Interesting facts about genetics

The Basics

Nucleotides are the alphabet of DNA. There are only four "letters" in DNA : adenine (A), thymine (T), guanine (G) and cytosine (C). They always go by pairs, A with T, and G with C. Such pairs are called "base pairs".

Almost every cell in our body contains a complete copy of our genome. The exceptions are egg/sperm cells, which only carry half of our genome, as well as red blood cells and some white blood cells, which have no DNA at all (otherwise blood transfusions would often cause an immune reaction, like organ transplants).

If unfolded the DNA in each cell's nucleus would be 2 metres long. Humans have an estimated 100 trillion cells. In other words, if the all the DNA from every cell in a person's body were patched up together they would form a strand of 200 billion kilometres, or more than 1,000 times the distance between Earth and the Sun.

Mitochondrial DNA is found outside the cell's nucleus, and therefore outside of the chromosomes. It consists of only 16,569 base pairs.

A SNP (single nucleotide polymorphism) is a mutation in a single base pair. Depending on what section of DNA is affected these mutations can have no effect at all (it is usually the case for SNP's defining Y-DNA and mtDNA haplogroups), a change in physical appearance (e.g. eye colour), an improvement of health (e.g. increased immunity), a increased susceptibility to a disease (e.g. diabetes), or a genetic disease (e.g. cystic fibrosis).

The Chromosomes

• A human genome is made of 3,000 million base pairs, split into 46 chromosomes.
• There are in fact 23 pairs of chromosomes, each person inheriting a maternal and paternal copy of each. Pairs of chromosomes are numbered from the largest (chromosome 1) to the smallest (chromosome 21). Chromosome 22 ought to be the smallest, but it was later discovered than chromosome 21 was smaller, and the established ordered was kept.
• The sex-determining chromosomes (X and Y) are the only pair that is not symmetrical in size. The Y-chromosome possess 60 millions bases, against 153 millions for the X chromosome.
• The reason why the Y chromosome is so much smaller than the X chromosome is that the latter possess genes that attack the Y chromosome. In response the Y chromosome has had to shut down a lot of its non-coding DNA so as to better protect itself.
• In some rare cases people are born with one extra chromosome. Those born with three chromosome 21 have Down's syndrome. Other possibilities is an extra X chromosome, leading to Klinefelter's syndrome (XXY), XYY syndrome, Triple X syndrome, XXYY syndrome, 48, XXXX, or 49, XXXXX. An extra copy of any other chromosome normally results in miscarriages. Some very rare cases of autosomal trisomies can survive to birth, notably when it affects chromosomes 13 or 18, but result in seriously shortened life expectancy.
• Humans, like most animals, are diploid, meaning that they have only two sets of chromosomes. However that is not the case of all life beings. Plants in particular are often polyploid. There are varieties of wheat that are tetraploid (four sets of chromosomes) and others that are hexaploid (six sets of chromosomes). Some strawberries can be decaploid (ten sets of chromosomes). Polyploid animals include the goldfish, salmons, and salamanders. Polyploidy occurs in some human tissues like muscles or the liver. When two or three spermatozoids fertilise an ovum at the same time, a human foetus will be triploid or tetraploid. However almost all such pregnancies end as miscarriage and those that do survive to term typically die shortly after birth.

The Human Genome

• The first complete human genome was only decoded in 2007. The two first individuals who got their full genome sequenced that year were Craig Venter and James D. Watson.
• A human genome is identical at 98% to a chimpanzee's genome. In comparison, two random human beings are in average 99.5% identical. Gorillas are 97% identical to either humans or chimps, meaning that humans are more chimp-like than gorillas.
• Most of our genome is made of junk DNA. This junk is composed either of deactivated genes that were once useful for our non-human ancestors (like a tail), or parasitic DNA from virus that have entered our genome and replicated themselves hundreds or thousands of times over the generations, but serve no purpose. Genome size is therefore not related to the complexity of life. For example, the genome of the unicellular Amoeba dubia has been reported to contain more than 200 times the amount of DNA in humans.

