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Salim Al Babili, Ph.D., KAUST
Food Genomics

To Boost Crop Resilience, We Need to Read Our Plants’ Genetic Codes

By Salim Al Babili, Ph.D.
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Salim Al Babili, Ph.D., KAUST

In just 30 years, worldwide food production will need to nearly double to feed the projected population of 9 billion people. Challenges to achieving food security for the future include increasing pressures of global warming and shifting climatic belts, a lack of viable agricultural land, and the substantial burdens on freshwater resources. With the United Nations reporting nearly one billion people facing food insecurity today, our work must begin now.

A key research area to meet this crisis is in developing crops resilient enough to grow in a depleting environment. That’s why we need to search for ways to improve crop resilience, boost plant stress resistance and combat emerging diseases. Researchers around the world, including many of my colleagues at Saudi Arabia-based King Abdullah University of Science and Technology (KAUST), are exploring latest genome editing technologies to develop enough nutritious, high-quality food to feed the world’s growing population.1

Where We’ve Been, and Where We Need to Go

Farmers have been genetically selecting crop plants for thousands of years, choosing superior-looking plants (based on their appearance or phenotype) for breeding. From the early 20th century, following breakthroughs in understanding of genetic inheritance, plant breeders have deliberately cross-bred crop cultivars to make improvements. In fact, it was only a few decades ago that Dr. Norman Borlaug’s development of dwarf wheat saved a billion lives from starvation.

However, this phenotypic selection is time-consuming and often expensive—obstacles that today’s global environment and economy don’t have the luxury of withstanding.

Because phenotypic selection relies on traits that are already present within the crop’s genome, it misses the opportunity to introduce resilient features that may not be native to the plant. Features like salt tolerance for saltwater irrigation or disease resistance to protect against infections could yield far larger harvests to feed more people. This is why we need to explore genome editing methods like CRISPR, made popular in fighting human diseases, to understand its uses for agriculture.

What Our Research Shows

We can break down these issues into the specific challenges crops face. For instance, salt stress can have a huge impact on plant performance, ultimately affecting overall crop yields. An excess of salt can impede water uptake, reduce nutrient absorption and result in cellular imbalances in plant tissues. Plants have a systemic response to salt stress ranging from sensing and signaling to metabolic regulation. However, these responses differ widely within and between species, and so pinpointing associated genes and alleles is incredibly complex.2

Researchers must also disentangle other factors influencing genetic traits, such as local climate and different cultivation practices.

Genome-wide association studies, commonly used to scan genomes for genetic variants associated with specific traits, will help to determine the genes and mutations responsible for individual plant responses.3 Additionally, technology like drone-mounted cameras could capture and scan large areas of plants to measure their characteristics, reducing the time that manual phenotyping requires. All of these steps can help us systematically increase crops’ resilience to salt.

Real-world Examples

“Quinoa was the staple ‘Mother Grain’ that fueled the ancient Andean civilizations, but the crop was marginalized when the Spanish arrived in South America and has only recently been revived as a new crop of global interest,” says Mark Tester, a professor of plant science at KAUST and a colleague of mine at the Center for Desert Agriculture (CDA). “This means quinoa has never been fully domesticated or bred to its full potential even though it provides a more balanced source of nutrients for humans than cereals.”

In order to further understand how quinoa grows, matures and produces seeds, the KAUST team combined several methods, including cutting-edge sequencing technologies and genetic mapping, to piece together full chromosomes of C. quinoa. The resulting genome is the highest-quality quinoa sequence to date, and it is producing information about the plant’s traits and growth mechanisms.4,5

The accumulation of certain compounds in quinoa produces naturally bitter-tasting seeds. By pinpointing and inhibiting the genes that control the production of these compounds, we could produce a sweeter and more desirable crop to feed the world.

And so, complexity of science in food security increases when we consider that different threats affect different parts of the world. Another example is Striga, a parasitic purple witchweed, which threatens food security across sub-Saharan Africa due to its invasive spread. Scientists, including my team, are focused on expanding methods to protect the production of pearl millet, an essential food crop in Africa and India, through hormone-based strategies for cleansing soils infested with Striga.6

Other scientists with noteworthy work in the area of crop resilience include that of KAUST researchers Simon Krattinger, Rod Wing, Ikram Blilou and Heribert Hirt; with work spanning from leaf rust resistance in barley to global date fruit production.

