Progress 03/01/18 to 02/28/23
Outputs
Target Audience:For the application research, we focused on small farmers in urban areas in Mid-Atlantic region and local residents who are interesting in backyard gardening; for scientific research, we provided information of heavy metal tolerance mechanisms to those whose research is in plant heavy metal accumulation and tolerance and environmental heavy metal pollutions. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Two postdocs were recurited to the project during the grant period and trained for biotechnoligy-related skills and knoweldge. Two undergraduated students were also trained for plant biotechnology skills. How have the results been disseminated to communities of interest?Applicable part of the research was presented to Urban farmers in the mid-atlantic region through presentation at Mid-Atlantic Urban Agriculture Summit in 2021. Scientific part of research were presentated as two poster presentations and one oral presentation in 1890 ARD symposium in 2022. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
During the grant period, we conducted various greenhouse experiments to examine both leafy and root based vegetables for their accumulation and tolerance to different heavy metals. The heavy metals we tested included chromium, lead, cadmium and copper. The vegetables tested included onion, kale and lettuce for leafy consumption, and radish and beet for root consumption. Four varieties for each species were included. The results suggested that different species response to different heavy metals differentily. More importantly, different varieties within the species showed a dramatic difference in accumulating heavy metals in their edible parts. The results confirmed our hypothesis:heavy metal accumulation in the edible parts of vetetables varied not only between species, but also among varieties within the species. The findings are essential to advising urban farmers on what species and varieties within species should be selected to grow on potentially contaminted urban soils. In examination of purslane's heavy metal accumulation and tolerance in response to arsenic and chromium, we confirmed one specific purslane accession that significantly accumulated hexavalent chromium in its shoots, however such accumulation did not inhibit its growing, instead Cr6+ promoted its growth. We also identified two purslane accessions that are resistant to arsenic through preventing arsenic transporting to above ground tissues. Thses accessions together with susceptible accessions were used to conduct transcriptome analysis to understand mechanisms of purslane arsenic and chromium tolerance. Transcriptome analysis were conducted in purslane in response to chromium. Because of lack of reference genome, the de novo analysis were conducted. Based on bioinformatic analysis, in general, chromium treatment affected significantly more genes expression in roots than their shoot. This is true for both chromuim resistant and susceptible accessions. However, the clusters of genes altered their expressions are different between chromium tolerant and susceptible accessions. For chromium tolerant accession, clusters of kinase activity and ion binding activity genes were significantly upregulated and transmembrane transport activity genes were downregulated in its roots. However, in the shoot tissue, the oppsite was found with kinase activity and ion binding activity were down regulated and transport activity was up regulated. In addition, response to stress was all down regulated in both root and shoot sduggesting that Cr6+ treatment does not consider as a stress for Cr tolerant accession. For Cr susceptible accession, the clusters of kinase activity and ion binding activitygenes were significanlt upregulated in both root and shoot tissues, but the transporting activity genes were significantly down regulated in both root and shoot tissues.Such difference in response to Cr6+ treatment between Cr tolerant and susceptible accessions may suggest a molecular mechanism in control of Cr6+ transport. In consistence with its susceptibility to Cr6+, genes responding to stress were significantly up regulated in its shoot upon Cr6+ treatment. Based on these analysis, we suggested two potential molecular explainations on Cr tolerance in purslane: 1) although Cr6+ is toxic to plants, upon uptaken into its root, it may be converted into Cr3+ where Cr3+ is essential element for plant growth, therefore it is not only toxic but even promotes its growing as we showed previously; 2) when taking up Cr6+ and transporting from root to shoot, the activated transmembrane transporters in shoots will transport Cr6+ into vacule and store them there to avoid causing damages to plants. However, considering Cr6+ growth promoting effects, we believe that the first explanation could be the case and is warranting for further investigation. Identification of gene(s) encoding enzymes that can convert Cr6+ to Cr3+ in Cr tolerant purslane would be the key for future study. We also donducted transcriptome analysis with purslane accessions responding differentially to arsenic. Through comparative bioinformatic analysis, we identified homologous