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Edae EA, Kosgey Z, Bajgain P, Ndung'u KC, Gemechu A, Bhavani S, Anderson JA, Rouse MN. The genetics of Ug99 stem rust resistance in spring wheat variety 'Linkert'. Front Plant Sci 2024; 15:1343148. [PMID: 38516672 PMCID: PMC10954791 DOI: 10.3389/fpls.2024.1343148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024]
Abstract
Wheat stem rust caused by Puccinia graminis f. sp. tritici (Pgt) threatens wheat production worldwide. The objective of this study was to characterize wheat stem rust resistance in 'Linkert', a variety with adult plant resistance effective to emerging wheat stem rust pathogen strain Ug99. Two doubled haploid (DH) populations and one recombinant inbred line (RIL) population were developed with 'Linkert' as a stem rust resistant parent. Hard red spring wheat variety 'Forefront' and genetic stock 'LMPG' were used as stem rust susceptible parents of the DH populations. Breeding line 'MN07098-6' was used as a susceptible parent of the RIL population. Both DH and RIL populations with their parents were evaluated both at the seedling stage and in the field against Pgt races. Genotyping data of the DH populations were generated using the wheat iSelect 90k SNP assay. The RIL population was genotyped by genotyping-by-sequencing. We found QTL consistently associated with wheat stem rust resistance on chromosome 2BS for the Linkert/Forefront DH population and the Linkert/MN07098-6 RIL population both in Ethiopia and Kenya. Additional reliable QTL were detected on chromosomes 5BL (125.91 cM) and 4AL (Sr7a) for the Linkert/LMPG population in Ethiopia and Kenya. Different QTL identified in the populations reflect the importance of examining the genetics of resistance in populations derived from adapted germplasm (Forefront and MN07098-6) in addition to a genetic stock (LMPG). The associated markers in this study could be used to track and select for the identified QTL in wheat breeding programs.
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Affiliation(s)
- Erena A. Edae
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Zennah Kosgey
- Kenya Agricultural and Livestock Research Organization (KALRO), Food Crops Research Centre, Njoro, Kenya
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Kimani C. Ndung'u
- Kenya Agricultural and Livestock Research Organization (KALRO), Food Crops Research Centre, Njoro, Kenya
| | - Ashenafi Gemechu
- Ethiopian Institute of Agriculture, Debre Zeit Agricultural Research Center, Bishoftu, Ethiopia
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - James A. Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Matthew N. Rouse
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, Saint Paul, MN, United States
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McCradden MD, Joshi S, Anderson JA, London AJ. A normative framework for artificial intelligence as a sociotechnical system in healthcare. Patterns (N Y) 2023; 4:100864. [PMID: 38035190 PMCID: PMC10682751 DOI: 10.1016/j.patter.2023.100864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Artificial intelligence (AI) tools are of great interest to healthcare organizations for their potential to improve patient care, yet their translation into clinical settings remains inconsistent. One of the reasons for this gap is that good technical performance does not inevitably result in patient benefit. We advocate for a conceptual shift wherein AI tools are seen as components of an intervention ensemble. The intervention ensemble describes the constellation of practices that, together, bring about benefit to patients or health systems. Shifting from a narrow focus on the tool itself toward the intervention ensemble prioritizes a "sociotechnical" vision for translation of AI that values all components of use that support beneficial patient outcomes. The intervention ensemble approach can be used for regulation, institutional oversight, and for AI adopters to responsibly and ethically appraise, evaluate, and use AI tools.
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Affiliation(s)
- Melissa D. McCradden
- Department of Bioethics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics & Genome Biology Research Program, Peter Gilgan Center for Research & Learning, Toronto, ON, Canada
- Division of Clinical & Public Health, Dalla Lana School of Public Health, Toronto, ON, Canada
| | - Shalmali Joshi
- Department of Biomedical Informatics, Department of Computer Science (Affliate), Data Science Institute, Columbia University, New York, NY, USA
| | - James A. Anderson
- Department of Bioethics, The Hospital for Sick Children, Toronto, ON, Canada
- Institute for Health Policy, Management, and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Alex John London
- Department of Philosophy and Center for Ethics and Policy, Carnegie Mellon University, Pittsburgh, PA, USA
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DeHaan LR, Anderson JA, Bajgain P, Basche A, Cattani DJ, Crain J, Crews TE, David C, Duchene O, Gutknecht J, Hayes RC, Hu F, Jungers JM, Knudsen S, Kong W, Larson S, Lundquist PO, Luo G, Miller AJ, Nabukalu P, Newell MT, Olsson L, Palmgren M, Paterson AH, Picasso VD, Poland JA, Sacks EJ, Wang S, Westerbergh A. Discussion: Prioritize perennial grain development for sustainable food production and environmental benefits. Sci Total Environ 2023; 895:164975. [PMID: 37336402 DOI: 10.1016/j.scitotenv.2023.164975] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/02/2023] [Accepted: 06/15/2023] [Indexed: 06/21/2023]
Abstract
Perennial grains have potential to contribute to ecological intensification of food production by enabling the direct harvest of human-edible crops without requiring annual cycles of disturbance and replanting. Studies of prototype perennial grains and other herbaceous perennials point to the ability of agroecosystems including these crops to protect water quality, enhance wildlife habitat, build soil quality, and sequester soil carbon. However, genetic improvement of perennial grain candidates has been hindered by limited investment due to uncertainty about whether the approach is viable. As efforts to develop perennial grain crops have expanded in past decades, critiques of the approach have arisen. With a recent report of perennial rice producing yields equivalent to those of annual rice over eight consecutive harvests, many theoretical concerns have been alleviated. Some valid questions remain over the timeline for new crop development, but we argue these may be mitigated by implementation of recent technological advances in crop breeding and genetics such as low-cost genotyping, genomic selection, and genome editing. With aggressive research investment in the development of new perennial grain crops, they can be developed and deployed to provide atmospheric greenhouse gas reductions.
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Affiliation(s)
- Lee R DeHaan
- The Land Institute, 2440 E. Water Well Rd, Salina, KS 67401, USA.
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN 55108, USA
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN 55108, USA
| | - Andrea Basche
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 1875 N. 38th St, 279 PLSH, Lincoln, NE 68583-0915, USA
| | - Douglas J Cattani
- Department of Plant Science, University of Manitoba, 66 Dafoe Rd, Winnipeg, MB R3T 2N2, Canada
| | - Jared Crain
- Department of Plant Pathology, Kansas State University, 1712 Claflin Rd, 4024 Throckmorton PSC, Manhattan, KS 66506, USA
| | - Timothy E Crews
- The Land Institute, 2440 E. Water Well Rd, Salina, KS 67401, USA
| | - Christophe David
- ISARA, Agroecology and Environment Research Unit, 23 rue Jean Baldassini, 69364 Lyon, France
| | - Olivier Duchene
- ISARA, Agroecology and Environment Research Unit, 23 rue Jean Baldassini, 69364 Lyon, France
| | - Jessica Gutknecht
- Department of Soil, Water, and Climate, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN 55108, USA
| | - Richard C Hayes
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Pine Gully Rd, NSW 2650, Australia
| | - Fengyi Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center of Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, 2 Cuihu N Rd, Wuhua District, Kunming 650106, China
| | - Jacob M Jungers
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN 55108, USA
| | - Søren Knudsen
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, 1799, Copenhagen, Denmark
| | | | - Steve Larson
- USDA-ARS, Forage and Range Research, 696 North 1100 East, Logan, UT 84321, USA
| | - Per-Olof Lundquist
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Box 7080, 750 07 Uppsala, Sweden
| | - Guangbin Luo
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| | - Allison J Miller
- Saint Louis University, Donald Danforth Plant Science Center, 975 N Warson Rd, Olivette, MO 63132, USA
| | - Pheonah Nabukalu
- NESPAL, University of Georgia, 2356 Rainwater Rd, Tifton, GA 31793, USA
| | - Matthew T Newell
- NSW Department of Primary Industries, Cowra Agricultural Research Station, 296 Binni Creek Rd, Cowra, NSW 2794, Australia
| | - Lennart Olsson
- Lund University Centre for Sustainability Studies, P.O. Box 170, SE-221 Lund, Sweden
| | - Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| | | | | | - Jesse A Poland
- King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | | | - Shuwen Wang
- The Land Institute, 2440 E. Water Well Rd, Salina, KS 67401, USA
| | - Anna Westerbergh
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Box 7080, 750 07 Uppsala, Sweden
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Hay WT, Anderson JA, Garvin DF, McCormick SP, Busman M, Vaughan MM. Elevated CO 2 Can Worsen Fusarium Head Blight Disease Severity in Wheat but the Fhb1 QTL Provides Reliable Disease Resistance. Plants (Basel) 2023; 12:3527. [PMID: 37895995 PMCID: PMC10610529 DOI: 10.3390/plants12203527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/03/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023]
Abstract
Fusarium head blight (FHB) is a destructive fungal disease of wheat that causes significant economic loss due to lower yields and the contamination of grain with fungal toxins (mycotoxins), particularly deoxynivalenol (DON). FHB disease spread and mycotoxin contamination has been shown to worsen at elevated CO2, therefore, it is important to identify climate-resilient FHB resistance. This work evaluates whether wheat with the Fhb1 quantitative trait locus (QTL), the most widely deployed FHB resistance locus in wheat breeding programs, provides reliable disease resistance at elevated CO2. Near-isogenic wheat lines (NILs) derived from either a highly FHB susceptible or a more FHB resistant genetic background, with or without the Fhb1 QTL, were grown in growth chambers at ambient (400 ppm) and elevated (1000 ppm) CO2 conditions. Wheat was inoculated with Fusarium graminearum and evaluated for FHB severity. At elevated CO2, the NILs derived from more FHB-resistant wheat had increased disease spread, greater pathogen biomass and mycotoxin contamination, and lower rates of DON detoxification; this was not observed in wheat from a FHB susceptible genetic background. The Fhb1 QTL was not associated with increased disease severity in wheat grown at elevated CO2 and provided reliable disease resistance.
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Affiliation(s)
- William T. Hay
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N, University Street, Peoria, IL 61604, USA; (S.P.M.); (M.B.); (M.M.V.)
| | - James A. Anderson
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA; (J.A.A.); (D.F.G.)
| | - David F. Garvin
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA; (J.A.A.); (D.F.G.)
| | - Susan P. McCormick
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N, University Street, Peoria, IL 61604, USA; (S.P.M.); (M.B.); (M.M.V.)
| | - Mark Busman
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N, University Street, Peoria, IL 61604, USA; (S.P.M.); (M.B.); (M.M.V.)
| | - Martha M. Vaughan
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N, University Street, Peoria, IL 61604, USA; (S.P.M.); (M.B.); (M.M.V.)
