Source: DARTMOUTH COLLEGE submitted to NRP
CYTOKININS AND THE TRANSCRIPTIONAL REGULATION OF ROOT ARCHITECTURE AND PHOSPHORUS UPTAKE IN RICE
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
Reporting Frequency
Annual
Accession No.
1018608
Grant No.
2019-67013-29191
Cumulative Award Amt.
$417,000.00
Proposal No.
2018-06406
Multistate No.
(N/A)
Project Start Date
Mar 1, 2019
Project End Date
Feb 28, 2023
Grant Year
2019
Program Code
[A1152]- Physiology of Agricultural Plants
Recipient Organization
DARTMOUTH COLLEGE
8000 CUMMINGS HALL
HANOVER N H,NH 03755
Performing Department
Biological Sciences
Non Technical Summary
The root systems of plants perform such critical functions as the absorption of nutrients and water from the soil, the storage of food and nutrients, and the anchoring of the plant to the soil. The optimal root system for crop growth varies depending on the local environmental conditions. There is therefore a need to better understand the mechanisms that control root system architecture and nutrient uptake, particularly in cereal crops because these are the foundation of our food supply. In this project, the role the plant hormone cytokinin plays in regulating the growth and development of roots as well as their ability to take up nutrients from the soil will be characterized. The studies will be performed in rice, which is an important crop worldwide, and which shares similar root system characteristics with other cereal crops. The experimental focus is on a key family of transcription factors that mediate the cytokinin response, with their role evaluated by generating and characterizing mutants that alter their activity. The role the transcription factors play in regulating root system architecture will be quantified and these results correlated with their effects on gene regulation. In addition, their role in phosphorus uptake and distribution will be characterized, phosphorus being one of the most limiting nutrients for plant growth. Insights into contamination of food by the poison arsenic will also be obtained because the same uptake system used for phosphate acquisition in plants also mediates the acquisition of arsenic. The results from this project will form a basis for improving plant productivity through foundational studies on root system architecture and nutrient uptake, with the information obtained from rice having significance for other agronomically important crops such as maize, wheat, barley, rye, and sorghum.
Animal Health Component
(N/A)
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2061530101020%
2061530102020%
2061530105020%
2061530104015%
2061530108015%
2061530302010%
Goals / Objectives
Cytokinins are phytohormones that regulate growth and development in plants, including the root system architecture (RSA). The overall goal of this project is to determine the role that cytokinin-mediated gene regulation plays in the control of RSA in rice, and to then extend this to the uptake of phosphorus, which is one of the most limiting nutrients for plant growth. For this purpose, we will take a mutant-based approach focused on the type-B RRs, which mediate the cytokinin transcriptional response. The objectives of this proposal are as follows:Objective 1. To phenotypically characterize the role the type-B RRs play in regulating the RSA. This will be accomplished by characterizing the effects of mutants on various components of the RSA, and linking these to changes in meristematic and cytokinin activity.Objective 2. To determine the gene-regulatory networks mediated through action of the type-B RRs in control of RSA. This will be accomplished by use of RNA-Seq for gene expression analysis and ChIP-Seq to identify direct targets of type-B RRs.Objective 3. To characterize the role the type-B RRs play in the root developmental response to phosphorus availability. This will be accomplished by examining the effects of mutants on phosphorus-linked changes in the RSA, gene expression, and phosphorus uptake. Additionally, due to the link of phosphorus uptake to arsenic uptake, we will also characterize the effects of type-B RR mutants on the uptake and distribution of the poison arsenic in rice.
Project Methods
The overall goal of this project is to determine the role that cytokinin-mediated gene regulation plays in the control of root system architecture (RSA) in rice, and to then extend this to the uptake of phosphorus, which is one of the most limiting nutrients for plant growth. For this purpose, we will take a mutant-based approach focused on the type-B RRs, which mediate the cytokinin transcriptional response.To determine the roles of type-B RRs in regulating RSA, we will employ loss- and gain-of-function mutants to evaluate root growth responses to cytokinin, determine the basis for differences in root growth of mutants by examining meristem activity and cell elongation, determine the basis for the decreased lateral root growth observed in the type-B rr mutants, and correlate these root growth responses with regions of cytokinin activity.To determine the roles of type-B RRs in regulating gene expression in roots, we will employ RNA-Seq to compare gene expression in type-B rr mutants to wild type and use ChIP-Seq with type-B RRs to determine which genes are direct targets.To determine the roles of type-B RRs in regulating the root growth response to phosphorus deficiency, we will examine the effects of type-B rr mutants on the RSA, gene expression, and P-uptake and distribution during the P-deficiency response. Due to the overlapping role of P-transport with that of arsenic, we will also examine the type-B rr mutants for effects on arsenic uptake and distribution.Results from these studies will be communicated to the audiences by publication in scientific journals, by press releases alerting audiences to these publications, and by presentations at scientific conferences. Success of the project will be assessed by the collection and analysis of the data described above, each of which will generate quantifiable results, and by publication of results in peer-reviewed scientific journals.

