Source: UNIVERSITY OF CALIFORNIA, DAVIS submitted to
A SYNOPTIC APPROACH TO PHYSIOLOGICAL BREEDING FOR DROUGHT RESILIENCE IN BEAN
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1022320
Grant No.
2020-67013-30913
Cumulative Award Amt.
$475,000.00
Proposal No.
2019-05625
Multistate No.
(N/A)
Project Start Date
Jun 1, 2020
Project End Date
May 31, 2024
Grant Year
2020
Program Code
[A1152]- Physiology of Agricultural Plants
Project Director
Buckley, T. N.
Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671
Performing Department
Plant Sciences
Non Technical Summary
This project will measure several physiological traits that influence the yield of common beans under drought. We will use a combination of traditional direct measurements and optical (remote sensing) methods to enable measurement of an unprecedented number of varieties (320). This work will discover genetic markers for traits that improve yield in drought, which breeders can then use to produce new varieties to sustain bean yields with less water.
Animal Health Component
30%
Research Effort Categories
Basic
40%
Applied
30%
Developmental
30%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2021410108150%
2031410102050%
Knowledge Area
203 - Plant Biological Efficiency and Abiotic Stresses Affecting Plants; 202 - Plant Genetic Resources;

Subject Of Investigation
1410 - Beans (dry);

Field Of Science
1081 - Breeding; 1020 - Physiology;
Goals / Objectives
(1) Measure a wide range of physiological traits and yield components in 300 genotypes of common bean with known genealogy as part of a MAGIC population and 20 genotypes of tepary bean, in the field under two irrigation treatments (well-watered and droughted);(2) Quantify how traits and yield components act individually and in concert to determine yield resilience in drought, by applying results from Objective #1 to a synoptic yield model that includes a physiological model of biomass accumulation; and(3) Use results from Objective #2 to identify traits with the greatest potential impact on yield resilience under drought, and then identify genomic regions associated with those traits by applying results from Objective #1 to genotyping data for our mapping populations.
Project Methods
We will phenotype 300 genotypes of field-grown common bean (P. vulgaris) and 20 genotypes of drought-tolerant tepary bean (P. acutifolius) under two irrigation treatments (irrigated and drought), in two growing seasons. The P. vulgaris genotypes comprise an established MAGIC population that has been genotyped using a 6K SNP platform and phenotyped for seed yield and seed size for three years under irrigated conditions and two years under drought stress.We will use a hierarchical phenotyping approach to quantify a range of parameters that collectively drive variations in the resilience of yield in drought. In a subset of 16 genotypes, we will directly measure the main determinants of seasonal canopy photosynthesis (stomatal conductance, photosynthetic capacity, leaf area index.)In all 320 genotypes, we will estimate these parameters using a range of remotely sensed proxies. We will also directly measure yield, harvest index (HI) and the components of HI in all 320 genotypes, as well as parameters of water relations that influence stomatal behavior, and carbon isotope discrimination, an integrated measure of intrinsic water use efficiency.We will use an innovative, synoptic model-guided analysis to quantify the contribution of each trait to drought resilience of yield, thus identifying key target traits. We will then use genotyping data to identify genomic regions associated with those traits, to inform future breeding efforts. Additional outcomes of our approach include (i) the ability to predict how drought resilience would be affected by pyramided changes in multiple traits, enabled by our unique modeling approach, and (ii) an exceptionally rich dataset with which to validate and refine high-throughput optical proxy measurements for future work, provided by our hierarchical phenotyping approach.