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Thai K, Tsiandoulas KH, Stephenson EA, Menna-Dack D, Zlotnik Shaul R, Anderson JA, Shinewald AR, Ampofo A, McCradden MD. Perspectives of Youths on the Ethical Use of Artificial Intelligence in Health Care Research and Clinical Care. JAMA Netw Open 2023; 6:e2310659. [PMID: 37126349 PMCID: PMC10152306 DOI: 10.1001/jamanetworkopen.2023.10659] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Importance Understanding the views and values of patients is of substantial importance to developing the ethical parameters of artificial intelligence (AI) use in medicine. Thus far, there is limited study on the views of children and youths. Their perspectives contribute meaningfully to the integration of AI in medicine. Objective To explore the moral attitudes and views of children and youths regarding research and clinical care involving health AI at the point of care. Design, Setting, and Participants This qualitative study recruited participants younger than 18 years during a 1-year period (October 2021 to March 2022) at a large urban pediatric hospital. A total of 44 individuals who were receiving or had previously received care at a hospital or rehabilitation clinic contacted the research team, but 15 were found to be ineligible. Of the 29 who consented to participate, 1 was lost to follow-up, resulting in 28 participants who completed the interview. Exposures Participants were interviewed using vignettes on 3 main themes: (1) health data research, (2) clinical AI trials, and (3) clinical use of AI. Main Outcomes and Measures Thematic description of values surrounding health data research, interventional AI research, and clinical use of AI. Results The 28 participants included 6 children (ages, 10-12 years) and 22 youths (ages, 13-17 years) (16 female, 10 male, and 3 trans/nonbinary/gender diverse). Mean (SD) age was 15 (2) years. Participants were highly engaged and quite knowledgeable about AI. They expressed a positive view of research intended to help others and had strong feelings about the uses of their health data for AI. Participants expressed appreciation for the vulnerability of potential participants in interventional AI trials and reinforced the importance of respect for their preferences regardless of their decisional capacity. A strong theme for the prospective use of clinical AI was the desire to maintain bedside interaction between the patient and their physician. Conclusions and Relevance In this study, children and youths reported generally positive views of AI, expressing strong interest and advocacy for their involvement in AI research and inclusion of their voices for shared decision-making with AI in clinical care. These findings suggest the need for more engagement of children and youths in health care AI research and integration.
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Affiliation(s)
- Kelly Thai
- Department of Bioethics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genetics & Genome Biology, Peter Gilgan Centre for Research & Learning, Toronto, Ontario, Canada
| | - Kate H Tsiandoulas
- Department of Bioethics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elizabeth A Stephenson
- Labatt Family Heart Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Dolly Menna-Dack
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Randi Zlotnik Shaul
- Department of Bioethics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - James A Anderson
- Department of Bioethics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute for Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Melissa D McCradden
- Department of Bioethics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genetics & Genome Biology, Peter Gilgan Centre for Research & Learning, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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Kusunose Y, Rossi JJ, Van Sanford DA, Alderman PD, Anderson JA, Chai Y, Gerullis MK, Jagadish SVK, Paul PA, Tack JB, Wright BD. Sustaining productivity gains in the face of climate change: A research agenda for US wheat. Glob Chang Biol 2023; 29:926-934. [PMID: 36416581 PMCID: PMC10107672 DOI: 10.1111/gcb.16538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Wheat is a globally important crop and one of the "big three" US field crops. But unlike the other two (maize and soybean), in the United States its development is commercially unattractive, and so its breeding takes place primarily in public universities. Troublingly, the incentive structures within these universities may be hindering genetic improvement just as climate change is complicating breeding efforts. "Business as usual" in the US public wheat-breeding infrastructure may not sustain productivity increases. To address this concern, we held a multidisciplinary conference in which researchers from 12 US (public) universities and one European university shared the current state of knowledge in their disciplines, aired concerns, and proposed initiatives that could facilitate maintaining genetic improvement of wheat in the face of climate change. We discovered that climate-change-oriented breeding efforts are currently considered too risky and/or costly for most university wheat breeders to undertake, leading to a relative lack of breeding efforts that focus on abiotic stressors such as drought and heat. We hypothesize that this risk/cost burden can be reduced through the development of appropriate germplasm, relevant screening mechanisms, consistent germplasm characterization, and innovative models predicting the performance of germplasm under projected future climate conditions. However, doing so will require coordinated, longer-term, inter-regional efforts to generate phenotype data, and the modification of incentive structures to consistently reward such efforts.
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Affiliation(s)
| | | | | | | | | | - Yuan Chai
- University of MinnesotaMinneapolisMinnesotaUSA
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Djordjevic D, McFadyen A, Anderson JA. Ethical challenges and opportunities in the development and approval of novel therapeutics for rare diseases. J Med Access 2023; 7:27550834231177507. [PMID: 37323852 PMCID: PMC10262601 DOI: 10.1177/27550834231177507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/05/2023] [Indexed: 06/17/2023]
Abstract
The development of novel therapeutics for rare "orphan" diseases has brought a growing tension between the desire to accelerate access to these breakthrough therapies and the need to generate quality evidence regarding their safety and efficacy. Accelerating the pace of drug development and approval may facilitate the rapid delivery of benefits to patients and cost savings for research and development, which theoretically improves affordability of drugs for the health system. However, several ethical challenges arise with expedited approval, compassionate release of drugs, and subsequent study of drugs in "real-world" settings. In this article, we explore the changing landscape of drug approval and the ethical challenges expedited approval creates for patients, caregivers, clinicians, and institutions, and propose tangible strategies to maximize the benefits of "real-world" data acquisition while mitigating risks to patients, clinicians, and institutions.
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Negash T, Edae EA, Tilahun L, Anderson JA, Rouse MN, Bajgain P. Genome-wide association mapping for field and seedling resistance to the emerging Puccinia graminis f. sp. tritici race TTRTF in wheat. Plant Genome 2022; 15:e20274. [PMID: 36263894 DOI: 10.1002/tpg2.20274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Stem rust of wheat (Triticum spp.), caused by Puccinia graminis f. sp. tritici (Pgt), is one of the most impactful wheat diseases because of its threat to global wheat production. While disease mitigation has primarily been achieved through the deployment of resistant wheat varieties, emerging new virulent races continue to pose risks to the crop. For example, races such as Ug99 (TTKSK), TKTTF, and TTRTF have caused epidemics in different wheat growing regions of the world in recent years. A continual search for new and effective sources of resistance is therefore necessary to safeguard wheat production. This study assessed a breeding panel from the Ethiopian Institute of Agricultural Research (EIAR) wheat breeding program for seedling and field plant resistance to TTRTF and reports genomic regions conferring resistance to TTRTF. Trait correlations (r) were medium to strong (range = .38-.71) and heritabilities were moderate (.32-.56). Association analysis for resistance to TTRTF resulted in detection of 20 markers in 11 chromosomes; the marker S1B_175439851 was associated with resistance at both seedling and adult plant stages. Models with two to four QTL combinations reduced seedling and field disease severity by 12-48 and 9-17%, respectively. Genomic prediction for TTRTF resistance resulted in low to moderately-high predictions (mean correlations of .25-.47). Identification of resistant lines and QTL in the EIAR population is expected to assist in selection toward improved resistance to TTRTF. Specifically, the application of genomic selection (GS) in identifying resistant lines in future related breeding populations will further assist breeding efforts against this new stem rust pathogen race.
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Affiliation(s)
- Tamrat Negash
- Ethiopian Institute of Agricultural Research, Kulumsa, Ethiopia
| | - Erena Aka Edae
- Dep. of Plant Pathology, Univ. of Minnesota, St. Paul, MN, USA
| | - Lidiya Tilahun
- Ethiopian Institute of Agricultural Research, Kulumsa, Ethiopia
| | - James A Anderson
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, St. Paul, MN, USA
| | - Matthew N Rouse
- Dep. of Plant Pathology, Univ. of Minnesota, St. Paul, MN, USA
- USDA-ARS, Cereal Disease Laboratory, St. Paul, MN, 55108, USA
| | - Prabin Bajgain
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, St. Paul, MN, USA
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Hay WT, Anderson JA, Garvin DF, McCormick SP, Vaughan MM. Fhb1 disease resistance QTL does not exacerbate wheat grain protein loss at elevated CO 2. Front Plant Sci 2022; 13:1034406. [PMID: 36518513 PMCID: PMC9742602 DOI: 10.3389/fpls.2022.1034406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
Fusarium head blight, a devastating cereal crop disease, can cause significant yield losses and contaminate grain with hazardous fungal toxins. Concerningly, recent evidence indicates that substantial grain protein content loss is likely to occur in wheat that is moderately resistant to head blight when it is grown at elevated CO2. Although wheat breeders in North America utilize a number of resistance sources and genes to reduce pathogen damage, the Fhb1 gene is widely deployed. To determine whether Fhb1 is associated with the protein content loss at elevated CO2, twelve near-isogenic spring wheat lines from either a susceptible or moderately susceptible genetic background, and with, or without the Fhb1 QTL, were grown at ambient and elevated CO2 conditions. The near-isogenic lines were evaluated for differences in physiology, productivity, and grain protein content. Our results showed that the Fhb1 QTL did not have any significant effect on plant growth, development, yield, or grain protein content at ambient or elevated CO2. Therefore, other factors in the moderately susceptible wheat genetic background are likely responsible for the more severe grain protein loss at elevated CO2.
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Affiliation(s)
- William T. Hay
- Mycotoxin Prevention and Applied Microbiology Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, USDA, Peoria, IL, United States
| | - James A. Anderson
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - David F. Garvin
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - Susan P. McCormick
- Mycotoxin Prevention and Applied Microbiology Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, USDA, Peoria, IL, United States
| | - Martha M. Vaughan
- Mycotoxin Prevention and Applied Microbiology Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, USDA, Peoria, IL, United States
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Anderson JA, McCradden MD, Stephenson EA. Response to Open Peer Commentaries: On Social Harms, Big Tech, and Institutional Accountability. Am J Bioeth 2022; 22:W6-W8. [PMID: 35593914 DOI: 10.1080/15265161.2022.2075977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
| | - Melissa D McCradden
- The Hospital for Sick Children
- Peter Gilgan Centre for Research and Learning
- Dalla Lana School of Public Health
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Tamang BG, Monnens D, Anderson JA, Steffenson BJ, Sadok W. The genetic basis of transpiration sensitivity to vapor pressure deficit in wheat. Physiol Plant 2022; 174:e13752. [PMID: 36281842 PMCID: PMC9543498 DOI: 10.1111/ppl.13752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/12/2022] [Accepted: 07/26/2022] [Indexed: 05/10/2023]
Abstract
Genetic manipulation of whole-plant transpiration rate (TR) response to increasing atmospheric vapor pressure deficit (VPD) is a promising approach for crop adaptation to various drought regimes under current and future climates. Genotypes with a non-linear TR response to VPD are expected to achieve yield gains under terminal drought, thanks to a water conservation strategy, while those with a linear response exhibit a consumptive strategy that is more adequate for well-watered or transient-drought environments. In wheat, previous efforts indicated that TR has a genetic basis under naturally fluctuating conditions, but because TR is responsive to variation in temperature, photosynthetically active radiation, and evaporative demand, the genetic basis of its response VPD per se has never been isolated. To address this, we developed a controlled-environment gravimetric phenotyping approach where we imposed VPD regimes independent from other confounding environmental variables. We screened three nested association mapping populations totaling 150 lines, three times over a 3-year period. The resulting dataset, based on phenotyping nearly 1400 plants, enabled constructing 63-point response curves for each genotype, which were subjected to a genome-wide association study. The analysis revealed a hotspot for TR response to VPD on chromosome 5A, with SNPs explaining up to 17% of the phenotypic variance. The key SNPs were found in haploblocks that are enriched in membrane-associated genes, consistent with the hypothesized physiological determinants of the trait. These results indicate a promising potential for identifying new alleles and designing next-gen wheat cultivars that are better adapted to current and future drought regimes.