Heredity

• Although autosomal DNA is inherited equally from each parent, a few genetic diseases seem to be worse when inherited from one's father (e.g. Huntingdon's disease), because mutations occur or repeat themselves at a higher rate in men, and increase with the father's age. This is also why older fathers (over 40 years old) have higher chances of having children suffering from schizophrenia, depression or autism.
• Some genes have different functions depending on whether they are inherited from one's father or mother. These are called imprimted genes. For example, the maternal copy of a gene on chromosome 15 is known as UBE3A, while the paternal copy is SNRPN. Inheriting two paternal copies or missing the maternal copy causes Prader-Willi syndrome, whereas two maternal copies or a deletion of the paternal copy leads to the very different Angelman syndrome.
• Rather than inheriting a homosexual gene, gay men tend to have several older brothers (including abortions and miscarriages). The reason is that the mother's body accumulates antibodies against genes responsible for the masculinisation of the foetus' brain at each pregnancy with a boy. The risk of male homosexuality therefore increases with the number of boy carried by a mother before. This does not apply to girls.

Neurotransmitters

• Neurotransmitters such as serotonin, dopamine, adrenaline and noradrenaline influence our mood and personality. Their levels is influenced by our environment, but the sensitivity of the brain to these neurotransmitters is genetically determined.
• Low serotonin levels increase depression, anxiety, risk of suicide and violence. Carbohydrates and cholesterol both increase serotinin levels.
• Excessive dopamine can lead to schizophrenia. Too low dopamine levels engender boredom and low activity, and in extreme cases Parkinson Disease. The long variants (7-repeat or more) of the dopamine receptor D4 (DRD4) causes dopamine to be consumed more quickly by the brain. People with this variant will usually have more novelty-seeking, thrill-seeking and adventurous personality than average to compensate for naturally lower dopamine levels.

Immunity

• Some people possess a deletion on the CCR5 gene, which makes them more resistant to smallpox, HIV, plague and other viruses (e.g. West Nile virus). This mutation is commonest in North-East Europe.
• The ABO blood type is related to cholera resitance, with AB confering the strongest resistance, and O the weakest. On the other hand, the O blood group seems to be the most resistant against malaria and syphilis, and less susceptible to many kinds of cancers.
• Many genetic diseases survived natural selection because they confer immunity against epidemic diseases. For instance, the CFTR mutation causing cystic fibrosis protects against the dysentry and fever of typhoid. Sickle-cell anaemia and thalassaemia are both protective against malaria. Genetic resistance to TB has for side-effect an increased susceptibility for osteoporosis. Tay-Sachs disease, mostly found among people of Ashkenazi Jewish ancestry, is also protective against TB.
• Studies have shown that men and women are most attracted to the smell of people with the most different immune system from their own. This is also a way of Nature to prevent inbreeding. Differences in immune systems can be identified by comparing our HLA types, among other genes of the major histocompatibility complex (MHC).

Source: http://www.eupedia.com
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IT SKIPS A GENERATION

Long before they understood why the strategy worked, farmers knew how to crossbreed plants to obtain more desirable traits. Even today, a farmer who knows nothing about genetics can tell you that when a blue type of corn crosses with a yellow one, the offspring are blue. However, the farmer might add, if you cross a corn plant with small ears with a large-eared one, the offspring will have ears that are intermediate in size. Without any knowledge of genetics, the farmer has just told you a great deal about how the genes for blue color and for ear size work.

Gregor Mendel, an Austrian monk often described as the “father of genetics,” worked with pea plants in the 1860s to understand how traits are passed from one generation to the next. Mendel made his discoveries by making crosses between true-breeding pea plant populations with different characteristics and keeping careful track of the characteristics of their offspring. Sometimes, when he transferred pollen from one tall plant to another tall plant (like in the cross shown in the F1 generation of Figure 1.1), some of the offspring were tall but some also were short. Where was this shortness coming from, if not from the parental populations?

“It skips a generation”—the shortness was coming from the grand-parental populations. Shortness, the recessive trait, was masked by the tall dominant traitin the “hybrid” or F1 generation. In essence, the shortness was hidden because of sexual recombination. Each offspring receives one copy of a gene from its mother and one from its father.