Progress 03/01/19 to 02/28/23

Outputs
Target Audience:The target audiences are students, researchers, and members of the public interested in science, plant biology, and agriculture. They were reached through efforts that include laboratory instruction and the dissemination of scientific results through publications. Changes/Problems:The research project was impacted due to the COVID-19 pandemic. Phased re-openings to research occurred, concurrent with the vaccine rollout, which as of summer 2022 allowed for full lab occupancy to perform benchwork and to access facilities. Restrictions on international travel during the pandemic delayed fulfilling personnel positions for this research project. What opportunities for training and professional development has the project provided?Swadhin Swane (post-doc) Identification and characterization of CRISPR-cas9 alleles for generation of loss-of-function mutations. Development of molecular tools for characterization of type-B RRs. He is being trained in molecular biology, plant physiology, and genetics. Sitwat Aman (post-doc) ICP-MS analysis of HK and type-B RR mutant lines. Identification and characterization of CRISPR-cas9 alleles for generation of loss-of-function mutations. She is being trained in molecular biology, plant physiology, and genetics. Kasey Hernandez (PhD student) Characterization of growth phenotypes for CRISPR-cas9 mutant lines. He is being trained in molecular biology, plant physiology, and genetics. How have the results been disseminated to communities of interest?Results have been disseminated to communities of interest through publications generated over the length of the award, including research papers and review articles. 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: The root systems of plants perform such critical functions as the absorption of nutrients and water from the soil, the storage of food and nutrients, and the anchoring of the plant to the soil. The optimal root system for crop growth varies depending on the local environmental conditions. There is therefore a need to better understand the mechanisms that control root system architecture and nutrient uptake, particularly in cereal crops because these are the foundation of our food supply. To address this issue, we characterized the role the plant hormone cytokinin plays in regulating the growth and development of roots of the cereal crop rice. For this purpose, we a genetically characterized a key family of transcription factors that mediate cytokinin signaling, as well as collaborated on the genetic characterization of cytokinin receptors in rice. Novel as well as conserved roles for cytokinin signal transduction in the control of rice growth and development were uncovered as compared to the role in a non-cereal plant species. Cytokinin signal transduction was revealed to affect rice throughout its life cycle, including effects on root and shoot growth, grain yield, and flower development. Analysis of gene expression, use of reporters for cytokinin activity, and characterization of mutant phenotypes, pointed to a key role for cytokinin in regulating meristematic regions that dictate growth and architecture of the root and grain-producing panicle. These results demonstrate the importance of the plant hormone cytokinin and a specific family of transcription factors in regulating growth and development of a major crop species, and have significance for other agronomically important crops such as maize, wheat, barley, rye, and sorghum. Objective 1. To phenotypically characterize the role the type-B RRs play in regulating the root system architecture (RSA). The initial focus of these studies was to characterize the effects of loss-of-function and gain-of-function type-B RR mutants on rice growth and development, including the RSA, as described in our publications arising from this project. Our recent focus has been to characterize the role of the KMD F-box proteins in rice, our prior research indicating that these target the type-B RRs for degradation. We have used a CRISPR-cas9 approach to target four members of the rice KMD family and isolated various KMD mutant combinations for phenotypic characterization. Phenotypes of the triple and quadruple mutant combinations of the KMDs are consistent with the rice plants exhibiting an increase in cytokinin activity, but without the deleterious growth effects found when type-B RRs are overexpressed. Objective 2. To determine the gene-regulatory networks mediated through action of the type-B RRs in control of RSA. The initial focus of these studies was to characterize cytokinin-dependent gene expression for both LOF and GOF type-B RR mutants; consistent with predictions, the LOF lines exhibited cytokinin hyposensitivity in roots and shoots, whereas the GOF overexpression lines exhibited enhanced cytokinin sensitivity. To facilitate the identification of regions where the type-B RRs regulate gene expression, we developed a fluorescence reporter optimized for rice and this past reporting cycle characterized transgenic lines containing this reporter. The reporter exhibits cytokinin-dependent changes in expression, is expressed in roots and shoots in zones consistent with heightened cytokinin signaling. Novel differences from Arabidopsis were observed in the meristematic tissues. Objective 3. To characterize the role that cytokinin and the type-B RRs play in the developmental response to nutrient availability. Through our initial focus on the analysis of LOF and GOF type-B RR mutants in rice, we uncovered a role for the type-B RRs and cytokinin in the regulating the number of leaf silica-cell files, which provide mechanical stability and improve resistance to pathogens. Our recent focus has been on the broader role that cytokinin may play in regulating metals homeostasis in rice, in particular how cytokinin affects nutrient availability in the rice seed because of its worldwide significance as a food source. We performed ICP-MS analysis on the rice seed, taking advantage of our LOF and GOF lines for the type-B RR and HK genes. Of particular significance is the finding for a potential role of cytokinin in regulating calcium levels in the seed.