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Affiliation(s)
- Bishal G. Tamang
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMinnesotaUSA
| | - Daniel Monnens
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMinnesotaUSA
| | - James A. Anderson
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMinnesotaUSA
| | | | - Walid Sadok
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMinnesotaUSA
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Tandukar Z, Chopra R, Frels K, Heim B, Marks MD, Anderson JA. Genetic dissection of seed characteristics in field pennycress via genome-wide association mapping studies. Plant Genome 2022; 15:e20211. [PMID: 35484973 DOI: 10.1002/tpg2.20211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Field pennycress (Thlaspi arvense L.) is a new winter annual cash cover crop with high oil content and seed yield, excellent winter hardiness, early maturation, and resistance to most pests and diseases. It provides living cover on fallow croplands between summer seasons, and in doing so reduces nutrient leaching into water sources, mitigates soil erosion, and suppresses weed growth. The first ever genome-wide association study (GWAS) was conducted on a pennycress diversity panel to identify marker trait associations with important seed size and composition related traits. The entire population was phenotyped in three total environments over 2 yr, and seed area, length, width, thousand grain weight, total oil, and total protein were measured post-harvest with specialized high-throughput imaging and near-infrared spectroscopy. Basic unbiased linear prediction values were calculated for each trait. Seed size traits tended to have higher entry mean reliabilities (0.76-0.79) compared with oil content (0.51) and protein content (0.37). Genotyping-by-sequencing identified 33,606 high quality genome-wide single nucleotide polymorphism (SNPs) that were coupled with phenotypic data to perform GWAS for seed area, length, width, thousand grain weight, total oil, and total protein content. Fifty-nine total marker-trait associations were identified revealing genomic regions controlling each trait. The significant SNPs explained 0.06-0.18% of the total variance for that trait in our population. A list of candidate genes was identified based on their functional annotations and characterization in other species. Our results confirm that GWAS is an efficient strategy to identify significant marker-trait associations that can be incorporated into marker-assisted selection pipelines to accelerate pennycress breeding progress.
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Affiliation(s)
- Zenith Tandukar
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, USA
| | - Ratan Chopra
- Dep. of Plant and Microbial Biology, Univ. of Minnesota, Saint Paul, MN, USA
| | - Katherine Frels
- Dep. of Agronomy and Horticulture, Univ. of Nebraska, Lincoln, NE, USA
| | - Brett Heim
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, USA
| | - M David Marks
- Dep. of Plant and Microbial Biology, Univ. of Minnesota, Saint Paul, MN, USA
| | - James A Anderson
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, USA
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13
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Nunn A, Rodríguez‐Arévalo I, Tandukar Z, Frels K, Contreras‐Garrido A, Carbonell‐Bejerano P, Zhang P, Ramos Cruz D, Jandrasits K, Lanz C, Brusa A, Mirouze M, Dorn K, Galbraith DW, Jarvis BA, Sedbrook JC, Wyse DL, Otto C, Langenberger D, Stadler PF, Weigel D, Marks MD, Anderson JA, Becker C, Chopra R. Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates. Plant Biotechnol J 2022; 20:944-963. [PMID: 34990041 PMCID: PMC9055812 DOI: 10.1111/pbi.13775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/28/2021] [Accepted: 12/23/2021] [Indexed: 05/20/2023]
Abstract
Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high-quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe non-coding RNAs, pseudogenes and transposable elements, and highlight tissue-specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome-wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.
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Affiliation(s)
- Adam Nunn
- ecSeq Bioinformatics GmbHLeipzigGermany
- Department of Computer ScienceLeipzig UniversityLeipzigGermany
| | - Isaac Rodríguez‐Arévalo
- GeneticsFaculty of BiologyLudwig Maximilians UniversityMartinsriedGermany
- Gregor Mendel Institute of Molecular Plant Biology GmbHAustrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC)ViennaAustria
| | - Zenith Tandukar
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | - Katherine Frels
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNEUSA
| | | | | | - Panpan Zhang
- Institut de Recherche pour le DéveloppementUMR232 DIADEMontpellierFrance
- Laboratory of Plant Genome and DevelopmentUniversity of PerpignanPerpignanFrance
| | - Daniela Ramos Cruz
- GeneticsFaculty of BiologyLudwig Maximilians UniversityMartinsriedGermany
- Gregor Mendel Institute of Molecular Plant Biology GmbHAustrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC)ViennaAustria
| | - Katharina Jandrasits
- GeneticsFaculty of BiologyLudwig Maximilians UniversityMartinsriedGermany
- Gregor Mendel Institute of Molecular Plant Biology GmbHAustrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC)ViennaAustria
| | - Christa Lanz
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| | - Anthony Brusa
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | - Marie Mirouze
- Institut de Recherche pour le DéveloppementUMR232 DIADEMontpellierFrance
- Laboratory of Plant Genome and DevelopmentUniversity of PerpignanPerpignanFrance
| | - Kevin Dorn
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMNUSA
- USDA‐ARSSoil Management and Sugarbeet ResearchFort CollinsCOUSA
| | - David W Galbraith
- BIO5 InstituteArizona Cancer CenterDepartment of Biomedical EngineeringUniversity of ArizonaSchool of Plant SciencesTucsonAZUSA
| | - Brice A. Jarvis
- School of Biological SciencesIllinois State UniversityNormalILUSA
| | - John C. Sedbrook
- School of Biological SciencesIllinois State UniversityNormalILUSA
| | - Donald L. Wyse
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | | | | | - Peter F. Stadler
- Department of Computer ScienceLeipzig UniversityLeipzigGermany
- Max Planck Institute for Mathematics in the SciencesLeipzigGermany
| | - Detlef Weigel
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| | - M. David Marks
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMNUSA
| | - James A. Anderson
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | - Claude Becker
- GeneticsFaculty of BiologyLudwig Maximilians UniversityMartinsriedGermany
- Gregor Mendel Institute of Molecular Plant Biology GmbHAustrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC)ViennaAustria
| | - Ratan Chopra
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMNUSA
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14
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Helmers AJ, Anderson JA, Kirsch RE. Caregiver COVID-19 Vaccination Status in Pediatric Hospitals-Ethics of Exclusion. JAMA Pediatr 2022; 176:441-442. [PMID: 35226057 DOI: 10.1001/jamapediatrics.2021.6582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Andrew J Helmers
- Department of Critical Care Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Bioethics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - James A Anderson
- Department of Bioethics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Roxanne E Kirsch
- Department of Critical Care Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Bioethics, The Hospital for Sick Children, Toronto, Ontario, Canada
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15
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McCradden MD, Anderson JA, A Stephenson E, Drysdale E, Erdman L, Goldenberg A, Zlotnik Shaul R. A Research Ethics Framework for the Clinical Translation of Healthcare Machine Learning. Am J Bioeth 2022; 22:8-22. [PMID: 35048782 DOI: 10.1080/15265161.2021.2013977] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The application of artificial intelligence and machine learning (ML) technologies in healthcare have immense potential to improve the care of patients. While there are some emerging practices surrounding responsible ML as well as regulatory frameworks, the traditional role of research ethics oversight has been relatively unexplored regarding its relevance for clinical ML. In this paper, we provide a comprehensive research ethics framework that can apply to the systematic inquiry of ML research across its development cycle. The pathway consists of three stages: (1) exploratory, hypothesis-generating data access; (2) silent period evaluation; (3) prospective clinical evaluation. We connect each stage to its literature and ethical justification and suggest adaptations to traditional paradigms to suit ML while maintaining ethical rigor and the protection of individuals. This pathway can accommodate a multitude of research designs from observational to controlled trials, and the stages can apply individually to a variety of ML applications.
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Affiliation(s)
- Melissa D McCradden
- Department of Bioethics, The Hospital for Sick Children
- Genetics and Genome Biology, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning
- Division of Clinical & Public Health, Dalla Lana School of Public Health
| | - James A Anderson
- Department of Bioethics, The Hospital for Sick Children
- Institute for Health Management Policy, & Evaluation, University of Toronto
| | - Elizabeth A Stephenson
- Labatt Family Heart Centre, The Hospital for Sick Children
- Department of Pediatrics, The Hospital for Sick Children
| | - Erik Drysdale
- Genetics and Genome Biology, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning
| | - Lauren Erdman
- Genetics and Genome Biology, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning
- Vector Institute
- Department of Computer Science, University of Toronto
| | - Anna Goldenberg
- Department of Bioethics, The Hospital for Sick Children
- Vector Institute
- Department of Computer Science, University of Toronto
- CIFAR
| | - Randi Zlotnik Shaul
- Department of Bioethics, The Hospital for Sick Children
- Department of Pediatrics, The Hospital for Sick Children
- Child Health Evaluative Sciences, The Hospital for Sick Children
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16
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Bajgain P, Li C, Anderson JA. Genome-wide association mapping and genomic prediction for kernel color traits in intermediate wheatgrass (Thinopyrum intermedium). BMC Plant Biol 2022; 22:218. [PMID: 35477400 PMCID: PMC9047355 DOI: 10.1186/s12870-022-03616-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Intermediate wheatgrass (IWG) is a novel perennial grain crop currently undergoing domestication. It offers important ecosystem benefits while producing grain suitable for human consumption. Several aspects of plant biology and genetic control are yet to be studied in this new crop. To understand trait behavior and genetic characterization of kernel color in IWG breeding germplasm from the University of Minnesota was evaluated for the CIELAB components (L*, a*, b*) and visual differences. Trait values were used in a genome-wide association scan to reveal genomic regions controlling IWG's kernel color. The usability of genomic prediction in predicting kernel color traits was also evaluated using a four-fold cross validation method. RESULTS A wide phenotypic variation was observed for all four kernel color traits with pairwise trait correlations ranging from - 0.85 to 0.27. Medium to high estimates of broad sense trait heritabilities were observed and ranged from 0.41 to 0.78. A genome-wide association scan with single SNP markers detected 20 significant marker-trait associations in 9 chromosomes and 23 associations in 10 chromosomes using multi-allelic haplotype blocks. Four of the 20 significant SNP markers and six of the 23 significant haplotype blocks were common between two or more traits. Evaluation of genomic prediction of kernel color traits revealed the visual score to have highest mean predictive ability (r2 = 0.53); r2 for the CIELAB traits ranged from 0.29-0.33. A search for candidate genes led to detection of seven IWG genes in strong alignment with MYB36 transcription factors from other cereal crops of the Triticeae tribe. Three of these seven IWG genes had moderate similarities with R-A1, R-B1, and R-D1, the three genes that control grain color in wheat. CONCLUSIONS We characterized the distribution of kernel color in IWG for the first time, which revealed a broad phenotypic diversity in an elite breeding germplasm. Identification of genetic loci controlling the trait and a proof-of-concept that genomic selection might be useful in selecting genotypes of interest could help accelerate the breeding of this novel crop towards specific end-use.
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Affiliation(s)
- Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
| | - Catherine Li
- Department of Crop Sciences, University of Illinois, Urbana-Champaign, IL, 61801, USA
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
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17
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Bajgain P, Brandvain Y, Anderson JA. Influence of Pollen Dispersal and Mating Pattern in Domestication of Intermediate Wheatgrass, a Novel Perennial Food Crop. Front Plant Sci 2022; 13:871130. [PMID: 35574146 PMCID: PMC9096613 DOI: 10.3389/fpls.2022.871130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Intermediate wheatgrass (IWG) is a perennial forage grass that is currently being domesticated as a grain crop. It is a primarily wind-pollinated outcrossing species and expresses severe inbreeding depression when self-pollinated. Characterization of pollen dispersal, mating parameters, and change in genetic diversity due to pollen movement is currently lacking in IWG. In this study, we examined pollen dispersal in an IWG selection nursery by evaluating 846 progeny from 15 mother plants and traced their parentage to 374 fathers. A set of 2,500 genomic loci was used to characterize the population. We assigned paternity to 769 (91%) progeny and the average number of fathers per mother plant was 37, from an average of 56 progeny examined per mother. An extensive number (80%) of pollination events occurred within 10 m of the mother plants. Pollination success was not correlated with trait attributes of the paternal genotypes. Mating system analysis confirmed that IWG is highly outcrossing and inbreeding was virtually absent. Neither genetic diversity nor the genome-estimated trait values of progeny were significantly affected by pollinator distance. The distance of pollinator in an IWG breeding nursery therefore was not found to be a major contributor in maintaining genetic diversity. These findings reveal the pollen dispersal model in IWG for the first time and its effect on genetic diversity, which will be valuable in designing future IWG breeding populations. Information generated and discussed in this study could be applied in understanding gene flow and genetic diversity of other open-pollinated species.
