Bingyu Y.; Cui, Guowen; Ji, Jing; Kuang, Xiao; Ervin, Erik H.; Zhang, Xunzhong (PLOS, 2018-06-25)
    Soil salinization is a major factor limiting crop growth and development in many areas. Switchgrass (Panicum virgatum L.) is an important warm-season grass species used for biofuel production. The objective of this study was to investigate antioxidant metabolism, proline, and protein variation associated with alkali-salt tolerance among 30 switchgrass lines and identify metabolic markers for evaluating alkali-salt tolerance of switchgrass lines. The grass lines were transplanted into plastic pots containing fine sand. When the plants reached E5 developmental stage, they were subjected to either alkali-salt stress treatment (150 mM Na+ and pH of 9.5) or control (no alkali-salt stress) for 20 d. The 30 switchgrass lines differed in alkali-salt tolerance as determined by the level of leaf malondialdehyde (MDA), antioxidant enzyme activity [(superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX)], proline and protein. Alkali-salt stress increased MDA, proline, SOD, reduced CAT activity, but its effect on protein and APX varied depending on lines. Wide variations in the five parameters existed among the 30 lines. In general, the lines with higher CAT activity and lower proline content under alkali-salt stress had less MDA, exhibiting better alkali-salt tolerance. Among the five parameters, CAT can be considered as valuable metabolic markers for assessment of switchgrass tolerance to alkali-salt stress.
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    Assessment of drought tolerance of 49 switchgrass (Panicum virgatum) genotypes using physiological and morphological parameters
    Liu, Yiming; Zhang, Xunzhong; Tran, Hong T.; Shan, Liang; Kim, Jeongwoon; Childs, Kevin L.; Ervin, Erik H.; Frazier, Taylor P.; Zhao, Bingyu Y. (2015-09-22)
    Background Switchgrass (Panicum virgatum L.) is a warm-season C4 grass that is a target lignocellulosic biofuel species. In many regions, drought stress is one of the major limiting factors for switchgrass growth. The objective of this study was to evaluate the drought tolerance of 49 switchgrass genotypes. The relative drought stress tolerance was determined based on a set of parameters including plant height, leaf length, leaf width, leaf sheath length, leaf relative water content (RWC), electrolyte leakage (EL), photosynthetic rate (Pn), stomatal conductance (g s), transpiration rate (Tr), intercellular CO2 concentration (Ci), and water use efficiency (WUE). Results SRAP marker analysis determined that the selected 49 switchgrass genotypes represent a diverse genetic pool of switchgrass germplasm. Principal component analysis (PCA) and drought stress indexes (DSI) of each physiological parameter showed significant differences in the drought stress tolerance among the 49 genotypes. Heatmap and PCA data revealed that physiological parameters are more sensitive than morphological parameters in distinguishing the control and drought treatments. Metabolite profiling data found that under drought stress, the five best drought-tolerant genotypes tended to have higher levels of abscisic acid (ABA), spermine, trehalose, and fructose in comparison to the five most drought-sensitive genotypes. Conclusion Based on PCA ranking value, the genotypes TEM-SEC, TEM-LoDorm, BN-13645-64, Alamo, BN-10860-61, BN-12323-69, TEM-SLC, T-2086, T-2100, T-2101, Caddo, and Blackwell-1 had relatively higher ranking values, indicating that they are more tolerant to drought. In contrast, the genotypes Grif Nebraska 28, Grenville-2, Central Iowa Germplasm, Cave-in-Rock, Dacotah, and Nebraska 28 were found to be relatively sensitive to drought stress. By analyzing physiological response parameters and different metabolic profiles, the methods utilized in this study identified drought-tolerant and drought-sensitive switchgrass genotypes. These results provide a foundation for future research directed at understanding the molecular mechanisms underlying switchgrass tolerance to drought.
