DEFENSE VERSUS SYMBIOSIS: HOST GENETIC CONTROL OF NODULATION SPECIFICITY IN SOYBEAN

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: TERMINATED
• Funding Source: AFRI COMPETITIVE GRANT
• Reporting Frequency: Annual
• Accession No.: 0218942
• Grant No.: 2009-65300-05663
• Project No.: KY0ZHU3
• Proposal No.: 2009-01903
• Program Code: 91610
• Project Start Date: Sep 1, 2009
• Project End Date: Aug 31, 2013
• Grant Year: 2009

Project Director
Zhu, H.

Recipient Organization
UNIVERSITY OF KENTUCKY
500 S LIMESTONE 109 KINKEAD HALL
LEXINGTON,KY 40526-0001

Performing Department
Plant and Soil Sciences

Non Technical Summary
Legumes represent the second most important family of crop plants. One of the defining features of legumes is their ability to form a root symbiosis with nitrogen-fixing soil bacteria, collectively called rhizobia. A significant property of the symbiosis is its host specificity, which is controlled at multiple levels involving both rhizobial and host genes. Understanding of the host genetic control mechanisms involved in determination of host specificity will enable breeding for enhanced nitrogen fixation in crop legumes and facilitate the study of the molecular ecology of nitrogen-fixing symbiosis. A number of single dominant genes (e.g, Rj2, Rj4 and Rfg1) that restrict nodulation with specific rhizobial strains have been identified in soybean since 1960s. These dominant genes restrict nodulation through recognition of incompatible rhizobial strains, resembling those `gene-for-gene' interactions between plants and pathogens. The observation that the Rj2 allele is located within a disease resistance (R) gene cluster on the soybean linkage group J has led to the speculation that the dominant nodulation restriction genes may encode plant R proteins that play an important role in limiting the host range of rhizobia. The goal of this project is to map and clone the soybean genes Rj2 and Rfg1, taking advantage of the availability of genetic and genomic tools in soybean. Cloning and characterization of these genes will not only provide novel insights into the evolution of host specificity in legume nodulation but also contribute to our understanding of the similarities and contrasts between pathogenic and symbiotic plant-microbe interactions.

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
201	1820	1080	100%

Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1820 - Soybean;

Field Of Science
1080 - Genetics;

Keywords

soybean

nodulation specificity

symbiosis

nitrogen fixation

legume

Goals / Objectives
Legumes represent the second most important family of crop plants. One of the defining features of legumes is their ability to form a root symbiosis with nitrogen-fixing soil bacteria, collectively called rhizobia. A significant property of the symbiosis is its host specificity, which is controlled at multiple levels involving both rhizobial and host genes. Understanding of the host genetic control mechanisms involved in determination of host specificity will enable breeding for enhanced nitrogen fixation in crop legumes and facilitate the study of the molecular ecology of nitrogen-fixing symbiosis. A number of single dominant genes (e.g, Rj2, Rj4 and Rfg1) that restrict nodulation with specific rhizobial strains have been identified in soybean since 1960s. These dominant genes restrict nodulation through recognition of incompatible rhizobial strains, resembling those gene-for-gene interactions between plants and pathogens. The observation that the Rj2 allele is located within a disease resistance (R) gene cluster on the soybean linkage group J has led to the speculation that the dominant nodulation restriction genes may encode plant R proteins that play an important role in limiting the host range of rhizobia. The goal of this project is to map and clone the soybean genes Rj2 and Rfg1, taking advantage of the availability of genetic and genomic tools in soybean. Cloning and characterization of these genes will not only provide novel insights into the evolution of host specificity in legume nodulation but also contribute to our understanding of the similarities and contrasts between pathogenic and symbiotic plant-microbe interactions.

Project Methods
We will carry out fine mapping of the Rj2 and Rfg1 loci using F2 populations derived from soybean lines that show contrasting nodulation phenotypes. To do this, we will take advantage of the available genomic resources of soybean, including the soybean physical map (www.soybase.org) and the recently released whole genome draft sequences (http://www.phytozome.net/soybean). Fine mapping will allow us to delimit the candidate genes within a small genetic interval. We will take various strategies to validate the candidate gene(s). First, we will transfer the candidate genes into the genetic background of normally nodulated soybean lines through Agrobacterium rhizogenes-mediated hairy root transformation, in order to test if the transgenic roots can convert the nodulation phenotype into a non-nodulation phenotype. Second, we will use a virus-induced-gene-silencing (VIGS) approach to knock down the expression of the candidate genes. The BPMV (bean pod mottle virus) vector will be used for the proposed experiments.

Progress 09/01/09 to 08/31/13

Outputs
Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? We trained a postdoc and a graduate student using the grant. How have the results been disseminated to communities of interest? The PI was invited to give the following presentations: Symbiosis specificity in the legume-rhizobial symbiosis. Shanxi Agricultural University, Taigu, China, September 4, 2013 How do legumes choose their symbiotic partners in the rhizosphere? International Workshop on Agricultural Resource Utilization and Soil Quality Improvement. Nanjing Agricultural University, Nanjing, China, October 27-31, 2012 How do legumes choose their symbiotic partners in the rhizosphere? College of Agriculture, Yangzhou University, Yangzhou, China, October 24, 2012 Genetic control of symbiosis specificity in soybeans, 14th Molecular & Cellular Biology of the Soybean Conference, 2012, Des Moines, Iowa R you friend or foe? R-gene controlled host specificity in the legume-rhizobial symbiosis, Model Legume Congress 2011, France What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? We have successfully cloned theRj2 and Rfg1genes. We showed that Rj2 and Rfg1 are allelic genes encoding a member of the Toll-interleukin receptor/nucleotide-binding site/leucine-rich repeat (TIR-NBS-LRR) class of plant resistance (R) proteins. Our discovery is consistent with recent reports describing rhizobial T3SS and its secreted effectors that play an important role in modulation of host range, and suggests that establishment of a root nodule symbiosis requires the evasion of plant immune responses triggered by rhizobial effectors. This finding may also offer novel strategies to enhance symbiotic nitrogen fixation in crop legumes. For example, the nodulation-restrictive R genes may be manipulated so that a host can deterministically interact with rhizobial inoculants with high nitrogen-fixing efficiency and exclude those indigenous strains that are highly competitive but with very low nitrogen-fixing efficiency.