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Affiliation(s)
- Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Yaniv Brandvain
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, United States
| | - James A. Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
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18
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Whitney K, Gracia-Gomez G, Anderson JA, Simsek S. Time Course Metabolite Profiling of Fusarium Head Blight-Infected Hard Red Spring Wheat Using Ultra-High-Performance Liquid Chromatography Coupled with Quadrupole Time of Flight/MS. J Agric Food Chem 2022; 70:4152-4163. [PMID: 35298172 DOI: 10.1021/acs.jafc.1c08374] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Wheat is an important food crop, yet its value is reduced by fungal infections (ex. Fusarium graminearum). Metabolite profiling is a useful tool for explaining resistance mechanisms. By analyzing near-isogenic lines (NILs) with contrasting Fhb1 alleles and three wheat varieties, a time course resulting in 61 relevant metabolites was studied. The presence of one metabolite as resistant related constitutive late in the time course was detected. Results confirm the presence of hydroxycinnamic acid amides conjugated with polyamine derivatives (hydroxycinnamic acid amides, HCAAs), which have been shown to induce thickening of cell walls. These compounds are shared by resistant and susceptible genotypes with no difference in intensities but vary in time as early- or late-occurring, suggesting that for the NIL studied here, HCAAs were a normal part of the host reaction. Overall, metabolites synthesized as a result of infection were observed regardless of susceptibility but occurred at different times after infection.
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Affiliation(s)
- Kristin Whitney
- Department of Food Science & Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Gerardo Gracia-Gomez
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58108, United States
| | - James A Anderson
- Department of Agronomy & Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, Minnesota 55108, United States
| | - Senay Simsek
- Department of Food Science & Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, Indiana 47907, United States
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19
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Potts L, Douglas A, Perez Calderon LJ, Anderson JA, Witte U, Prosser JI, Gubry-Rangin C. Chronic Environmental Perturbation Influences Microbial Community Assembly Patterns. Environ Sci Technol 2022; 56:2300-2311. [PMID: 35103467 PMCID: PMC9007448 DOI: 10.1021/acs.est.1c05106] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Acute environmental perturbations are reported to induce deterministic microbial community assembly, while it is hypothesized that chronic perturbations promote development of alternative stable states. Such acute or chronic perturbations strongly impact on the pre-adaptation capacity to the perturbation. To determine the importance of the level of microbial pre-adaptation and the community assembly processes following acute or chronic perturbations in the context of hydrocarbon contamination, a model system of pristine and polluted (hydrocarbon-contaminated) sediments was incubated in the absence or presence (discrete or repeated) of hydrocarbon amendment. The community structure of the pristine sediments changed significantly following acute perturbation, with selection of different phylotypes not initially detectable. Conversely, historically polluted sediments maintained the initial community structure, and the historical legacy effect of chronic pollution likely facilitated community stability. An alternative stable state was also reached in the pristine sediments following chronic perturbation, further demonstrating the existence of a legacy effect. Finally, ecosystem functional resilience was demonstrated through occurrence of hydrocarbon degradation by different communities in the tested sites, but the legacy effect of perturbation also strongly influenced the biotic response. This study therefore demonstrates the importance of perturbation chronicity on microbial community assembly processes and reveals ecosystem functional resilience following environmental perturbation.
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Affiliation(s)
- Lloyd
D. Potts
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Alex Douglas
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Luis J. Perez Calderon
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James A. Anderson
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Ursula Witte
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James I. Prosser
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Cécile Gubry-Rangin
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
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20
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Rauf Y, Bajgain P, Rouse MN, Khanzada KA, Bhavani S, Huerta-Espino J, Singh RP, Imtiaz M, Anderson JA. Molecular Characterization of Genomic Regions for Adult Plant Resistance to Stem Rust in a Spring Wheat Mapping Population. Plant Dis 2022; 106:439-450. [PMID: 34353123 DOI: 10.1094/pdis-03-21-0672-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Adult plant resistance (APR) to wheat stem rust has been one of the approaches for resistance breeding since the evolution of the Ug99 race group and other races. This study was conducted to dissect and understand the genetic basis of APR to stem rust in spring wheat line 'Copio'. A total of 176 recombinant inbred lines (RILs) from the cross of susceptible parent 'Apav' with Copio were phenotyped for stem rust resistance in six environments. Composite interval mapping using 762 genotyping-by-sequencing markers identified 16 genomic regions conferring stem rust resistance. Assays with gene-linked molecular markers revealed that Copio carried known APR genes Sr2 and Lr46/Yr29/Sr58 in addition to the 2NS/2AS translocation that harbors race-specific genes Sr38, Lr37, and Yr17. Three quantitative trait loci (QTLs) were mapped on chromosomes 2B, two QTLs on chromosomes 3A, 3B, and 6A each, and one QTL on each of chromosomes 2A, 1B, 2D, 4B, 5D, 6D, and 7A. The QTL QSr.umn.5D is potentially a new resistance gene and contributed to quantitative resistance in Copio. The RILs with allelic combinations of Sr2, Sr38, and Sr58 had 27 to 39% less stem rust coefficient of infection in all field environments compared with RILs with none of these genes, and this gene combination was most effective in the U.S. environments. We conclude that Copio carries several genes that provide both race-specific and non-race-specific resistance to diverse races of stem rust fungus and can be used by breeding programs in pyramiding other effective genes to develop durable resistance in wheat.
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Affiliation(s)
- Yahya Rauf
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Matthew N Rouse
- Cereal Disease Lab, United States Department of Agriculture, St. Paul, MN 55108, U.S.A
| | - Khalil A Khanzada
- Cereal Disease Research Institute, Pakistan Agricultural Research Council, University of Karachi 75270, Pakistan
| | - Sridhar Bhavani
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, 06600, Mexico
| | - Julio Huerta-Espino
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, 06600, Mexico
| | - Ravi P Singh
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, 06600, Mexico
| | - Muhammad Imtiaz
- Global Wheat Program, International Maize and Wheat Improvement Center, National Agricultural Research Center, Islamabad 44000, Pakistan
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
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21
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Altendorf KR, DeHaan LR, Larson SR, Anderson JA. QTL for seed shattering and threshability in intermediate wheatgrass align closely with well-studied orthologs from wheat, barley, and rice. Plant Genome 2021; 14:e20145. [PMID: 34626160 DOI: 10.1002/tpg2.20145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Perennial grain crops have the potential to improve agricultural sustainability but few existing species produce sufficient grain yield to be economically viable. The outcrossing, allohexaploid, and perennial forage species intermediate wheatgrass (IWG) [Thinopyrum intermedium (Host) Barkworth & D. R. Dewey] has shown promise in undergoing direct domestication as a perennial grain crop using phenotypic and genomic selection. However, decades of selection will be required to achieve yields on par with annual small-grain crops. Marker-aided selection could accelerate progress if important genomic regions associated with domestication were identified. Here we use the IWG nested association mapping (NAM) population, with 1,168 F1 progeny across 10 families to dissect the genetic control of brittle rachis, floret shattering, and threshability. We used a genome-wide association study (GWAS) with 8,003 single nucleotide polymorphism (SNP) markers and linkage mapping-both within-family and combined across families-with a robust phenotypic dataset collected from four unique year-by-location combinations. A total of 29 quantitative trait loci (QTL) using GWAS and 20 using the combined linkage analysis were detected, and most large-effect QTL were in common across the two analysis methods. We reveal that the genetic control of these traits in IWG is complex, with significant QTL across multiple chromosomes, sometimes within and across homoeologous groups and effects that vary depending on the family. In some cases, these QTL align within 216 bp to 31 Mbp of BLAST hits for known domestication genes in related species and may serve as precise targets of selection and directions for further study to advance the domestication of IWG.
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Affiliation(s)
- Kayla R Altendorf
- USDA-ARS Forage Seed and Cereal Research Unit, Prosser, WA, 99350, USA
| | | | - Steve R Larson
- USDA-ARS Forage & Range Research Lab, Logan, UT, 84322, USA
| | - James A Anderson
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, St. Paul, MN, 55108, USA
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22
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Pérez-Cadenas M, Asedegbega-Nieto E, Carter J, Anderson JA, Rodríguez-Ramos I, Guerrero-Ruiz A. Study of the Interaction of an Iron Phthalocyanine Complex over Surface Modified Carbon Nanotubes. Materials (Basel) 2021; 14:ma14154067. [PMID: 34361260 PMCID: PMC8347569 DOI: 10.3390/ma14154067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022]
Abstract
Carbon nanotubes (CNT) were prepared by a modified chemical vapor deposition (CVD) method. The synthesized carbon materials were treated with acidic and basic solutions in order to introduce certain surface functional groups, mainly containing oxygen (OCNT) or amine (ACNT) species. These modified CNTs (OCNT and ACNT) as well as the originally prepared CNT were reacted with a non-ionic Fe complex, Iron (II) Phthalocyanine, and three composites were obtained. The amount of metal complex introduced in each case and the interaction between the complex and the CNT materials were studied with the aid of various characterization techniques such as TGA, XRD, and XPS. The results obtained in these experiments all indicated that the interaction between the complex and the CNT was greatly affected by the functionalization of the latter.
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Affiliation(s)
- María Pérez-Cadenas
- Departamento Química Inorgánica y Técnica, Facultad de Ciencias UNED, Paseo Senda del Rey No. 9, 28040 Madrid, Spain; (E.A.-N.); (A.G.-R.)
- Correspondence:
| | - Esther Asedegbega-Nieto
- Departamento Química Inorgánica y Técnica, Facultad de Ciencias UNED, Paseo Senda del Rey No. 9, 28040 Madrid, Spain; (E.A.-N.); (A.G.-R.)
| | - Jonathan Carter
- Surface Chemistry and Catalysis Group, Department Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK; (J.C.); (J.A.A.)
| | - James A. Anderson
- Surface Chemistry and Catalysis Group, Department Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK; (J.C.); (J.A.A.)
| | | | - Antonio Guerrero-Ruiz
- Departamento Química Inorgánica y Técnica, Facultad de Ciencias UNED, Paseo Senda del Rey No. 9, 28040 Madrid, Spain; (E.A.-N.); (A.G.-R.)