Progress 06/01/20 to 05/31/24

Outputs
Target Audience:We communicated outcomes of work funded by this grant to other scientists in the fields of plant and crop physiology, remote sensing and plant ecology, through journal publications and presentations at research conferences. We also communicated research outcomes and plans to a variety of stakeholders, mostly growers and farm advisors,at the UC Davis Dry Bean Field Dayin 2022. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project supported the training and career development of several undergraduate and graduate students and a postdoctoral researcher: Postdoc Chris Wong was supported by the project for three years, and has recently begun a tenure-track faculty position. Project funds supported Chris' attendance at several conferences. Graduate students Marshall Pierce and Colleen Mills were both supported by this project for one summer quarter, and received extensive training and experience in both water relations and gas exchange methods, as well as experience in data analysis and writing scientific papers. Pierce is now a faculty member at a junior college and Mills is continuing her PhD studies. Undergraduate students Yasmin Wadhwani and Juliet Han gained extensive training in laboratory-based physiological measurements. How have the results been disseminated to communities of interest?The results of this study have been disseminated to communities of interest in several ways. Firstly, we have published two manuscripts describing the tower-based high throughput phenotyping method. Secondly, we have submitted, and are currently revising, a manuscript describing the core physiological results; this manuscript received a decision of "accept pending revisions" and will be resubmitted in late summer 2024. Thirdly, we are currently drafting a manuscript describing the greenhouse root growth experiments. Finally, we presented these results at several academic research conferencesand a grower/advisor field day. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Impact of the project: We identified physiological traits that helped bean plants continue growing despite cessation of irrigation after flowering. We verified that two lines of common bean and four of tepary bean conformed more closely to an ideal behavior in which growth and water use were slower under irrigated conditions, but not greatly suppressed during drought, thus enabling plants to convert limited water supply into maximal yield. This behavior would be beneficial in rainfed (non-irrigated) conditions or in locations where irrigation is otherwise scarce or limited. These results, combined with our remote sensing-based inference of these key physiological traits across many diverse genotypes of common bean and tepary bean for which genetic data are available, will help bean breeders produce new drought-resilient varieties of bean plants. Our results also demonstrate the exceptional drought resilience of tepary bean, suggesting that efforts should be increased to improve the palatability of this high-yielding yet drought-resilient bean species. (1) Measure a wide range of physiological traits and yield components in 300 genotypes of common bean with known genealogy as part of a MAGIC population and 20 genotypes of tepary bean, in the field under two irrigation treatments (well-watered and droughted). We planted 264 genotypes (including the eight parents of the MAGIC population with n=4 plots, and 256 genotypeswith n=1 plot per treatment). We measured physiological traits directly in the eight parent genotypes, and indirectly in allgenotypes using remote sensing techniques, in two campaigns: one at flowering, and one four weeks later, after 3 weeks ofterminal drought was imposed in half of the plots. Directly-measured physiological traits included photosynthetic capacity,stomatal conductance (at 0800, 1100 and 1400), midday leaf water potential, and osmotic pressure at full turgor. We alsocollected 6-10 pods per plot to measure yield components, and collected a full harvest in all plots to measure yield. We also conducted three rounds of a greenhouse experiment to quantify differences in rooting depth and water extractionprofiles. We also developed, and demonstrated in the field, a novel method for high-throughput estimation of physiological traits using a tower-based remote sensing system. We validated this approach and found that it can predict physiological traits with high reliability. This novel development can accelerate pre-breeding research to identify diversity in the physiological traits that contribute to yield under drought and other stressors. (2) Quantify how traits and yield components act individually and in concert to determine yield resilience in drought, byapplying results from Objective #1 to a synoptic yield model that includes a physiological model of biomass accumulation. We verified that two common bean genotypes and four tepary bean genotypes conformed more closely than most genotypes to an ideotype in which stomatal conductance is constitutively lower under irrigated conditions, but is not dramatically suppressed under conditions of terminal drought. Such an ideotype would be beneficial in rainfed conditions or in locations where irrigation is otherwise scarce or limited. Our results show that this ideotype was achieved partly through smaller declines in plant hydraulic conductance during drought (less "hydraulic vulnerability"), and partly also by smaller increases in evaporative demand, and hence less water loss for a given level of stomatal opening, due to smaller increase in canopy temperature. We found no evidence that photosynthetic capacity (light and CO2-saturated photosynthetic rate, i.e., independent of stomatal limitations) was directly and negatively impacted by terminal drought. Our greenhouse experimental data also do not support the hypothesis that faster vertical root growth contributes to differences in drought resilience. We are currently processing yield components from the final field season and will combine the physiological trait analysis described above with yield and yield component data to further assess the drivers of yield resilience per se. (3) Use results from Objective #2 to identify traits with the greatest potential impact on yield resilience under drought, and thenidentify genomic regions associated with those traits by applying results from Objective #1 to genotyping data for our mappingpopulations. All genomic and physiological data are in hand to complete this objective. We will conduct the genomic analysis as soon as yield component measurements are complete.