In this way, gene combinations are shuffled with every generation and new types may appear. Many of the early discoveries in genetics occurred in plants. Plants have a few special characteristics that make them ideal for studying genetics. From one known cross, many genetically similar “siblings” are produced. Pea pods, like the ones Mendel worked with, produce about five peas, and a cucumber has hundreds of seeds. Furthermore, some plants (but not all) have the remarkable capability of being able to fertilize their own flowers. This means that the same plant can be both the male and female parent of a seed. Therefore, scientists can easily and naturally create whole populations of genetically identical individuals.

The cross in Figure 1.1 resulted from two true-breeding individuals. The F1 generation would have contained 5–10 seeds that were genetically identical to one another for the alleles that determine height (all had the Tt alleles). To make the F2 generation, Mendel had two options: He could self-pollinate the plants, or he could cross two different individuals of the F1 generation. Regardless of which method he used, in the F2 generation, the individuals would not all be genetically identical!

Tomato’s Genome Sequence Finally Cracked!

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Though science has still not replied to the eternal question of whether tomato is a fruit or a vegetable, it has stepped closer to answering it. The full genome sequence of tomato has been discovered by an international team of scientists, working across nationalities. Not only has the team cracked the genetic code of cultivated tomato but also that of the wild variety. It is being hoped that this development would help farmers grow tastier and more nutritious varieties of tomatoes in the future.

1) The Genetic Code

The full genome sequence of tomato, Solanum lycopersicum, has been named “Heinz 1706” and it has been published in the science journal “Nature.” Describing the details of the genetic code, the scientists said that all the 35,000 genes of tomato are well displayed in this sequence along with their functional parts, orientation, types, and relative positions. The researchers found that the tomatoes were made up of about 35,000 genes, arranged on 12 chromosomes and each of those genes is responsible for any characteristic that tomato shows. The “Nature” article describes the genetic results, “The tomato genome sequence provides insights into fleshy fruit evolution.” Apart from the domesticated or cultivated tomato, the researchers have also been able to crack the genetic sequence of its wild relative Solanum pimpinellifolium. James Giovannoni, who works at the “Boyce Thompson Institute for Plant Research at Cornell University," shows his excitement through words, “For any characteristic of the tomato, whether it’s taste, natural pest resistance or nutritional content, we’ve captured virtually all those genes.” Giovannoni further adds, “Tomato genetics underlies the potential for improved taste every home gardener knows and every supermarket shopper desires and the genome sequence will help solve this and many other issues in tomato production and quality.”

2) The Significance

In the US alone, tomatoes are worth $2 billion pie of the market share and Britain dabbles in $980 million worth of tomato business a year. In the rest of the world too, tomatoes are an inherent part of daily diet in all forms. Therefore, their consumption depends, to a large extent, on their quality. It is no wonder then that the scientists are excited about the possibilities arising out of knowing tomato’s genetic code. One of the main benefits would be for the researchers to identify links between tomato genes and the characteristics like taste, shape, color and nutrition level shown by various tomatoes. The scientists will also be able to pinpoint the specific environmental factors that enhance or affect the overall health of tomato crops. Graham Seymour, a member of the scientific team working on this project, and a professor of biotechnology at the “Nottingham University”, explains, “Tomatoes are one of the most important fruit crops in the world, both in terms of the volume that we eat and the vitamins, minerals and other phytochemicals that both fresh and processed tomato products provide to our diets.”

3) The Team

It was an international collaboration between more than a dozen countries that was named the “Tomato Genomics Consortium” and was entrusted with the responsibility to identify the genetic sequence of this popular fruit/vegetable of the world. The researchers, who were members of this Consortium, belonged to various nationalities, such as Argentina, Germany, China, France, India, Israel, the Netherlands, South Korea, Italy, Spain, Belgium, Japan, United Kingdom, and the US.

