Source: PENNSYLVANIA STATE UNIVERSITY submitted to NRP
ESTABLISHMENT OF AN EPIGENETIC CROP IMPROVEMENT STRATEGY IN MULTIPLE CROP SPECIES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
1022787
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Jun 1, 2020
Project End Date
Mar 31, 2025
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
PENNSYLVANIA STATE UNIVERSITY
208 MUELLER LABORATORY
UNIVERSITY PARK,PA 16802
Performing Department
Plant Science
Non Technical Summary
Epigenetics is the study of how genes are expressed to influence plant behavior. Epigenetic breeding involves new methods that allow manipulation of gene expression patterns to render plants more environmentally resilient and vigorous in growth. These approaches, incorporating non-GMO methods and grafting, can serve to rapidly enhance traits like stress tolerance and yield, where progress is generally extremely slow and incremental using traditional methods. Development of innovative crop breeding strategies to address challenges of climate change will be important to enhancing yield stability in the future.
Animal Health Component
30%
Research Effort Categories
Basic
70%
Applied
30%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011848104014%
2011460104014%
2031848108010%
2031460108010%
2062420208052%
Knowledge Area
206 - Basic Plant Biology; 203 - Plant Biological Efficiency and Abiotic Stresses Affecting Plants; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1460 - Tomato; 1848 - Canola; 2420 - Noncrop plant research;

Field Of Science
1040 - Molecular biology; 2080 - Mathematics and computer sciences; 1080 - Genetics;
Goals / Objectives
The project is comprised of theseprimary objectives:1. To identify and characterize the genetic networks that underpin epigenetic reprogramming in plants, in association with the RNA-directed DNA methylation(RdDM) pathway, stress-responsive histone deacetylation/acetylation activity, and transcriptome regulation. These experiments use Arabidopsis thaliana as a model plant species.2. To establish a crop breeding method that employs epigenetic reprogramming to derive novel phenotypic variation that enhances crop resilience and growth vigor, and incorporates crossing and grafting strategies. These experiments use tomato, canola and strawberry as primary focus crops.3. To characterize the role of epigenetics in perennial plant development and trans-seasonal regrowth potential. These experiments incorporate both fundamental studies of RdDM-based mechanisms in overwintering/regrowth, and applied studies on the employment of epigenetics in the enhancement of perennial plant growth vigor, involving poplar trees and alfalfa forage crops as primary models.
Project Methods
1. The Mackenzie lab discovered and developed the MSH1 epigenetic reprogramming system in plants. MSH1 is a nuclear gene in plants that encodes a mitochondrial and plastid targeted protein. Mutation or disruption of MSH1 results in a unique condition of epigenetic reprogramming that can be manipulated to create transgenerational epigenetic memory lines, grafting rootstocks, and crossing lines for epigenetic breeding. Outcomes from MSH1 manipulation can create measureable increases in plant stress resilience and enhanced growth vigor/yield.Methods used in the study of MSH1-generated materials include sRNA sequencing, RNA sequencing, genome-wide methylation (bisulfite) sequencing, network-based enrichment analyses, double mutant analyses. Computational efforts involve data integration and modeling. Our group developed a novel, publicly available, DNA methylation analysis method, Methyl-IT, that employs signal detection and machine learning to identify genes that undergo methylation changes following epigenetic reprogramming. This method, combining DNA methylation variation and gene expression analysis, provides higher resolution analysis than either data analysis method alone.2. The suppression of MSH1 is achieved through CRISPR Cas9 or RNAi transgene-mediated suppression.Plant grafting methods are optimized for the particular crop and follow standard procedures, followed by harvesting of seed from the grafted scion for subsequent testing. Double mutant analysis is carried out in Arabidopsis, designed to identify key components in the networks that control the epigenetic reprogramming process.3. Crop performance testing is carried out initially within greenhouse conditions, followed by field testing that is conducted at the Russell Larson Agricultural Research Center at Rock Springs.Crop field testing involves tomato and canola, with strawberry planned for 2021.

Progress 06/01/20 to 09/30/20

Outputs
Target Audience:Research being conducted will have impact on the following audiences: 1. Canola breeding and production communities in which we have developed epigenetically modified canola lines that are now under field testing. 2. Strawberry breeders in which we have developed epigenetically modified strawberry lines that will enter a novel grafting program for field testing. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?One graduate student, Dr. Hardik Kundarya, has completed his Ph.D. degree training on the MSH1 project, and serves as a primary author of three publications for 2020. Two additional graduate students, Mr. Isaac Dopp and Ms. Ha Eun Jeh are currently being trained on this project. Mr. Dopp is developing skills in confocal microscopy and plant genetics, and serves as a coauthor on the Yang et al. 2020 (Nat Comm) publication. Ms. Jeh is developing skills in electron microscopy and immunocytology, and is preparing her first manuscript for submission in December, 2020. How have the results been disseminated to communities of interest?Presentations of this work were made at multiple workshops and several general audience articles were written on the work. What do you plan to do during the next reporting period to accomplish the goals?In the coming year we expect to report on: 1. Epigenetic enhanced growth gene pathways that account for vigor. 2. Proteins that interact with MSH1 to provide insight to the mechanisms involved in plant stress sensing. 3. Testing of epigenetic breeding outcomes in canola.

