Progress 04/01/18 to 03/31/20
Outputs
Target Audience:Farmers of Common Beans and Black-eyed Peas (a.k.a. cowpea when dry and purple-hulled peas when green) are the targets of this project. These legumes are some of the most important, traditional crops of the southeastern United States, with Black-Eyed Peas being the highest net income generators per acre among the vegetables produced in this region. Like most legumes, beans and cowpeas are sensitive to abiotic stresses affecting their roots, especially those associated with aluminum toxicity, drought conditions or salinization. The PI for this project has one of the few legume genomics/breeding programs in the region that is evaluating these traits but was missing the transcriptomic and proteomic evaluations of tolerant genotypes needed to support further varietal improvement. Overall the goal of this project has been to improve the PI's legume genetics research using molecular markers derived from newest biotechnology tools. With this in mind, the professional development grant has alllowed the PI and his graduate student, Mr. David Hickok, to visit a mentor, Dr. Ted Thannhauser, at USDA Soil, Plant and Animal Nutrition Laboratory located at Cornell University in Ithaca, New York. The USDA laboratory has the advantage of being fully integrated from proteomics to basic plant physiology, currently managed by an Aluminum stress expert, Dr. Miguel Pineros, the division supervisor at the USDA facility, helped Dr. Blair plan the hydroponics experiment. Germplasm of bean/cowpea has been provided by Dr. Kisha and Dr. Morris as well as sourced internationally and at Univ of Nebraska. Dr. Ray Glahn, also of the USDA lab in Ithaca helped train the graduate student on plant physiology and resulting plant nutrition outcomes. During the time of the project two next generation sequencers were purchased for the lab of the PI and were put into place with training from the company, Illumina Inc. on their use in transcriptome analysis. Training was split up into two events one for the MiSeq and one for the nextSeq. A basic bacterial genome coverage library was run on the first of these machines, while a sample transcriptome library of tomato was run on the NextSeq using RNA-seq protocols common in genomics. All of this was done to train the PI and graduate student on analysis of gene expression for Aluminum treated roots of cowpeas or beans. Changes/Problems:Unfortunately, a tornado hit TSU's greenhouse in Nashville and whatever survived of the new hydroponic system will have to be transferred to a replacement hoophouse next year. This was the major setback to the project but occurred at the end of the time period so the laboratory training proceeded well. ? What opportunities for training and professional development has the project provided?Multiple opportunities for training and professional development were provided by the project both to the PI and to the two graduate students, one PhD and one MS candidate, across 2018-20 time frame. Apart from the transcriptome/proteome training we had instruction on root scanning and growth of plants in hydroponic system for root imaging. . Dr. Blair's PhD student Daniel Demissie was in contact with USDA staff Eric Shaff and others to modify our TSU system to resemble that of Cornell's. The MS student had contact with Dr. Thannhauser for proteomics / transcriptomics training especially with single cell types and then with Dr. Pineros for plant physiology and Dr. Glahn for nutritional work.? How have the results been disseminated to communities of interest?Publications are underway for the PhD student and a proposal has been submtted by the MS student for the remaining 1 to 1.5 years of his MS program. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
So far a Shallow pots Hydroponic assay technique has been developed for screening 150 genotypes of common bean at a time in TSU greenhouse. This was useful for GWAS diversity panel called the Andean Bean Diversity Panel (ADP) developed under a USAID/USDA funding by various university and USDA collaborators. The assay was tried on 5 commercial cowpea varieties and 1 control but did not owrk well due to poor root growth of this species after transfer to hydroponic solution. Deep pot and shallow tray assays were also tested for cowpea but were also problematic. The first graduate student (PhD candidate for 2020 - Daniel Demissie) obtained data for a chapter of his disseration on common bean; while the second graduate student (MS candidate for 2021 - David Hickok) was trained in cowpea hydroponics and in next generation sequencing at TSU and proteomics / transcriptomics at USDA-Ithaca. Proteomics training was by Dr. Thannhauser as the mentor for the capacity building project with two visits of the graduate student and the PI to Cornell / USDA-Ithaca first in summer 2019 and second in spring 2020). Experimental design benefitted from this exchange especially with USDA-Ithaca plant physiologist and nutritional physiologist, Dr. Miguel Pineros and Dr. Ray Glahn, respectively. Results using next generation sequencerss in transcriptome and genome sequencing are being analyzed but in total two runs of 40 Gb (giga base pairs 40,000,000,000 nucleotides) of paried end reads were generated from the new Illumina sequencers intalled in the PI's laboratory. These will be used for teaching purposes in the TSU biotechnology program. The MS student was also trained by Dr. Suping Zhou who had expertise already in aluminum treatment of tomatoes with micro-dissection and single cell type proteomics and transcriptomics taught in her Cell Tissue Culture class at TSU. All this training has been useful for perfecting RNA extraction techniques and evaluation of transcriptome / proteomic data.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Wu J, Wang LF, Fu J, Chen J, Zhang J, Zhang SL, Wei SH, Tang YS, Zhu J, Lei L, Chen ML, Geng Q, Liu CL, Wu L, Li XM, Wang X, Wang Z, Wang Q, Xing S, Zhang H, Blair MW*, Wang S* (2019) Resequencing of 683 common bean genotypes identifies yield component trait associations across a north-south cline. Nature Genetics.
