Genetics

In this page below you will find classical experiments of genetics by Mendel in 1866 and the corresponding genes discovered in XXI century. There are also experiments by Thomas Morgan in the fly room at University of Columbia in 1910’s and by Frederick Griffith in 1932 on the transformation of bacteria explained by Avery, McLeod and McCarthy in bacteriophage T2 among many others. Epigenetics examples and other genetics topics.

GENETICS EXPERIMENTS
R/S Griffith experiment

Avery, McLeod  T2 experiment

Beadle And Tatum experiment

Enzyme mutations

Compare monogenetic diseases to complex diseases and  multiple effects of many genes as in the article provided on COVID-19 genetic risks using whole genome GWAS, TWAS, among other techniques.7,491 critically-ill cases compared with 48,400 controls to discover variants within genes involved in interferon signalling (IL10RB, PLSCR1), leucocyte differentiation (BCL11A), and blood type antigen secretor status (FUT2). Using transcriptome-wide association were found reduced expression of a membrane flippase (ATP11A), and increased mucin expression (MUC1), increased myeloid cell adhesion molecules (SELE, ICAM5, CD209) and increased  coagulation factor F8, all of which are potentially druggable targets.

You have available a second article on Alzheimer’s disease (AD) in a genome-wide association study totaling 111,326 clinically diagnosed/‘proxy’ AD cases and 677,663 controls. 75 risk loci were found (42  new) involving amyloid/tau pathways and highlight 31 genes in tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. More info at https://www.nature.com/articles/s41588-022-01024-z

 

MENDEL’S EXPERIMENTS

Mutations in Mendel’s genes.

Round versus wrinkled (R vs r): encoding starch branching enzyme I (SBEI). In the mutant allele, a transposon is inserted into the open reading frame (large triangle), disrupting both transcription (larger transcript) and translation in mutant lines. Yellow versus green cotyledons (I vs i): encoding a stay-green protein (SGR). In the mutant allele, a six nucleotide insertion in the coding sequence leads to a two amino acid insertion in the translated protein, disrupting gene function. Other amino acid changes in the signal peptide are not thought to disrupt function. Seed coat (and flower) colour (A vs a): encoding a basic helix–loop–helix transcription factor (bHLH). In the most common mutant allele, a single nucleotide change at an intron junction disrupts RNA processing leading to a transcript with an additional eight nucleotides and a truncated protein. Tall versus dwarf plants (Le vs le): encoding gibberellic acid 3-oxidase. A single nucleotide substitution in the coding sequence leads to an alanine (A) to threonine (T) substitution at position 229 that reduces the activity of the enzyme.

Pea genome cultivar “Caméor” was published in 2019 in Nature Genetics magazine. It contains 7 chromosomes, 4.5 Gbp, over 75% of retro transposons and transposons. These 7 chromosomes are related to the 7 Mendel pure features and the sequence is longer than human genome (3.000.000.000 bp) and it was analysed the symbol marked genes corresponding to the storage protein as the main storage protein legumin (similar to the main storage protein of milk named casein or ovalbumin in eggs) in the following image. Vicillin and convicillin are storage globular proteins and possible allergens in peas.

Comparing expected and observed proportions in genetics using Pearson’s Chi Square

Calculate the Pearson Chi Square formula (Observed -Expected)2/Expected with degrees of freedom (rows-1)x(columns-1).

