Genetics in Food Processing Part 1 - Genetic Modification and Food

February 2023

Introduction

Food biotechnology is the application of biological techniques to food crops, animals, and microorganisms to improve the quality, quantity, and safety of ingredients and foods. This includes traditional food manufacturing processes, including using yeast in baking and brewing, bacteria and fungi in cheese manufacturing and processing fermented foods such as kimchi, kombucha, sauerkraut, and sourdough bread.

Random variation from genetic recombination and mutation occurs naturally in all living things resulting in the evolution of new variants and species through natural selection. Whole genome profiling through genetic sequencing has uncovered many of the mysteries of DNA and inheritance. The development of molecular tools in biology that can isolate specific genes and insert them into particular parts of a genome has given us many new insights into the molecular biology of cells for research applications in medicine and our food industry.

Even before this specific tailoring of genes using molecular biology, we have taken advantage of natural genetic variation through the classical breeding of plants, animals, and microorganisms that started around 10,000 years ago when humankind settled and cultivated wild populations of plants and animals. By carefully choosing offspring of selective crosses between hybrids, cultivars and breeds, our ancestors produced domesticated variants suited to agricultural and food production. This type of selective breeding is time-consuming. What we see today in crops, livestock, and even our domestic pets are a snapshot of 10,000 years of natural selection for convenience and temperament. More recent developments have taken place in the following key areas.

  1. Meaningful change to crop and livestock variants takes decades and includes many different factors such as nutrition, flavour and taste, convenience, and suitability can take decades. It involves transferring an indefinite range of genes between individuals of compatible species. In classical breeding programmes, the immediately visible or detectable desirable traits were selected for, such as colour, and structures that were associated with successful harvests (e.g. shorter plants), increased yield (e.g. high grain numbers per plant), or animals that produce twins. These positive traits may be selected alongside less visible negative traits closely located on the genome or genetically linked metabolically, meaning visual classical selection could result in loss or gain of disease resistance or nutritional factors.
  2. Some of the resulting hybrid vigour demonstrated from adventitious cross breeding may arise in plants from multiple copies of chromosomes being conserved in the offspring. Commonly organisms contain two sets of chromosomes in cells (diploid), and naturally occurring crosses resulting in numerous copies arising (polyploidy) may be responsible for critical evolutionary jumps (e.g., wheat) by generating offspring with fewer recessive traits being expressed and more dominant traits being over-expressed. Thus larger, more robust, higher yielding offspring rise, and through this, heterosformorms are the basis of many historical crop improvements via plant breeding programmes.
  3. The passing on of undesirable, not readily visible traits during selection is not entirely random but is not easily predictable. Negative characteristic as disease susceptibility carried over into subsequent generations can, after many generations of backcrossing, be removed at least to some degree to produce a suitable commercial variety or breed. With molecular biology technologies, we were able to identify precisely how genetic material is transferred between organisms and how genetic mutations can impact the subsequent tangible (phenotypic) expression of genetic traits.  Emergent technologies have scaled our initial forays into molecular biology so that the whole cellular system can be characterised by genomics, transcriptomics, proteomics, and metabolomics. These uncover how genetic code is interpreted in the processing (transcription and translation) of genes into proteins so that their impact on metabolic processes can be defined. These technologies have already provided rapid advances in the development of therapeutics, e.g., vaccines genetically engineered to give immunity to the SARS-CoV-2 virus responsible for the COVID-19 pandemic, and the identification and treatment of inheritable diseases, e.g. Duchenne muscular dystrophy.