4) The Future

It took the international Consortium many years and millions of dollars to find out the first genome sequence in case of tomato. However, the scientists are hopeful that further studies in this direction would yield results at a much less cost because they will have initial findings to work with. Besides, buoyed by the tomato findings, scientists are also ready to work on fruits like strawberries, apples, bananas, etc to identify their genome sequence and work for their improvement too. As Giovannoni explains, “Now we can start asking a lot more interesting questions about fruit biology, disease resistance, root development and nutritional qualities.”

Tomato has many health benefits, especially when eaten raw. Now armed with the genetic information, it is going to be much easier for the scientists to provide significant inputs to the farmers to grow better varieties of tomatoes as well as other fruits and vegetables. As for that cup of salsa, it is gonna get better now!

Image Courtesy: malcolmallison.lamula.pe, ifood.tv

Read more at http://www.ifood.tv/blog/tomato-s-genome-sequence-finally-cracked#0p0AgEfPPI8EqMFi.99

Tomato Genome Decoded: Researchers To Publish Fruit's DNA Sequence In Full

By: Jennifer Welsh, LiveScience Staff Writer
Published: 05/30/2012 01:07 PM EDT on LiveScience
For years scientists have slaved away, trying to piece together the genes that make up the ripe, red goodness that is the tomato. They have finally published the fleshy fruit's genome in full.
The genome of any species is the DNA code that is stored as a blueprint inside every cell of every individual of that species. The DNA letters, called base pairs, are organized into genes, which are translated into proteins, the building blocks and machinery of every cell.
Decoding these genes can help researchers understand the different types of proteins found in organisms, and how these proteins make that species different from every other species. These kinds of insights from the genome could help crop researchers improve the yield, nutritional content, disease resistance, taste and color of tomatoes, they say.
"For any characteristic of the tomato, whether it's taste, natural pest resistance or nutritional content, we've captured virtually all those genes," study researcher James Giovannoni, of Cornell University, said in a statement. "Tomato genetics underlies the potential for improved taste every home gardener knows and every supermarket shopper desires and the genome sequence will help solve this and many other issues in tomato production and quality."
Generic and wild genomes
The researchers sequenced the genome of the tomato species Solanum lycopersicum, of the variety "Heinz 1706," as their type tomato. These tomatoes possess some 35,000 genes arranged on 12 chromosomes (large arrangements of hundreds of genes packed into one strand), the researchers said.

The researchers also sequenced the garden tomato's wild ancestor, Solanum Pimpinellifolium.
Knowing the sequence of one tomato can help seed companies and plant breeders get a grasp on what makes different varieties, like heirloom tomatoes, different from the generic grocery tomato.
Because the variability between two varieties is pretty small, it's easier to use the Heinz 1706 genome as a guide, and pinpoint the differences that lead to changes in color, taste, texture, size and shapethat distinguish one variety from another.
Tomato vs. potato
The genome is also important in learning why the tomato is so different from its genetic relatives in the nightshade family of flowering plants, which includes the potato, pepper and even coffee. Scientists want to know what genes have changed that gives each of these species their distinct flavor and look.
"Now we can start asking a lot more interesting questions about fruit biology, disease resistance, root development and nutritional qualities," Giovannoni said.
Tomatoes represent a $2 billion market in the United States alone. The USDA estimates that Americans consume, on average, more than 72 pounds (33 kilograms) of tomato products annually. Researchers have even developed a robot tomato harvester to go into space (or just use here on Earth).

The tomato decoded: holds more genes than humans

The tomato has always been a complex fruit. Or is it a vegetable? Either way. Tomato, tomahto, right?
The tomato, which is considered a fruit by botanists and a vegetable to the US government, has been demystified by a consortium of plant geneticists from 14 countries who spent nine years decoding the tomato genome with the hopes of breeding better, tastier fruits.
Specifically, the scientists sequenced the genomes of both Heinz 1706, a variety used to make ketchup, and the tomato’s closest wild relative, Solanum pimpinellifolium, which is grown in Peru, according to The New York Times.
The researchers reported that tomatoes possess some 35,000 genes arranged on 12 chromosomes. "For any characteristic of the tomato, whether it's taste, natural pest resistance or nutritional content, we've captured virtually all those genes," James Giovannoni, a scientist at the Boyce Thompson Institute for Plant Research, told Phys.org