Normal autosomes 2 genes

Example of Pearson Chi Square:

MENDEL’S LAWS

Law of Segregation: When gametes form, alleles are separated so that each gamete carries only one allele for each gene

Law of Independent Assortment: The segregation of alleles for one gene occurs independently to that of any other gene*

Principle of Dominance: Recessive alleles will be masked by dominant alleles†

* The law of independent assortment does not hold true for genes located on the same chromosome (i.e. linked genes)

† Not all genes show a complete dominance hierarchy – some genes show co-dominance or incomplete dominance

ABO human blood types

ABO is an antigen system of sugars located on the surface of red blood cells discovered by Landstein in 1901. Type A antigens are made mainly of N-acetylgalactosamin polysaccharides and type B of galactose polysaccharides and O type does not have any type of sugar. The gene responsible for ABO system is a glucosyltransferase located in chromosome 9, 9q34.1-q34.2, 7 exons and 18 kb and the difference between A and B types are 7 nucleotides producing 4 aminoacid mutations L266M, G268A. Type O allele is a delection of guanine 261 producing a frameshift and a protein without enzymatic activity. People have antigen A have antibody against B and viceversa.

There are many other antigens on the red blood cell membrane. One of the most well known is the Kell or K antigen present in 9%  of Caucasian people.

Rh system consist of  a surface protein in the red blood cell.

Fur colours of Labrador retriever dogs 

Labrador retriever dogs have dominant/recessive allels for B/b body color genes and epistatic/hipostatic allels for E/e avoiding or allowing dominant traits.

The three recognised colours of Labrador Retrievers result from differences in two genetic loci that affect pigment expression. The first of these affects the colour of the dark pigment, eumelanin, and is referred to as the B (brown) locus. TYRP1 (tyrosinase related protein 1) is localised to melanosomes, the cellular organelles that produce and store pigments, and serves to catalyze oxidation of eumelanin precursors. In dogs, three mutations in the TYRP1 gene have been identified, one resulting in a truncation of the protein, the other two leading to an amino acid deletion or a single amino acid substitution in the sequence of the protein. All of these mutations are found across the range of dogs, and hence are thought to have preceded the divergence of distinct breeds, and all three are found within Labrador Retrievers. Each of the mutations appears to eliminate or significantly reduce enzymatic activity, and the colouration phenotypes (the visible traits) produced by the three mutations are indistinguishable.

These represent recessive mutations in the TYRP1 gene, and since mammals have two copies of each gene, one from each parent, an animal with at least one copy of the fully functioning TYRP1 protein (represented as ‘B’) will display the dominant trait, black pigmentation, while to display brown pigmentation, both copies of this gene must be mutant alleles (collectively represented as ‘b’). Thus a dog with the genotypes BB or Bb will express black eumelanin, while brown eumelanin will be seen in dogs with the bb genotype.

Eumelanin distribution

A second gene affects whether these eumelanin pigments will be expressed in the fur or solely in the skin. Called the ‘extension’ (E) trait, this is directed by the melanocortin 1 receptor (MC1R). This receptor signals the pigment-producing cell in response to melanocortins and results in deposition of eumelanin into the hair. Mutations in this protein have been shown to be involved in pale or red colour phenotypes in a range of species, including humans, horses, pigs, cattle, mice, fur seals, mammoths and the Kermode bear, as well as colouration in whiptail lizards.

A recessive mutation in this E gene truncates the protein, producing a non-functional receptor incapable of directing eumelanin deposition in the fur. Among dogs, this mutation is unique to yellow Labrador Retrievers and Golden Retrievers and is thought to have arisen in the retriever population before these individual breeds became distinct. The exact mutation has also been found to underlie the colouration of white coyotes found around Newfoundland, having apparently passed into that population through interbreeding with a Golden Retriever.

As with the B locus, presence of a single copy of the functional receptor gene (‘E’) will result in the dominant phenotype: presence of eumelanin in the fur. If both copies of this gene are the recessive mutated variant (‘e’), the dog will have no eumelanin in its fur. Such a dog will appear yellow, with eumelanin evident only in the skin of the nose, lips, eye rims and foot pads, of a colour determined by the B locus. A variant of the functional MC1R allele that produces a facial ‘mask’ in other breeds of dogs (Em) is also present in Labradors, but since the colour of the mask is determined by the B locus, in Labradors the mask this gene produces is indistinguishable from the overall coat colour.