The ability to change biology at the genetic level has been recognised since the discovery that ionising radiation (e.g. X-rays) and genotoxic chemical agents (e.g. ethyl methanesulphonate) can damage DNA, giving rise to genetic mutations. The transfer of DNA fragments and genes between bacteria or viruses to bacteria has been understood as a natural phenomenon for many years. They have provided the initial tools to manipulate specific genes in plants and animals. Fragments of transferred DNA will change the expression of the host DNA in specific ways, including the expression of a new protein or changing the activity of biochemical pathways so that they are up-regulated, down-regulated, or switched off completely. Herbert Boyer and Stanley Cohen were the first to demonstrate such recombinant technologies by inserting DNA from one bacterium into another in 1973. This research led to insulin production from a transgenic technology in 1978, using transferred fragments of bacterial DNA containing the DNA sequence for insulin. The transferred fragment was called a plasmid, a self-replicating bacterial DNA particle that, in this case, had the bacterial DNA for replicating and the inserted DNA for human insulin. [1]

The demand for insulin was as a treatment for diabetes and there are around 150–200 million people requiring insulin therapy worldwide [2]. The treatment of diabetes has seen many advances since this first demonstration in the 1970s, and medical insulin is typically made via fermentation using genetically modified bacteria that have the human gene for insulin biosynthesis.

The agri-food sector has utilised transgenic biotechnology for a similar length of time. It was discovered that certain bacteria could be exploited to prevent ice formation on the leaves of glasshouse crops [3]. The new recombinant DNA technology enabled genes to be silenced to produce bacteria naturally found on plants but modified, so less ice nucleation occurs, protecting plants from frost damage [4, 5]. The resulting so called ice-minus strain of Pseudomonas syringae became the first genetically modified organism (GMO) to be released into the environment. Strawberry and potato crops were sprayed with the ice-minus strain of P. syringae around 1987 to provide improved protection against frost. This targeted approach was subsequently used in developing new plant crop cultivars, and later fish and livestock, and was termed genetic modification (GM). It is also known as genetic engineering, bioengineering, genetic manipulation, gene technology and recombinant DNA technology. Where foreign genetic material, for example, from another species, is transferred into the genome of a recipient, it may be termed transgenics. The collective term ‘Genetically Modified Organisms’ is used frequently in regulatory documents and scientific literature to describe the deliberate introduction of DNA by human intervention into plants, animals, and micro-organisms. GMOs are officially defined in EU legislation as ‘organisms in which the genetic material (DNA) has been altered in a way that does not occur naturally by mating or natural recombination’. UK regulations have, until recently, taken a common position as EU states towards GM use in the supply of food and feed. The European ‘Organic’ food sector has also adopted a comprehensive ban on GMOs and ingredients derived from GMO sources. For food flavourings, for example, many are produced using fermentation technologies, potentially with genetically modified microorganisms (GMMs) at some point in the manufacturing process. The following European Flavour Association (EFFA) summary table illustrates the current regulatory position. [6].  

Table 1 - Current Status of EU/UK Flavouring Ingredients in Standard and 'Organic' Food Supply

In agriculture, the most utilised transgenes to date have been those responsible for herbicide resistance in plants. The major crops that have this modification have a gene from bacteria that has an herbicide insensitive form of an essential enzyme. The commonly used herbicide glyphosate inhibits the functioning of a critical enzyme used by all plants (not animals) to synthesise essential amino acids. Only herbicide resistant plants will survive the application of broad spectrum herbicides like glyphosate that, when applied would otherwise kill all plant types whether crop or weeds [7].

In the 1970s, GM methods using recombinant DNA technology offered the potential to enhance agri-food industry breeding programmes for food and feed crops, ornamental plants and animals. The aim was to speed up the selection of genetic traits. Typical breeding improvements used established transgenic GM techniques that introduced genetic material from unrelated species using Agrobacterium tumefaciens mediated transformation. Alternatively, biolistic methods were used, which involved  firing particles of genetic material into cells and was dramatically termed the ‘gene gun’ method. These both required expensive selection programmes using herbicide, bioluminescence or antibiotic resistance marker genes attached to the functional gene transferred. This was done, so the identification of successful transfer of the transgene constructs into new crops or livestock was made possible. Despite these marker traits being silenced or removed in the subsequent breeding programs, concerns remain that the particular herbicide and antibiotic resistance genes could enter the environment and cause harm. As a precaution, regulatory authorities typically restrict antibiotic resistance markers (ARMs), for example, to antibiotics with an established record of use and no clinical importance. In 2004, a working party of the British Society for Antimicrobial Chemotherapy stated, “There are no objective scientific grounds to believe that bacterial antibiotic resistance genes will migrate to bacteria to create new clinical problems.” They investigated routes where these genes could enter the environment but were ‘unable to identify a credible scenario whereby new drug-resistant bacteria would be created’ [8].