Publications


    Progress 03/01/21 to 02/28/22

    Outputs
    Target Audience:The target audiences are students, researchers, and members of the public interested in science, plant biology, and agriculture. They were reached through efforts that include laboratory instruction and the dissemination of scientific results through publications. Changes/Problems:The research project was impacted due to the COVID-19 pandemic. Phased re-openings to research have occurred, concurrent with the vaccine rollout, which now allow for an increased ability to perform benchwork and to access facilities. In addition, restrictions on international travel during the pandemic delayed fulfilling personnel positions for this research project. What opportunities for training and professional development has the project provided?Swadhin Swane (post-doc) Identification of CRISPR-cas9 alleles for members of the KMD family. Development of molecular tools for characterization of type-B RRs. He is being trained in molecular biology, plant physiology, and genetics. Sitwat Aman (post-doc) ICP-MS analysis of HK and type-B RR mutant lines. Identification and characterization of CRISPR-cas9 alleles for members of the KMD family. She is being trained in molecular biology, plant physiology, and genetics. Kasey Hernandez (PhD student) Characterization of growth phenotypes for CRISPR-cas9 KMD lines. He is being trained in molecular biology, plant physiology, and genetics. Hai Nguyen (PhD student) Development of molecular tools for characterization of type-B RRs. He is being trained in molecular biology and genetics of rice. How have the results been disseminated to communities of interest?Results have been disseminated to communities of interest through the following publications: Shakeel*, S.N., Swadhin*, S., Aman, S., and Schaller, G.E. (2021) Interaction of cytokinin and ethylene in the regulation of primary root growth and development. In: Rhizobiology: Molecular Physiology of Plant Roots (SoumyaMukherjee, FrantišekBaluška, eds.) Signaling and Communication in Plants. Springer Springer, Cham. pp. 195-238. https://doi.org/10.1007/978-3-030-84985-6_13 (* equal contribution) G. Eric Schaller served as a co-editor for a Frontiers in Plant Science special research topic issue: Hejatko, J. Brenner, W.G., Hoyerova, K. and Schaller, G.E., eds. (2022) Cytokinins as Central Regulators of Plant Growth and Development. Lausanne: Frontiers Media SA. doi: 10.3389/978-2-88974-277-6 What do you plan to do during the next reporting period to accomplish the goals?We will continue with the objectives 1-3 from our proposal, with an emphasis upon objectives 2 and 3 to take advantage of molecular tools and genetic lines we have generated that will facilitate these objectives.