Publications

  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Wong CYS, Jones T, McHugh D, Gilbert ME, Pets P, Palkovic A, Buckley TN*, Magney TS* (2023) TSWIFT: Tower spectrometer on wheels for investigating frequent timeseries for high-throughput phenotyping of vegetation physiology. Plant Methods 19:1-15 (*co-last author) (10.1186/s13007-023-01001-5)
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Scoffoni C, Albuquerque C, Buckley TN, Sack L (2023) The dynamic multi-functionality of leaf water transport outside the xylem. New Phytologist 239:2099-2107 (10.1111/nph.19069)
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Coleman D, Windt C, Buckley TN, Merchant A (2023) Leaf relative water content at 50% stomatal conductance measured by non-invasive NMR is linked to climate of origin in nine species of eucalypt. Plant, Cell & Environment 46:3791-3805 (doi.org/10.1111/pce.14700)
  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Triplett G, Buckley TN, Muir CD (2024) Amphistomy increases leaf photosynthesis more in coastal than montane plants of Hawaiian 'ilima (Sida fallax). American Journal of Botany 111:e16284 (10.1002/ajb2.16284)
  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Watts JL, Dow GJ, Buckley TN, Muir CD (2024) Does stomatal patterning in amphistomatous leaves minimize the CO2 diffusion path length with leaves of Arabidopsis thaliana? AoB PLANTS 16:plae015 (10.1093/aobpla/plae015)
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2024 Citation: Mills C, Bartlett MK, Buckley TN (2024) The poorly-explored stomatal response to temperature at constant evaporative demand. Plant, Cell & Environment (in press) (10.1111/pce.14911)
  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Baird AS, Medeiros CD, Caringella MA, Bowers J, Hii M, Liang J, Matsuda J, Pisipati K, Pohl C, Simon B, Tagaryan S, Buckley TN, Sack L (2024) How and why do diverse species break a developmental trade-off? Elucidating the association of trichomes and stomata across species. American Journal of Botany (in press)
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2024 Citation: Ochoa M, Henry C, John G, Medeiros C, Pan R, Scoffoni C, Buckley TN, Sack L (2024) Pinpointing the causal influences of stomatal anatomy and behavior on leaf conductance from minimum to maximum. Plant Physiology (in press)
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2024 Citation: Wood J, Detto M, Browne M, Kraft N, Konings A, Fisher JB, Trugman A, Medeiros C, Vinod N, Buckley TN, Sack L (2024) Upscaling hydraulic mechanisms from leaves to plants to forests under climate change. Integrative and Comparative Biology (in press)


Progress 06/01/22 to 05/31/23

Outputs
Target Audience:During the review period (June 2022-May 2023), outcomes of work funded by this grant were communicated to otherscientists in the fields of plant and crop physiology, remote sensing and plant ecology, through journal publications andpresentations at research conferences. We also communicated research outcomes and plans to a variety of stakeholders at the UC Davis Dry Bean Field Day on 01 Sep 2022. Changes/Problems:Several technical failures and other issues impacted our experiments in 2022. First, field crews failed to properly align subsurface drip lines with planting beds, resulting in uneven water distribution between planting rows in each bed. This impacted emergence and establishment in both irrigated and drought treatments. We believe that we can account for differences in establishment using RGB (visible light) images from our tower-based remote sensing system, when quantifying biomass production and yield across genotypes. Second, field crews caused flooding of a portion of the droughted field early in the drought treatment. This reduced replication of genotypes in the drought treatment. Third, our laboratory osmometer failed in fall 2022, leading to a four-month delay in processing osmotic samples as the device was being repaired. These measurements were finally completed in June 2023. Fourth, the graduate students at UC Davis went on strike in fall 2023, which further delayed processing of samples, including yield and yield components. The latter two problems caused delays which led us to request a no-cost extension of the project through May 2024, so that we can complete and publish the measurements and analyses central to the project's objectives. What opportunities for training and professional development has the project provided?A postdoctoral fellow, Chris Wong, supported by the project was trained in physiological measurement techniques, data analysis and remote sensing instrumentation. Project funds also supported Chris' attendance at the American Geophysical Union conference in December 2022to present his research and meet other scientists. This is the premier conference for remote sensing research. A graduate student, Colleen Mills, was supported by the project for the summer quarter of 2022, and was trained in physiological measurement techniques. One undergraduate student, Yasmin Wadhwani,was supported part-time through the 2022-2023 academic year to process physiological samples from the 2022 field season. How have the results been disseminated to communities of interest?We published two papers describing the tower-based remote sensing technique developed and applied in this project for complementing low-throughput direct physiological measurements with high-throughput indirect optical measurements. What do you plan to do during the next reporting period to accomplish the goals?We plan to continue and complete our quantification of yield components, yield itself, and stable carbon isotope discrimination in leaf and seed samples. When those data are available, we will conduct an integrative analysis of how physiological traits and yield components together determine genetic variation in yield resilience to terminal drought across genotypes in the MAGIC population. We anticipate three publications will arise from this work: one describing the reduced-stomatal-conductance ideotype and the underlying physiological mechanisms, one describing the results of the greenhouse experiments to quantify genetic variation in rooting depth and depth of water extraction across genotypes, and one describing the integrative analysis of the determinants of yield resilience under drought.