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Altendorf KR, Larson SR, DeHaan LR, Crain J, Neyhart J, Dorn KM, Anderson JA. Nested association mapping reveals the genetic architecture of spike emergence and anthesis timing in intermediate wheatgrass. G3 (Bethesda) 2021; 11:6124305. [PMID: 33890617 PMCID: PMC8063084 DOI: 10.1093/g3journal/jkab025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/07/2021] [Indexed: 11/16/2022]
Abstract
Intermediate wheatgrass (Thinopyrum intermedium) is an outcrossing, cool season grass species currently undergoing direct domestication as a perennial grain crop. Though many traits are selection targets, understanding the genetic architecture of those important for local adaptation may accelerate the domestication process. Nested association mapping (NAM) has proven useful in dissecting the genetic control of agronomic traits many crop species, but its utility in primarily outcrossing, perennial species has yet to be demonstrated. Here, we introduce an intermediate wheatgrass NAM population developed by crossing ten phenotypically divergent donor parents to an adapted common parent in a reciprocal manner, yielding 1,168 F1 progeny from 10 families. Using genotyping by sequencing, we identified 8,003 SNP markers and developed a population-specific consensus genetic map with 3,144 markers across 21 linkage groups. Using both genomewide association mapping and linkage mapping combined across and within families, we characterized the genetic control of flowering time. In the analysis of two measures of maturity across four separate environments, we detected as many as 75 significant QTL, many of which correspond to the same regions in both analysis methods across 11 chromosomes. The results demonstrate a complex genetic control that is variable across years, locations, traits, and within families. The methods were effective at detecting previously identified QTL, as well as new QTL that align closely to the well-characterized flowering time orthologs from barley, including Ppd-H1 and Constans. Our results demonstrate the utility of the NAM population for understanding the genetic control of flowering time and its potential for application to other traits of interest.
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Affiliation(s)
- Kayla R Altendorf
- USDA-ARS, Forage Seed and Cereal Research Unit, Irrigated Agriculture Research and Extension Center, Prosser, WA 99350, USA
| | | | - Lee R DeHaan
- USDA-ARS, Forage Range and Research Lab, Utah State University, Logan, UT 84322, USA
| | - Jared Crain
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Jeff Neyhart
- GEMS Informatics Initiative, University of Minnesota, St. Paul, MN 55108, USA
| | - Kevin M Dorn
- USDA-ARS, Soil Management and Sugarbeet Research, Fort Collins, CO 80526, USA
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
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Abstract
AC Taber is a hard red spring wheat cultivar that has had long-lasting resistance to the leaf rust fungus Puccinia triticina. The objective of this study was to determine the chromosome location of the leaf rust resistance genes in AC Taber. The leaf rust-susceptible cultivar Thatcher was crossed with AC Taber to develop an F6 recombinant inbred line (RIL) population. The RILs and parents were evaluated for segregation of leaf rust resistance in five field plot tests and in two seedling tests to race BBBDB of P. triticina. A genetic map of the RIL population was developed using 90,000 single nucleotide polymorphism markers with the Illumina Infinium iSelect 90K wheat bead array. Quantitative trait loci (QTLs) with significant effects for lower leaf rust severity in the field plot tests were found on chromosomes 2BS and 3BS. The same QTLs also had significant effects for lower infection type in seedlings to leaf rust race BBBDB. The gene on 2BS was the adult plant resistance gene Lr13, and the gene on 3BS mapped to the same region as the adult plant resistance gene Lr74 and other QTLs for leaf rust resistance. Kompetitive allele-specific PCR assay markers linked to the 2BS and 3BS regions were developed and should be useful for marker-based selection of these genes.
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Affiliation(s)
- J A Kolmer
- Cereal Disease Laboratory, U.S. Department of Agriculture Agricultural Research Service, St. Paul, MN 55108
| | - M K Turner
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
| | - M N Rouse
- Cereal Disease Laboratory, U.S. Department of Agriculture Agricultural Research Service, St. Paul, MN 55108
| | - J A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
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McCradden MD, Joshi S, Mazwi M, Anderson JA. Ethical limitations of algorithmic fairness solutions in health care machine learning. Lancet Digit Health 2021; 2:e221-e223. [PMID: 33328054 DOI: 10.1016/s2589-7500(20)30065-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 01/14/2023]
Affiliation(s)
- Melissa D McCradden
- Department of Bioethics, The Hospital for Sick Children, Toronto, ON, Canada.
| | - Shalmali Joshi
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada
| | - Mjaye Mazwi
- Department of Critical Care Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - James A Anderson
- Department of Bioethics, The Hospital for Sick Children, Toronto, ON, Canada
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McCradden MD, Joshi S, Anderson JA, Mazwi M, Goldenberg A, Zlotnik Shaul R. Patient safety and quality improvement: Ethical principles for a regulatory approach to bias in healthcare machine learning. J Am Med Inform Assoc 2020; 27:2024-2027. [PMID: 32585698 PMCID: PMC7727331 DOI: 10.1093/jamia/ocaa085] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/01/2020] [Indexed: 12/27/2022] Open
Abstract
Accumulating evidence demonstrates the impact of bias that reflects social inequality on the performance of machine learning (ML) models in health care. Given their intended placement within healthcare decision making more broadly, ML tools require attention to adequately quantify the impact of bias and reduce its potential to exacerbate inequalities. We suggest that taking a patient safety and quality improvement approach to bias can support the quantification of bias-related effects on ML. Drawing from the ethical principles underpinning these approaches, we argue that patient safety and quality improvement lenses support the quantification of relevant performance metrics, in order to minimize harm while promoting accountability, justice, and transparency. We identify specific methods for operationalizing these principles with the goal of attending to bias to support better decision making in light of controllable and uncontrollable factors.
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Affiliation(s)
- Melissa D McCradden
- Bioethics Department, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - James A Anderson
- Bioethics Department, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute for Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
- Joint Centre for Bioethics, University of Toronto, Toronto, Ontario, Canada
| | - Mjaye Mazwi
- Department of Critical Care Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anna Goldenberg
- Vector Institute, Toronto, Ontario, Canada
- Genetics and Genome Biology, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- CIFAR, Toronto, Ontario, Canada
| | - Randi Zlotnik Shaul
- Bioethics Department, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Child Health Evaluative Sciences, The Hospital for Sick Children, Peter Gilgan Centre for Research, Toronto, Ontario, Canada
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Sallam AH, Manan F, Bajgain P, Martin M, Szinyei T, Conley E, Brown-Guedira G, Muehlbauer GJ, Anderson JA, Steffenson BJ. Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat. Plant Genome 2020; 13:e20051. [PMID: 33217209 DOI: 10.1002/tpg2.20051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
Germplasm collections are rich sources of genetic variation to improve crops for many valuable traits. Nested association mapping (NAM) populations can overcome the limitations of genome-wide association studies (GWAS) in germplasm collections by reducing the effect of population structure. We exploited the genetic diversity of the USDA-ARS wheat (Triticum aestivum L.) core collection by developing the Spring Wheat Multiparent Introgression Population (SWMIP). To develop this population, twenty-five core parents were crossed and backcrossed to the Minnesota spring wheat cultivar RB07. The NAM population and 26 founder parents were genotyped using genotyping-by-sequencing and phenotyped for heading date, height, test weight, and grain protein content. After quality control, 20,312 markers with physical map positions were generated for 2,038 recombinant inbred lines (RILs). The number of RILs in each family varied between 58 and 96. Three GWAS models were utilized for quantitative trait loci (QTL) detection and accounted for known family stratification, genetic kinship, and both covariates. GWAS was performed on the whole population and also by bootstrap sampling of an equal number of RILs from each family. Greater power of QTL detection was achieved by treating families equally through bootstrapping. In total 16, 15, 12, and 13 marker-trait associations (MTAs) were identified for heading date, height, test weight, and grain protein content, respectively. Some of these MTAs were coincident with major genes known to control the traits, but others were novel and contributed by the wheat core parents. The SWMIP will be a valuable source of genetic variation for spring wheat breeding.
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Affiliation(s)
- Ahmad H Sallam
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Fazal Manan
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Matthew Martin
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Tamas Szinyei
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Emily Conley
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
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28
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McCradden MD, Anderson JA, Zlotnik Shaul R. Accountability in the Machine Learning Pipeline: The Critical Role of Research Ethics Oversight. Am J Bioeth 2020; 20:40-42. [PMID: 33103980 DOI: 10.1080/15265161.2020.1820111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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Affiliation(s)
| | | | - James A Anderson
- Department of Bioethics, The Hospital for Sick Children, Toronto, Canada
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Byrd KB, Lorenz AA, Anderson JA, Wallace CSA, Moore-O'Leary KA, Isola J, Ortega R, Reiter ME. Quantifying drought's influence on moist soil seed vegetation in California's Central Valley through remote sensing. Ecol Appl 2020; 30:e02153. [PMID: 32348601 DOI: 10.1002/eap.2153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/20/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
California's Central Valley, USA is a critical component of the Pacific Flyway despite loss of more than 90% of its wetlands. Moist soil seed (MSS) wetland plants are now produced by mimicking seasonal flooding in managed wetlands to provide an essential food resource for waterfowl. Managers need MSS plant area and productivity estimates to support waterfowl conservation, yet this remains unknown at the landscape scale. Also the effects of recent drought on MSS plants have not been quantified. We generated Landsat-derived estimates of extents and productivity (seed yield or its proxy, the green chlorophyll index) of major MSS plants including watergrass (Echinochloa crusgalli) and smartweed (Polygonum spp.) (WGSW), and swamp timothy (Crypsis schoenoides) (ST) in all Central Valley managed wetlands from 2007 to 2017. We tested the effects of water year, land ownership and region on plant area and productivity with a multifactor nested analysis of variance. For the San Joaquin Valley, we explored the association between water year and water supply, and we developed metrics to support management decisions. MSS plant area maps were based on a support vector machine classification of Landsat phenology metrics (2017 map overall accuracy: 89%). ST productivity maps were created with a linear regression model of seed yield (n = 68, R2 = 0.53, normalized RMSE = 10.5%). The Central Valley-wide estimated area for ST in 2017 was 32,369 ha (29,845-34,893 ha 95% CI), and 13,012 ha (11,628-14,396 ha) for WGSW. Mean ST seed yield ranged from 577 kg/ha in the Delta Basin to 365 kg/ha in the San Joaquin Basin. WGSW area and ST seed yield decreased while ST area increased in critical drought years compared to normal water years (Scheffe's test, P < 0.05). Greatest ST area increases occurred in the Sacramento Valley (~75%). Voluntary water deliveries increased in normal water years, and ST seed yield increased with water supply. Z scores of ST seed yield can be used to evaluate wetland performance and aid resource allocation decisions. Updated maps will support habitat monitoring, conservation planning and water management in future years, which are likely to face greater uncertainty in water availability with climate change.