    Impacts
    What was accomplished under these goals? Objective 1. To phenotypically characterize the role the type-B RRs play in regulating the RSA. To this end, we characterized the effects of both loss-of-function and gain-of-function mutants on rice growth and development, including the RSA, as described in two publications (Worthen et al, 2019; Yamburenko et al, 2020). The results from the LOF and GOF mutant studies indicate that careful balance of cytokinin signaling activity needs to be maintained to assure optimal growth and development. Our current focus is on the role of the KMD F-box proteins in rice, our prior research indicating that these target the type-B RRs for degradation. We have used a CRISPR-cas9 approach to target four members of the rice KMD family and isolated various KMD mutant combinations that are currently being phenotypically characterized. LOF mutations of the KMD genes are predicted to result in an increase in type-B RR and cytokinin activity, but not have the drastic effects found when type-B RR are overexpressed. Objective 2. To determine the gene-regulatory networks mediated through action of the type-B RRs in control of RSA. Cytokinin-dependent gene expression has been examined for both LOF and GOF type-B RR mutants and, consistent with predictions, the LOF lines exhibit cytokinin hyposensitivity in roots and shoots, whereas the GOF overexpression lines exhibit enhanced cytokinin sensitivity. To facilitate the identification of regions where the type-B RRs regulate gene expression, we have developed a fluorescence reporter optimized for rice and are currently characterizing transgenic lines containing this reporter. The reporter exhibits cytokinin-dependent changes in expression, with initial observations indicating some novel differences from Arabidopsis in the meristematic tissues. Objective 3. To characterize the role that cytokinin and the type-B RRs play in the developmental response to nutrient availability. A surprising finding from our analysis of LOF and GOF type-B RR mutants in rice, was uncovering a role for the type-B RRs and cytokinin in the number of leaf silica-cell files, which provide mechanical stability and improve resistance to pathogens. In particular, type-B RR LOF mutants displayed an increase in the number of silica-cell files, indicating that cytokinin likely suppresses this developmental pathway. To gain broader insight into the role of cytokinin in regulating metals homeostasis in rice, we are performing ICP-MS analysis of rice seeds, taking advantage of our LOF and GOF lines for the type-B RR and HK genes. Initial results suggest alterations in key elements involved in rice growth and development and we are now repeating and expanding on this analysis.

    Publications

    • Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Shakeel*, S.N., Swadhin*, S., Aman, S., and Schaller, G.E. (2021) Interaction of cytokinin and ethylene in the regulation of primary root growth and development. In: Rhizobiology: Molecular Physiology of Plant Roots (Soumya Mukherjee, Frantiaek Baluaka, eds.) Signaling and Communication in Plants. Springer Springer, Cham. pp. 195-238. https://doi.org/10.1007/978-3-030-84985-6_13 (* equal contribution)
    • Type: Books Status: Accepted Year Published: 2022 Citation: Hejatko, J. Brenner, W.G., Hoyerova, K. and Schaller, G.E., eds. (2022) Cytokinins as Central Regulators of Plant Growth and Development. Lausanne: Frontiers Media SA. doi: 10.3389/978-2-88974-277-6


