Increasing Crop Yield Through Smart Approaches In Trait Discovery

This year, genetically modified crops will be planted on an estimated 470 million acres worldwide. The core biotech traits deployed in crops were developed and commercialized over 20 years ago using recombinant DNA technology. Since the introduction of successful traits to protect against pests, the agriculture industry invested in the mass screening of individual plant genes to improve crop yield without ever gaining traction in the identification of new yield traits or seeing a return on investment for the effort.

In early 2018, members of the Yield10 team published a paper entitled Metabolic Engineering to Increase Crop Yield: From Concept to Execution. This paper asserts that complex traits such as yield are likely to involve multiple genes, and smart approaches must be developed in order to successfully identify and commercialize promising new yield traits.

The paper also discusses how trait discovery programs incorporating in silico analyses of plant metabolism and gene networks can move trait discovery beyond trial and error approaches and towards rational design strategies. Yield10’s research is founded upon the belief that complex traits such as crop yield are likely multigenic, and the exhaustive and expensive screening of random gene combinations to achieve yield gains is not realistic. Instead, the company emphasizes the use of metabolic models that employ flux-balance analysis used to determine the contribution of individual genes to a trait, or for further review of metabolic pathways for synthetic design. Regulatory association networks provide a transcriptome-based view of the plant and can lead to the identification of transcription factors that control the expression of multiple genes affecting a trait.

The paper also cites various external factors impacting development in terms of both cost and timelines for the ultimate goal of commercialization.

Research at Yield10 is using predictive models to identify novel gene targets capable of increasing seed and biomass yields in key crops such as camelina, canola, soybean, corn, sorghum, rice, and others.

Core to Yield10’s process is a metabolic engineering approach where the team is focused on optimizing the flow of carbon from its initial capture in leaf tissue through its deposition in seed or biomass. This paper references Yield10’s own trait discovery program, a platform designed to move beyond trial-and-error approaches and towards rational design strategies.

Yield10 has reported results with C3003, a trait that acts as a transporter and is based on a gene in algae which has been deployed in camelina and canola and produced significant increases in seed yield. Using C3003 to probe the flow of carbon through Camelina, Yield10 researchers identified a highly upregulated plant gene which it has named C3004.

In September 2018, Yield10 reported promising results for novel yield trait C3004 in growth chamber studies conducted using Yield10’s Camelina platform. In this study, Camelina plant lines containing C3004 grew vigorously, and the best lines produced increases in seed yield in a range of 26% to 65% as compared to control plants. Given the promising results, Yield10 researchers are planning field tests of C3004, as well as deploying C3004 as a Crispr-cas9 genome-edited trait in oilseed and other crops.

Yield10 believes that new approaches must be utilized to capitalize on advances in technology and that the recent stance by the US and other global regulatory bodies appears committed to addressing global food security by spurring innovation. This sentiment is shared by many in the agricultural biotech space who were encouraged by the USDA’s recent guidance on genome-editing in plants comparing the use of genome-editing in plants as akin to plant breeding, and therefore not subject to the complex regulatory path required to commercially introduce GMO crops. The advances in technology combined with a clarification of the regulatory path for traits achieved through genome editing is leading many to believe a new wave of innovation in agriculture is coming capable of capturing the interest of the agricultural, consumer, and investment communities.

In Yield10’s research, the use of these models from the perspective of the company’s trait discovery and development program are detailed extensively, and one day may make significant impacts on the cost and timeline for developing new yield traits for major row crops – all of which could help in the challenge of addressing global food security challenges.

These findings are described in the article entitled Metabolic engineering to increase crop yield: From concept to execution, recently published in the journal Plant ScienceThis work was conducted by Frank A. Skraly, Madana M.R. Ambavaram, Oliver Peoples, and Kristi D. Snell from Yield10 Bioscience, Inc.

About The Author

FAS
Frank A. Skraly

Frank is a senior director and scientific researcher at Yield 10.

MMA
Madana M.R. Ambavaram

Accomplished ‘Plant Molecular Geneticist’ with more than 10 years of experience in both industry and academia. Demonstrated experience working with multiple crop plants (Maize, Rice, Soybean, Switchgrass etc.) to study extreme or specialized environmental conditions using functional genomics approach. Proficient in characterizing the molecular, biochemical and physiological changes conferred by transgenes and their effect on biomass and yield related traits. Expertise in several computational biology techniques, including, but not limited to, transcriptome-based gene regulatory association network analysis for gene discovery to enable step changes in plant productivity. Exhibits strong communication and organizational skills and an ability to work effectively in coordinating research efforts in a team environment and across research groups.

Oliver Peoples

Oliver P. Peoples, Ph.D. was named President and Chief Executive Officer of Metabolix in October 2016 in conjunction with the transition to Yield10 Bioscience as the Company's core business. Dr. Peoples was a co-founder of Metabolix and served as our Chief Scientific Officer from January 2000 until October 2016, and was previously our Vice President of Research and Development. Dr. Peoples has served as a director since June 1992. Prior to founding Metabolix, Dr. Peoples was a research scientist with the Department of Biology at the Massachusetts Institute of Technology where he emerged as a pioneer of the new field of metabolic pathway engineering and its applications in industrial biotechnology. The research carried out by Dr. Peoples at MIT established the fundamental tools and methods for engineering bacteria and plants to produce Mirel biopolymers. Dr. Peoples has published numerous peer reviewed academic papers and is an inventor of over 90 patents and patent applications worldwide. Dr. Peoples received a Ph.D. in Molecular Biology from the University of Aberdeen, Scotland..

Kristi D. Snell

My career has focused on the metabolic engineering of plants and bacteria to produce value-added products. Through metabolic engineering, one can redirect a portion of an organism's metabolism to produce a target product, such as a molecule or polymer, or to enhance the organism's growth and yield.

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