|
Progress 04/01/18 to 03/31/19
Outputs
Target Audience:Farmers of Common Beans and Black-eyed Peas (a.k.a. cowpea when dry and purple-hulled peas when green) are the targets of this project. These legumes are some of the most important, traditional crops of the southeastern United States, being the highest net income generators per acre among the vegetables produced in this region. Like most legumes, beans and cowpeas are sensitive to abiotic stresses affecting their roots, especially those associated with aluminum toxicity, drought conditions or salinization. The PI for this project has one of the few legume genomics/breeding programs in the region that is evaluating these traits but is missing the transcriptomic and proteomic evaluations of tolerant genotypes needed to support further varietal improvement. Overall the goal of this project has been to improve the PI's legume genetics research using molecular markers derived from newest biotechnology tools. With this in mind, the professional development grant has alllowed the PI to visita mentor, Dr. Ted Thannhauser, at USDA Soil, Plant and Animal Nutrition Laboratory located at Cornell University in Ithaca, New York. The USDA laboratory has the advantage of being fully integrated from proteomics to basic plant physiology, currently managed by an Aluminum stress expert, Dr. Miguel Pineros, the division supervisor at the USDA facility, who is also willing to collaborate with Dr. Blair. Germplasm of salt-tolerant bean/cowpea has been provided by Dr. Kisha and Dr. Morris as well as sourced internationally and at Univ of Nebraska.Academic audience is also important for the results of this grant. Changes/Problems:A no costextension was requested due to the nature of conducting collaborative research at Cornell USDA in the summer months, with planning in 2018 and execution in 2019 using the intervening semesters for setting up research at TSU especially the hydroponic greenhouse system. What opportunities for training and professional development has the project provided?Dr. Blair has visited the USDA facility of Dr. Thannhauser for one week in the summer of 2018 and is planning a longer visit for the summer of 2019. The first visit led to instruction on root scanning and growth of plants in hydroponic system for root imaging. Dr. Blair's student Daniel Demissies was in contact with USDA staff Eric Shaff and others to modify our TSU system to resemble that of Cornell's. How have the results been disseminated to communities of interest?publications so far have discussed genotype selection but a dissertation has been completed with screening of cowpea root systems in the hydroponic system What do you plan to do during the next reporting period to accomplish the goals?A plan is in place to conduct the aluminum stress experiments at TSU in the deep and shallow hydrponic tanks and to take samples to Cornell for analysis at the USDA lab or Dr. Thannhauser. This will take place in July and August of 2019.
Impacts
What was accomplished under these goals?
So far aShallow pots Hydroponic assay technique has been developed for screening 100 plus genotypes of common bean or cowpea at a time in TSU greenhouse. This is useful for RIL screening and GWAS results using transcriptome or genome sequence data. Deep pot technique also developed and in process of being used for the first time. It will be useful for RNA extraction and evaluation of transcriptome or proteome.
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2019
Citation:
Darkwa K, Mohammed H, Ambachew D, Blair MW, Asfaw A (in revisions) Genetic parameters estimation for drought adaptation traits in Mesoamerican common beans. Journal of Crop Improvement.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2019
Citation:
Wu J, Wang LF, Fu J, Chen J, Zhang J, Zhang SL, Wei SH, Tang YS, Zhu J, Lei L, Chen ML, Geng Q, Liu CL, Wu L, Li XM, Wang X, Wang Z, Wang Q, Xing S, Zhang H, Blair MW*, Wang S* (in revisions) Resequencing of 683 common bean genotypes identifies yield component trait associations across a north-south cline. Nature Genetics.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Assefa T, Rubyogo JC, Mahama AA, Cannon EKS, Brown AV, Rao IM, Blair MW, Cannon SB (2019) A Review of Breeding and Genomics Resources for Common Bean (Phaseolus vulgaris L.) Molecular Breeding 39:20.
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Hacisalihoglu G, Blair MW (2019) What we know about zinc in soils and plants for improving global food production security. . In Special Issue : (eds.) Z Rengel Achieving Sustainable Crop Nutrition Chp16 - Micronutrients: advances in understanding zinc cycling in soils, uptake/use by plants and ways of optimising zinc use efficiency in crop production. Publisher: Burleigh Dodds Science Publishing
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Yahaya D, Denwar N, Blair MW (2019) Evaluation of USDA Cowpea (Vigna unguiculata (L.) Walp) Genotypes for Drought Tolerance Conditions in the Northern Region of Ghana. Agricultural Sciences
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Yahaya D, Denwar N, Mohammed M, Blair MW (2019) Screening of Cowpea (Vigna unguiculata (L.) Walp) Genotypes for Enhanced N2 Fixation And Water Use Efficiency Under Field Conditions In Ghana. American Journal of Plant Sciences 10 (4)
|
|