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    Elucidation and analyses of the regulatory networks of upland and lowland ecotypes of switchgrass in response to drought and salt stresses
    Zuo, Chunman; Tang, Yuhong; Fu, Hao; Liu, Yiming; Zhang, Xunzhong; Zhao, Bingyu Y.; Xu, Ying (PLOS, 2018-09-24)
    Switchgrass is an important bioenergy crop typically grown in marginal lands, where the plants must often deal with abiotic stresses such as drought and salt. Alamo is known to be more tolerant to both stress types than Dacotah, two ecotypes of switchgrass. Understanding of their stress response and adaptation programs can have important implications to engineering more stress tolerant plants. We present here a computational study by analyzing time-course transcriptomic data of the two ecotypes to elucidate and compare their regulatory systems in response to drought and salt stresses. A total of 1,693 genes (target genes or TGs) are found to be differentially expressed and possibly regulated by 143 transcription factors (TFs) in response to drought stress together in the two ecotypes. Similarly, 1,535 TGs regulated by 110 TFs are identified to be involved in response to salt stress. Two regulatory networks are constructed to predict their regulatory relationships. In addition, a time-dependent hidden Markov model is derived for each ecotype responding to each stress type, to provide a dynamic view of how each regulatory network changes its behavior over time. A few new insights about the response mechanisms are predicted from the regulatory networks and the time-dependent models. Comparative analyses between the network models of the two ecotypes reveal key commonalities and main differences between the two regulatory systems. Overall, our results provide new information about the complex regulatory mechanisms of switchgrass responding to drought and salt stresses.
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    Physiological Evaluation of Alkali-Salt Tolerance of Thirty Switchgrass (Panicum virgatum) Lines
    Hu, Guofu; Liu, Yiming; Zhang, Xunzhong; Yao, Fengjiao; Huang, Yan; Ervin, Erik H.; Zhao, Bingyu Y. (PLOS, 2015-07-06)
    Soil salt-alkalization is a major limiting factor for crop production in many regions. Switchgrass (Panicum virgatum L.) is a warm-season C4 perennial rhizomatous bunchgrass and a target lignocellulosic biofuel species. The objective of this study was to evaluate relative alkali-salt tolerance among 30 switchgrass lines. Tillers of each switchgrass line were transplanted into pots filled with fine sand. Two months after transplanting, plants at E5 developmental stage were grown in either half strength Hoagland’s nutrient solution with 0 mM Na+ (control) or half strength Hoagland’s nutrient solution with 150 mM Na+ and pH of 9.5 (alkali-salt stress treatment) for 20 d. Alkali-salt stress damaged cell membranes [higher electrolyte leakage (EL) ], reduced leaf relative water content (RWC), net photosynthetic rate (Pn), stomatal conductance (gs), and transpiration rate (Tr). An alkali-salt stress tolerance trait index (ASTTI) for each parameter was calculated based on the ratio of the value under alkali-salt stress and the value under non-stress conditions for each parameter of each line. Relative alkali-salt tolerance was determined based on principal components analysis and cluster analysis of the physiological parameters and their ASTTI values. Significant differences in alkali-salt stress tolerance were found among the 30 lines. Lowland lines TEM-SEC, Alamo, TEM-SLC and Kanlow were classified as alkali-salt tolerant. In contrast, three lowland lines (AM-314/MS-155, BN-13645-64) and two upland lines (Caddo and Blackwell-1) were classified as alkali-salt sensitive. The results suggest wide variations exist in alkali-salt stress tolerance among the 30 switchgrass lines. The approach of using a combination of principal components and cluster analysis of the physiological parameters and related ASTTI is feasible for evaluating alkali-salt tolerance in switchgrass.
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    SacB-SacR Gene Cassette As the Negative Selection Marker to Suppress Agrobacterium Overgrowth in Agrobacterium-Mediated Plant Transformation
    Liu, Yiming; Miao, Jiamin; Traore, Sy; Kong, Danyu; Liu, Yi; Zhang, Xunzhong; Nimchuk, Zachary L.; Liu, Zongrang; Zhao, Bingyu Y. (2016)
    Agrobacterium overgrowth is a common problem in Agrobacterium-mediated plant transformation. To suppress the Agrobacterium overgrowth, various antibiotics have been used during plant tissue culture steps. The antibiotics are expensive and may adversely affect plant cell differentiation and reduce plant transformation efficiency. The SacB-SacR proteins are toxic to most Agrobacterium tumefaciens strains when they are grown on culture medium supplemented with sucrose. Therefore, SacB-SacR genes can be used as negative selection markers to suppress the overgrowth of A. tumefaciens in the plant tissue culture process. We generated a mutant A. tumefaciens strain GV2260 (recA-SacB/R) that has the SacB-SacR cassette inserted into the bacterial genome at the recA gene locus. The mutant Agrobacterium strain is sensitive to sucrose but maintains its ability to transform plant cells in both transient and stable transformation assays. We demonstrated that the mutant strain GV2260 (recA-SacB/R) can be inhibited by sucrose that reduces the overgrowth of Agrobacterium and therefore improves the plant transformation efficiency. We employed GV2260 (recA-SacB/R) to generate stable transgenic N. benthamiana plants expressing a CRISPR-Cas9 for knocking out a WRKY transcription factor.