Looking Ahead

Magdy Mahfouz, an associate professor of bioengineering at KAUST and another CDA colleague, is looking to accelerate and expand the scope of next-generation plant genome engineering, with a specific focus on crops and plant responses to abiotic stresses. His team recently developed a CRISPR platform that allows them to efficiently engineer traits of agricultural value across diverse crop species. Their primary goal is to breed crops that perform well under climate-related stresses.

“We also want to unlock the potential of wild plants, and we are working on CRISPR-guided domestication of wild plants that are tolerant of hostile environments, including arid regions and saline soils,” says Mahfouz.

As climate change and population growth drastically alters our approach to farming, no singular tool may meet the urgent need of feeding the world on its own. By employing a variety of scientific and agricultural approaches, we can make our crops more resilient, their cultivation more efficient, and their yield more plentiful for stomachs in need worldwide. Just as technology guided Dr. Bourlag to feed an entire population, technology will be the key to a food secure 21st century.

References

  1. Zaidi, SS. et al. (2019). New plant breeding technologies for food security. Science. 363:1390-91.
  2. Morton, M. et al. (2018). Salt stress under the scalpel – dissecting the genetics of salt tolerance. Plant J. 2018;97:148-63.
  3. Al-Tamimi, N. et al. (2016). Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping. Nature Communicat. 7:13342.
  4. Jarvis, D.E., et.al. (2017). The genome of Chenopodium quinoa. Nature. 542:307-12.
  5. Saade. S., et. al. (2016). Yield-related salinity tolerance traits identified in a nested association mapping (NAM) population of wild barley. Sci Reports. 6:32586.
  6. Kountche, B.A., et.al. (2019). Suicidal germination as a control strategy for Striga hermonthica (Benth.) in smallholder farms of sub‐Saharan Africa. Plants, People, Planet. 1: 107– 118. https://doi.org/10.1002/ppp3.32
FSMA

Company Resources Critical to FSMA Implementation

By Maria Fontanazza
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FSMA

In Part II of Food Safety Tech’s Q&A with Kathy Wybourn, Director Food & Beverage, USA & Canada at DNV-GL, we discuss FSMA preparedness and alignments of the regulation with GFSI.

Food Safety Tech: Now that we’re in the compliance phase, how prepared are food companies to meet FSMA requirements?

Read Part I: Embracing Big Data as an Asset to Your CompanyKathy Wybourn: It depends. Food companies must want to stay informed and make the necessary changes. What is critical in this change is the resources and organization, and not the size of a company. We still see large companies that are not ready for FSMA, same as with smaller companies. It comes down to what they have done proactively to keep up with the regulations, understanding the preventive pieces of that and the shift within their organization.

There are two pieces: It’s about being informed, plus the company’s culture for change. It comes down to management commitment. If you don’t have the management commitment to move an organization to being compliant with FSMA, you can be informed, but the culture isn’t there to support it.

FST: GFSI recently released Version 7.1 to incorporate more harmonization with FSMA. Any thoughts on this new version?

Wybourn: I was in the Technical Work Group for Version 7 guidance document. Adding in the food fraud and food defense components, and the new 7.1 Version brings the GFSI benchmark document closer to FSMA around suppliers and the use of non-approved suppliers.

It puts more requirements on the food manufacturer if they have supplier problems. For example, if there’s an interruption in the supply of a critical ingredient and you don’t have another supplier that’s going through the preventive hazard. It’s very important to know how to follow the requirements around non-approved suppliers. It all fits with the bigger picture of supply chain risks and transferring risks from a supplier (those things you don’t know about), understanding your suppliers and having a contingency plan. And if you don’t have that formal approval through your system, what are the requirements around using a non-approved supplier.

FST: How can the BRC FSMA Readiness Module help food companies with the Preventive Controls rule?