Impacts
What was accomplished under these goals? Impact of the project: the study and data analysis are still underway, so we have not yet generated any firm conclusions that can be used by the plant breeding community. Preliminary analysis of physiological data suggest that two common bean genotypes and all tepary bean genotypes conform more closely than most genotypes to an ideotype in which stomatal conductance is constitutively lower under irrigated conditions, but is not dramatically suppressed under conditions of terminal drought. Such an ideotype could be beneficial in rainfed conditions or in locations where irrigation is otherwise scarce or limited. Our results also suggest that this ideotype might be achieved, in part, by lower, yet less vulnerable, plant hydraulic conductance. We have found no evidence of significant suppression of photosynthetic capacity (light and CO2-saturated photosynthetic rate, i.e., independent of stomatal limitations) under terminal drought conditions. (1) Measure a wide range of physiological traits and yield components in 300 genotypes of common bean with known genealogy as part of a MAGIC population and 20 genotypes of tepary bean, in the field under two irrigation treatments (well-watered and droughted); In 2022, we planted 264 genotypes (including the eight parents of the MAGIC population with n=4 plots, and 256 genotypes with n=1 plot per treatment). We measured physiological traits directly in the eight parent genotypes, and indirectly in all genotypes using remote sensing techniques, in two campaigns: one at flowering, and one four weeks later, after 3 weeks of terminal drought was imposed in half of the plots. Directly-measured physiological traits included photosynthetic capacity, stomatal conductance (at 0800, 1100 and 1400), midday leaf water potential, and osmotic pressure at full turgor.We also collected 6-10 pods per plot to measure yield components, and collected a full harvest in all plots to measure yield. We are currently in the process of measuring yield components and yield and expect these measurements to be complete by fall. We also collected leaf samples from all plots to measure stable carbon isotope discrimination, and will subsample seeds from the yield component samples for isotope measurements once the yield component measurements have been completed. We anticipate that the isotope measurements will be completed by the end of 2023, but this will depend on the queue at the stable isotope facility. We also conducted two more rounds of a greenhouseexperiment to quantify differences in rooting depth and water extraction profiles. The third round was harvested in June 2023 and samples are currently being processed. We anticipate those data will be available for analysis and publication in the fall. (2) Quantify how traits and yield components act individually and in concert to determine yield resilience in drought, by applying results from Objective #1 to a synoptic yield model that includes a physiological model of biomass accumulation. (3) Use results from Objective #2 to identify traits with the greatest potential impact on yield resilience under drought, and then identify genomic regions associated with those traits by applying results from Objective #1 to genotyping data for our mapping populations. Achievement of these objectives awaits yield measurements and finalization of the other analyses described above.

