Chicken DNA, Part 2: Genetics, Genomes, Genomics & More

By Doug Ottinger
This is the second in a six-part series on poultry genetics by Doug Ottinger. The third article coming in the June-July issue will look at how genetic research changed the skin and feathers in chickens.

Chicken DNA, Part 1

In the last article, I wrote about the history of early genetic studies and the important role that research in poultry genetics played, not only for the poultry industry, but for many other fields of life sciences.

Notable advances were made during the first half of the 20th century in the understanding of poultry genet-ics, as well as a growing understanding of the chicken genome itself (the term genome refers to the entire collection of genes and DNA that holds the genetic code for a living organism). While the understanding of DNA had not yet been fully developed, researchers compiled numerous lists that documented every proven genetic concept known about the chicken.

Many of these studies went much further than just finding out about the genetic material of the chicken. Vast amounts of knowledge and understanding were gained in the fields of endocrinology, embryology, pathology and histology (the studies of the micro-scopic structure of tissue). Much of the work done on  chickens and in numerous cases, other poultry and birds, was found to be transferable to other animal organisms, including humans.

My last article more-or-less stopped with research done through the end of the 1940s and at the latest, early 1950s. As the 1950s and 1960s progressed, much of the developmental research gradually shifted from the family-farm concept, to the larger, corporate agriculture we know today.

The 1950s and 1960s
If you look at the advertising trends in the poultry industry trade periodicals throughout the 1950s and into the early ’60s, you can see movement from general breeds and ads for small mom-and-pop hatcheries, to a general trend of hybrid strains of layers and broiler birds developed by larger hatcheries and corporate firms able to spend money on research and proprietary product development. Most of these strains were given fancy number or letter-number designations that sounded more like the government’s latest rocket or fighter jet than a simple chicken that would just lay a lot of nice, tasty eggs. This was, after all, during the peak years of the space program, and anything that sounded remotely turbo-charged and rocket-fueled was superior to the old farm hen that people had known in their youth! Concentration began to be placed on poultry as a sole, specialized operation, rather than an integral part of, or an addition to a diversified, family farm operation. (For decades, there had been large poultry operations, but smaller diversified family farms also figured largely into the total production picture across the North America.) It was during this time that a large shift was made from individual breeds and the genetic breed purity that most producers knew to hybridized strains of layers and broilers, which were touted as top secrets of the hatchery industry.

Most of these firms spared very little expense in their advertising budgets. Readers were faced with a litany of ads for the new hybrid birds, and the perils to befall them if they failed to buy the given strain of layer being advertised. If they did not buy and raise Zingerdoodle’s XT307 proprietary, hybridized-strain of laying chicken the next spring (available, of course, only from Zingerdoodle’s Hatchery), their entire operation would be doomed for bankruptcy within a year. Large pharmaceutical companies joined the fray. Poultry publication readers were bombarded with full-page and double-page ads that explained, in scientific-sounding terms, why it was necessary to buy bags of whatever type of antibiotic they were producing, and virtually free-feed the stuff every time you fed your poultry, whether they needed it or not.

Often the advertisements made it sound like the addition of the antibiotic was the only way you could prevent your birds from all dropping dead from the next horrible, pathological monster hiding just around the corner of every poultry house. Woe to those who were too parsimonious to give their animals only the best that the drug-company had to sell. All you had to do was read the advertisement to know that you were risking an imminent epidemic and financial collapse because you failed to buy and feed the antibiotic to even a perfectly well flock!

By the late 1970s and early 1980s, many small operations had closed, taking with them, not only a way of life, but also a great majority of the few poultry farms that still relied on self-sufficiency, old methods and, in some cases, limited supplies of old breeds and genetic material.

How Chicken Genes Work
And now, with a little history about some of these studies and industry changes in place, let’s jump into the genetics of the birds themselves. We will also take a look at the research today, and how it  is changing.

Within the cells of each living organism exists a specialized biochemical coding that makes that organism unique. We as human beings are all unique and different from one another. Even identical twins, so scientific studies tell us, have various differences that can develop within that coding, making them unique from each other. And so it is with chickens, as well as the other types of poultry that we know and love. While birds within a flock, especially commercial flocks, may look like carbon copies of each other, each bird’s genetic coding is actually unique to that bird, and many subtle differences exist between the individual birds.

The nucleus, or center part, of each cell in the chicken contains 39 pairs of chromosomes, or 78 individual chromosomes (compared to 23 pairs in humans, 41 pairs in the turkey or 40 in the duck). Each one of these chromosomes is made up of strands of a complex, molecular, chemical compound, called DNA or deoxyribose nucleic acid. Attached to the sides of each chromosome are those little things called genes. Actually, the best description for the genes is that they are just shorter segments of DNA. As most of us learned in high school biology class, it is these genes, or individual coding segments, in all of their varied and virtually unlimited combinations that make each individual animal or plant look the way that it does. It is these strands and segments of DNA that hold the “coding” for each individual organism.

In humans, as well as most mammals, the chromosomes are all pretty much the same size within each cell. However, in chickens, as well as most avian, or bird species, the chromosomes vary in size within the cell. Most mammalian chromosomes are classified as macro chromosomes.