The potential benefits of GM technology compared to traditional breeding are described as follows:

  1. GM enables a focussed selection of diverse traits for improvement programmes.
  2. It is a more expedient route to breeding and selection. Desired change can be achieved in fewer generations.
  3. Lower cost of generating new varieties and breeds.
  4. Allows greater precision in selecting characteristics and reduces the risk of random occurrence of undesirable traits.
  5. Lower labour and energy inputs are required in developing new varieties and breeds.
  6. Lower agricultural inputs as outcomes of new breeding programmes. These include reduced fertiliser and water requirements that facilitate improved soil management, such as the use of ‘no-till’ soil cultivation made possible using herbicide resistant crops.
  7. Reduced amounts of crop protection agents used in agriculture. See the later section headed 'Insect pest management in crops'.
  8. Improved processing characteristics, including storage and shelf-life stability, result in reduced food supply chain waste.

Some of the traits targeted include, but are not limited to, improved yield; resistance to insect pests and diseases; herbicide tolerance; drought resistance; tolerance to high salinity; improved nutritional content; removal of allergens; enhanced organoleptic properties. The early application of genetic engineering using transgenic bacteria (P. syringae) to reduce ice nucleation on the leaves of frost-susceptible crop plants was developed as a now discontinued product called Frostban™. Since then, the most commercialised GMOs have been soybean, maize, cotton and oilseed rape. Specific case studies of where GM technology has been used to improve production and processing are now described.

Allergens

The removal of allergens or toxic components includes ongoing research to produce non-allergenic peanut/groundnut (Arachis hypogaea) [9] and wheat (Triticum aestivum) varieties. Having a coeliac-safe wheat is particularly challenging because gluten is a complex mixture of about 100 proteins encoded by many genes. One team solved this problem by silencing a master regulator of prolamin accumulation in wheat grains. [10] Protection against allergens can be built into commodity crops, including rice (Oryza sativa). In 2007, transgenic anti-allergy rice was developed to protect against Japanese cedar pollinosis in sufferers. The seeds of the transformed plants expressed 7crp gene-modified cedar pollen allergens (Cry j 1 & 2) that provoke only a low-level antibody reaction. However, this protects a full allergenic response by triggering a mucosal immune response to cedar pollen allergens [11, 12, 13, 14]. Currently, no studies have found that proteins from modified crops trigger allergic responses any differently than from non-modified organisms in allergic subjects. There needs to be more research looking at the potential for allergens from modified organisms to trigger allergic responses in previously unaffected subjects more frequently than from exposure to unmodified organisms. The lack of evidence of proteins from GM organisms triggering new allergic reactions is not proof of it not occurring, but further research is required to build an evidence base. [15, 16, 17]

Impacts on yield

Despite the crop improvements brought about through genetic engineering, there is little evidence to indicate that increased crop yields over the past 20 years have been any greater for GM crops than for non-GM crops. That does not mean there has been no economic, environmental and sustainability gains and the realisation of potential yields through various crop management improvements. [18].

There has been a great deal of interest in improving the sustainability of nitrogen fertilisation by manipulating symbiotic nitrogen fixation in crop plants. With the advent of new molecular biology tools, it is now understood that mycorrhizal root symbiosis evolved in land plants hundreds of millions of years before the development of legume-rhizobia symbiotic nitrogen fixation. Recent research has shown that over 196 genes are involved in effective symbiosis and root nodulation. The transfer of nodulation properties from legumes to non-legumes, such as cereal crops, is one strategy to improve yield. This is likely a key area of future developments [19].

