Charting the Way
The Alpaca Research Foundation and the Morris Animal Foundation are Embarking on a Joint Research Effort to Map the Alpaca Genome
By Patricia A. Craven, PhD
The Alpaca Research Foundation and the Morris Animal Foundation are about to launch the most ambitious alpaca research project to date, construction of a medium resolution map of the alpaca genome. Genome maps have now been produced for numerous species including human, mouse, rat, pig, cow, dog and cat. Construction of the alpaca map will not just bring the alpaca industry up to date, it will propel us into the modern genetic arena. The initial work to map the alpaca genome will be conducted by Dr. Warren E. Johnson at the Laboratory of Genomic Diversity, National Cancer Institute, National Institutes of Health, Frederick Maryland. This laboratory has successfully produced a map of the cat genome and is currently working on maps of the macaque and the African elephant. The team is widely regarded as being extremely well qualified for the job.
Construction of the map of the alpaca genome will provide the basic tools that will be used in future studies to develop genetic tests to predict the inheritance of recessive traits including congenital defects and fiber characteristics. It is important to emphasize here that the current project will not result in identification of any genes or establishment of linkage of any traits with genetic markers. Before we can even begin to try to identify genes which are responsible for inherited traits we must first assemble the basic tools of investigation, ie a medium resolution genome map. That is the goal of the study which is currently being initiated. We can’t reach this goal without the help of alpaca breeders. But before we ask for help it is important to us that each of you has the opportunity to understand what we will learn from this pursuit and how we will make use of this information in the future.
It is always best to start at the beginning. What do we mean by the term "genome?" Each cell of a particular organism, except for the germ cells (eggs and sperm), contains the same amount and sequences of DNA in the nucleus. This DNA is called genomic DNA or simply the genome. Genes are arranged in a linear fashion along the genome much like cities and towns are positioned along the length of a highway. The genome contains all of the genes and thereby all of the genetic information for that particular organism. Fortunately for gene mappers, the genome also contains a large number of markers which are interspersed between the genes or actually are part of a gene. Markers in between the genes are called type II markers and those located on a gene are called type I markers. Markers are small regions of the genome which are easy to measure. They occur at the same place on the genome of each individual in a particular species.
Currently, only about 80 markers have been identified in the alpaca genome. These 80 markers have not yet been placed on a map, meaning that we do not know whether they are evenly dispersed along the entire length of the genome or clustered together. While it is possible in principle to develop genetic tests for inherited traits based on linkage analysis, without first obtaining a map, the availability of a map will greatly facilitate the process, increase the accuracy of these tests and provide the tools needed for future work directed at identifying the genes involved. The availability of a genome map will also enable investigators to determine whether a particular trait is transmitted by a single gene and thus amenable to linkage analysis or whether markers for a particular trait map to different regions of the genome, thus indicating multigenic causation. A thorough explanation of linkage analysis can be found in a previous article entitled "Mapping the Alpaca Genome" which appeared in the Autumn 2001 issue of Alpacas Magazine and is available on the ARF website. Suffice it to say that linkage analysis employs easy to measure markers, which are located so close to defective genes that they are usually inherited together, to identify carriers of defective genes in families.
Mapping the genome occurs in several stages. The first stage involves identifying and placing 1000 type II markers along the length of the genome. Type II markers occur in many different forms and thus are useful for paternity testing and linkage analysis in families. The more markers that are identified and the closer together they are, the higher the resolution of the map. Moreover, the more markers that are identified the more likely it is that a gene of interest will occur near enough to a marker so that the marker can be used to help track the inheritance of the gene and eventually to actually identify the gene. For those of you who shy away from technical discussions, let me assure you that the basic approach to constructing a map of DNA is extremely straight forward in principle and in fact intuitive. Imagine a road map of the United States. The single length of Rte 66 which starts in Chicago and ends in Los Angeles represents the alpaca genome The cities and towns along the highway represent markers. Now imagine you could cut Rte 66 up into a thousand overlapping pieces and shake them up. How would you go about putting the map back together? The principle is simple. The closer two cities are to each other on the map the more likely they are to appear on the same overlapping fragment of highway.
