Is it possible to automate agrigenomics?

Genomics is a field of molecular biology that is transforming the future of agricultural practices. When combined with open, integrated automation solutions, it can significantly boost innovation and achieve scalable results.

Video Credit: Automata

Fundamentals of agrigenomics

Agricultural genomics, widely known as agrigenomics, leverages genomics to enhance efficiency and sustainability in crop cultivation and livestock breeding within the agricultural industry.

By employing advanced technologies like next-generation sequencing (NGS), agrigenomics helps farmers, breeders, and researchers identify genetic markers linked to desired or undesired traits, enabling more informed decisions in cultivation and breeding.

As an emerging science with transformative potential, agrigenomics promises to positively impact food security, especially in the face of environmental challenges brought about by climate change and a growing global population.

Applications of agricultural genomics

Agrigenomics covers a wide range of applications that are vital to human, animal, plant, and environmental health. Key applications include:

Crop improvement

Utilizing genomic data helps uncover the genetic foundations of desirable traits like disease resistance, crop yield, and drought tolerance. This knowledge supports the development of new genetically modified crop varieties with enhanced, beneficial characteristics.¹

Livestock improvement

Genetic data about livestock populations can be utilized to select desirable traits, such as growth rate, meat quality, improved milk yield, and resistance to disease and infection.²

Biofuel production

Agrigenomics can offer valuable insights into metabolic pathways and genes, helping optimize biofuel production, a renewable energy source in growing demand.³

Microbiome studies

Gaining a deeper understanding of the microbiome in livestock guts or soil can provide valuable insights into livestock digestion and plant health. This knowledge can enhance agricultural outcomes and contribute to improved animal and plant health.

Biodiversity and conservation

By increasing our understanding of the genetic diversity in livestock and crops, agrigenomics can play a vital role in improving the efficacy of conservation efforts.⁴

Traceability

Agrigenomics can be used to trace the origin of animal products. By matching the genetic makeup of a specific batch of crops or meat to its source, it ensures authenticity and quality.

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The importance of agrigenomics

Agrigenomics holds significant importance for the broader population, not just those directly involved in agriculture. By opening up potential improvements in the yield and quality of animal and crop products, it plays an increasingly crucial role in addressing climate change, food insecurity, and the challenges posed by a growing global population.^1,2,5

Its ability to accelerate biofuel production and promote more sustainable agricultural practices makes agrigenomics essential in meeting the rising demand for renewable energy as the climate crisis progresses.³

Climate change is also impacting habitats and ecosystems, resulting in a loss of biodiversity.⁶ The loss of carbon sinks (for example, peatlands and rainforests) is exacerbating the effects of climate change. By developing a greater understanding of biodiversity and intensifying efforts to restore it, this positive feedback loop may be slowed.⁴

Beyond enhancing food security and environmental health, agrigenomics has applications in microbiome studies and traceability, which can improve health outcomes for both animals and humans.

Scientists can utilize genetic data to better understand the genetic basis of disease in plants and animals. By developing strategies to prevent or resist disease, plant and animal health improvements will ultimately lead to higher-quality food products for humans.¹

The benefits of open, integrated automation in agrigenomics

Agrigenomics is a rapidly expanding field with an increasing need for scalability as the demand for environmental sustainability and food security intensifies in response to the climate crisis and a growing global population.

The sector stands to gain significantly by adopting open, integrated automation solutions like Automata’s LINQ platform, which provides several key advantages for genomics in agriculture.^7,8

Scalability and efficiency

The use of open, integrated automation can reduce manual tasks and streamline processes in genomic research.⁹ Automating DNA extraction and sequencing allows samples to be processed quickly, consistently, and reproducibly, while also increasing the number of samples that can be handled.

Automata has recently worked with The Francis Crick Institute to automate sample library preparation as part of genomics and NGS workflows.

Automata’s quality control solution helped one lab reduce its setup time for genomics workflows from 370 minutes to just 15 minutes and its manual touchpoints from 1388 to 7. Applying this to agrigenomics applications could lead to increases in efficiency, scalability, and cost-effectiveness.

Data integration

An open platform allows for the integration of data from a variety of sources. In agrigenomics, this means combining genotypic data (such as DNA sequences) with phenotypic data (such as crop yield, disease resistance, or animal growth rates).

Integrating these data types enables comprehensive analysis and enhances decision-making, leading to the development of genetically modified plants or animals with desirable traits.

Faster time to insight

The automation and integration of processes can significantly reduce the time between collecting samples and deriving actionable insights or data.

Farmers, researchers, and breeders can make informed decisions more quickly, a crucial advantage given that many applications of agrigenomics address urgent issues like climate change.

Enhanced knowledge base

Open automation systems combined with cloud-based orchestration software can facilitate knowledge exchange and collaboration, contributing to a more comprehensive understanding of plant and animal genomes and their interactions with the environment.

Such knowledge has important implications for conservation and biodiversity efforts, which would greatly benefit from large-scale genomic studies and the integration of data from multiple research efforts.

LINQ automation for agriginomics

Fully automated agricultural genomics solutions are the perfect solution for agrigenomics applications. They offer scalability, greater processing efficiency, and accelerated time to insight.

References and further reading

1. Labant M. Agrigenomics Yields a Next-Gen Cornucopia: Benefits of genome editing and molecule-sensing technologies in agriculture include more sustainable crops and healthier foods. Genet Eng Biotechnol News. 2019;39(11):24-26, 28. doi:10.1089/gen.39.11.09
2. Suminda GGD, Ghosh M, Son YO. The Innovative Informatics Approaches of High-Throughput Technologies in Livestock: Spearheading the Sustainability and Resiliency of Agrigenomics Research. Life. 2022;12(11):1893. doi:10.3390/life12111893
3. Misra N, Panda PK, Parida BK. Agrigenomics for Microalgal Biofuel Production: An Overview of Various Bioinformatics Resources and Recent Studies to Link OMICS to Bioenergy and Bioeconomy. OMICS J Integr Biol. 2013;17(11):537-549. doi:10.1089/omi.2013.0025
4. Supple MA, Shapiro B. Conservation of biodiversity in the genomics era. Genome Biol. 2018;19(1):131. doi:10.1186/s13059-018-1520-3
5. Berman J, Zhu C, Pérez-Massot E, et al. Can the world afford to ignore biotechnology solutions that address food insecurity? Plant Mol Biol. 2013;83(1-2):5-19. doi:10.1007/s11103-013-0027-2
6. How are climate change and biodiversity loss linked? Accessed August 17, 2023. https://www.nhm.ac.uk/discover/how-are-climate-change-and-biodiversity-loss-linked.html
7. Meldrum D. Automation for Genomics, Part One: Preparation for Sequencing. Genome Res. 2000;10(8):1081-1092. doi:10.1101/gr.101400
8. Meldrum D. Automation for Genomics, Part Two: Sequencers, Microarrays, and Future Trends. Genome Res. 2000;10(9):1288-1303. doi:10.1101/gr.1574009. Tegally H, San JE, Giandhari J, De Oliveira T. Unlocking the efficiency of genomics laboratories with robotic liquid-handling. BMC Genomics. 2020;21(1):729. doi:10.1186/s12864-020-07137-1

Acknowledgments

Produced from materials originally authored by Automata Technologies Ltd.

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When two architects from Zaha Hadid’s research lab first approached robotics, their idea was to explore applications specific to architectural engineering.

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