Impacts on nutrition

Vitamin A: Research has targeted increased provitamin A (b-carotene) content in rice, intending to help to prevent blindness resulting from vitamin A deficiency (VAD) among children in South and South East Asia. VAD may affect up to 20% of children in the Philippines and 190 million under 5year olds globally. “The vitamin A rice project was considered a scientific breakthrough because it was the first case of pathway engineering (The Golden Rice Tale by Ingo Potrykus), and the first high level b-carotene rice plants were reported in 2000 [20]. So-called “Golden Rice” was found to be an effective source of vitamin A for human consumption [21] and the first field trial was completed in Louisiana, USA, in September 2004. Regulatory food safety approval followed in Australia and New Zealand (2017), Canada and the USA (2018), and the Philippines (2019). The first commercially grown rice was harvested in the Philippines in October 2022, following approval for cultivation in 2021 [22].

Vitamin E: a natural, fat soluble, dietary antioxidant comprising a group of tocopherol related compounds, with a-tocopherol being of primary importance for human nutrition. Rich dietary sources include cereal grains, nuts, and a range of leafy vegetables but maize, for example is a poor source of a-tocopherol.  Researchers at the Donald Danforth Plant Science Centre in Missouri, USA announced in 2003 that by inserting a gene extracted from barley into a common type of maize, they had created a strain that overexpresses a key tocopherol biosynthesis enzyme, homogentisic acid geranylgeranyl transferase (HGGT). Crops grown with the modification produce corn with six times the usual amount of vitamin E [23].

Omega-3 fatty acids: several GM research projects exist to develop crops with elevated levers of essential fatty acids, including omega-3. For example, oilseed rape (OSR) cultivars that produce omega-3 fatty acid, DHA (docosahexaenoic acid), thus minimising the reliance on fish as the primary source of omega-3. However, soya remains the primary target for developing improved fatty acid biofortification [18, 24].

Biofortification and removing anti-nutritional factors: cassava is an edible tuberous root that is resistant to drought, diseases, and pests and is a significant source of carbohydrates in tropical areas. However, the cassava plant tissues contain enzymes responsible for cyanogenesis that can cause cyanide poisoning if consumed without appropriate processing. The Bio Cassava Plus Project was set up as an international multi-centre research team led by Ohio State University, to produce GM cassava with improved nutritional value. Tubers would contain enough vitamins, minerals, and protein to provide poorer communities and the malnourished with a day's worth of nutrition in a single meal while reducing the cyanogen content. Several reported incidents have occurred when lethal levels of cyanide have been released from otherwise edible plant tissues because of sub-optimal processing [25]. Successful greenhouse trials subsequently led to field trials [18]. Many examples of biofortification are subject to current research or have produced results with crops already approved and, on the market, [24].

Effect on animal feed quality

Phytate - a GM maize has been developed that could help improve the nutritional value of livestock feed and reduce pollution. Initial research was carried out by the Chinese Academy of Agricultural Sciences (CAAS). GM maize produces corn containing high levels of the phytase enzyme. This enzyme helps livestock digest phosphorus enclosed in the indigestible form of phytate. Animals lack phytase in their system. As a result, farmers add the enzyme to animal feed to help livestock digest phosphorus. The CAAS scientists isolated the gene that produces phytase from a species of the fungus Aspergillus and inserted it into fodder maize kernels. Preliminary tests have shown that compared to traditional varieties, the rate of seed germination, growth speed and yield of the GM maize was no different. Potential cost savings exist if conventional feed additives are replaced by modified fodder maize. Also, phosphorus pollution from animal waste is a serious problem, and improved phosphorous digestibility could provide environmental benefits by decreasing runoff into surface waters. At least 12 crop species have now been engineered with a phytase gene for the expression of the phytase enzyme for improving sustainable phosphorus utilisation. [26]

Insect pest management in crops

The soil bacterium Bacillus thuringiensis (Bt) have genes that code for proteins that, when incorporated into a plant genome via genetic engineering, results in the production of a Bt protein that, when ingested, disrupts cells in the target insect’s digestive system, resulting in death. A range of Bt proteins may be incorporated into a crop to target different insect species or to protect against tolerance to a Bt toxin that can evolve. Bt plant-incorporated protectants (PIPs) have been incorporated into various crops, e.g. Bt maize, aubergine (eggplant), cotton and poplar trees. [18]