    Progress 03/01/20 to 02/28/21

    Outputs
    Target Audience:The target audiences are students, researchers, and members of the public interested in science, plant biology, and agriculture. They will be reached through efforts that include laboratory instruction and the dissemination of scientific results through publications, conference presentations, and press releases. Changes/Problems:Due to the COVID-19 pandemic, Dartmouth College was closed to on-campus research except for basic maintenance of stocks from mid-March to June, at which point one person per lab group was allowed on site at a time. This reduced the ability to perform the benchwork described in the proposal. The university entered into phase I research in June with one person per lab group on site at a time, and in July entered phase II research with additional researchers allowed in labs although restricted by physical distancing guidelines, which allowed for a resumption of benchwork related to the project aims. What opportunities for training and professional development has the project provided?Maria Yamburenko (post-doc) Characterization of type-B RR LOF and GOF lines, and of HK LOF lines. She is being trained in molecular biology, plant physiology, and genetics. Swadhin Swane (post-doc) Isolation and identification of CRISPR-cas9 alleles for members of the KMD family. Characterization of type-B RR reporter lines. He is being trained in molecular biology, plant physiology, and genetics. Sitwat Aman (post-doc) ICP-MS analysis of HK and type-B RR mutant lines. She is being trained in molecular biology, plant physiology, and genetics. How have the results been disseminated to communities of interest?Results have been disseminated to communities of interest through the following publications: 1. Burr*, C.A., Sun*, J., Yamburenko*, M.V., Willoughby, A., Hodgens, C., Boeshore, S.L., Elmore, A., Atkinson, J., Nimchuk, Z.L., Bishopp, A., Schaller, G.E., and Kieber, J.J. (2020) The HK5 and HK6 cytokinin receptors mediate diverse developmental pathways in rice. Development. 147:191734. doi: 10.1242/dev.191734. (* equal contribution) 2. Yamburenko*, M.V., Worthen*, J.M., Zeenat, A., Azhar, B.J., Swain, S., Couitt, A.R., Shakeel, S.N., Kieber, J.J., Schaller, G.E. (2020) Functional analysis of the rice type-B response regulator RR22. Frontiers Plant Sci. 11:577676. doi: 10.3389/fpls.2020.577676. (* equal contribution) Outreach: G. Eric Schaller served as a co-editor with Hejatko, J., Brenner, W.G., Hoyerova, K. on a Frontiers in Plant Science special research topic issue (Cytokinins as central regulators of plant growth and development), as a means to raise awareness and highlight the significance of cytokinins. What do you plan to do during the next reporting period to accomplish the goals?We will continue with the objectives 1-3 from our proposal, with increased emphasis upon objectives 2 and 3 now that we have refined the molecular tools and approaches that will facilitate these objectives.