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Affiliation(s)
- Kristin B Byrd
- USGS Western Geographic Science Center, P.O. Box 158, Moffett Field, California, 94035, USA
| | - Austen A Lorenz
- USGS Western Geographic Science Center, P.O. Box 158, Moffett Field, California, 94035, USA
- USGS Western Ecological Research Center, 800 Business Park Drive, Suite D, Dixon, California, 95620, USA
| | - James A Anderson
- USGS Western Geographic Science Center, P.O. Box 158, Moffett Field, California, 94035, USA
- Golder Associates Inc., 18300 NE Union Hill Road #200, Redmond, Washington, 98052, USA
| | - Cynthia S A Wallace
- USGS Western Geographic Science Center, 520 Park Avenue, ENRB Building, Room 106, Tucson, Arizona, 85719, USA
| | - Kara A Moore-O'Leary
- Pacific Southwest Region, Inventory and Monitoring Program, U.S. Fish and Wildlife Service, 3020 State University Drive East, Sacramento, California, 95819, USA
| | - Jennifer Isola
- Sacramento National Wildlife Refuge Complex, U.S. Fish and Wildlife Service, 752 County Road 99W, Willows, California, 95988, USA
| | - Ricardo Ortega
- Grassland Water District, 200 W. Willmott Avenue #5501, Los Banos, California, 93635, USA
| | - Matthew E Reiter
- Point Blue Conservation Science, 3820 Cypress Drive #11, Petaluma, California, 94954, USA
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Sallam AH, Conley E, Prakapenka D, Da Y, Anderson JA. Improving Prediction Accuracy Using Multi-allelic Haplotype Prediction and Training Population Optimization in Wheat. G3 (Bethesda) 2020; 10:2265-2273. [PMID: 32371453 PMCID: PMC7341132 DOI: 10.1534/g3.120.401165] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/29/2020] [Indexed: 02/01/2023]
Abstract
The use of haplotypes may improve the accuracy of genomic prediction over single SNPs because haplotypes can better capture linkage disequilibrium and genomic similarity in different lines and may capture local high-order allelic interactions. Additionally, prediction accuracy could be improved by portraying population structure in the calibration set. A set of 383 advanced lines and cultivars that represent the diversity of the University of Minnesota wheat breeding program was phenotyped for yield, test weight, and protein content and genotyped using the Illumina 90K SNP Assay. Population structure was confirmed using single SNPs. Haplotype blocks of 5, 10, 15, and 20 adjacent markers were constructed for all chromosomes. A multi-allelic haplotype prediction algorithm was implemented and compared with single SNPs using both k-fold cross validation and stratified sampling optimization. After confirming population structure, the stratified sampling improved the predictive ability compared with k-fold cross validation for yield and protein content, but reduced the predictive ability for test weight. In all cases, haplotype predictions outperformed single SNPs. Haplotypes of 15 adjacent markers showed the best improvement in accuracy for all traits; however, this was more pronounced in yield and protein content. The combined use of haplotypes of 15 adjacent markers and training population optimization significantly improved the predictive ability for yield and protein content by 14.3 (four percentage points) and 16.8% (seven percentage points), respectively, compared with using single SNPs and k-fold cross validation. These results emphasize the effectiveness of using haplotypes in genomic selection to increase genetic gain in self-fertilized crops.
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Affiliation(s)
| | - Emily Conley
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
| | | | - Yang Da
- Department of Animal Science, and
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
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33
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Bajgain P, Zhang X, Anderson JA. Dominance and G×E interaction effects improve genomic prediction and genetic gain in intermediate wheatgrass (Thinopyrum intermedium). Plant Genome 2020; 13:e20012. [PMID: 33016625 DOI: 10.1002/tpg2.20012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/30/2020] [Indexed: 06/11/2023]
Abstract
Genomic selection (GS) based recurrent selection methods were developed to accelerate the domestication of intermediate wheatgrass [IWG, Thinopyrum intermedium (Host) Barkworth & D.R. Dewey]. A subset of the breeding population phenotyped at multiple environments is used to train GS models and then predict trait values of the breeding population. In this study, we implemented several GS models that investigated the use of additive and dominance effects and G×E interaction effects to understand how they affected trait predictions in intermediate wheatgrass. We evaluated 451 genotypes from the University of Minnesota IWG breeding program for nine agronomic and domestication traits at two Minnesota locations during 2017-2018. Genet-mean based heritabilities for these traits ranged from 0.34 to 0.77. Using four-fold cross validation, we observed the highest predictive abilities (correlation of 0.67) in models that considered G×E effects. When G×E effects were fitted in GS models, trait predictions improved by 18%, 15%, 20%, and 23% for yield, spike weight, spike length, and free threshing, respectively. Genomic selection models with dominance effects showed only modest increases of up to 3% and were trait-dependent. Cross-environment predictions were better for high heritability traits such as spike length, shatter resistance, free threshing, grain weight, and seed length than traits with low heritability and large environmental variance such as spike weight, grain yield, and seed width. Our results confirm that GS can accelerate IWG domestication by increasing genetic gain per breeding cycle and assist in selection of genotypes with promise of better performance in diverse environments.
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Affiliation(s)
- Prabin Bajgain
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | - Xiaofei Zhang
- The Alliance of Bioversity International and International Center for Tropical Agriculture, Cali, Colombia
| | - James A Anderson
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN, USA
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Hassanein M, Anderson JA. Refusal of animal-derived medical products in a paediatric setting: Ethical issues. Paediatr Child Health 2020; 26:99-102. [PMID: 33747306 DOI: 10.1093/pch/pxz171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/10/2019] [Indexed: 11/13/2022] Open
Abstract
Many medical products that are widely available and commonly used are of animal origin, which can be problematic for those who identify as followers of a particular religion, or have moral commitments or dietary preferences that prohibit or restrict the ingestion of animal products. Given that people are becoming more conscious of the products they ingest, however, we suspect this might be an issue in the foreseeable future, particularly in a multicultural and diverse community like Toronto, Canada. Failure to provide services sensitive to these beliefs and preferences may result in a refusal of medical treatment. In this paper, we aim to identify and explore issues relating to the refusal of animal-derived medical products in paediatric settings by exploring three clinical cases.
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Affiliation(s)
- Maram Hassanein
- Department of Bioethics, The Hospital for Sick Children, Toronto, Ontario
| | - James A Anderson
- Department of Bioethics, The Hospital for Sick Children, Toronto, Ontario.,Institute for Health Policy Management and Evaluation, University of Toronto, Toronto, Ontario.,Joint Centre for Bioethics, University of Toronto, Toronto, Ontario
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Saba T, Burnett JW, Li J, Wang X, Anderson JA, Kechagiopoulos PN, Wang X. Assessing the environmental performance of NADH regeneration methods: A cleaner process using recyclable Pt/Fe3O4 and hydrogen. Catal Today 2020. [DOI: 10.1016/j.cattod.2019.01.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Liu W, Kolmer J, Rynearson S, Chen X, Gao L, Anderson JA, Turner MK, Pumphrey M. Identifying Loci Conferring Resistance to Leaf and Stripe Rusts in a Spring Wheat Population ( Triticum aestivum) via Genome-Wide Association Mapping. Phytopathology 2019; 109:1932-1940. [PMID: 31282284 DOI: 10.1094/phyto-04-19-0143-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A previous genome-wide association study (GWAS) for leaf rust (caused by Puccinia triticina) resistance identified 46 resistance quantitative trait loci (QTL) in an elite spring wheat leaf rust resistance diversity panel. With the aim of characterizing the pleiotropic resistance sources to both leaf rust and stripe rust (caused by P. striiformis f. sp. tritici), stripe rust responses were tested in five U.S. environments at the adult-plant stage and to five U.S. races at the seedling stage. The data revealed balanced phenotypic distributions in this population except for the seedling response to P. striiformis f. sp. tritici race PSTv-37. GWAS for stripe rust resistance discovered a total of 21 QTL significantly associated with all-stage or field resistance on chromosomes 1B, 1D, 2B, 3B, 4A, 5A, 5B, 5D, 6A, 6B, 7A, and 7B. Previously documented pleiotropic resistance genes Yr18/Lr34 and Yr46/Lr67 and tightly linked genes Yr17-Lr37 and Yr30-Sr2-Lr27 were also detected in this population. In addition, stripe rust resistance QTL Yrswp-2B.1, Yrswp-3B, and Yrswp-7B colocated with leaf rust resistance loci 2B_3, 3B_t2, and 7B_4, respectively. Haplotype analysis uncovered that Yrswp-3B and 3B_t2 were either tightly linked genes or the same gene for resistance to both stripe and leaf rusts. Single nucleotide polymorphism markers IWB35950, IWB74350, and IWB72134 for the 3B QTL conferring resistance to both rusts should be useful in incorporating the resistance allele(s) in new cultivars.
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Affiliation(s)
- Weizhen Liu
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430070, China
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - James Kolmer
- Cereal Disease Laboratory, U.S. Department of Agriculture Agricultural Research Service, St. Paul, MN 55108, U.S.A
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55018, U.S.A
| | - Sheri Rynearson
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, U.S. Department of Agriculture Agricultural Research Service, Pullman, WA 99164-6430, U.S.A
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Liangliang Gao
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66502, U.S.A
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - M Kathryn Turner
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
- The Land Institute, Salina, KS 67401, U.S.A
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6430, U.S.A
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Kolmer JA, Bernardo A, Bai G, Hayden MJ, Anderson JA. Thatcher wheat line RL6149 carries Lr64 and a second leaf rust resistance gene on chromosome 1DS. Theor Appl Genet 2019; 132:2809-2814. [PMID: 31280341 DOI: 10.1007/s00122-019-03389-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 06/28/2019] [Indexed: 05/05/2023]
Abstract
The leaf rust resistance gene Lr64 in the Thatcher wheat RL6149 was mapped to chromosome 6AL with SNP and KASP markers and a second leaf rust resistance gene was mapped to chromosome 1DS. RL6149, a near-isogenic line of Thatcher wheat, carries leaf rust resistance gene Lr64 on chromosome arm 6AL. The objective of this study was to develop molecular markers that can be easily used to select wheat lines with Lr64. RL6149 was crossed with Thatcher and F2 plants derived from a single F1 plant were advanced to F6 lines by single seed descent. The 100 F7 recombinant inbred lines (RIL) were inoculated with two races of P.triticina that differed widely for virulence in order to identify resistant and susceptible RIL. Thirty RIL that differed for resistance and the parental lines were genotyped with the 90 K Infinium iSelect single nucleotide polymorphism (SNP) array to find closely linked markers with Lr64. Seven linked SNPs on chromosome arm 6AL were converted into Kompetitive Allele Specific PCR (KASP) markers that were genotyped on the 100 RIL. A genetic linkage map for the seven KASP markers spanned 19.1 cM on chromosome arm 6AL. KASP marker K-IWB59855 was tightly linked to Lr64. A second unexpected gene for leaf rust resistance also segregated in the F7 lines. Four KASP markers that spanned 18.6 cM located the gene on chromosome 1DS. The KASP marker K-IWB38437 was tightly linked to the second leaf rust resistance gene.
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Affiliation(s)
- J A Kolmer
- United States Department of Agriculture - Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, 55108, USA.
| | - A Bernardo
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - G Bai
- United States Department of Agriculture - Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - M J Hayden
- Agriculture Victoria Research, AgriBio, Bundoora, VIC, 3083, Australia
- School of Applied Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - J A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
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Kuzay S, Xu Y, Zhang J, Katz A, Pearce S, Su Z, Fraser M, Anderson JA, Brown-Guedira G, DeWitt N, Peters Haugrud A, Faris JD, Akhunov E, Bai G, Dubcovsky J. Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping. Theor Appl Genet 2019; 132:2689-2705. [PMID: 31254024 PMCID: PMC6708044 DOI: 10.1007/s00122-019-03382-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/12/2019] [Accepted: 06/16/2019] [Indexed: 05/21/2023]
Abstract
A high-resolution genetic map combined with haplotype analyses identified a wheat ortholog of rice gene APO1 as the best candidate gene for a 7AL locus affecting spikelet number per spike. A better understanding of the genes controlling differences in wheat grain yield components can accelerate the improvements required to satisfy future food demands. In this study, we identified a promising candidate gene underlying a quantitative trait locus (QTL) on wheat chromosome arm 7AL regulating spikelet number per spike (SNS). We used large heterogeneous inbred families ( > 10,000 plants) from two crosses to map the 7AL QTL to an 87-kb region (674,019,191-674,106,327 bp, RefSeq v1.0) containing two complete and two partial genes. In this region, we found three major haplotypes that were designated as H1, H2 and H3. The H2 haplotype contributed the high-SNS allele in both H1 × H2 and H2 × H3 segregating populations. The ancestral H3 haplotype is frequent in wild emmer (48%) but rare (~ 1%) in cultivated wheats. By contrast, the H1 and H2 haplotypes became predominant in modern cultivated durum and common wheat, respectively. Among the four candidate genes, only TraesCS7A02G481600 showed a non-synonymous polymorphism that differentiated H2 from the other two haplotypes. This gene, designated here as WHEAT ORTHOLOG OF APO1 (WAPO1), is an ortholog of the rice gene ABERRANT PANICLE ORGANIZATION 1 (APO1), which affects spikelet number. Taken together, the high-resolution genetic map, the association between polymorphisms in the different mapping populations with differences in SNS, and the known role of orthologous genes in other grass species suggest that WAPO-A1 is the most likely candidate gene for the 7AL SNS QTL among the four genes identified in the candidate gene region.