genes ABCC1 and ABCC2 in purslane. ABCC1 and ABCC2 play important roles in arsenic transportation. In Arabidopsis, both ABCC1 and 2 are located on vacuole membrane to help transfer excessive arsenic from cytoplasm to vacuoles to be stored and de-toxified. In the purslane transcriptome data, we identified 2 ABCC1 homolgs and 8 ABCC2 homologs in both root and shoots. However, contrary to other species such Arabidopsis, both ABCC1 and 2 in purslane were downregulated in arsenic tolerant accession compared to arsenic sensitive accession. Such down regulation is more signifiant in roots than in shoots. We cloned ABCC2 gene from purslane and RT-PCR analysis demonstrated that it is more highly induced by arsenic in arsenic sensitive accession than in arsenic tolerant accession. These results suggest that ABCC1 and ABCC2 in purslane may play a different role in arsenic transportation than in other studied species. In puralnce, ABCC1 and 2 may help transporting arsenic from root to shoot, where in orther species they help to transport arsenic from cytoplasm to vacuoles. Identify the promoters and signaling peptide on their amino acid sequences would help us to further understand mechanisms that ABCC1/2 genes in purslane in control of arsenic transportation.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Ren S, Cerven V, Huang J, Atalay A, Jiang G, Githinji L (2021) Genetic variation of leafy vegetables on lead and chromium accumulation in their edible parts. Mid-Atlantic Urban Agriculture Conference, Oct. 12-14, 2021.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Ren S, Huang J, Moon H, Jiang G, Atalay A, Rutto L (2022) Finding the neglected treasure from wild species for crop production and food securities. 1890 ARD 20th Biennial Research Symposium 2022, Atlanta, April 2-5, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Cerritos Z, Huang J, Ren S (2022) Genetic variation of chromium accumulation and transcriptome response to chromium stress in Purslane. 1890 ARD 20th Biennial Research Symposium 2022, Atlanta, April 2-5, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Joseph D, Huang J, Ren S (2022) Genetic variation of arsenic accumulation, cloning and expression analysis of PoABCC2 in response to Arsenic in Purslane. 1890 ARD 20th Biennial Research Symposium 2022, Atlanta, April 2-5, 2022.
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Progress 03/01/21 to 02/28/22
Outputs
Target Audience:Small farmers in urban areas through presentation in Mid-Atlantic Urban Agriculture Summit Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?A postdoctoral research associate partially involved in this project and got trained on transcriptome analysis. How have the results been disseminated to communities of interest?The applicable part of research in this project was presented to urban farmers in the mid-atlantic region. This was accomplished through a presentation of the leafy vetetables on their lead and chromium accumulations at Mid-Atlantic Urban Agriculture Summit in 2021. What do you plan to do during the next reporting period to accomplish the goals?During the last grant period, we will continue to further dessect the transcriptome data and indentify genes and pathways that related to both arsenic and chromium stress tolerance.
Impacts
What was accomplished under these goals?
During this grant period, we have further analyzed transcriptomic data to identify potential candidate genes that are responsible for arsenic stress. We compared RNA-seq data between arsenic-tolerant and arsenic sensitive purslane accessions under arsenic-treatment conditions. Literature reported that ABCC1 and ABCC2 play important roles in arsenic transportation. Both proteins are located on vacuole membranes to help transfer excessive arsenic from cytoplasm to vacuoles so that arsenic won't affect plants' growth. Double knockout of ABCC1 and ABCC2 would lead to plants becoming sensitive to arsenic. We identified both ABCC1 and ABCC2 genes from purslane transcriptome data. 2 ABCC1 homologs existed in both roots and shoots transcriptome profiles, while 8 ABCC2 homologs were identified in both roots and shoots expression profiles. Contrary to those from other species, both ABCC1s and ABCC2s in purslane were downregulated in arsenic-tolerant accession compared to arsenic-sensitive accession. These down regulations were more dramatic in roots than in shoots. In previous research, we cloned ABCC2 gene from purslane, RT-PCR analysis showed that it is more highly induced by arsenic in arsenic-sensitive accession than in arsenic-tolerant accession. Our current analysis is consistant with our previous findings indicating that ABCC1 and ABCC2 in purslane may play a different role in arsenic transportation than in other studied species. Our findings warrant further study to clone both genes and examine their cellular localizations, and their functions in plant arsenic tolerance.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Ren S., Cerven V.,Huang J., Githinji L., Atalay A., and Jiang G. (2021) Genetic Variation of Leafy Vegetables on Lead and Chromium Accumulations in their edible parts. Mid-Atlantic Urban Agriculture Summit, Oct. 12-14, 2021.