Wybourn: If you’re a BRC-certified site, it gives you guidance on what is needed to be FSMA ready. BRC benchmarked and identified what was missing in the standard and created a module that minimizes the gap. It gives you guidance and reference to the actual CFR and explains what’s needed.

FSMA

FDA Awards Nearly $22 Million to States for Produce Safety Rule

By Food Safety Tech Staff
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FSMA

FDA has awarded $21.8 million to 42 states to support the implementation of the FSMA Produce Safety rule. The State Produce Implementation Cooperative Agreement Program (CAP) provides states with the resources to enable the following:

  • Form a multi-year plan to implement a produce safety system
  • Education, outreach and technical assistance
  • Prioritize farming operations covered by the rule
  • Develop programs to address the needs of farming communities

According to FDA, “the intended outcomes of this cooperative agreement program are to:

Advance efforts for a nationally integrated food safety system (IFSS)
Plan, establish, and/or enhance state and territorial produce safety programs.
Encourage the safe production of fresh fruits and vegetables.
Promote understanding and compliance with the requirements of the Produce Safety Rule.”

Applicants were classified into five tiers of funding eligibility based on the number of farms growing covered produce within the jurisdiction. The agency has also provided a list of funding award amounts by state.

Learn more about FSMA at the 2016 Food Safety Consortium | December 7–8, 2016 | Schaumburg, IL | VIEW AGENDA

 

Stack of papers and folders

Supplier Documentation: To Automate or Not to Automate

By Maria Fontanazza
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Stack of papers and folders

Q&A Part I: Hiring and Training, Understanding FSMA Remain Big Industry ChallengesIn part two of Food Safety Tech’s Q&A with TraceGains, Anthony Arocha (customer success consultant), Rajan Gupta (vice president of customer success), and Jason Ulrich (customer success manager) explain the factors at play surrounding the lack of supplier documentation in the food industry.

Food Safety Tech: Just 44% of respondents said they automate supplier documents. What information can you glean from this? Why aren’t more companies automating?

Arocha: Companies understand that using technology is essential to manage the increasing demands on accurate food safety documentation and verification. For many companies, it is likely to be just a timing and resource issue as to why they have not yet adopted automation—timing as in they have not yet reached the pain threshold required to justify the new cost to implement and to have a resource to support or focus on it. As companies grow and new budgets get created, it is just a matter of time before they will have to include automation help if they have not already.

Gupta: I believe lack of internal respect for QA and thus lack of education and funding are key contributors to this area. Most of the quality staff is stuck doing daily activities with limited time to explore options to make their processes better. Lack of empowerment to make business process changes is also a large factor in not adopting technology. Marc states that the companies have silos as indicated by the transparency gains from technology—while that is true, the root cause of this may be that the various groups within an organization have never really paid attention to FSQA areas and thus never envisioned having access to information that can help the organization proactively manage risk and increase food safety awareness.

Ulrich: This is all about people money, and time. The industry as a whole doesn’t have enough in quality departments. The lack of qualified individuals available in QA departments has always been an issue. The money is usually used to improve production and other departments except quality. That leaves the limited resources in the department with very little time to review and implement new processes or software.

Food Safety ad Quality Assurance Survey, TraceGains
2016 Annual TraceGains Food Safety & Quality Assurance (FSQA) Professional Survey (Figure courtesy of TraceGains)

FST: Regarding supplier documentation management, where are companies falling short?

Arocha: Supplier document management is not easy. You are at the mercy of your vendors. I think the biggest issue is trying to do everything too fast versus having a risk-based approach and focusing on the top priority items first. Build on success. If you try to do too much too fast, it is hard to pick out the success stories easily and can become overwhelming.

Gupta: Anthony is right but he is also stating the obvious problem – “mercy of vendors”. We believe that technology such as TraceGains Network can improve efficiency greatly in sharing documentation and risk-based data, but lack of education and rapid acceptance within the industry of new approaches hinders innovation and limits already stretched resources to take shortcuts that may not be the best course of action long-term.

Ulrich:  In addition to what Marc, Anthony and Raj stated most are afraid to challenge the supplier. There is a fear of making them angry or asking for too much.