Before they are served to our table, crop improvement

Naturally, we judge the foods based on their appearances such as color, shape, smell, and arrangement. Domestic crops have traits that are significantly different from their wild relatives. Undoubtedly tomato is red, banana is yellow, the carrot is orange. But how they end up being what they are on our plates? Can you imagine eating a banana with large seeds, a carrot in purple color, or tomato in black color? What happened to those fruits and vegetables? Which is their true color? You may wonder. Plants in the same genus can vary significantly in appearance due to their abilities to accommodating environment cues. But for domestic crops, particularly the plants that are grown for human consumption, are not undergoing natural evolution but are selected by artificial breeding for better appearance, delicious taste, easy harvest, and nutritional values.

Far before we know anything about genetics, farmers had known for millennia that crossbreeding between two different traits result in variations in the offsprings. Hybrid vigor or heterosis has been observed and applied to crop improvement before we knew them. This is how the early crops are selected based on their performance score, farmers collect seeds from the best performers and crossbreed among them for several generations. Thanks to the father of modern genetics, Gregor Mendel who opened the door that leads to modern molecular genetic manipulations. He did a series of studies using pea which is the model plant that displaying visible and distinguishing traits such as height, pod shape and color, seed/pea shape and color, and flower position and color. By crossing the different types of peas, Mendel successfully discovered the patterns of the traits heredity, namely the Laws of Mendelian Inheritances. According to his theories, genes that determined the traits are either recessive (denoted by small letter) or dominant (denoted by capital letter). The dominant allele of a gene will exhibit its trait in any combination (AA, Aa, aA). Yet the recessive allele will only exhibit its trait if both of the alleles are recessive (aa). The ratio of each type of trait can be calculated based on the parent’s genotype. Those early findings revealed that phenotypes are controlled by genetic materials that once were considered as a myth.

Traditional breeders grow the chosen ones with special horticultural practices to enforce a selection bar/pressure, including using chemicals or boosters to increase yields or other desired traits such as flower size and color, fruit size and color, tolerance to diseases, or pests, etc. The offsprings will exhibit a curve of normality, which is a bell-shaped curve that has fewer numbers of the two extremes traits which are the worst and the best, and the majority are the ones that show average. Then the plant that has the best traits will be cross-pollinated with a plant that is excellent in other traits. For example, plant A has large fruit but in low quantity, while plant B produces a lot of fruits but in small sizes. Then predictably the cross-pollination between A and B will result in various combinations of size and yield including the plant with a lot of large fruits. This process is repeated for several generations until the best combination of traits is achieved. For instance, Honeycrisp apple gets its famous texture and flavor by blending from multiple parent apple species, which took decades of years of effort involving thousands of trees to produce just one special cultivar. All the efforts are well worth it, isn’t it?

How far are the chosen ones could be different from their wild ancestors? Let’s take a look at wild banana (Musa sp.), which is no longer commercially produced, there are large seeds within the creamy flesh that is unpleasant to eat. Carrots and tomatoes were once purple back then, the purple pigment tends to leach a dark dye onto whatever they are cooked with. Bright colors such as red, orange, and yellow were believed as the best. Although their current bright colors are considered as normal and common, they are not naturally evolved but selected by early crop breeders. However, recent studies showed that purple color is an indicator of rich in anthocyanin which is a beneficial antioxidant to consume. As more and more people turn to healthy food and diet, it’s not surprising to find some “ancient” types of fruits and vegetables that are in different colors on the market.

Diversity can also be created by using different selection strategies with a focus on different parts of the crop. Brassica oleracea, the plant that includes many common vegetables includes cabbage, broccoli, cauliflower, Brussels sprouts, kohlrabi, and kale. The uncultivated form, known as wild cabbage that is native to coastal southern and western Europe. From the same ancestor, there are diversified cultivars selected with a different strategy on different parts of the plant. Cabbage (Brassica oleracea var. capitata f. alba) is the product of the selection for terminal buds. Brussels sprouts (Brassica oleracea var. gemmifera) are obtained from the selection of lateral buds. Kohlrabi (Brassica oleracea var. gongylodes) is selected from the stem. Broccoli (Brassica oleracea var. italica) is the selection for the stems and flowers. Cauliflower (Brassica oleracea var. botrytis) is the selection or flower clusters only. Leaves selection on Brassica oleracea gave rise to the cultivation of kale (Brassica oleracea var. sabellica).

Almost all plants can be crossed for traits improvement. Ornamental industries often cross for large and showy flowers with bright attractive colors. However, the conventional crossing is a tedious job that requires a large number of workloads on planting, recording, manual pollination, replanting, and selection. Now we know that most valuable phenotypes are controlled by multiple genes which increase the uncertainty of segregation in the offspring. Good phenotypes might be suppressed due to the gene‘s recessive property. The combination of the genes of an offspring is random, thus require multiple generations to produce the desired genotype. It is cost-ineffective because the offspring may not be able to follow the trend or the need for the market. Especially those crops seeking resistance to diseases and pests, as the pathogen might evolve from time to time.