Dog size variability

Diversity of body size in different types of dog is produced in part because different expression of gene IGF1 according to Plassais et al, 2022.
MORGAN’S EXPERIMENTS
Thomas Morgan in the fly room laboratory at University of Columbia discovered a single male fly with white eyes (1910)  instead of the brilliant red eyes of wild-type Drosophila melanogaster, this fly had white eyes. In the F1 generation all flies were red-eyed, and in F2 ratio were not 3:1 expected according to Mendel’s laws, because he discovered white eyes genes must be in chromosome X.

In a experiment using flies with black body or vestigial wings they do not find 9:3:3:1 Mendel proportion. Calculate the Pearson’s Chi Square.

Here you can see why the previous results are possible due to meiosis recombination.

The recombination frequency between y and w is low, so they are close together on the map. Recombination between y and v is more frequent, so they are farther apart. The recombination frequencies are converted to map units (also called centimorgans, cM); one map unit is equivalent to an average recombination frequency of 0.01 (one percent). 50 cM means 50% of recombination, genes far away in the same chromosome or in different chromosomes.

EPIGENETICS

Environment and behaviors, such as diet and exercise, can result in epigenetic changes, it affect gene expression in different ways. Types of epigenetic changes include:

DNA Methylation turns genes “off” and demethylation turns genes “on.” It is highly specific and always happens in a region in which a cytosine nucleotide is located next to a guanine nucleotide that is linked by a phosphate; this is called a CpG site. DNA methyltransferases (DNMTs) are the family of enzymes responsible for DNA methylation. To date, four DNMTs have been identified in mammals: DNMT1, DNMT2, DNMT3a and DNMT3b.

Histone modification: Chemical groups can be added or removed from histones and change whether a gene is unwrapped or wrapped (“on” or “off”). E.g. methylation of a particular lysine (K9) on a specific histone (H3) that marks silent DNA is widely distributed throughout heterochromatin. This is the type of epigenetic change that is responsible for the inactivated X chromosome of females. In contrast, methylation of a different lysine (K4) on the same histone (H3) is a marker for active genes.

Non-coding RNA: control gene expression by attaching to coding RNA, along with certain proteins, to break down the coding RNA so that it cannot be used to make proteins. Non-coding RNAs (ncRNAs) are classified in small (less than 200 nt, and typically much shorter) and long (greater than 200 nt and often much longer) species. Small ncRNAs are generally derived from larger RNA precursor molecules, by cleavage with RNAse III-family enzymes (typically Drosha and Dicer) and include microRNAs (miRNAs), short interfering RNAs (siRNAs), PIWI-interacting RNAs (piRNAs), and repeat-associated RNAs (rasiRNAs), among others.

Examples of epigenetic changes can affect your DNA in different ways:

  1. Infections with  Mycobacterium tuberculosis can cause changes to histones in some of your immune cells that result in turning “off” the IL-12B gene. Turning “off” the IL-12B gene weakens your immune system and improves the survival of Mycobacterium tuberculosis
  1. Cancer: increased DNA methylation that results in decreased BRCA1 gene expression raises your risk for breast or other cancers; and colorectal cancers have increased methylation at the SEPT9 gene. Hypermethylation of CpG islands can cause tumors by shutting off tumor-suppressor genes, including O6-methylguanine-DNA methyltransferase (MGMT), MLH1 cyclin-dependent kinase inhibitor 2B (CDKN2B), and RASSF1A.
  1. Nutrition During Pregnancy
    Dutch Hunger Winter Famine (1944-1945): 60 years after the famine, researchers looked at methylation levels in people whose mothers were pregnant with them during the famine. These people had increased methylation at some genes and decreased methylation at other genes compared with their siblings who were not exposed to famine before their birth These differences in methylation could help explain why these people had an increased likelihood for more likely to develop certain diseases such as heart disease, schizophrenia, and type 2 diabetes. Perhaps the Dutch Hunger Winter added a methyl group to fetuses born to starving mothers, which made some genes less active — and continued to do so for life. Famine individuals had, 6 decades later, less DNA methylation of the imprinted IGF2 gene compared with their unexposed, same-sex siblings.
  2. Epigenetics and Development: Your muscle cells and nerve cells have the same DNA but work differently. A nerve cell transports information to other cells in your body. A muscle cell has a structure that aids in your body’s ability to move. Epigenetics allows the muscle cell to turn “on” genes to make proteins important for its job and turn “off” genes important for a nerve cell’s job.
  3. Epigenetics and Age: A newborn had the highest DNA methylation, the 103-year-old had the lowest DNA methylation, and the 26-year-old had a DNA methylation level between the newborn and 103-year-old.
  4. Epigenetics and Reversibility: Smoking can result in epigenetic changes. For example, at certain parts of the AHRR gene, smokers tend to have less DNA methylation than non-smokers.
  5. Mental retardation: Fragile X syndrome is the most frequently inherited mental disability, particularly in males. The syndrome is caused by an abnormality in the FMR1 (fragile X mental retardation 1) gene.  A methylation turns the gene off, stopping the FMR1 gene from producing an important protein called fragile X mental retardation protein. Loss of this specific protein causes fragile X syndrome. Fragile X syndrome is not the only disorder associated with mental retardation that involves epigenetic changes. Other such conditions include Rubenstein-Taybi, Coffin-Lowry, Prader-Willi, Angelman, Beckwith-Wiedemann, ATR-X, and Rett syndromes

The fragile X mental retardation 1 gene (FMR1)-related disorder fragile X syndrome (FXS) is the most common heritable form of cognitive impairment and the second most common cause of comorbid autism. FXS usually results when a premutation trinucleotide CGG repeat in the 5′-untranslated region of the FMR1 gene (CGG 55–200) expands over generations to a full mutation allele (CGG >200). This expansion is associated with silencing of the FMR1 promoter via an epigenetic mechanism that involves DNA methylation of the CGG repeat and the surrounding regulatory regions. Decrease in FMR1 transcription is associated with loss of the FMR1 protein that is needed for typical brain development.


Hypermethylation of FMR1 in Fragile X syndrome (FXS). The CGG repeats (yellow) are located in the 5′-untranslated region (UTR) of the FMR1 gene. In the general population (<55 CGG repeats), the FMR1 gene is transcribed to mRNA and then translated to the Fragile X mental retardation protein (FMRP). Patients with FXS have expanded CGG repeats (>200 repeats, termed full mutation). The CGG repeats expansion leads to the hypermethylation (red circles) of CGG repeats and the upstream promoter region of the FMR1 gene. Consequently, the gene is silenced, and FMRP is absent. The absence of FMRP leads to FXS.
The fragile X mental retardation protein (FMRP) is an RNA-binding protein encoded by the Fmr1 gene, which regulates the transport, stability, and translation of hundreds of brain RNAs, many of which are critically involved in synaptic function.
CG repeats are located on the Xq27.3 loci.

Pharmacological therapy studies of FXS
The drugs namely 5-azacytidine and 5-aza deoxycytidine are responsible for taking off DNA methylation. Also, these two drugs were applied to the cell lines of FXS patients and at the locus of the gene, FMR1 eliminate DNA methylation is removed and to repair incomplete FMRP production histone rectifications were moved to the transcriptionally active configuration.
L-acetyl carnitine and valproic acid, considered an important treatment option in FXS, and these drugs are generally regarded as histone deacetylates.

Gene therapy of FXS

CRISPR/Cas9 gene-editing tool has been considered important in the treatment of FXS because pluripotent stem cells of FXS patients, this CRISPR/Cas9 gene-editing tool has been used to dock the expanded CGG triplet repeats, which results in the demethylation of the FMR1 promoter and reactivation of FMRP production. Lately, the Cas9 tool, with no alterations in the sequence of DNA has been allowed to target editing of DNA methylation.