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Progress 03/01/20 to 02/28/21
Outputs
Target Audience:
Nothing Reported
Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?During this grant period, we have a Postdoctoral research associate being recurited on this project for about 5 months and trained for scientific mewthodoligy related to the project. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?Detail analysis of the trasnscriptome will be the major target for next reporting period, Eventually we will identify some promising genes that are important for Cr tolerance in crop species. In addition, we will test Cr and Pb accumulation in two different rooty vegetables (radish and beet) with 4 varieties each species included.
Impacts
What was accomplished under these goals?
During this grant period, we donducted transcriptome analysis to identify the expression profiles in response to chromium treatment. Two different puralsne accessions, one with chromium sensitive and the other chromium tolerance were selected and subjected to a 24 hour 200ppm Cr6+ treatment (with water as control treatment). Roots and shoots were collected seperately after treatment completed. All treatments and tissue collections were biologivcally triplicated. Total RNAs were isolated and subjected for RNA-seq analysis. Overall, 1043 millions clean reads were obtained from all samples and at least 40M clean reads were received from each sample. After de novo analysis, at least 71% of clean reads from each library were mapped to existing genes in all available database. With a log 2 fold as significantl cut off, we analysed expression difference between Cr6+ treated and control samples for both Cr tolerant and sensitive accessions. For accession GT, a Cr tolerance purslane, significant amount of genes were altered in their expression in root after Cr6+ treratment, where more than 10000 gene clusters were upregulated and about 9000 gene clusters were down regulated by Cr6+ treatment. Much less gene clusters were affected by Cr6+ treatment in their shoot tissues with only 2746 gene clusters up and 2049 gene cluster down regulated by Cr6+ treatment. Similar trends were observed for accession EG, a Cr sensitive purslane accession, with about 7000 gene clusters up and 7000 down in root tissues and about 4000 up and 2700 down regulated in shoot tissues in response to Cr6+ treatment. GO enrichment analysis were conducted to identify the pathways that is related to the Cr6+ treatment or the response to the treatment. In general, kinase activity, transmembrane transport activity and ion binding activity are the most affected by Cr6+ treatment in both root and shoot tissues. For GT accession, Kinase activity and ion binding activity were significantly uregulated, while transmembrane transport activity is down regulated by Cr6+ treatment in roots. However, in shoot tissues, exact opposite was fund with kinase activity and ion binding activity were down regulated and transport activity upregulated. In addition, response to stress was all down regulated in both root and shoot tissues indicating that Cr6+ treatment for GT accession does not consider as a stress for Cr tolerant accession. In consistance, photosynthesis pathway genes were significantly upregulated in shoots by Cr6+ treatment. This finding supports our observation that after Cr6+ treatment, accession GT grew better and even doubled biomass comparing to untreated control. For EG accession, where it is sensitive to Cr6+ treatment, kinase activity and ion binding activity were significantly up regulated by Cr6+ treatment in both root and shoot tissues, but transmembrane transport activity were significantly down regulated by Cr6+ treatment in roots and shoots. Such response difference between Cr tolerant and Cr sensitive purslane accessions to Cr6+ treatment may suggest a molecular mechanism in control of Cr6+ transport. Furthermore, in consistant with the sensitivity to Cr6+, genes responding to stress were significantly up regulated in EG shoots upon Cr6+ treatment, and genes controlling photosynthesis were drastically downregulated by Cr6+ treratment. This transcriptome analysis suggests two potential molecular explainations on Cr tolerance in GT accession: 1) although Cr6+ is toxic to plants, upon uptaken into GT roots, it may be converted into Cr3+ where Cr3+ is essential element for plants (as well as animal) growth, therefore it is not only toxic but even promote its growing as we demonstrated previously; 2) when taking up Cr6+ and transporting from roots to shoots, the activated transmembrane transporters in shoots will transport Cr6+ into vacule and stored it there to avoid causing damage to the plants. However, considering our previous findings where Cr6+ treatment significantly promotes its biomass growing, we hypotheses that the first explanation could be the case and is warranting for further invistigation.