Publications

  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Pierrat, Zoe Amie, Jacob Bortnik, Bruce Johnson, Alan Barr, Troy Magney, David R. Bowling, Nicholas Parazoo, Christian Frankenberg, Ulli Seibt, and Jochen Stutz. "Forests for forests: combining vegetation indices with solar-induced chlorophyll fluorescence in random forest models improves gross primary productivity prediction in the boreal forest." Environmental Research Letters 17, no. 12 (2022): 125006.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Cheng, Rui, Troy S. Magney, Erica L. Orcutt, Zoe Pierrat, Philipp K�hler, David R. Bowling, M. Syndonia Bret-Harte et al. "Evaluating photosynthetic activity across Arctic-Boreal land cover types using solar-induced fluorescence." Environmental Research Letters 17, no. 11 (2022): 115009.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Martini, David, Karolina Sakowska, Georg Wohlfahrt, Javier Pacheco?Labrador, Christiaan van der Tol, Albert Porcar?Castell, Troy S. Magney et al. "Heatwave breaks down the linearity between sun?induced fluorescence and gross primary production." New phytologist 233, no. 6 (2022): 2415-2428.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Pierrat, Zoe, Troy Magney, Nicholas C. Parazoo, Katja Grossmann, David R. Bowling, Ulli Seibt, Bruce Johnson et al. "Diurnal and seasonal dynamics of solar?induced chlorophyll fluorescence, vegetation indices, and gross primary productivity in the boreal forest." Journal of Geophysical Research: Biogeosciences 127, no. 2 (2022): e2021JG006588.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Nelson, Peter R., Andrew J. Maguire, Zoe Pierrat, Erica L. Orcutt, Dedi Yang, Shawn Serbin, Gerald V. Frost et al. "Remote sensing of tundra ecosystems using high spectral resolution reflectance: opportunities and challenges." Journal of Geophysical Research: Biogeosciences 127, no. 2 (2022): e2021JG006697.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: ME Gilbert (2023) Flowers of a South African succulent plant predict tomorrow's weather, synchronizing flower opening with pollinator activity. Functional Ecology 37:1407-1420
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Gilbert, Matthew E., Rochelle C. Deriquito, Sarah B. Lam, and Sam Roth. "METHODS FOR FINDING THE LOCATION OF HISTORICAL PHOTOGRAPHS FOR REPEAT PHOTOGRAPHY." Madro�o 69, no. 3 (2023): 252-262.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Momayyezi, Mina, Aleca M. Borsuk, Craig R. Brodersen, Matthew E. Gilbert, Guillaume Th�roux?Rancourt, Daniel A. Kluepfel, and Andrew J. McElrone. "Desiccation of the leaf mesophyll and its implications for CO2 diffusion and light processing." Plant, Cell & Environment 45, no. 5 (2022): 1362-1381.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Buckley, Thomas N., Ethan H. Frehner, and Brian N. Bailey. "Kinetic factors of physiology and the dynamic light environment influence the economic landscape of short?term hydraulic risk." New Phytologist 238, no. 2 (2023): 529-548.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Vinod, Nidhi, Martijn Slot, Ian R. McGregor, Elsa M. Ordway, Marielle N. Smith, Tyeen C. Taylor, Lawren Sack, Thomas N. Buckley, and Kristina J. Anderson?Teixeira. "Thermal sensitivity across forest vertical profiles: patterns, mechanisms, and ecological implications." New Phytologist 237, no. 1 (2023): 22-47.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Verslues, Paul E., Julia Bailey-Serres, Craig Brodersen, Thomas N. Buckley, Lucio Conti, Alexander Christmann, Jos� R. Dinneny et al. "Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress." The Plant Cell 35, no. 1 (2023): 67-108.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Wu, Genghong, Chongya Jiang, Hyungsuk Kimm, Sheng Wang, Carl Bernacchi, Caitlin E. Moore, Andy Suyker et al. "Difference in seasonal peak timing of soybean far-red SIF and GPP explained by canopy structure and chlorophyll content." Remote sensing of environment 279 (2022): 113104.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Han, Jimei, Christine Y?Y. Chang, Lianhong Gu, Yongjiang Zhang, Eliot W. Meeker, Troy S. Magney, Anthony P. Walker et al. "The physiological basis for estimating photosynthesis from Chl a fluorescence." New Phytologist 234, no. 4 (2022): 1206-1219.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Yang, Julia C., Troy S. Magney, Loren P. Albert, Andrew D. Richardson, Christian Frankenberg, Jochen Stutz, Katja Grossmann et al. "Gross primary production (GPP) and red solar induced fluorescence (SIF) respond differently to light and seasonal environmental conditions in a subalpine conifer forest." Agricultural and Forest Meteorology 317 (2022): 108904.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Fletcher, Leila R., Christine Scoffoni, Colin Farrell, Thomas N. Buckley, Matteo Pellegrini, and Lawren Sack. "Testing the association of relative growth rate and adaptation to climate across natural ecotypes of Arabidopsis." New Phytologist 236, no. 2 (2022): 413-432.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: He, Nianpeng, Pu Yan, Congcong Liu, Li Xu, Mingxu Li, Koenraad Van Meerbeek, Guangsheng Zhou et al. "Predicting ecosystem productivity based on plant community traits." Trends in Plant Science (2022).
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Rajewicz, Paulina A., Chao Zhang, Jon Atherton, Shari Van Wittenberghe, Anu Riikonen, Troy Magney, Beatriz Fernandez-Marin, Jose Ignacio Garcia Plazaola, and Albert Porcar-Castell. "The photosynthetic response of spectral chlorophyll fluorescence differs across species and light environments in a boreal forest ecosystem." Agricultural and Forest Meteorology 334 (2023): 109434.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Sun, Ying, Lianhong Gu, Jiaming Wen, Christiaan van Der Tol, Albert Porcar?Castell, Joanna Joiner, Christine Y. Chang et al. "From remotely sensed solar?induced chlorophyll fluorescence to ecosystem structure, function, and service: Part IHarnessing theory." Global Change Biology (2023).
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Sun, Ying, Jiaming Wen, Lianhong Gu, Joanna Joiner, Christine Y. Chang, Christiaan van der Tol, Albert Porcar?Castell et al. "From remotely?sensed solar?induced chlorophyll fluorescence to ecosystem structure, function, and service: Part IIHarnessing data." Global Change Biology (2023).
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Wong, Christopher YS, Matthew E. Gilbert, Marshall A. Pierce, Travis A. Parker, Antonia Palkovic, Paul Gepts, Troy S. Magney, and Thomas N. Buckley. "Hyperspectral remote sensing for phenotyping the physiological drought response of common and tepary bean." Plant Phenomics 5 (2023): 0021.