    Impacts
    What was accomplished under these goals? Impact: The root systems of plants perform such critical functions as the absorption of nutrients and water from the soil, the storage of food and nutrients, and the anchoring of the plant to the soil. The optimal root system for crop growth varies depending on the local environmental conditions. There is therefore a need to better understand the mechanisms that control root system architecture and nutrient uptake, particularly in cereal crops because these are the foundation of our food supply. To address this issue, we are characterizing the role the plant hormone cytokinin plays in regulating the growth and development of roots of the cereal crop rice. For this purpose, we continued with a genetic characterization for a key family of transcription factors that mediate cytokinin signaling, as well as collaborated on the genetic characterization of cytokinin receptors in rice. Novel as well as conserved roles for cytokinin signal transduction in the control of rice growth and development were uncovered as compared to the role in a non-cereal plant species. Cytokinin signal transduction was revealed to affect rice throughout its lifecycle, including effects on root and shoot growth, grain yield, and flower development. Analysis of gene expression, use of reporters for cytokinin activity, and characterization of mutant phenotypes, pointed to a key role for cytokinin in regulating meristematic regions that dictate growth and architecture of the root and grain-producing panicle. These results demonstrate the importance of the plant hormone cytokinin and a specific family of transcription factors in regulating growth and development of a major crop species, and have significance for other agronomically important crops such as maize, wheat, barley, rye, and sorghum. Objective 1. To phenotypically characterize the role the type-B RRs play in regulating the RSA. To this end, we are characterizing the effects of mutants on various components of the RSA. We previously generated single and higher order mutant combinations for four type-B RRs (RR21, 22, 23, and 24) using a CRISPR-cas9 gene editing approach, and have continued to exploit these lines for the analysis of rice growth and development. As a complement to the CRISPR-cas9-based approach, we (1) four loss-of-function (LOF) Tos17 insertion alleles of RR22. The results from the LOF and GOF mutant studies indicate that careful balance of cytokinin signaling activity needs to be maintained to assure optimal growth and development. Objective 3. To characterize the role that cytokinin and the type-B RRs play in the developmental response to nutrient availability. A surprising finding from our analysis of LOF and GOF type-B RR mutants in rice, was uncovering a role for the type-B RRs and cytokinin in the number of leaf silica-cell files, which provide mechanical stability and improve resistance to pathogens. In particular, type-B RR LOF mutants displayed an increase in the number of silica-cell files, indicating that cytokinin likely suppresses this developmental pathway. To gain broader insight into the role of cytokinin in regulating metals homeostasis in rice, we have now performed ICP-MS analysis of rice seeds from LOF and GOF lines involving type-B RR and HK mutants. Initial results are consistent with effects of cytokinin signal transduction on Si levels as well as pointing to broader roles for cytokinin in regulating homeostasis of other key elements required for rice growth and development. @font-face { panose-1:2 4 5 3 5 4 6 3 2 4; mso-font-charset:0; mso-generic- mso-font-pitch:variable; mso-font-signature:-536870145 1107305727 0 0 415 0;}@font-face { panose-1:2 15 5 2 2 2 4 3 2 4; mso-font-charset:0; mso-generic- mso-font-pitch:variable; mso-font-signature:-536859905 -1073732485 9 0 511 0;}@font-face { panose-1:2 0 5 3 0 0 0 2 0 4; mso-font-alt:"Helvetica Neue LT Std"; mso-font-charset:0; mso-generic- mso-font-pitch:variable; mso-font-signature:-452984065 1342208475 16 0 1 0;}p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-unhide:no; mso-style-qformat:yes; mso-style-parent:""; margin:0in; mso-pagination:widow-orphan; ; mso-ascii- mso-ascii-theme-font:minor-latin; mso-fareast- mso-fareast-theme-font:minor-latin; mso-hansi- mso-hansi-theme-font:minor-latin; mso-bidi- mso-bidi-theme-font:minor-bidi;}p {mso-style-priority:99; mso-margin-top-alt:auto; margin-right:0in; mso-margin-bottom-alt:auto; margin-left:0in; mso-pagination:widow-orphan; ; mso-fareast-}p.Default, li.Default, div.Default {mso-style-name:Default; mso-style-unhide:no; mso-style-parent:""; margin:0in; mso-pagination:widow-orphan; mso-layout-grid-align:none; text-autospace:none; ; mso-fareast- mso-fareast-theme-font:minor-latin; mso-bidi- }.MsoChpDefault {mso-style-type:export-only; mso-default-props:yes; mso-ascii- mso-ascii-theme-font:minor-latin; mso-fareast- mso-fareast-theme-font:minor-latin; mso-hansi- mso-hansi-theme-font:minor-latin; mso-bidi- mso-bidi-theme-font:minor-bidi;}div.WordSection1 {page:WordSection1