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Affiliation(s)
- Saarah Kuzay
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yunfeng Xu
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Junli Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Andrew Katz
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Zhenqi Su
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Max Fraser
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Noah DeWitt
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | | | - Justin D Faris
- USDA-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA.
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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Bajgain P, Zhang X, Anderson JA. Genome-Wide Association Study of Yield Component Traits in Intermediate Wheatgrass and Implications in Genomic Selection and Breeding. G3 (Bethesda) 2019; 9:2429-2439. [PMID: 31147390 PMCID: PMC6686922 DOI: 10.1534/g3.119.400073] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/23/2019] [Indexed: 11/18/2022]
Abstract
Intermediate wheatgrass (Thinopyrum intermedium, IWG) is a perennial grain crop with high biomass and grain yield, long seeds, and resistance to pests and diseases. It also reduces soil erosion, nitrate and mineral leaching into underground water tables, and sequesters carbon in its roots. The domestication timeline of IWG as a grain crop spans only 3 decades, hence it lags annual grain crops in yield and seed characteristics. One approach to improve its agronomic traits is by using molecular markers to uncover marker-trait associations. In this study, we performed association mapping on IWG breeding germplasm from the third recurrent selection cycle at the University of Minnesota. The IWG population was phenotyped in St Paul, MN in 2017 and 2018, and in Crookston, MN in 2018 for grain yield, seed length, width and weight, spike length and weight, and number of spikelets per spike. Strong positive correlations were observed among most trait pairs, with correlations as high as 0.76. Genotyping using high throughput sequencing identified 8,899 high-quality genome-wide SNPs which were combined with phenotypic data in association mapping to discover regions associated with the yield component traits. We detected 154 genetic loci associated with these traits of which 19 were shared between at least two traits. Prediction of breeding values using significant loci as fixed effects in genomic selection model improved predictive abilities by up to 14%. Genetic mapping of agronomic traits followed by using genomic selection to predict breeding values can assist breeders in selecting superior genotypes to accelerate IWG domestication.
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Affiliation(s)
- Prabin Bajgain
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN and
| | - Xiaofei Zhang
- Department of Horticultural Science, North Carolina State University, Raleigh, NC
| | - James A Anderson
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN and
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Tamang BG, Schoppach R, Monnens D, Steffenson BJ, Anderson JA, Sadok W. Variability in temperature-independent transpiration responses to evaporative demand correlate with nighttime water use and its circadian control across diverse wheat populations. Planta 2019; 250:115-127. [PMID: 30941570 DOI: 10.1007/s00425-019-03151-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
Nocturnal transpiration, through its circadian control, plays a role in modulating daytime transpiration response to increasing evaporative demand, to potentially enable drought tolerance in wheat. Limiting plant transpiration rate (TR) in response to increasing vapor pressure deficit (VPD) has been suggested to enable drought tolerance through water conservation. However, there is very little information on the extent of diversity of TR response curves to "true" VPD (i.e., independent from temperature). Furthermore, new evidence indicate that water-saving could operate by modulating nocturnal TR (TRN), and that this response might be coupled to daytime gas exchange. Based on 3 years of experimental data on a diverse group of 77 genotypes from 25 countries and 5 continents, a first goal of this study was to characterize the functional diversity in daytime TR responses to VPD and TRN in wheat. A second objective was to test the hypothesis that these traits could be coupled through the circadian clock. Using a new gravimetric phenotyping platform that allowed for independent temperature and VPD control, we identified three and fourfold variation in daytime and nighttime responses, respectively. In addition, TRN was found to be positively correlated with slopes of daytime TR responses to VPD, and we identified pre-dawn variation in TRN that likely mediated this relationship. Furthermore, pre-dawn increase in TRN positively correlated with the year of release among drought-tolerant Australian cultivars and with the VPD threshold at which they initiated water-saving. Overall, the study indicates a substantial diversity in TR responses to VPD that could be leveraged to enhance fitness under water-limited environments, and that TRN and its circadian control may play an important role in the expression of water-saving.
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Affiliation(s)
- Bishal G Tamang
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Twin Cities, MN, USA
| | - Rémy Schoppach
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Twin Cities, MN, USA
- Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Daniel Monnens
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Twin Cities, MN, USA
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, Twin Cities, MN, USA
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Twin Cities, MN, USA
| | - Walid Sadok
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Twin Cities, MN, USA.
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41
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Xin Y, Zhang N, Wang X, Li Q, Ma X, Qi Y, Zheng L, Anderson JA, Zhang Z. Efficient synthesis of the Cu-SAPO-44 zeolite with excellent activity for selective catalytic reduction of NO by NH3. Catal Today 2019. [DOI: 10.1016/j.cattod.2018.08.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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42
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Potts LD, Perez Calderon LJ, Gontikaki E, Keith L, Gubry-Rangin C, Anderson JA, Witte U. Effect of spatial origin and hydrocarbon composition on bacterial consortia community structure and hydrocarbon biodegradation rates. FEMS Microbiol Ecol 2019; 94:5047303. [PMID: 29982504 PMCID: PMC6166136 DOI: 10.1093/femsec/fiy127] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/26/2018] [Indexed: 12/30/2022] Open
Abstract
Oil reserves in deep-sea sediments are currently subject to intense exploration, with associated risks of oil spills. Previous research suggests that microbial communities from deep-sea sediment (>1000m) can degrade hydrocarbons (HCs), but have a lower degradation ability than shallow (<200m) communities, probably due to in situ temperature. This study aimed to assess the effect of marine origin on microbial HC degradation potential while separating the influence of temperature, and to characterise associated HC-degrading bacterial communities. Microbial communities from 135 and 1000 m deep sediments were selectively enriched on crude oil at in situ temperatures and both consortia were subsequently incubated for 42 days at 20°C with two HC mixtures: diesel fuel or model oil. Significant HC biodegradation occurred rapidly in the presence of both consortia, especially of low molecular weight HCs and was concomitant with microbial community changes. Further, oil degradation was higher with the shallow consortium than with the deep one. Dominant HC-degrading bacteria differed based on both spatial origin of the consortia and supplemented HC types. This study provides evidence for influence of sediment spatial origin and HC composition on the selection and activity of marine HC-degrading bacterial communities and is relevant for future bioremediationdevelopments.
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Affiliation(s)
- Lloyd D Potts
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom.,Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Fraser Noble Building, Elphinstone Road, Aberdeen, AB24 3UE, United Kingdom
| | - Luis J Perez Calderon
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom.,Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Fraser Noble Building, Elphinstone Road, Aberdeen, AB24 3UE, United Kingdom
| | - Evangelia Gontikaki
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom
| | - Lehanne Keith
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom
| | - Cécile Gubry-Rangin
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom
| | - James A Anderson
- Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Fraser Noble Building, Elphinstone Road, Aberdeen, AB24 3UE, United Kingdom
| | - Ursula Witte
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UL, United Kingdom
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43
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Singh L, Anderson JA, Chen J, Gill BS, Tiwari VK, Rawat N. Development and Validation of a Perfect KASP Marker for Fusarium Head Blight Resistance Gene Fhb1 in Wheat. Plant Pathol J 2019; 35:200-207. [PMID: 31244566 PMCID: PMC6586189 DOI: 10.5423/ppj.oa.01.2019.0018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/16/2019] [Accepted: 03/31/2019] [Indexed: 05/25/2023]
Abstract
Fusarium head blight (FHB) is a devastating wheat disease with a significant economic impact. Fhb1 is the most important large effect and stable QTL for FHB resistance. A pore-forming toxin-like (PFT) gene was recently identified as an underlying gene for Fhb1 resistance. In this study, we developed and validated a PFT-based Kompetitive allele specific PCR (KASP) marker for Fhb1. The KASP marker, PFT_KASP, was used to screen 298 diverse wheat breeding lines and cultivars. The KASP clustering results were compared with gel-based gene specific markers and the widely used linked STS marker, UMN10. Eight disagreements were found between PFT_KASP and UMN10 assays among the tested lines. Based on the genotyping and sequencing of genes in the Fhb1 region, these genotypes were found to be common with a previously characterized susceptible haplotype. Therefore, our results indicate that PFT_KASP is a perfect diagnostic marker for Fhb1 and would be a valuable tool for introgression and pyramiding of FHB resistance in wheat cultivars.
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Affiliation(s)
- Lovepreet Singh
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742,
USA
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108,
USA
| | - Jianli Chen
- Department of Plant, Soil, and Entomological Sciences, University of Idaho, Aberdeen, ID 83210,
USA
| | - Bikram S Gill
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, Kansas, KS 66506,
USA
| | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742,
USA
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742,
USA
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44
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McCradden MD, Anderson JA. The Last Refuge of Privacy. AJOB Neurosci 2019; 10:25-28. [PMID: 31070559 DOI: 10.1080/21507740.2019.1595786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Melissa D McCradden
- a The Hospital for Sick Children and Vector Institute for Artificial Intelligence
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45
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Potts LD, Perez Calderon LJ, Gubry-Rangin C, Witte U, Anderson JA. Characterisation of microbial communities of drill cuttings piles from offshore oil and gas installations. Mar Pollut Bull 2019; 142:169-177. [PMID: 31232291 DOI: 10.1016/j.marpolbul.2019.03.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/03/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
Drill cuttings (DC) are produced during hydrocarbon drilling operations and are composed of subsurface rock coated with hydrocarbons and drilling fluids. Historic disposal of DC at sea has resulted in the formation of large piles on the seabed that may be left in situ following infrastructure decommissioning. This study provides a first insight into the microbial abundance, diversity and community structure of two DC piles from North Sea oil and gas installations. The abundance of both bacteria and archaea was lower in DC than in surrounding natural sediments. Microbial diversity and richness within DC were low but increased with distance from the piles. Microbial community structure was significantly different in DC piles compared to nearby natural sediments. DC bacterial communities were dominated by Halomonas, Dietzia and Dethiobacter. The presence of such organisms suggests a potential function of hydrocarbon degradation ability and may play an active role in DC pile remediation.
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Affiliation(s)
- Lloyd D Potts
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom; Chemical and Materials Engineering, School of Engineering, University of Aberdeen, Aberdeen, United Kingdom.
| | - Luis J Perez Calderon
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom; Chemical and Materials Engineering, School of Engineering, University of Aberdeen, Aberdeen, United Kingdom
| | - Cecile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ursula Witte
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - James A Anderson
- Chemical and Materials Engineering, School of Engineering, University of Aberdeen, Aberdeen, United Kingdom
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46
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Liu Y, McCue AJ, Yang P, He Y, Zheng L, Cao X, Man Y, Feng J, Anderson JA, Li D. Support morphology-dependent alloying behaviour and interfacial effects of bimetallic Ni-Cu/CeO 2 catalysts. Chem Sci 2019; 10:3556-3566. [PMID: 30996947 PMCID: PMC6432614 DOI: 10.1039/c8sc05423a] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 02/07/2019] [Indexed: 01/24/2023] Open
Abstract
The dependence of alloying behavior and interfacial effects on the support morphology is revealed, in which homogeneous Ni–Cu nanoalloys were induced by polyhedron ceria.