Progress 06/01/21 to 05/31/22

Outputs
Target Audience:During the review period (June 2021-May 2022), outcomes of work funded by this grant were communicated to other scientists in the fields of plant and crop physiology, remote sensing and plant ecology, through journal publications and presentations at research conferences. Changes/Problems:Two problems arose during the 2021 field season that reduced our ability to complete the initially planned objectives. First, damaged irrigation lines led to patchy water supply shortly after planting, causing wide variation in seed emergence and establishment; this was subsequently magnified by destruction of many plots by pests (jackrabbits) and weed pressure (bindweed).Second, an unexpectedly early and severe rainfall event in October 2021 occurred just before harvest, preventing field access for several weeks and thereby preventing a successful harvest. To minimize the risks of similar issues occurring in 2022, we have shifted the entire season forward by one month (planting on 04-05 May 2022 vs. 05-06 June 2021) and planted in a different field area that has much lower weed pressure and a history of fewer pest problems. The earlier planting date will ensuregreater moisture in the soil profile and less severe atmospheric water demand during germination and establishment, which should improve uniformity across plots. Earlier planting should also lead to earlier harvest, which will greatly reduce the chance that rain will interfere with harvest plans. What opportunities for training and professional development has the project provided?A postdoctoral fellow, Chris Wong, supported by the project was trained in physiological measurement techniques, data analysis and remote sensing instrumentation. Project funds also supported Chris' attendance at the American Geophysical Union conference in December 2021 to present his research and meet other scientists. This is the premier conference for remote sensing research. A graduate student, Marshall Pierce, was supported by the project for the summer quarter of 2021, and was trained in physiological measurement techniques. Pierce completed his Masters degree in fall 2021 and is now employed as an agricultural inspector for Venutura County. Two undergraduate students were supported during the summer 2021 field campaigns and during the period of planting preparation for the 2022 season. They were trained in a variety of methods, including physiological measurements, soil moisture measurements, and harvest index measurements. How have the results been disseminated to communities of interest?No final results have been determined from this project, nor therefore disseminated. We will prepare final analyses disseminate results after the 2022 field season. What do you plan to do during the next reporting period to accomplish the goals?In 2022, we will repeat the physiological and remote sensing measurements from the 2021 field campaign. We will also measure yield, yield components, and carbon isotope discrimination in harvested seeds,which we were unable to do in 2021 due to severe early-seasonrainfall. In addition we will perform a repeat of the greenhouse rooting depth experiment to determine soil water extraction profiles.After completion of data collection,we will synthesize results from both field seasons, perform the analyses described in project Objectives 2 and 3, and prepare several manuscripts describing the results for publication.

Impacts
What was accomplished under these goals? Impact of the project: the study and data analysis are still underway, so we have not yet generated any firm conclusions that can be used by the plant breeding community. Our preliminary data suggest there there are few or no significant differences in physiological traits related to drought tolerance among the lines that we examined. This would suggest that differences in the resilience of bean yield under drought are caused by other factors such as biomass partitioning. However, we caution that these conclusions are preliminary and await confirmation from our second field season, scheduled for 2022 (planting occurred in early May 2022). (1) Measure a wide range of physiological traits and yield components in 300 genotypes of common bean with known genealogy as part of a MAGIC population and 20 genotypes of tepary bean, in the field under two irrigation treatments (well-watered and droughted); We measured physiology and hyperspectral traits across genotypes under well-watered and drought conditions (water withheld after flowering), largelyas planned. Physiology measurements were successful. We were able to collect hyperspectral data concurrent with the physiological measurements using a drone and handheld hyperspectral device. High-temporal-frequency hyperspectral measurements with the tower system were successful for a subset of plots, but the tower was unable to resolve plots beyond a certain distance due to the low angle of attack. We also measured depth profiles of soil water content using neutron backscatter detecter soil moisture probes in 96 plots. Preliminary analysis suggests there were no consistent genotype-by-environment interactions in any physiological traits. We also measured pod harvest index in xxxx genotypes and found no genotype by environment interactions. We were unable to obtain yield data, however, because an unexpectedly severe and early rainfall occurred just prior to the scheduled harvest date, preventing field access for several weeks. We performed a greenhouse root depth experiment in spring 2022 on 17 focus genotypes. Preliminary analysis suggest no consistent differences in rooting depth among genotypes in response to drought. Root biomass measurements are currently underway to determine whether the depth profile of rooting, rather than maximum rooting depth per se, differed among genotypes. We are also planting a second roundof the same experiment in which we will measure terminal water content at different depths in the soil column to determine whether the depth profile of water extraction differs among genotypes and aligns with differences in the depth profile of root biomass. (2) Quantify how traits and yield components act individually and in concert to determine yield resilience in drought, by applying results from Objective #1 to a synoptic yield model that includes a physiological model of biomass accumulation. (3) Use results from Objective #2 to identify traits with the greatest potential impact on yield resilience under drought, and then identify genomic regions associated with those traits by applying results from Objective #1 to genotyping data for our mapping populations. Achievement of these objectives awaits yield results from the 2022 field season.