    Publications

    • Type: Journal Articles Status: Accepted Year Published: 2020 Citation: Burr*, C.A., Sun*, J., Yamburenko*, M.V., Willoughby, A., Hodgens, C., Boeshore, S.L., Elmore, A., Atkinson, J., Nimchuk, Z.L., Bishopp, A., Schaller, G.E., and Kieber, J.J. (2020) The HK5 and HK6 cytokinin receptors mediate diverse developmental pathways in rice. Development. 147:191734. doi: 10.1242/dev.191734. (* equal contribution)
    • Type: Journal Articles Status: Accepted Year Published: 2020 Citation: Yamburenko*, M.V., Worthen*, J.M., Zeenat, A., Azhar, B.J., Swain, S., Couitt, A.R., Shakeel, S.N., Kieber, J.J., Schaller, G.E. (2020) Functional analysis of the rice type-B response regulator RR22. Frontiers Plant Sci. 11:577676. doi: 10.3389/fpls.2020.577676. (* equal contribution)


    Progress 03/01/19 to 02/29/20

    Outputs
    Target Audience:The target audiences are students, researchers, and members of the public interested in science, plant biology, and agriculture. They have been reached through efforts that include laboratory instruction and the dissemination of scientific results through publications and conference presentations. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Maria Yamburenko (post-doc) Characterization of type-B RR LOF and GOF lines. She is being trained in molecular biology, plant physiology, and genetics. Yan Zubo (post-doc) Identification of CRISPR-cas9 alleles for members of the KMD family. He is being trained in molecular biology, plant physiology, and genetics. How have the results been disseminated to communities of interest?Results have been disseminated to communities of interest through seminars and publications. Seminars by G. Eric Schaller on the transcriptional mechanisms for cytokinin dependent control of growth and development: 1. Auxins and Cytokinins in Plant Development International Symposium (July 1-5, 2018). Prague, Czech Republic (Invited Speaker and Session Chair). 2. Ghent University, Ghent, Belgium (May 28, 2019) (Invited Speaker). Publications: 1. Worthen, J.M., Yamburenko, M.V., Lim, J., Nimchuk, Z.L., Kieber, J.J., and Schaller, G.E. (2019) Type-B response regulators of rice play key roles in growth, development, and cytokinin signaling. Development 146, dev174870. doi:10.1242/dev.174870 2. Zubo, Y. and Schaller, G.E. (2020) Role of the cytokinin-activated type-B response regulators in hormone crosstalk. Plants. 9:166. doi:10.3390/plants9020166 What do you plan to do during the next reporting period to accomplish the goals?We will continue with the objectives 1-3 from our proposal, with increased emphasis upon objectives 2 and 3 now that we have refined the molecular tools and approaches that will facilitate these objectives.

