An Agency Effort To Sequence Genomes
It's not a simple process
to map and sequence the
genome of an animal. Geneticist
Hans Cheng and colleagues at
Avian Disease and
Oncology Laboratory used the
DNA of the Red Jungle
line combined with that of
a White Leghorn chicken,
to the one shown
here, to create a genetic
map of the chicken. ARS
scientists are also mapping
the genomes of the pig, cow,
Though mapping the human genome received a lot of media
attention, scientists have been performing the same studies in other
animalswith much less fanfare. Researchers from around the world are
mapping, or have mapped, the genomes of several farm animals. In addition to
helping with the study of agriculture, this work may help further the
understanding of human health.
It's not a simple process to map and sequence the genome of an
animal. It takes years to do the research. And it takes plenty of money. The
National Institutes of Health's (NIH) National Human Genome Research Institute
has contributed tens of millions of dollars to various sequencing centers
working on other animal genomes. The U.S. Department of Agriculture's
Agricultural Research Service (ARS) and
Cooperative State Research, Education, and Extension Service have also
contributed millions, as have universities and foreign governments.
"In the long run, it makes great business sense for all these
organizations to fund genomic research," says Ronnie D. Green, ARS national
program leader for Food Animal Production and leader of ARS animal genomic
ARS scientists are working with collaborators to map the
chicken, honey bee, cow, and pig genomes to learn more about these animals and
what information they can provide for the study of humans.
scientists and cooperators
throughout the world are in the
stages of completing a
bacterial artificial chromosome
map of the
cow. From this map,
the cow genome is already being
genome should be
useful for selecting cows that
resist disease or
| The "Original Chicken"
Donates Blueprint to Science
The campus of Michigan State University is home to Female #256,
the Red Jungle Fowl (Gallus gallus) chicken whose blood samples gave
researchers the 1 billion DNA units needed to create the first high-quality
draft sequence of the chicken genome. She appears no worse for wear, despite
her advanced age of 7 years. Wild Red Jungle Fowl are the ancestors of today's
chickens. The breed has survived at large for about 8,000 yearsrare for a
wild ancestor of a domesticated animal.
Chickens were chosen for mapping because they are the premier
nonmammalian vertebrate model organisms. They're one of the primary models for
embryology and development since they grow inside an egg rather than a mother's
uterus, making for easier study. Chickens are also a major model for research
on viruses and cancer.
The framework for this genome sequence came from Jerry Dodgson,
a molecular biologist at Michigan State University at East Lansing, and ARS
geneticist Hans H. Cheng and colleagues at the nearby ARS Avian Disease and
Worker bees remove the mummified
remains of larvae infected
the chalkbrood fungus Ascosphaera
apis. ARS scientists are
the completed bee genome to
help understand bee responses
Dodgson created a physical map with Female #256's DNA. Cheng
created a genetic map using DNA from progeny of Male #10394a member of
the same Red Jungle Fowl lineand a White Leghorn female from an
experimental inbred line of chickens. The team used these two maps as the basis
for sequencing chicken genes.
NIH funded the project, and the sequence is now online at
A genetic map is a broad overview that shows the order of genes.
A physical map shows the actual distance between genes. Using a driving
analogy, the genetic map is like an Interstate map, and the physical map is
like a local street map. Use of common genetic markers as landmarks allows for
integration of the two types of maps. Aligning the genetic map with the genome
sequence greatly facilitates scientific efforts to determine the function of
each gene and how it influences traits.
Chicks atop a picture of a
genetic map of a chicken.
The new chicken genome will
make it much easier to locate
especially those for
complex traits like disease
| At East
Lansing, ARS maintains more than 50 inbred lines of chickens ideally suited for
genetic studies. The collectionbegun in the 1930sis one of the best
in the world.
Over the years, many universities have given up their living
collections because maintenance costs were too high. Cheng says, "It's ironic
that when the best tool for genetically analyzing these lines arrived, many
universities no longer had the chickens around to analyze."
Cheng says that the new genome map to guide the search for genes
makes a night-and-day difference. He went almost overnight from having 2,000
genetic markers to having potentially 3 million.