In an analogous way, Dr. Johnson and his colleagues will cut up the alpaca genome into thousands of overlapping fragments by controlled irradiation of a cell line which they grow from the skin of a pedigreed male alpaca The amount of radiation they use will determine the number of fragments they get. It follows that the more fragments that are obtained, the higher the resolution of the resulting map. To put it another way, a high resolution map will contain a larger number of cities which are closer together than those on a low resolution map. Once it is determined which markers are on each fragment of the genome, the data is fed into a computer which uses highly automated programs to place the markers in their proper sequence based on the principle that the closer two markers are to each other on the map the more likely they are to appear on the same overlapping fragment of DNA. Once the type II markers are placed on the map, 600 type I markers will be placed. Type I markers do not vary in form and can not be used for either paternity testing or linkage analysis. Instead Type I markers, being located on the genes themselves, can help investigators obtain very specific information about the identity of the gene involved in transmitting a specific trait. Since type I markers on the alpaca genome map occur in the same relative place as they do on the genome maps of other species, they are also extremely useful as "anchor loci." In other words, the type I markers make up the scaffolds that facilitate comparisons among genome maps from a variety of species.
Once Dr. Johnson and his colleagues have a medium resolution map of the alpaca genome, it will be lined up and compared to similar maps from other species including human. There is a great deal of similarity among genome maps for various species. The complete nucleotide sequence of the human genome is now known and several thousand genes have been identified. By comparing the alpaca genome map with the human genome map, educated guesses can be made concerning the location and identity of genes involved in inherited disorders and other traits in the alpaca. Knowing where to look for a "candidate gene" on the alpaca map based on comparisons with the maps from other species will be an important aid in identifying genes of interest to the alpaca industry.
How we proceed in identifying alpaca genes is like a series of ever smaller concentric circles. Availability of a medium resolution map of the alpaca genome will stimulate a great deal of interest in breeding trials and pedigree analysis to establish the pattern of inheritance of various characteristics of interest in alpacas. Highly automated genome scanning will then be done to determine whether the inheritance of a particular marker, as tracked by DNA analysis of a blood sample, can be associated with the inheritance of a particular trait. Once a linked marker is identified, a genetic test can be developed to predict the occurrence of that trait in families. In addition, identification of a linked marker will allow us to pinpoint on the map, the approximate location of the gene responsible for that trait. The location can be further refined by looking for additional markers which are even closer, employing the principle that the closer a marker is to the gene of interest, the more likely it is to be inherited together with the gene. Eventually a comparison with other genome maps will lead to the identification of a "candidate gene." Once a candidate gene is identified and the protein it produces is known, experiments can be designed to test the hypothesis that that protein is altered in the affected alpaca. Once the actual gene responsible for the trait is identified unequivocal tests for the occurrence of that gene in unrelated alpacas can be developed.
Only a few years ago genetic testing in alpacas seemed an unattainable goal. But look at the enormous progress that has been made with the human genome. Genetic testing will only become more available and more cost efficient in the future. Let’s boldly take the first step. Let’s make the map!
Additional Reading
Gelehrter, T. D., Collins, F.S. and Ginsburg, D. Principles of Medical Genetics, Williams and Wilkins, 1998.
Craven, PA, Mapping the Alpaca Genome, Alpacas Magazine, Autumn, 2001.
Patricia Craven is adjunct Research Professor at the University of Pittsburgh, Medical School, and serves on the Board of Directors of the Alpaca Research Foundation. She and her husband Bryan own Cherry Ridge Alpacas in Creekside, PA.
Glossary
Genome: The complete DNA sequence of an organism containing its complete genetic information.
Linkage: Coinheritance of two or more genes or markers because they are in close proximity on the genome.
Markers: Segments of DNA which are easy to detect. Type II markers occur in between genes and Type I markers are part of a gene.
Candidate gene: A gene which is present in a region of the genome which also contains markers which have been linked to a specific disease by following their inheritance in affected families. The protein product of a candidate gene also has characteristics suggesting that it may be the actual disease-associated gene.