Publications
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Progress 03/01/19 to 02/29/20
Outputs
Target Audience:
Nothing Reported
Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?A post doc was recurited to the project and got trained on both techniques and knowledgy on heavy plant metal accumulation and related molecular approaches in understanding mechanisms of heavy metal transport and accumulation. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, we will focus on transcriptome analysis to identify potential genes and gene networks regulating purslane's heavy metal transport and accumulation, specifically focusing on chromium and arsenic. RNA-seq will be conducted and clean data will be bioinformactally analyzed. DEGs and enriched pathways will be identified in responding to heavy metal treatment. We will also conduct greemhouse experiments to test purslane's ability to grow on coal ash-contained growth medium to test its capacity to extract heavy metals (As, Cr, and Pb) from coal ashes.
Impacts
What was accomplished under these goals?
During the last grant period, we quantified both chromoium and lead accumulation in leafy vegetables focusing on edible parts. After treating three times with 200ppm of either Cr 6+ or Pb2+ during growing season, we found that all 4 kales accumulated more than 100mg/kg chromium in their edible parts. However, dramatic variations were observed among lettuce varieties. Only variety Ruby accumulated similar amount of chromium as kales did, other three varieties accumulated significantly less in their edible parts, with Butter-Crunch only accumulated about 5mg/kg, 20 times less than kales' accumulation. On the other hand, all kale varieties accumulated very little lead (less than 3 mg/kg), but big variation existed among lettuce veraities ranging from 2 mg/kg (Prize-Head) to over 180 mg/kg (Ruby). These results clearly demonstrated that heavy metal accumulation in the edible parts isvaried, not only between species but also among varieties within the same species. This finding is essential to advising urban farmers on what species and varieties within species should be selected to gorw on potentially contaminated soils. From basic research point of view, lettuce variety Ruby could be an interesting material for understanding heavy metal transport and accumulation since it accumulated both chromium and lead at significantly high level. In addition, we also conducted chromium and arsenic treatments among different purslane accessions (accessions were selected based on previous experiments on chromium or arsenic accumulation). Total RNAs were extracted from both shoot anf rooot tissues and will be subjected to transcriptome analysis through RNA-seq technologiy.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Genetic variation of copper stress tolerance and shoot copper accumulation in Purslane. 2019. JournaL of Biotech Research 10: 213-222
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Progress 03/01/18 to 02/28/19
Outputs
Target Audience:
Nothing Reported
Changes/Problems:In our original project, we proposed to directly grow purslane in farms with potential heavy metal contaminations. After discussing with Dominion Power staff, we found that coal ash generated by their company contained all three heavy metals that we proposed to evaluate. This provide us a better opportunity to test purslane's ability to remidiate all three heavy metals together. Therefore we will adjust our project and test purslane directly on coal ash contained soil mixture in our greenhouse experiment. This will provide better infomration for puslane's potential of remidiate heavy metals from contaminated environments. What opportunities for training and professional development has the project provided?Although not supported by this project, we did use this project to train a post doctoral associate in handling of greenhouse experiments for heavy metal related research. A new postdoctoral associate was recurited to the project at the beginning of the second year period. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, we will start to conduct the research to identify potential genes that are responsible for chromium tolerance from purslane. We will aslo condinue to conduct experiment on the rest of vegetables for their heavy metal tolerance. In addition, we will test the possibility of using purslane to remove heavy metals from coal ash. In January of 2019, we talked to a Dominion Power representative to discuss the project and they agreed to provide us withthe coal ash needed for our experiments.
Impacts
What was accomplished under these goals?
During the first year, we multiplied purslane seeds from relative accessions that will be used for the project. We obtained seeds of three leafy vegetables (kale, lettuce and onion), two fruit vegetable (pepper and tomato), and three root vegetables (carrot, radish and beet). Each vegetable selected contains 4 different varieties. A greenhose experiment was conducted for leafy vegetables for their tolerance to chromium and lead. Phenotypic observation revealed that different vegetables have different capacity to tolerate heavy metal contamination. Both chromium and lead do not affect onion growth significantly while they do affect growth of kale and lettuce. Furthermore, different varieties within the same species (kale and lettuce) showed different response to chromium and lead treatment with some varieties was significantly inhibited for its gorwth and some did not show any difference comparing to the control treatment. Chromium and lead accumulation in their ediable parts are under investigated. Our preliminary results confirmed our hypothysis and indicate that we should be able to select certain species and varieties within the species that fit for the use in urban agriculture settings in concern of heavy metal contaminations.
Publications
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