Sharbel: Comparative genomics of apomictic plants: advancing novel tools for niche breeding
Date: December 2017
Term: 2 years
Status: Completed
Researcher(s): Timothy Francis Sharbel; Global Institute for Food Security (GIFS), University of Saskatchewan, Philippe Riggault, Gydle
SaskCanola Investment: $47,150
Total Project Cost: n/a
Funding Partners: ADF, GIFS
Project Summary
Researchers at the University of Saskatchewan conducted a two-year project to further the discovery and subsequent genetic transformation for the introduction of apomixis technology into agriculture crops. Apomixis technology would provide an enormous advance to crop breeding by significantly shortening the production time of novel hybrid varieties, and by enabling the exploitation of traits previously too complex to harness using standard breeding approaches. Researchers completed a gold-standard assembled genome of a model system of the sexual Boechera stricta, and are in the process of finalizing the assemblies of a further three apomictic genomes from the same genus. Researchers are continuing to integrate the project data with various projects underway in the Sharbel lab to accelerate progress in transferring apomixis to crops, including canola, wheat and maize.
Crop breeding typically requires many (8 to 10) generations in order to produce a new and improved variety at considerable costs. Apomixis, a naturally occurring form of asexual reproduction in plants that is found in several plant families, is a tool that would potentially significantly reduce both the time and costs associated with developing novel crop varieties. Apomictic plants produce normal seeds containing embryos that grow into plants that are genetic clones of themselves, regardless of their homo- or heterozygous state on a genome-wide scale. Apomixis technology would provide an enormous advance to crop breeding by significantly shortening the production time of novel hybrid varieties, and by enabling the exploitation of traits previously too complex to harness using standard breeding approaches.
Researchers at the University of Saskatchewan initiated a two-year project in 2015 to further the discovery and subsequent genetic transformation for the introduction of apomixis technology into agriculture crops. The genus Boechera, a wild relative of Brassica, was selected as an ideal model system to compare sexual and apomictic reproduction and associated life history traits. Project objectives were to: i) use a hybrid sequencing approach (short and long read sequencing), in addition to Irys optical genome mapping, to assemble the complex genomes of three sexual and three apomictic Boechera, and ii) to perform a genome-wide isoform analysis of microdissected reproductive tissues from the same plants. To address the challenges during the assembly and analysis of the genomes under investigation, researchers used complementary state- of the art high throughput or new-generation sequencing (NGS) together with mapping technologies and innovative bioinformatics software tools designed to integrate data from these technologies into accurate genome representations.
For the project, researchers developed a single diploid sexual genotype of Boechera and samples were sent to NRGene for whole genome sequencing. From the same genotype, two RNA samples from each of the following: leaf, stem, and flower were delivered for Ilumina sequencing at NRC. Furthermore, a comparative genome-sequencing (short and long read sequencing), single-molecule mapping and mRNA isoform analysis project was completed in three sexual and three apomictic members of the genus Boechera. The researchers have completed a gold-standard assembled genome of a sexual Boechera stricta, and are in the process of finalizing the assemblies of a further three apomictic genomes from the same genus, using the sexual genome as a reference.
Overall, all of the research data has been collected, and researchers are in the process of performing high-powered bioinformatics and statistical analyses of the remaining apomictic genomes, in addition to the sequenced and mapped mRNA isoform spectra isolated from ovules from each individual. Researchers are working on integrating the project data with the various projects underway in the Sharbel lab to accelerate progress in transferring apomixis to crops, including canola, wheat and maize. Apomixis would enable hybrids to be tested in the first generation, thus providing more rapid and accurate data to breeders for making advancement decisions, and will have significant influences on industry at a number of levels.
Full Report PDF: Comparative genomics of apomictic plants: advancing novel tools for niche breeding