"This map makes it much easier to find genesespecially
those for complex traits like disease resistance," he says. "It eliminates a
lot of guesswork. It's like suddenly having the complete 'parts list' for a
Before the map, Cheng had found what he thinks are three genes
that confer resistance to Marek's disease, his chief interest. "This genome
sequence will be an immense help in finding the rest of the resistance genes,"
Cheng says. "We found the genes using a unique, integrated functional genomics
approach that combines DNA, RNA, and protein methods. The genome sequence will
only enhance our power and accuracy."
Chemist Tim Smith and cattle
wrangler Randy Scott record
growth and health data of a
heifer to look for correlation
markers and performance
at the U.S. Meat Animal
Research Center in
He expects many other payoffs, including improved vaccines for
Marek's and other serious diseases. "We'll also learn how to grow a more
nutritious, tastier, and healthier chicken," Cheng says. "From the ARS
viewpoint, mapping and sequencing the chicken genome makes sense because
poultry and egg products are a $25 billion industry and poultry is the
number-one meat consumed in the United States."
ARS scientists have been on the forefront of research both to
breed a better honey bee and to manage the welfare and productivity of this
Humans have a vested interest in Apis mellifera; the
honey bee's pollination of 90-plus flowering crops results in yield and quality
improvements worth more than $14 billion annually. And don't forget the
delectable byproduct of such pollination: honey.
Many dangers, from blood-sucking mites to disease
organisms, constantly threaten to undermine the honey bee's efforts, keeping
scientists on a fast-track search for new ways to safeguard the insectand
agriculture, no less. Now, a rough draft of A. mellifera's genome is at
hand, and bee researchers are gobbling up the wealth of information.
Molecular biologists Steve Kappes
(left) and John Keele use
sequences and genomic sequence
to assemble sequences and
determine bovine gene structure
and regulatory sites.
"As an organism whose social order rivals our own in many ways,
the honey bee will serve as a natural system for further agricultural studies,
including social behavior, cognition, and immune system function," Joseph Jen,
Under Secretary for USDA's Research, Education, and Economics, noted shortly
after the genome draft's January 2004 completion.
The honey bee's entire blueprint for life is only about
one-tenth the length of the human genome. Still, writing that first draft was
no easy task; the feat took a dedicated team of scientistsled by Baylor
College of Medicine in Houstonabout a year to complete using the latest
in genome-sequencing technology and several million dollars in funding.
Kevin Hackett, ARS's national program leader for bees and
pollination in Beltsville, Maryland, lists some of the exciting new research
avenues that the honey bee genome has opened up: identifying genetic markers to
expedite bee-breeding efforts, for example, to improve crop pollination, winter
survival, and defensiveness against Africanized bees; host-pathogen modeling
studies to better control organisms that cause honey bee diseases; and
genome-driven studies to fine-tune honey bee nutrition and pollination.
The chip that geneticist
Gary Rohrer is holding allows
him to evaluate more than
380 pigs for genetic
variations at 6
regions of the genome. This
information will help
which genes affect reproduction
"If you can locate the 'smelling' genes of bees," says Hackett,
"you can use the information to improve their diet through supplementation as
well as their ability to foragewith greater pollination resulting."
Jay Evans and Katherine Aronstein, ARS entomologists who
participated in the honey bee genome project, are using information from the
advance to identify immune system genes that keep bees healthy. Of particular
emphasis is characterizing genes involved in potential resistance to the
bacterium Paenibacillus larvae, which causes foulbrood disease in honey
bee larvae. Along with insect pests, parasites, and other pathogens, foulbrood
outbreaks in U.S. hives cause $5 million annually in crop-pollination
At their respective labs in Beltsville and in Weslaco, Texas,
Evans and Aronstein are studying a handful of genes and gene products, or
proteins, that may stymie honey bee diseases. One tantalizing lead is abaecin,
a peptide that honey bees produce to varying degrees when attacked by
"We know these bees are responding to foulbrood by producing
abaecin," Evans says. "But we're not sure whether a bee that produces more of
this peptide is indeed foulbrood resistant."
The bacterium Paenibacillus larvae
Entomologist Jay Evans and technician
Armstrong use genomic data
to define honey bee genes involved
resistance to the bacterium.
| With the
honey bee genome, it's possible to cast a wider net for other such genes and
characterize them in hopes of eventually using the information to improve honey
bee breeding and management, he adds.