GENE THERAPY
What is gene therapy?

Gene therapy is a medical approach that treats or prevents disease by correcting the underlying genetic problem instead of using drugs or surgery.
The objectives of gene therapy is to introduce a new gene into cells to help fight a disease or to introduce a non-faulty copy of a gene to stand in for the altered copy causing disease.

Types of therapeutic approaches

Strategies of gene therapy

CRISP-CAS9 GENE EDITION

The CRISPR-Cas9 system consists of two key molecules: an enzyme called Cas9, a pair of ‘molecular scissors’ that can cut the two strands of DNA at a specific location in the genome so that bits of DNA can then be added or removed and a piece of RNA called guide RNA (gRNA) about 20 bases long located within a longer RNA scaffold. The scaffold part binds to DNA and the pre-designed sequence ‘guides’ Cas9 to the right part of the genome. This makes sure that the Cas9 enzyme cuts at the right point in the genome.

Gene therapies are being used to treat a small number of diseases as you can see in the following table. Many more gene therapies are undergoing research to make sure that they will be safe and effective. Genome editing is a promising technique also under study that doctors hope to use soon to treat disorders in people.

APPROVED GENE THERAPIES

Spinal muscular atrophy gene edition

Spinal muscular atrophy (SMA) is a severe childhood monogenic disease resulting from loss or dysfunction of the gene encoding survival motor neuron 1 (SMN1). The incidence of this disease is approximately 1 in 10,000 live births, with a carrier frequency of 1 in 54. SMA is characterized by the degeneration and loss of lower motor neurons, which leads to muscle atrophy. More than 90% of untreated patients with SMA Type 1 will not survive or will need permanent ventilatory support by 2 years of age.

The most expensive drug in the world, 2.000.000 $ per dose, drug named onasemnogene abeparvovec (Zolgensma®) is a novel gene therapy medicine, FDA-approved in May 2019 for the treatment of SMA and  by EMA in March 2020 to treat babies and young children with SMA.

The SMN protein is made by two genes, the SMN1 and SMN2 genes. Patients with spinal muscular atrophy lack the SMN1 gene but have the SMN2 gene, which mostly produces a ‘short’ SMN protein that cannot work properly on its own. A one-time intravenous administration of Zolgensma supplies a fully functioning copy of the human SMN1 gene enabling the body to produce enough SMN protein. This is expected to improve their muscle function, movement and survival of children with the disease.

At a similar price, atidarsagene autotemcel (Libmeldy®) is a gene therapy treatment for metachromatic leukodystrophy (MLD). It contains an autologous CD34+ cell enriched population that contains haematopoietic stem and progenitor cells transduced using a lentiviral vector encoding the human arylsulfatase A (ARSA) gene. 

MLD is a rare genetic disorder that causes lipids to build up in cells, particularly in the brain, spinal cord and peripheral nerves. This buildup is caused by a deficiency of an enzyme that helps break down lipids called sulfatides (ARSA enzyme).

Symptoms:

  • Loss of the ability to detect sensations, such as touch, pain, heat and sound.
  • Loss of intellectual, thinking and memory skills.
  • Loss of motor skills, such as walking, moving, speaking and swallowing.
  • Stiff, rigid muscles, poor muscle function and paralysis.
  • Loss of bladder and bowel function.
  • Gallbladder problems

Antibody drug conjugates for cancer

In the order of thousands of euros per treatment there are new drugs against cancer made of monoclonal antibodies linked to anticancer compounds. Examples: trastuzumab deruxtecan (Enhertu®) against metastasic HER2+ breast cancer (aggressive  20% breast cancer, 8000€/month)  or enfortumab vedotin (Padcev®) against metastasic urinary bladder cancer (7500 euros per 30 mg). There are over ongoing  80 clinical trials with similar drug type.