Publications

  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Trueba S, Theroux-Rancourt G, Earles JM, Buckley TN, Love D, Johnson DM, Brodersen C (2022) The 3D construction of leaves is evolutionarily coordinated with water use efficiency in conifers. New Phytologist 233:851-861 (10.1111/nph.17772)
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: De La Torre AR*, Sekhwal MK, Scott AD, Allen B, Neale DB, Chin ARO, Buckley TN* (2022) Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia. The Plant Journal 109:7-22 (*equal contributions) (10.1111/tpj.15592)
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Adams MA, Buckley TN, Binkley D, Neumann N, Turnbull TL (2021) CO2, nitrogen deposition and a discontinuous climate response drive water use efficiency in global forests. Nature Communications 12:1-9 (10.1038/s41467-021-25365-1)
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Wong CYS, Young DJN, Latimer AM, Buckley TN, Magney TS (2021) Remote sensing of coniferous tree ring growth in the Sierra Nevada. Remote Sensing of Environment 265:112635 (10.1016/j.rse.2021.112635)
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Wong CYS, Bambach N, Alsina M, McElrone A, Jones T, Buckley TN, Kustas W, Magney TS (2022) Detecting short-term stress and recovery events in a vineyard using tower-based remote sensing of photochemical reflectance index (PRI). Irrigation Science (10.1007/s00271-022-00777-z)
  • Type: Journal Articles Status: Accepted Year Published: 2022 Citation: Momayyezi, M. Rippner, D. Duong, F. Raja, PV. Brown, P. Kluepfel, D. Earles, M. Forrestel, E. Gilbert, M., and McElrone, A. (accepted). Structural and functional leaf diversity lead to variability in photosynthetic capacity across a range of Juglans regia genotypes. Plant, Cell and Environment.
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Bambach, N. E., Gilbert, ME. Paw U, KT. (2022). Introducing a dynamic photosynthetic model of photoinhibition, heat, and water stress in the next-generation land surface model ACASA. Agricultural and Forest Meteorology 312(15): 108702
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Th�roux-Rancourt, Guillaume, Adam B. Roddy, J. Mason Earles, Matthew E. Gilbert, Maciej A. Zwieniecki, C. Kevin Boyce, Danny Tholen, Andrew J. McElrone, Kevin A. Simonin, and Craig R. Brodersen. (2021). Maximum CO2 diffusion inside leaves is limited by the scaling of cell size and genome size. Proceedings of the Royal Society B 288(1945): 20203145
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Porcar-Castell, A., Malenovsk�, Z., Magney, T. et al. Chlorophyll a fluorescence illuminates a path connecting plant molecular biology to Earth-system science. Nat. Plants 7, 9981009 (2021).
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Han, J., Chang, C. Y. Y., Gu, L., Zhang, Y., Meeker, E. W., Magney, T. S., ... & Sun, Y. (2022). The physiological basis for estimating photosynthesis from Chl a fluorescence. New Phytologist 234:1206-1219