To encourage the emergence of new phenotypes, it often applies mutagens such as chemicals (ethyl methanesulfonate, dimethyl sulfate), or radioactivity (e.g., ultraviolet light, x-ray, gamma-ray) to induce mutation at random, which is known as mutagenesis. This method helped to create the desirable deeper color in the red grapefruit.

Protoplast fusion is one of the plant tissue cultures that isolates the cytoplasm by removing the cell wall from plant cell and fuse with another cell between species. For example, male sterility is transferred from radishes to red cabbage by fusing their cells. Male sterility helps plant breeders make hybrid crops easily. Protoplast fusion also can be applied to produce polyploid. Polyploidy is the phenomenon where the multiplication of the number of chromosomes has occurred within a crop. This eventual impact on the fertility of the crop. Seedless watermelons are created by crossing a plant that has two sets of chromosomes with another plant that has four sets of chromosomes. Therefore, the seedless fruit has three sets of chromosomes. The chemical colchicine is commonly used to double the chromosome sets to create polyploids.

Genetically modified organisms (GMOs) or simply known as transgenic plants are using recombinant DNA technology to introduce desired genetic traits. The gene to be transferred is packed with the necessary elements including an appropriate promoter, terminators, selectable markers, and origin(s) of replication in hosts, then subsequently engineered into a T-DNA binary vector. The vector replicates in Agrobacterium that used to infect the plant tissues, the T-DNA then delivers the target genes from Agrobacterium into plant cells by random insertion. The exogenous DNA can also be coated with heavy metal particles, such as gold, and fired into plant cells using a gene gun by mechanical force. The first transgenic crop is genetically engineered with the glyphosate-resistant trait, correspondently the gene that encodes for 5-enolpyruvoyl-shikimate-3-phosphate synthetase (EPSPS). Initially, the EPSPS gene was cloned and transfected into soybeans. Since 1996 genetically modified soybeans were made commercially available. In less than 10 years, 89% of corn, 94% of soybeans, and 89% of cotton produced in the United States were genetically modified as herbicide-tolerant. Most GMOs are gain-of-function mutants, meaning the gene is overexpressed in the crop to bring up new traits. But there are also loss-of-function GMOs, also known as gene silencing, the genes that responsible for certain phenotypes are knocked out so that the gene’s function is suppressed. For example, the nonbrowning Arctic Apples are created by the RNA-interference (RNAi) technique, the polyphenol oxidase (PPO) enzymes that responsible for the browning issues of apple flesh are destroyed by anti-PPO small RNAs. As a result, the Arctic apple’s flesh remains its original color after slicing so that the appearance and shelf life are improved.

Golden rice another successful transgenic crop that is developed to having beta-carotene (a precursor of vitamin A), which displays a “golden” color. Rice is a staple food crop for over half of the world’s population that provides 30 – 70 % of the energy intake for people in Asian countries. In an area that has the issue with a shortage of dietary vitamin A, it was found that about 670 thousand children under the age of 5 were suffered from problems of deficiency in vitamin A and another 500 thousand cases of irreversible childhood blindness. Golden rice that is enriched with vitamin A brings hope, life, and prosperity to those people.

Lastly, the gamechanger came to the stage of crop improvement. Clustered regularly interspaced short palindromic repeat (CRISPR) technology brings revolutionary breakthroughs for crop improvements. The CRISPR/cas9 gene-editing system cleaves DNA that is guided by a short synthetic gRNA sequence, the Cas9 nuclease enzyme binds to the target DNA and cleaves 3–4 bases off from the double DNA helix. Then the DNA repair mechanism allows the introduction of a few DNA bases into the genome. This process creates DNA sequences alterations by insertion or deletion of a few DNA bases. Compare to previous methods which are all random insertions. The mutation created by CRISPR is specific that can target any gene sequences precisely without segregation in offsprings. CRISPR breeding also only needs a significantly shorter time compared to conventional breeding methods. With more and more genomic maps and gene’s function being revealed, it’s possible to edit any sequences to create new phenotypes. As a new technique, CRISPR is of debating regarding regulations. The CRISPR modified crops are not considered GMOs in the United States but are facing more strict regulations in Europe.

Is GMO or CRISPR the solution for us? All of our food is genetic modified in some way. Manipulations of crop genetics have been changing our lives that not only playing a crucial role in developing disease-resistant crops but also improving the nutritional contents of the crops. The increasing human population and changes in climate experienced worldwide make it urgent to the production of food with high yield and enhanced adaptation to the environment, for which conventional breeding can barely meet the demand. However, we must be aware of the side effects of having GMOs in the ecosystem, which are still of debate and with areas remain unknown. Agriculture regulations, policies must be made based on science, environmental impacts, and social issues.