MODIFIED PIG HEART

Xenotransplantation risks provoking rejection, an immune response in the recipient that can cause the organ from another species to fail. A key problem is that antibodies produced by people recognize certain sugars on the surface of pig cells as foreign. Revivicor knocked out three genes for enzymes that enable pig cells to synthesize those sugars.

Six tweaks were additions of human genes: two anti-inflammatory genes, two genes that promote normal blood coagulation and prevent blood vessel damage, and two other regulatory proteins that help tamp down antibody response.

A final modification removed the gene for a growth hormone receptor to reduce the chance that a pig organ, roughly matched in size to the patient’s chest, will outgrow it once implanted.
If

Gene therapy for hemophilia A

Valoctocogene roxaparvovec (AAV5-hFVIII-SQ) is an adeno-associated virus 5 (AAV5)–based gene-therapy vector containing a coagulation factor VIII complementary DNA driven by a liver-selective promoter.

GENE THERAPY FOR BUTTERFLY SKIN DISEASE 

Recessive dystrophic epidermolysis bullosa (RDEB) is a lifelong genodermatosis associated with blistering, wounding, and scarring caused by mutations in COL7A1, the gene encoding the anchoring fibril component, collagen VII (C7). Beremagene geperpavec (B-VEC) is an engineered, non-replicating COL7A1 containing herpes simplex virus type 1 (HSV-1) vector, to treat RDEB skin. B-VEC restored C7 expression. Clinical trials show that B-VEC is a safe therapy promoting wound healing in patients with RDEB when it is applied several times, and after eight months all wounds in the skin were healed.

More info at this Nature Medicine article.

https://www.ccma.cat/324/avenc-en-el-tractament-de-la-pell-de-papallona-una-malaltia-genetica-i-incurable/noticia/3155042/

TRANSGENICS

Transgenic food article

transgenicsFRUITS  (pdf)

USA FDA APPROVED TRANSGENIC FOOD

Flavr Savr tomatoes were the first genetically modified plants, and they were modified to delay the ripening process, preventing tenderness and rot. The Flavr Savr contains a gene added by Calgene; a reversed antisense polygalacturonase gene which inhibits the production of this rotting enzyme. In addition to the antisense PG gene, contained within a bacterial plasmid, Calgene’s modified tomatoes also included the kanamycin-resistance (kanr) gene, which encoded the enzyme aminoglycoside-3′-phosphotransferase II. The enzyme was used as a marker for identifying plant cells carrying the antisense PG gene.

Del Monte Pinkglow Pineapple or variety Rose cost $50 It produces lower levels of the enzymes already in conventional pineapple that convert the pink pigment lycopene to the yellow pigment beta carotene. Lycopene is the pigment that makes tomatoes red and watermelons pink, so it is commonly and safely consumed and beta carotene is a yellow and orange pigment found in carrots and other colorful vegetables. Genes used in pineapple transformations to create Rose are:  phytoene synthase is overexpressed in an engineered plasmid converting geranylgeranyl pirophosphate to phytoene (a precursor of lycopene).  Lycopene cyclases are blocked by RNAi and they can not be converted to beta-carotenes.

The Arctic Fuji apple was genetically modified in the same non-browning trait as the Arctic Golden and Arctic Granny apples. Specifically, gene silencing reduces the expression of polyphenol oxidase (PPO) more than 90% using RNAi, thus delaying the onset of browning. When an apple is sliced or bruised, PPO reacts with chemicals in the fruit (polyphenolics), producing the browning effect we’re used to seeing. The enzyme is found in a number of plants, and is an evolutionary defense mechanism used to deter herbivorous insects. In apples, though, it’s only produced in small amounts.

AquAdvantage salmon is authorised by FDA and sold in USA from 2021. It has added a single copy of the opAFP-GHc2 construct, which consists of a promoter sequence from ocean pout directing production of a growth hormone protein using the coding sequence from Chinook salmon. AquaBounty’s transgenic salmon is currently not allowed on the European market. New foods and ingredients that are not previously sold in the European Union, the so-called novel foods, will only be allowed on the market if approved by the European Food Safety Authority (EFSA).