    Impacts
    What was accomplished under these goals? Impact: The root systems of plants perform such critical functions as the absorption of nutrients and water from the soil, the storage of food and nutrients, and the anchoring of the plant to the soil. The optimal root system for crop growth varies depending on the local environmental conditions. There is therefore a need to better understand the mechanisms that control root system architecture and nutrient uptake, particularly in cereal crops because these are the foundation of our food supply. To address this issue, we are characterizing the role the plant hormone cytokinin plays in regulating the growth and development of roots of the cereal crop rice. We generated mutations in a key family of transcription factors, demonstrated that these transcription factors play a major role in mediating the cytokinin response in rice, and characterized physiological effects of the transcription factor mutants upon rice growth and development. Novel as well as conserved roles for this family of transcription factors in the control of rice growth and development were uncovered as compared to their roles in a non-cereal plant species. Roles for the transcription factors were uncovered that affect rice throughout its lifecycle, including effects on root and shoot growth, grain yield, and flower development. A role for these cytokinin-regulated transcription factors in the control of root system architecture was demonstrated based on reductions in growth of the main seminal root as well as in the production of lateral roots. These results demonstrate the importance of the plant hormone cytokinin and a specific family of transcription factors in regulating growth and development of a major crop species, and have significance for other agronomically important crops such as maize, wheat, barley, rye, and sorghum. Objective 1. To phenotypically characterize the role the type-B RRs play in regulating the RSA. To this end, we are characterizing the effects of mutants on various components of the RSA. By employing a CRISPR-cas9 gene editing approach, single mutants were isolated for four type-B RRs (RR21, 22, 23, and 24), several independent lines for the triple mutant rr21/22/23, as well as wild-type siblings from these lines to act as controls. Novel as well as conserved roles for this family of transcription factors in the control of rice growth and development were uncovered as compared to their roles in a non-cereal plant species. Effects on root, shoot, panicle, and flower development were documented and quantified. Roots exhibited decreased growth on the seminal root along with a decrease in the production of lateral roots. The seminal root meristem was smaller than the wild type control, indicating a reduction in cell proliferation. Cross sections through the root suggested that there is also a decrease in the production of cortical cells, also consistent with a role for cytokinin in the regulation of root cell proliferation. The rr21/2/23 mutants exhibited a reduced cytokinin response based on a root growth assay as well as a a dark-induced leaf senescence assay. Results from this type-B RR loss-of-function analysis were included in a recent publication from our lab (Worthen et al. 2019). As a complement to our analysis of loss-of-function mutants, we have also overexpressed a type-B response regulator (RR22), characterization of these lines revealing a reduction in root and shoot growth, including decreased panicle branching and seed yield. The results from the loss- and gain-of-function mutant studies point to the careful balance of cytokinin signaling that needs to be maintained to assure optimal growth and development. Along with an analysis of type-B RR mutants, we are also initiating studies with KMD mutants, prior research having indicated that these F-box proteins can target the type-B RRs for degradation; CRISPR-cas9 constructs have been introduced in rice and we are currently identifying different mutant combinations for phenotypic characterization. Objective 2. To determine the gene-regulatory networks mediated through action of the type-B RRs in control of RSA. To this end, we have examined cytokinin-dependent gene expression for both loss-of-function and gain-of-function type-B RR mutants in roots and shoots by qRT-PCR. Consistent with predictions, the loss-of-function lines exhibit cytokinin hyposensitivity in roots and shoots, whereas the gain-of-function overexpression lines exhibit enhanced cytokinin sensitivity. These data are consistent with the effects of the mutants on growth and development being due to alterations in cytokinin-dependent gene expression. Data from the loss-of-function analysis was included in Worthen et al. 2019. This initial gene expression analysis by qRT-PCR serves as a starting point for a more global analysis by RNA-seq. We also analyzed cytokinin hormone cross-talk in detail from ChIP-seq dataset generated in Arabidopsis, as hormone interactions play a critical role in regulating RSA. Results from this analysis were included in a recent publication from our lab (Zubo and Schaller, 2020). Objective 3. To characterize the role the type-B RRs play in the root developmental response to phosphorus availability. To this end, we have examined the seedling growth phenotypes for wild-type and type-B RR mutant lines in a variety of hydroponic and agar-based growth media conditions, including under nutrient depletion conditions, to determine optimal conditions to examine nutrient uptake and effects on root growth. We have grown concurrent sets of wild-type and mutant plants to use for seed isolation, as this will allow us to make an initial assessment as to whether the distribution from root to seed of various nutrients including phosphorus is affected in the mutants. Arsenic content in seeds will also be evaluated because phosphorus uptake is linked to arsenic uptake, and so we will also characterize the effects of type-B RR mutants on the uptake and distribution of the poison arsenic in rice.

    Publications

    • Type: Journal Articles Status: Published Year Published: 2019 Citation: Worthen, J.M., Yamburenko, M.V., Lim, J., Nimchuk, Z.L., Kieber, J.J., and Schaller, G.E. (2019) Type-B response regulators of rice play key roles in growth, development, and cytokinin signaling. Development 146, dev174870. doi:10.1242/dev.174870
    • Type: Journal Articles Status: Published Year Published: 2020 Citation: Zubo, Y. and Schaller, G.E. (2020) Role of the cytokinin-activated type-B response regulators in hormone crosstalk. Plants. 9:166. doi:10.3390/plants9020166