This simply means that they are the largest chromosomes usually seen through high-powered microscopes. In the chicken (as well as most other birds), the majority of chromosomes are micro chromosomes, meaning that they are quite a bit smaller than their macro counterparts. Scientists who study such things tell us that there are five pairs of macro chromosomes within each chicken cell. There are another five pairs that fall somewhere in-between in size, so scientists just call them intermediary chromosomes. The other 29 pairs are micro chromosomes. The exception to the bird species are the hawks and eagles, or Falconiformes, which have mainly macro chromosomes. (I know, I know — hawks and eagles are not part of this article, but I just wanted to throw that in there so you have a piece of trivia that most of your friends don’t know! Now, if you really want to impress your friends, tell them that strands of DNA and chromosomes are measured in Angstrom units and that each Angstrom unit is approximately one ten-billionth of a meter long! Now aren’t you glad you decided to subscribe to Backyard Poultry?) Okay, okay! Enough stupid trivia! Let’s get back to chickens!

No discussion of genetics in any animal or organism that reproduces sexually can be complete without talking a little about some of the genetic processes involved in reproduction, or how nature determines which offspring become male, and which ones become female.

In mammals, the genetic makeup of the father’s sperm determines whether the new baby is male or female. Males and females each have a pair of sex-determining chromosomes in their cells. Each male cell contains one chromosome called the X chromosome, and another one called the Y chromosome. Females, on the other hand, have two X chromosomes in each of their cells. These cells are called X and Y because of the rudimentary shape of the chromosomes themselves. If you will think back to basic biology class, we all learned that when regular cells divide, they get complete, or whole, sets of chromosomes. However, when sex-cells (sperm and eggs) divide, they only get one-half of each pair of chromosomes. Thus, each egg (actually called oocytes when they are at this stage) will get one X chromosome from the mother. On the other hand, each sperm will either get one X chromosome, or one Y chromosome from the father. When the sperm and egg unite and form the new zygote, or brand new baby animal, each cell of the new animal will contain either an XX pair of chromosomes, and the new baby will consequently become a female, or each cell will contain one pair of XY chromosomes, and therefore that baby will become a male.

In birds however, the sex-determining chromosomes are not called X and Y. Instead, they are known as Z and W. Each male bird has one pair of ZZ chromosomes in its chromosomal collection. And each female bird has a pair of ZW chromosomes within its chromosomal makeup, or collection. When birds breed, each sperm carries one Z chromosome. Each oocyte, or egg, carries either one Z, or one W chromosome. Thus, the female in the species gives determination to the sexual-makeup of the new baby birds.

One will see the designations X and 0 used for male and female chromosomes in birds, as well as Z and W. This double-system of nomenclature goes back to the early days of genetic research. As noted previously, chromosomes in avian cells can, and do, vary greatly in size. In early microscopy, researchers were able to determine a male sex chromosome. However, in birds, the female sex chromosome is so small that it was not easily picked up during the research and viewing of genetic material. Thus, many early researchers concluded that an actual female sex chromosome did not exist.

When a few researchers did find what they thought was a small fragment of a female chromosome in some slides and preparations, it gave rise to the theory that female sex chromosomes in birds were either just rudimentary and not a working part of the genetic makeup, or that they actually degenerated as the fetus developed. Consequently, a designation of 0, or zero, was given to what they thought was simply an empty space in what would otherwise be a whole pair of chromosomes. This designation and belief still persists to this day in many articles and pieces of literature.

The ZW system, in which the female parent of a species gives rise to the determination of the sex of the offspring is not endemic to birds alone. Reptiles, some species of fish and amphibians, and butterflies all have a ZW sex-chromosome genome.

The Z, or male sexual chromosome, in chickens, carries a number of sex-linked genes. One of these is the dominant gene for barring on the feathers (B) (non-barred designated as simply b). This genetic factor was one of the earliest factors proven to determine sex-linked genetic traits. It was also one of the earliest studies that helped prove the heterogametic makeup of the female in avian species. Barred roosters, crossed with non-barred hens (i.e. Domi-nique or Barred-Rock males crossed with Rhode Island Red hens produced progeny that was all barred. However, barred hens crossed with non-barred roosters produced males that were barred and females which were non-barred).

These early studies gave rise to a new aspect in the hatchery industry: Namely, chicks that could be sexed, or sex-deter-mined, at time of hatching (vent-sexing, by sight, was being developed about this same time, especially in Japan, but was not yet an integral part of North American or European industry). Breeding barred females with non-barred males produced males that had had an enlarged creamy patch on the back of the head, which helped differentiate them from their female hatch mates. Other breeds, such as Delawares, also had sex-linked traits that could be used in the same way.

Not only were these birds easy to sex at time of hatching, but poultry men discovered that many of these crosses seemed to have extra vigor compared to some of the single breed strains that had been produced through more closed systems, such as line breeding. This helped give rise, eventually, to interest in hybridization of fowl and the proprietary strains commonly used in the industry today.