EUROPE APPROVED GMO FOOD

The foods approved by the European Union for food and feed uses  are:

  • Cotton GHB614xLL and Cotton25xMON1598 (Cotton) -its seeds are used as food, especially in the livestock industry-.
  • Maize 5307 (Corn)
  • Maize MON 87403 (Corn)
  • Maize 4114 (Corn)
  • Maize MON87411 (Corn)
  • Maize Bt11MIR162x1507xGA21 (Corn)
  • Soybean MON87751 (Soybean)
  • Oilseed rape Ms8xRf3 (Rape)
  • Maize 1507xNK603 (Corn)
  • XtendFlex soybeans (MON 87708 x MON 89788 x A5547-127)
  • The majority of above GM crops have been modified to be resistant to selected herbicides, usually a glyphosate or glufosinate based one. Genetically modified crops engineered to resist herbicides are now more available than conventionally bred resistant varieties. Most currently available genes used to engineer insect resistance come from the Bacillus thuringiensis (Bt) bacterium and code for delta endotoxins. Glyphosate, the active ingredient of Roundup herbicide works by inhibiting the enzyme 5-enolpyruvylshikimate-3- phosphate synthase (EPSPS), which catalyzes the penultimate step of the shikimate pathway leading to the conversion of shikimic acid to chorismate, the precursor for aromatic amino acids (tyrosine, phenylalanine, and tryptophan) and other secondary plant metabolites. Glyphosate competes with phosphoenolpyruvate (PEP), a substrate for the EPSPS enzyme, to form a very stable enzyme–herbicide complex that inhibits the product-formation reaction. In glyphosate-tolerant crops, expression of transgenic CP4 EPSP synthase enables weed control by allowing post-emergent herbicide application, whereas in susceptible plants, EPSPS is inhibited by GBH thus causing a cascade of metabolic effects that are associated with glyphosate toxicity.

Golden rice 2 is not authorized in the EU. It is a genetically modified to produce beta-carotene, which is not normally present in rice. Beta-carotene is converted into vitamin A when metabolized by the human body. We need vitamin A for healthier skin, immune systems, and vision. The genetic modification was made by the addition of two genes, phytoene synthase (Zmpsy1) from Zea mays and carotene desaturase (crtI) gene from the common soil bacterium, Pantoea ananatis.

EFSA have also authorised other non food plants as different carnations from Netherlands (Dianthus caryophyllus L.) genetically modified for flower colour.

As of April 2022 is pending authorization for genetically modified potato EH92-527-1 with an altered starch composition  and maize Bt genetically modified to provide protection against specific lepidopteran pests and tolerance to the herbicide glufosinate-ammonium.

There are near 1000 experimental authorization for GMO food by EFSA available here.

Therapeutic proteins from transgenic animals

There are many more examples from bacteria and fungi (e.g. insulin and other hormones)

Animal pharming example

ATryn is the first medicine produced using genetically engineered animals (2006 by EMA, 2009 by FDA). The transgenic animals designed to produce Atryn are goats whose genomes have been altered for the secretion of human antithrombin protein in their milk. Using recombinant DNA technology, scientists were able to attach the protein-coding region of the human antithrombin gene to a segment of DNA from a goat mammary gland gene that directs the release of the gene product into milk. The resulting recombinant gene, called a transgene, was then inserted into cells grown in cell culture in a laboratory. This enabled gene activity to be evaluated and cells containing the transgene to be generated for the subsequent production of transgenic animals. The recombinant human antithrombin (rhAT) was purified by heparin affinity chromatography from the goat milk. Antithrombin normally acts to inhibit coagulation, so a deficiency in anthithrombin makes the blood more prone to clot.   It is for patients who have a rare disease known as antithrombin (AT) deficiency.