Breeding for protein is an emerging goal for plant breeders. In recent years, the search for new plant-based alternative proteins has grown along with concerns about healthier lifestyle and the sustainability of global food systems. The demand for high quality plant protein as an alternative to protein sourced from animals is driven by multiple motivations: reducing the use of valuable water and land resources; addressing the environmental pollution caused by massive animal production and the associated supply chains; animal welfare; improvement of food safety, thereby yielding additional benefits for many vulnerable populations as well as improving health by decreasing the overall consumption of meat.

The motivation for expanding current resources of plant-based protein
 The economic potential of alternative protein increases the motivation for many breeding entities, research institutes, farmers, and food companies to focus on this relatively new segment. Plant proteins are needed for “feed” as well as “food,” but breeding for alternative protein involves intense and expensive research and development work, deep understanding of food industry needs and design of new plant breeding objectives, platforms and workflows.

Breeding entities, farmers, grain dealers, and food companies are all searching for the most suitable crop, with an optimal combination of traits for their products. All parts involved in the food supply chain seek crops that fit food industry requirements from isolating and processing the protein to integrating it in an high quality end product that addresses market demand.

For many years, soy was (and remains) the main source for alternative plant-based protein. Soy offers preferable agrotechnical traits and provides a high protein yield; it contains all essential amino acids and is considered a “complete protein” for human needs. Complete proteins are not enough, thus the food industry reflects demand for additional protein qualities such as natural taste, foaming, color and digestibility. Demand for these qualities creates opportunities to include other crops such as lentil, fava bean, chickpea, quinoa, and even hemp in various plant-based protein products.

Challenges in breeding for protein
Once a certain crop is chosen for a specific plant-based protein product, an extensive exploration process is launched by breeders and other R&D professionals to discern the best varieties for a given product. Agrotechnical traits are measured and collected from the field, and protein quantities and qualities are being measured in the lab.

This essential operational task creates a significant bottleneck for breeding companies that must extract seeds from thousands of plants in the field, deliver the seeds into labs, and execute various measurements within a limited period of time. The agricultural calendar determines a tight timeline within which breeders must determine which plants are candidates for the target product, and which should be sown in the field for additional examination in the following breeding season. This process involves the expense of highly qualified lab workers and bioinformaticians, as well as costly lab material and equipment. Plant breeding companies that breed for protein must invest significant resources in building special platforms for this goal, above and beyond their regular facilities.

When breeding for protein, financial and operational barriers are not the only challenges. To improve the accuracy and to speed up the process, nowadays, many breeders rely on genomic data. Genomic solutions turned into an integral and invaluable part of the whole trait discovery practice, enabling an understanding of the full genetic content of the plant and the detection of specific genes, their combinations and correlations between genes and traits. Measuring protein-related traits must be quick and accurate in high-throughput pipelines and carried out in conjunction with genotype screening of large numbers of plants. These traits are mainly quantitative traits which are affected by many different genes in different loci . This requires smarter sequencing, as well as efficient genotyping and analysis solutions.

A genotyping panel must be designed to describe the genetic material of plants in a specific breeding program to the greatest degree possible, as identifying the genetic signature for protein traits is essential for high-throughput screening of those progenies that potentially provide the best combination of desired protein related traits. The genotyping panel should describe polymorphism between parental lines that are the genetic source of the breeding program. Optimally, the panel will also enable imputation of markers to save money and increase genetic information. Genomic selection and marker association selection methods are utilized for the detection of protein-related genetic signature that represents the desired product—the seed for a drop with higher protein yield and improved protein traits.

Why get involved?
The road that leads to the enriched protein seed is complex and involves many challenges. When successful, this road benefits all participants in the supply chain, from breeding companies, farmers, and grain dealers to the food industry. Ultimately, some would say that humanity itself will derive the main profit from improvements in alternative plant-based proteins.

Arie Zackay, Ph.D.

Arie has recently joined NRGene as a computational biologist and a project manager. He holds a PhD. in Microbiology and Molecular Genetics from the Hebrew University of Jerusalem and a B.Sc. and M.Sc in bioinformatics from the Freie Universität Berlin. Arie has an extensive experience in developing various genomics and genotyping tools for the industry and academy. In the recent years he has been focusing on computational plant breeding and integration of genomics tools in the plant-breeding industry.

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