Publications

• Type: Journal Articles Status: Published Year Published: 2010 Citation: Yang S, Tang F, Gao M, Krishnan HB, Zhu H (2010) R gene-controlled host specificity in the legume-rhizobia symbiosis. Proceedings of the National Academy of Sciences USA 107:18735-18740
• Type: Journal Articles Status: Published Year Published: 2012 Citation: Wang D, Yang S, Tang F, Zhu H (2012) Symbiosis specificity in the legume-rhizobial mutualism. Cellular Microbiology 14:334-342

Progress 09/01/11 to 08/31/12

Outputs
OUTPUTS: Leguminous plants can enter into root nodule symbioses with nitrogen-fixing soil bacteria known as rhizobia. An intriguing but still poorly understood property of the symbiosis is its host specificity, which is controlled at multiple levels involving both rhizobial and host genes. The goal of this project was to clone the two soybean genes Rj2 and Rfg1 that restrict nodulation with specific strains of Bradyrhizobium japonicum and Sinorhizobium fredii, respectively. We have successfully cloned the two genes. We showed that Rj2 and Rfg1 are allelic genes encoding a member of the Toll-interleukin receptor/nucleotide-binding site/leucine-rich repeat (TIR-NBS-LRR) class of plant resistance (R) proteins. We are also working on clone another soybean gene Rj4 that controls nodulation specificity. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Our discovery is consistent with recent reports describing rhizobial T3SS and its secreted effectors that play an important role in modulation of host range, and suggests that establishment of a root nodule symbiosis requires the evasion of plant immune responses triggered by rhizobial effectors. This finding may also offer novel strategies to enhance symbiotic nitrogen fixation in crop legumes. For example, the nodulation-restrictive R genes may be manipulated so that a host can deterministically interact with rhizobial inoculants with high nitrogen-fixing efficiency and exclude those indigenous strains that are highly competitive but with very low nitrogen-fixing efficiency. We are also in the process of cloning another dominant soybean gene, called Rj4, that restricts nodulation with B. elkanii USDA61. Intriguingly Rj4 is not an R gene, and we believe that the result from this research will have significant impact in the area of plant-microbe interactions.

Publications

• No publications reported this period

Progress 09/01/10 to 08/31/11

Outputs
OUTPUTS: Leguminous plants can enter into root nodule symbioses with nitrogen-fixing soil bacteria known as rhizobia. An intriguing but still poorly understood property of the symbiosis is its host specificity, which is controlled at multiple levels involving both rhizobial and host genes. The goal of this project was to clone the two soybean genes Rj2 and Rfg1 that restrict nodulation with specific strains of Bradyrhizobium japonicum and Sinorhizobium fredii, respectively. We have successfully cloned the two genes. We showed that Rj2 and Rfg1 are allelic genes encoding a member of the Toll-interleukin receptor/nucleotide-binding site/leucine-rich repeat (TIR-NBS-LRR) class of plant resistance (R) proteins. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Our discovery is consistent with recent reports describing rhizobial T3SS and its secreted effectors that play an important role in modulation of host range, and suggests that establishment of a root nodule symbiosis requires the evasion of plant immune responses triggered by rhizobial effectors. This finding may also offer novel strategies to enhance symbiotic nitrogen fixation in crop legumes. For example, the nodulation-restrictive R genes may be manipulated so that a host can deterministically interact with rhizobial inoculants with high nitrogen-fixing efficiency and exclude those indigenous strains that are highly competitive but with very low nitrogen-fixing efficiency. We are also in the process of cloning another dominant soybean gene, called Rj4, that restricts nodulation with B. elkanii USDA61. Intriguingly Rj4 is not an R gene, and we believe that the result from this research will have significant impact in the area of plant-microbe interactions.

Publications

• No publications reported this period

Progress 09/01/09 to 08/31/10

Outputs
OUTPUTS: Leguminous plants can enter into root nodule symbioses with nitrogen-fixing soil bacteria known as rhizobia. An intriguing but still poorly understood property of the symbiosis is its host specificity, which is controlled at multiple levels involving both rhizobial and host genes. It is widely believed that the host specificity is determined by specific recognition of bacterially derived Nod factors by the cognate host receptor(s). We have cloned two soybean genes Rj2 and Rfg1 that restrict nodulation with specific strains of Bradyrhizobium japonicum and Sinorhizobium fredii, respectively. We show that Rj2 and Rfg1 are allelic genes encoding a member of the Toll-interleukin receptor/nucleotide-binding site/leucine-rich repeat (TIR-NBS-LRR) class of plant resistance (R) proteins. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The involvement of host R genes in the control of genotype-specific infection and nodulation reveals a common recognition mechanism underlying symbiotic and pathogenic host-bacteria interactions and suggests the existence of their cognate avirulence genes derived from rhizobia. This study suggests that establishment of a root nodule symbiosis requires the evasion of plant immune responses triggered by rhizobial effectors.

Publications

• Yang S, Tang F, Gao M, Krishnan HB, Zhu H (2010) R gene-controlled host specificity in the legume-rhizobia symbiosis. Proc Natl Acad Sci USA. 107(43):18735-40.