Aronstein has focused her work on a large family of receptors
that play roles in the bee's first line of defense against invading
microorganismswhat's known as innate, or inborn, immunity.
"The outcome of this genome sequencing research won't give
immediate results to the beekeeping industry," says Aronstein. "But it's
long-term research with huge potential for a better understanding of bee
biology and improvement of management practices."
Studying the Cow Genome
Steven M. Kappes, now ARS Deputy Administrator for Animal
Production and Protection, was one of the leaders of ARS's work on the bovine
genome at Clay Center, Nebraska. As director of the Roman L. Hruska U.S. Meat
Animal Research Center, Kappes worked with a dozen ARS scientists plus many
from around the world in developing the physical, bacterial artificial
chromosomeBACmap of the cow.
Research associate Laura
Decanini and technician
Andrew Ulsamer rate honey
bee colonies for signs of
The scientists first started this project in spring 2000 and are
in the final stages of putting the map together.
Though the scientists have not completed the BAC map,
researchers are using part of it to sequence the cow genome. "We are already
using the BAC map to find DNA markers," Kappes says.
The physical map was developed by researchers in the United
States and Australia, Canada, Brazil, France, New Zealand, and the United
Being able to sequence the genome may lead to new knowledge
about human health, particularly reproduction traits and immune functions. The
knowledge will also obviously help agricultural researchers. Based on evidence
from other species, Kappes believes we will be able to find genes that
influence feed efficiency in cattle. Cattle producers would use the information
to select cows that require less feed. Not only would this reduce the cost of
beef production, but it could also mean fewer nutrient and odor problems.
Kappes also notes the possibility of being able to identify cows
that are resistant to bovine spongiform encephalopathyor mad cow
diseaseby knowing what DNA changes are responsible for the resistance.
Then scientists would be able to breed cows naturally immune to the
The high-capacity DNA sequencer
being loaded by geneticists
Van Tassell (left) and Tad
Sonstegard will increase the
number of genetic markers available
for screening in livestock populations.
Many ARS scientists from around the country worked on the
cattle genome. Those that had an active role include geneticist Timothy P.L.
Smith of the Nebraska lab and Beltsville geneticists Curt Van Tassell and Tad
Sonstegard. Van Tassell found 25 regions in cattle genomes, called quantitative
trait loci, that may prove economically important to dairy producers.
Don't Forget the Pigs
Compared to the other animal genomes under study, the pig's has
the farthest to go. Animal geneticist Gary A. Rohrer at Clay Center is leading
ARS's efforts in sequencing the swine genome. "The sequencing effort is still
in its infancy and is evolving as we go," Rohrer explains.
An international consortium has completed the physical map and
has started to analyze it. Researchers can view this information at
Rohrer believes that it may take 3 to 5 years to complete the actual genome
Rohrer is part of the Swine Genome Sequencing Consortium, which
features representatives from governmental agencies and universities from
around the world. The group is still developing strategy on coordinating the
eventual sequencing work. They are also working to secure funding for the
project.By David Elstein,
Flores, Agricultural Research Service Information Staff.
This research is part of Food Animal Production, an ARS National
Program (#101) described on the World Wide Web at
Hans H. Cheng is
with the USDA-ARS Avian Disease and
Oncology Laboratory, 3606 E. Mount Hope Rd., East Lansing, MI 48823; phone
(517) 337-6758, fax (517) 337-6776.
Jay D. Evans is
with the USDA-ARS Bee
Research Laboratory, 10300 Baltimore Ave., Bldg. 476, BARC-East,
Beltsville, MD 20705; phone (301) 504-5143, fax (301) 504-8736.
Aronstein is with the USDA-ARS Kika
de la Garza Subtropical Agricultural Research Center, 2413 E. Highway 83,
#213, Weslaco, TX 78596; phone (956) 969-5008, fax (956) 969-5033.
Rohrer is with the USDA-ARS Roman L.
Hruska U.S. Meat Animal Research Center, Spur 18D, Clay Center, NE 68933;
phone (402) 762-4365, fax (402) 762-4390.
Steven M. Kappes is
with the ARS National
Program Staff, 5601 Sunnyside Ave., Beltsville, MD 20705-5140; phone (301)
504-5084, fax (301) 504-7302.
"An Agency Effort To Sequence Genomes" was published in
2005 issue of Agricultural Research magazine.