Impacts
What was accomplished under these goals? Goal 1: We have demonstrated association of RNA-directed DNA methylation and transcriptome changes that are associated with MSH1 (MUTS HOMOLOG 1)-directed memory and heritable enhancement through grafting (HEG) effects in Arabidopsis as a model plant species. These outcomes have been published in 2020 in Yang et al. (Nature Communications) and Kundariya et al. (Nature Communications). Goal 2. Within the Kundariya et al. publication, we have also demonstrated efficacy of HEG effects in large scale tomato field population trials. Grafting and field testing is now underway to test epigenetic breeding effects in canola. One large field trial is currently underway in Chile, and another is planned for the U.S. in 2021. In Strawberry, we have now successfully transformed plants with the MSH1 RNA interference (RNAi)transgene, and documented MSH1-like phenotypes emerging from the verified tranformant plants. Therefore, strawberry grafting experiments are currently underway. Goal 3. To understand the role of epigenetic variation in perennial growth phenotype, we have established a collaboration with a forest tree genomics expert at U.C. Davis (Dr. Andrew Groover) and we are currently developing poplar transformants for the MSH1 RNAi transgene and CRISPR knockdown constructions. We have also prepared anti-MSH1 antibodies to initiate experiments to localize MSH1 in perennial plant tissues. These experiments continue.

Publications

  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Yang, X, Sanchez R, Kundariya H, Maher T, Dopp I, Schwegel R, Virdi K, Axtell MJ, Mackenzie SA. 2020. Segregation of an MSH1 RNAi transgene produces heritable non-genetic memory in association with methylome reprogramming. Nat Commun. 11(1):2214. doi: 10.1038/s41467-020-16036-8.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Zhao N, Zhang L, Yang X, Mackenzie SA, Hu Z, Zhang M, Yang J. 2020. MutS HOMOLOG1 mediates fertility reversion via ORF220 substoichiometric shifting in cytoplasmic male sterile Brassica juncea. J. Exp. Bot., doi: 10.1111/pce.13895
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Henkhaus N, Bartlett M, Gang D, Grumet R, Haswell E, Jordon-Thaden I, Lorence A, Lyons E, Miller S, Murray S, Nelson A, Specht C, Tyler B, Wentworth T, Ackerly D, Baltensperger D, Benfey P, Birchler J, Chellamma S, Crowder R, Donoghue M, Dundore-Arias JP, Fletcher J, Gillespie K, Guralnick L, Hunter M, Kaeppler S, Kepinski S, Li F-W, Mackenzie S, McDade L, Min Y, Nemhauser J, Pearson B, Petracek P, Rogers K, Sakai A, Sickler D, Spady T, Taylor C, Wayne L, Wendroth O, Zapata F, Stern D. 2020. Plant Science Decadal Vision 2020-2030: Reimagining the potential of plants for a healthy and sustainable future. Plant Direct 4(8) e00252. http://dx.doi.org/10.1002/pld3.252
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Yang X, Mackenzie, SA. 2020. Approaches to whole-genome methylome analysis in plants. Methods Mol. Biol. 2093:15-31. doi: 10.1007/978-1-0716-0179-2_2.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2020 Citation: Kundariya H, Yang Y, Morton K, Sanchez R, Axtell MJ, Hutton SF, Fromm M, Mackenzie SA. 2020. MSH1-induced heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants. Nature Communications, in press.
  • Type: Journal Articles Status: Under Review Year Published: 2020 Citation: Dopp, IJ, Yang, X, Mackenzie SA. A new take on organelle-mediated stress sensing in plants. Tansley Insight, in review
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Sanchez R., Mackenzie SA. 2020. Integrative network analysis of differentially methylated and expressed genes for biomarker identification in leukemia. Sci Rept 10(1):2123. doi: 10.1038/s41598-020-58123-2.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Mackenzie SA, Kundariya H. 2020. Organellar protein multifunctionality and phenotypic plasticity in plants. Philos Trans R Soc Lond B Biol Sci. 375(1790):20190182. doi: 10.1098/rstb.2019.0182
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2020 Citation: Mackenzie, Sally. 2020. Incorporating Epigenetic Variation into Directed Breeding for Enhanced Crop Performance. Plant and Animal Genome Conference, San Diego, CA. January 11, 2020.