Since 1995, EPA has registered numerous cotton and maize PIPs that growers have widely adopted in the United States and other countries. For example:

  • Bt cotton PIPs designed to control lepidopteran (moth) larvae (budworms and bollworms).
  • Bt corn PIPs developed to control lepidopteran larvae (corn borers) and/or coleopterans (corn rootworm beetles). [27]

Although results are variable, Bt modified crops introduced between 1996 and 2015 have, in many locations, contributed to a statistically significant reduction in the gap between actual yield and potential yield when targeted insect pest pressure has been particularly high and has resulted in substantial damage to non-GE varieties and where conventional pesticide treatments did not provide adequate control. In areas of the United States where adoption of Bt maize or Bt cotton is high, there is statistical evidence that insect-pest populations are reduced regionally, and the reductions benefit both adopters and nonadopters of Bt crops. [18]

In experimental plots, the difference in yield between Bt and non-Bt varieties is sometimes demonstrated to be due to decreased insect damage to the Bt variety. However, in cases in which comparisons are not between true isolines (the identical cultivar with and without the modification) differences may be due to other characteristics of the Bt varieties or a combination of crop variety and decreased insect-pest damage. [18] This would also be true if Bt and non-Bt varieties were cultivated in different locations, by other growers or across seasons. These differences could confound the estimation of the apparent yield advantage of the Bt varieties. This is one example that highlights the challenges in quantifying the benefits of GMOs in real word applications, a problem for producers that need to be confident that they will realise a return on investment when adopting GMOs. However, this is true for any crop and animal husbandry strategies.

In all cases examined, the use of Bt crop varieties reduced the application of synthetic insecticides in those fields. In some cases, the use of Bt crop varieties has also been associated with reduced use of insecticides in fields with non-Bt types of the crop and other crops. This is thought to be due to reductions in the level of pest insects in the areas adjacent to Bt growing areas. A halo effect appears to be created. Crop insect pests are known to become resistant to the Bt toxin, and it is recognised that cropping strategies need to be adopted to reduce the development of resistant insect populations. [18]

By 2019 genetically modified crops were being grown by 18 million farmers worldwide, across 29 countries, on just under 190 million hectares of land. This represents roughly 12% of all cultivated land globally [28]. The most significant commercial impact has been observed for enhanced insect resistance and herbicide tolerance, which are single, specific gene transfers that provide plant protection [29]. They may have already provided improvements in crop yields globally, however, not in the USA, where the rate of yield improvement shows no difference between conventional and GM crops. There is evidence of improvements in the quality of the food supply and reductions in economical cost, energy usage, pesticide usage, fuel usage, soil erosion and carbon emissions. Critically, no scientifically documented evidence of harm to human health [18].

References
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Abbreviations
  • ARM Antimicrobial Resistance Marker
  • ARMG Antimicrobial Resistance Marker Gene
  • BE Bioengineered (USA)
  • CBE Cytidine Base Editor (or BE Base Editor)
  • CRISPR-Cas9 Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated system
  • GE Gene Editing
  • GM Genetically Modified
  • GMO Genetically Modified Organism
  • NBT New or Novel Breeding Techniques or Technologies
  • NPBT New or Novel Plant Breeding Techniques
  • PBT Precision Breeding Techniques
  • PCR Polymerase Chain Reaction
  • PIP Plant-Incorporated Protectant
  • TALEN Transcription Activator-Like Effector Nuclease
  • ZFN Zinc Finger Nuclease

Institute of Food Science & Technology has authorised the publication of the following Information Statement on Genetic Modification and Food. 

This Information Statement has been prepared by Dr Craig Duckham FIFST and Dr Wayne Martindale FIFST and peer-reviewed and approved by the IFST Scientific Committee. This Information Statement is dated February 2023. 

The Institute takes every possible care in compiling, preparing and issuing the information contained in IFST Information Statements, but can accept no liability whatsoever in connection with them. Nothing in them should be construed as absolving anyone from complying with legal requirements. They are provided for general information and guidance and to express expert professional interpretation and opinion, on important food-related issues.