Genetic Research Today:  Genomics
Today, a new and highly specialized field has emerged in the field of genetic studies. Known as “genomics,” this discipline comprises the study of genetics at a molecular level. More specifically, it is the study of DNA, DNA sequencing, bio-information, and the structure and function of the entire genome within an organism’s cells.

It is reported that the term “Genomics” was first coined and used by T.H. Roderick of Jackson Laboratories, of Bar Harbor, Maine, somewhere around 1987. Just like the study of genetics 100 years or so ago, the specialized study of genomics is growing and advancing at such an exponential rate that it has become difficult for researchers, even with our modern systems of data storage, sharing and retrieval, to keep up with all of the research, or to be able to currently catalog all of the research and findings in a totally coherent fashion.

Chickens Are Still Widely Studied
For those of us that love chickens, it probably comes as no surprise that chickens are still one of the most widely studied research animals in the fields of modern genetics and genomics. After all, most of us probably feel that chickens are just about as perfect an animal as ever lived on the face of the earth. However, beyond our perceived notions of perfection about our little feathered friends, there are reasons from a modern scientific basis that make studies of chicken genetics, at the molecular level, so important to world-wide research today. While not simple, or lacking in complexity by any means, chicken DNA and RNA (we will talk about RNA in just a minute) is still less complex than that of humans and many other mammals. The molecular structures can be more easily reproduced in a laboratory and can be manipulated much more easily, for research purposes.

The chicken was one of the first animals to have its entire genome mapped. In other words, we know (or at least think we know) where all of the chromosomes are, and most of the individual genes are at, on the individual chromosomes. I use the term “we think we know” because scientists are still finding out many things in this area. Toward the end of the 1940s, approximately 349 individual genes could be identified in the chicken genome. Twenty to 30 years ago, approximately 17,600 genes had been identified. And more recent research pegs the number in a range between 20,00 and 23,000 individual genes in the domestic fowl. In short, this little animal is so complex that even the brightest minds in science still haven’t figured it out.

In the late 1970s it was found that large amounts of chicken RNA (ribonucleic acid) could be reproduced in a laboratory setting. Within a cell there are the individual chromosomes and genes, which are made up of strands of DNA. These hold the genetic coding, directing and telling the proteins in the cell, what to do and what to make. However, it is the RNA that works as the messenger between these two molecular entities. During the past 35 to 40 years, RNA studies in histology, cell and molecular biology and genetics have become one of the leading areas of research. Where research once looked only at individual chromosomes and genes, it also now looks at RNA. It has been learned that abnormalities in the RNA structure, or damage to it, can be a large causative factor in genetically linked problems and abnormalities.

Researchers also discovered that chicken DNA was more simple and predictable to work with than many types of mammalian DNA. It was found time and again that results from avian genomic studies were linkable to human research, thus giving some direction to these studies in the early planning stages. One of the main reasons the entire chicken genome was mapped, was to increase our under-standing of the human genome. Simply put, studies in chicken genetics remain as viable and valuable today, as it was 75 or 100 years ago. Not only is the chicken studied for the sake of understanding the chicken itself, but it is studied to give us much information about ourselves, as well as many other organisms.

The next article in this series will talk about about skin and feather development, and how just a few changes in gene structure can make drastic changes in the looks of the bird. We will talk about a few interesting things that many people may or may not know (okay, call it more trivia). Until then, go to the hens in your coop and give them some love. Tell them that even though they are heterogametic, and no one really know how many genes they have, that you love them unconditionally and really could care less about what that Ottinger fellow wrote about them in Backyard Poultry.

HENS ARE HETEROGAMETIC
What does this mean? Heterogametic sex refers to the  sex of a species in which the gender chromosomes are not the same. For example, in humans, males, with an X and a Y sex chromosome, would be referred to as the heterogametic sex, and females having two X sex chromosomes would be referred to as the homogametic sex. Chickens have similar Y and Z chromosomal structures, except hens are the heterogametic sex, not the males.

Doug Ottinger lives in northwest Minnesota with his wife, Connie. They raise chickens, ducks and geese on their small hobby farm. Doug’s educational background is in agriculture, with an emphasis in poultry and avian genetics.

Sources:
• Pacific Poultryman, volume 64, numbers 7 and 8, July and August, 1958.
• www.ncbi.nlm.nih.gov/pmc/articles/PMC540272/micro and macro chromosomes
• www.bbc.co.uk/schools/gcsebitesize/science/portal.nifa.gov/…/0004227-current-and-sporadic-disease-problems-in-poultry
• usda.gov – research and education and eco-nomic information system.
• Hutt, F.B., Ph.D., D.Sc., Genetics of the Fowl, McGraw-Hill Book Company, 1949.
• Oxford Journals, Poultry Science (2006) 85 (12), oxfordjournals.org
• Sensen, C.W., editor, Essentials of Genomics and Bioinformatics, John Wiley and Sons, pub-lishers, 2002.
• Burt, D.W., Chicken Genome: Current Status and Future Opportunities, 2005. genome.chslp.org/content/15/12/1692.full
• U.S. National Library of Medicine, National Institute of Health, http//www.ncbi.nlm/pubmed/9354761
• www.sciencemag.org > 12 December 2014
• The RNA Society, rnasociety.org