Progress 06/01/20 to 05/31/21

Outputs
Target Audience:We presented the phenotyping system that we have developed for this study to a group of academic colleagues and a journal editor in May 2021. Changes/Problems:The only major change was postponing the first season due to COVID. What opportunities for training and professional development has the project provided?The postdoctoral associate employed under the project, Dr Chris Wong, has received extensive training and experience over the first year of the project. Dr Wong worked closely with co-PD Troy Magney to build and test the phenotyping tower system. They have tested the system in other field sites in the region. Dr Wong has also developed collaborations with other scientists at UC Davis not involved in the project, and has already submitted a manuscript with those authors (PD Buckley and co-PD Magney are also co-authors). Three undergraduate student interns were employed in the spring quarter 2021 (April and May) to assist with preparations for planting. The same three students have been extended through the summer and will work on the project at approximation 50% time through August, helping to collect field phenotyping data and process samples. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?We will conduct our first field season during the next reporting period (specifically, planting in early June and harvest in approximately September or October depending on weather). During and after this season, we will conduct the following measurements: - direct traditional measurements of physiological traits (photosynthetic capacity, stomatal conductance, and water relations parameters) in 16 genotypes, during each of three campaign weeks (one ~4 weeks days after sowing [DOS];one 2-3 weeks later, after imposition of drought in one set of blocks; and one another 2-3 weeks later) - indirect, tower-based proximal optical sensing of hyperspectral traits, both concurrent with the campaigns described earlier, and also several times a day for each plot throughout the growing season, for all 320 genotypes - canopy light interception measured using 1-m ceptometers placed beneath the canopies of eight genotypes in the control trial, and left in place continuously for the first month of growth. - canopy light interception as described above, but for 4 genotypes, measured in both control and drought treatments, beginning when drought is first imposed in the drought trial approximately 35 DOS. - soil moisture as a function of soil depth in 16 genotypes, using neutron moisture probe. - detailed tracking of phenology for 16 genotypes - days to flowering and days to seed maturity for all 320 genotypes - harvest index components for all 320 genotypes - carbon and nitrogen stable isotope discrimination for all 320 genotypes Isotopic, harvest index, and osmotic pressure measurements will be conducted in the fall and winter, after harvest is completed. After data collection is complete for the first field season, we will conduct an initial modeling exercise to quantify the contribution of different traits to resilience of yield under drought across genotypes.

Impacts
What was accomplished under these goals? Nothing has been accomplished under these goals, because the first field season was delayed due to COVID. We have however prepared and tested the tower-based phenotyping system and used other funding to acquire additional equipment that will aid in direct physiological phenotyping in the 2021 field season. Everything was prepared for planting for the summer 2021 field season in April and May. (Planting occurred in the first week of June, outside the current reporting period.)

Publications

  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Salter WT, Merchant A, Richards RA, Trethowan R, Buckley TN (2020) Wide variation in the suboptimal distribution of photosynthetic capacity in relation to light across genotypes of wheat. AoBP 12:plaa039 (doi.org/10.1093/aobpla/plaa039)
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Albuquerque CP, Scoffoni C, Brodersen C, Buckley TN, Sack L, McElrone AJ (2020) Coordinated decline of leaf hydraulic and stomatal conductances under drought is not linked to leaf xylem embolism for different grapevine cultivars. Journal of Experimental Botany 71:�7286-7300 (doi.org/10.1093/jxb/eraa392)
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Buckley TN (2021) Optimal carbon partitioning helps reconcile the apparent divergence between optimal and observed canopy profiles of photosynthetic capacity. New Phytologist (in press) (doi.org/10.1111/nph.17199)
  • Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Deng Z, Vice H, Gilbert ME, Adams MA, Buckley TN (2021) A double-ratio method (DRM) to measure fast, slow and reverse sap flows. Tree Physiology (in press)
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Chang CY, Guanter L, Frankenberg C, K�hler P, Gu L, Magney TS, et al (2020) Systematic assessment of retrieval methods for canopy far?red solar?induced chlorophyll fluorescence (SIF) using high?frequency automated field spectroscopy. Journal of Geophysical Research: Biogeosciences, 125, e2019JG005533. https://doi.org/10.1029/2019JG005533
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: He L, Magney TS, Dutta D, Yin Y, K�hler P, Grossmann K, Stutz J, Dold C, Hatfield J, Guan K, Peng B, Frankenberg C (2020) From the ground to space: Using solar?induced chlorophyll fluorescence (SIF) to estimate crop productivity. Geophysical Research Letters, 47, e2020GL087474. https://doi.org/10.1029/2020GL087474
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Meeker E, Magney TS, Bambach N, Momayyezi M, McElrone AJ (2021) Modification of a gas exchange system to measure active and passive chlorophyll fluorescence simultaneously under field conditions, AoB PLANTS, Volume 13, Issue 1, February 2021, plaa066, https://doi.org/10.1093/aobpla/plaa066