Development of wheat transformation and genome editing tools
Research project 28
Project researchers: Prof. Amir Sharon and Prof. Itay Mayrose

Wheat supplies about 20% of all calories and proteins consumed by humanity, rising up to 50% in some regions. Improvement of wheat varieties, such as for better yields and resistance to pathogens and environmental conditions requires the use of modern tools, in particular gene editing technologies. Compared with other crops, wheat is recalcitrant to genetic transformation. In addition, the large and polyploid wheat genome represents a challenge to efficient genome editing.

Our mission is to establish a reliable wheat transformation system in wheat, which will provide wheat transformation and genome editing services to the entire wheat research community in Israel.

The project has the following milestones: construction of a core facility, establishment of transformation in standard cultivars and later in local wheat cultivars, and development of a toolbox for CRISPR-mediated genome editing in wheat, including the design (bioinformatics) and application methods.

Our basic approach is transformation of immature wheat embryos of wheat cv. Fielder by the bacterium Agrobacterium tumefaciens with the aid of regeneration-promoting genes. In addition to wheat, we also develop transformation of the plant finger millet, which have an economical importance and are also used as model for C4 plants such as sugarcane and maize.

For performance of efficient genome editing, we will provide computational strategies for the optimal design of guide RNA (gRNA) sequences. The development will proceed in three phases: First, we will develop an artificial-intelligence based tool that considers the genomic context of the target DNA site and integrate several existing algorithms tools that were developed based on machine learning and deep learning strategies. Second, due to the long history of wheat domestication and improvement, the genetic pool of wheat consists of thousands of varieties, such that the use of the wheat reference genome as the sole input should result in reduced performance. Thus, our design tool will not be based on a single reference genome but will account for all available wheat varieties genomes. Third, due to its complex polyploid genome nearly all protein-coding genes in wheat belong to large families, and thus in many cases the editing of a single gene will not result in an evident phenotype. We will thus provide computational methodologies for designing guide RNAs that will target multiple members of a gene family. We will apply the designed tools to all protein-coding genes in the genomes of wheat and barley and will develop a dedicated web server that will enable researchers to view and download all predictions.

Red-wheat
sataria

We have completed the construction of our facility, established transformation protocols for wheat and finger millet, and generated our first wheat edited plants. The transformation of wheat cv. Fielder is highly stable with over 30% transformation rates and strong expression of the transgenes. We are using the systems to study genes that confer resistance to biotic (diseases) and abiotic (draught and salinity) and to introduce new traits to wheat, and working on improvement of the editing tools and development of transformation in local cultivars.

Prof. Amir Sharon 
Project researcher

The George S. Wise Faculty of Life Sciences, Tel-Aviv University.

The lab deals with two main areas:

1. Isolation of disease resistance genes from wild wheat species.

2. Biology of plant pathogenic fungi.

Prof. Itay Mayrose 
Project researcher

The George S. Wise Faculty of Life Sciences, Tel-Aviv University.

פרופ' איתי מירוז

Email: itaymay@tauex.tau.ac.il

Phone: +972-3-6407212

Website: Prof. Itay Mayrose

Research areas:

Plant evolution and phylogenetics.
Using comparative, bioinformatics approaches to gain insights into the evolutionary dynamics of plant genomes.
Developing novel computational tools, based on machine learning, reinforcement learning, and advanced probabilistic evolutionary models.

Research partners:

ד"ר ערבה שתיל-כהן

Dr. Arava Shatil Cohen
Director of the Center for Genomic Transformation and Editing

Email: aravashatil@tauex.tau.ac.il

Institution:
The George S. Wise Faculty of Life Sciences, Tel-Aviv University.

ד"ר ראקש קומר

Dr. Rakesh Kumar
Postdoctoral researcher

Institution:
The George S. Wise Faculty of Life Sciences, Tel-Aviv University.

Dr. Anna Rice

Dr. Anna Rice
Postdoctoral researcher, Bioinformatician

Institution:
The George S. Wise Faculty of Life Sciences, Tel-Aviv University.

Udi Landau
Bioinformatician

Institution:
The George S. Wise Faculty of Life Sciences, Tel-Aviv University.