The impregnation method is commonly employed to prepare supported multi-metallic catalysts but it is often difficult to achieve homogeneous and stable alloy structures. In this work, we revealed the dependence of alloying behavior on the support morphology by fabricating Ni–Cu over different shaped CeO2. Specifically, nanocube ceria favoured the formation of monometallic Cu and Ni-rich phases whereas polycrystalline and nanorod ceria induced the formation of a mixture of Cu-rich alloys with monometallic Ni. Surprisingly, nanopolyhedron (NP) ceria led to the generation of homogeneous Ni–Cu nanoalloys owing to the equivalent interactions of Ni and Cu species with CeO2 (111) facets which exposed relatively few coordinative unsaturated sites. More importantly, a strong interfacial effect was observed for Ni–Cu/CeO2-NP due to the presence of CeOx adjacent to metal sites at the interface, resulting in excellent stability of the alloy structure. With the aid of CeOx, NiCu nanoalloys showed outstanding catalytic behaviour in acetylene and hexyne hydrogenation reactions. This study provides valuable insights into how fully alloyed and stable catalysts may be prepared by tailoring the support morphology while still employing a universal impregnation method.
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Affiliation(s)
- Yanan Liu
- State Key Laboratory of Chemical Resource Engineering , Beijing University of Chemical Technology , Beijing , China . .,Beijing Engineering Center for Hierarchical Catalysts , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Alan J McCue
- Surface Chemistry and Catalysis Group , Department of Engineering , University of Aberdeen , Aberdeen , UK .
| | - Pengfei Yang
- State Key Laboratory of Chemical Resource Engineering , Beijing University of Chemical Technology , Beijing , China . .,Beijing Engineering Center for Hierarchical Catalysts , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Yufei He
- State Key Laboratory of Chemical Resource Engineering , Beijing University of Chemical Technology , Beijing , China . .,Beijing Engineering Center for Hierarchical Catalysts , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Lirong Zheng
- Institute of High Energy Physics , Chinese Academy of Sciences , Beijing , China
| | - Xingzhong Cao
- Institute of High Energy Physics , Chinese Academy of Sciences , Beijing , China
| | - Yi Man
- Beijing Research Institute of Chemical Industry , Sinopec Group , Beijing , China
| | - Junting Feng
- State Key Laboratory of Chemical Resource Engineering , Beijing University of Chemical Technology , Beijing , China . .,Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , Beijing , China
| | - James A Anderson
- Surface Chemistry and Catalysis Group , Department of Engineering , University of Aberdeen , Aberdeen , UK .
| | - Dianqing Li
- State Key Laboratory of Chemical Resource Engineering , Beijing University of Chemical Technology , Beijing , China . .,Beijing Engineering Center for Hierarchical Catalysts , Beijing University of Chemical Technology , Beijing 100029 , China
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Affiliation(s)
- Melissa D McCradden
- St Michael's Hospital, Neurosurgery, Toronto, Ontario, Canada.,Joint Centre for Bioethics, University of Toronto, Toronto, Ontario, Canada
| | - James A Anderson
- Joint Centre for Bioethics, University of Toronto, Toronto, Ontario, Canada.,The Hospital for Sick Children, Bioethics, Toronto, Ontario, Canada
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48
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Chopra R, Johnson EB, Daniels E, McGinn M, Dorn KM, Esfahanian M, Folstad N, Amundson K, Altendorf K, Betts K, Frels K, Anderson JA, Wyse DL, Sedbrook JC, David Marks M. Translational genomics using Arabidopsis as a model enables the characterization of pennycress genes through forward and reverse genetics. Plant J 2018; 96:1093-1105. [PMID: 30394623 DOI: 10.1111/tpj.14147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/05/2018] [Accepted: 10/26/2018] [Indexed: 05/05/2023]
Abstract
Thlaspi arvense (pennycress) has the potential for domestication as a new oilseed crop. Information from an extensive body of research on the related plant species Arabidopsis can be used to greatly speed this process. Genome-scale comparisons in this paper documented that pennycress and Arabidopsis share similar gene duplication. This finding led to the hypothesis that it should be possible to isolate Arabidopsis-like mutants in pennycress. This proved to be true, as forward genetic screens identified floral and vegetative pennycress mutants that were similar to mutants found in Arabidopsis. Extending this approach, it was shown that most of the pennycress genes responsible for the formation of oxidized tannins could be rapidly identified. The causative mutations in the pennycress mutants could be identified either by PCR amplification of candidate genes or through whole-genome sequencing (WGS) analysis. In all, WGS was used to characterize 95 ethyl methane sulfonate mutants, which revealed a mutation rate of 4.09 mutations per megabase. A sufficient number of non-synonymous mutations were identified to create a mutant gene index that could be used for reverse genetic approaches to identify pennycress mutants of interest. As proof of concept, a Ta-max3-like dwarf mutant and Ta-kcs5/cer60-like wax mutants deficient in the biosynthesis of long chain fatty acids were identified. Overall, these studies demonstrate that translational genomics can be used to promote the domestication of pennycress. Furthermore, the ease with which important findings could be made in pennycress makes this species a new potential model plant.
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Affiliation(s)
- Ratan Chopra
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Evan B Johnson
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Erin Daniels
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Michaela McGinn
- School of Biological Sciences, Illinois State University, Normal, IL, 61790, USA
| | - Kevin M Dorn
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Maliheh Esfahanian
- School of Biological Sciences, Illinois State University, Normal, IL, 61790, USA
| | - Nicole Folstad
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Kirk Amundson
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Kayla Altendorf
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, 55108, USA
| | - Kevin Betts
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, 55108, USA
| | - Katherine Frels
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, 55108, USA
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, 55108, USA
| | - Donald L Wyse
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, 55108, USA
| | - John C Sedbrook
- School of Biological Sciences, Illinois State University, Normal, IL, 61790, USA
| | - M David Marks
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
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49
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Szego MJ, Meyn MS, Shuman C, Zlotnik Shaul R, Anderson JA, Bowdin S, Monfared N, Hayeems RZ. Views from the clinic: Healthcare provider perspectives on whole genome sequencing in paediatrics. Eur J Med Genet 2018; 62:350-356. [PMID: 30503855 DOI: 10.1016/j.ejmg.2018.11.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 11/22/2018] [Accepted: 11/28/2018] [Indexed: 01/06/2023]
Abstract
Whole genome sequencing (WGS) is a transformative technology which promises improved diagnostic rates compared to conventional genetic testing strategies and tailored approaches to patient care. Due to the practical and ethical complexities associated with using WGS, particularly in the paediatric context, input from a broad spectrum of healthcare providers can guide implementation strategies. We recruited healthcare providers from the largest paediatric academic health science centre in Canada and conducted semi-structured qualitative interviews, exploring experiences with and perceptions of the opportunities and challenges associated with WGS. Interview transcripts were coded and analyzed thematically. Interviews were completed with 14 genetics professionals (geneticists and genetic counsellors) and 15 non-genetics professionals (physician sub-specialists and nurses). Genetics professionals ordered genetic tests more often and reported greater confidence on pre- and post-test genetic counselling compared to non-genetics professionals. Most healthcare providers endorsed WGS when a more specific test was either not available or not likely to yield a diagnosis. While genetics professionals raised concerns regarding the time demands associated with reviewing WGS variants, non-genetics professionals reflected concerns about knowledge and training. Providers' position on reporting secondary variants to parents drew upon but was not limited to the concept of best interests. Taken together, understanding practical and principled matters of WGS from healthcare providers' perspectives can guide ongoing efforts to implement WGS in paediatrics.
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Affiliation(s)
- M J Szego
- Joint Centre for Bioethics, University of Toronto, Toronto, Canada; St. Michael's Hospital, Toronto, Canada; Department of Family and Community Medicine, University of Toronto, Toronto, Canada; Dalla Lana School of Public Health, University of Toronto, Canada; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
| | - M S Meyn
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada; The Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada; Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada; Department of Paediatrics, University of Toronto, Toronto, Canada
| | - C Shuman
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada; Department of Genetic Counselling, The Hospital for Sick Children, Toronto, Canada; The Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada; Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - R Zlotnik Shaul
- Joint Centre for Bioethics, University of Toronto, Toronto, Canada; Department of Paediatrics, University of Toronto, Toronto, Canada; Department of Bioethics, The Hospital for Sick Children, Toronto, Canada; Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada
| | - J A Anderson
- Joint Centre for Bioethics, University of Toronto, Toronto, Canada; Department of Bioethics, The Hospital for Sick Children, Toronto, Canada
| | - S Bowdin
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada; The Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada; Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada; Department of Paediatrics, University of Toronto, Toronto, Canada
| | - N Monfared
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada; Department of Genetic Counselling, The Hospital for Sick Children, Toronto, Canada
| | - R Z Hayeems
- The Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Canada; Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada.
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Perez Calderon LJ, Gontikaki E, Potts LD, Shaw S, Gallego A, Anderson JA, Witte U. Pressure and temperature effects on deep-sea hydrocarbon-degrading microbial communities in subarctic sediments. Microbiologyopen 2018; 8:e00768. [PMID: 30444300 PMCID: PMC6562134 DOI: 10.1002/mbo3.768] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 12/24/2022] Open
Abstract
The Hatton-Rockall Basin (North-East Atlantic) is an area with potential for deep-sea (2,900 m) hydrocarbon exploration. Following the Deepwater Horizon oil spill, many investigations into the responses of sediment microbial communities to oil pollution have been undertaken. However, hydrostatic pressure is a parameter that is often omitted due to the technical difficulties associated with conducting experiments at high pressure (>10 MPa). In this study, sediments from 2,900 m in the Hatton-Rockall Basin, following a one-week decompression period in a temperature-controlled room at 5°C, were incubated in factorial combinations of 0.1 and 30 MPa, 5 and 20°C, and contamination with a hydrocarbon mixture or uncontaminated controls to evaluate the effect of these environmental variables on the bacterial community composition. Our results revealed varying effects of pressure, temperature, and oil contamination on the composition of the bacterial community within the sediment. Temperature was the strongest determinant of differences in the bacterial community structure between samples followed by pressure. Oil contamination did not exert a strong change in the sediment bacterial community structure when pressure and temperature conditions were held at in situ levels (30 MPa and 5°C). The γ-proteobacteria Pseudomonas and Colwellia, and several Bacteroidetes dominated communities at 30 MPa. In contrast, hydrocarbon degraders such as Halomonas, Alcanivorax, and Marinobacter decreased in relative abundance at the same pressure. This study highlights the importance of considering hydrostatic pressure in ex situ investigations into hydrocarbon-degrading deepwater microbial communities.
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Affiliation(s)
- Luis J Perez Calderon
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK.,Surface Chemistry and Catalysis Group, Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen, UK.,Marine Laboratory Aberdeen, Marine Scotland Science, Aberdeen, UK
| | - Evangelia Gontikaki
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK
| | - Lloyd D Potts
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK.,Surface Chemistry and Catalysis Group, Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen, UK
| | - Sophie Shaw
- Centre for Genome Enabled Biology and Medicine, University of Aberdeen, Aberdeen, UK
| | | | - James A Anderson
- Surface Chemistry and Catalysis Group, Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen, UK
| | - Ursula Witte
- Institute of Biological and Environmental Science, University of Aberdeen, Aberdeen, UK
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