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5-Animals: Genome map helping scientists build a better honeybee

                                  PART I
-------------------------------- GENET-news -------------------------------

TITLE:  Genome Map Helping Scientists Build a Better Honeybee
SOURCE: U.S. Department of Agriculture, Agricultural Research Service
        by Jan Suszkiw
DATE:   10 Jan 2005

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Genome Map Helping Scientists Build a Better Honeybee

With a map of the honeybee's entire genetic code in hand, Agricultural
Research Service (ARS) scientists are pursuing new ways to manage the
welfare and productivity of this important insect.

After all, humans have a vested interest in Apis mellifera; the
honeybee's pollination of 90-plus kinds of flowering crops each year
results in yield and quality improvements valued at more than $14 billion
in the United States alone. And that's not counting honey, the byproduct
of such pollination.

In January, a team led by scientists at Baylor College of Medicine in
Houston, Texas announced the completion of the first rough draft of the
honeybee genome, which is about one-tenth the length of that for humans.
Jay Evans and Katherine Aronstein, ARS members on the team, are now using
information from the advance to identify immune system genes that keep
honeybees healthy. Their efforts come at a time when insect pests,
parasites and diseases of honeybees cause an estimated $5 million
annually in crop-pollination losses.

Of particular interest to Evans, an entomologist in the ARS Bee Research
Laboratory in Beltsville, Md., and Aronstein, a molecular biologist in
the ARS Honey Bee Research Unit in Weslaco, Texas, is characterizing
genes involved in potential resistance to the bacterium Paenibacillus
larvae, which causes foulbrood disease in the insect's larvae. One
tantalizing lead is abaecin, a small protein that may be part of a
resistance response in some bees to foulbrood infection.

Mapping the honeybee genome opens up other exciting research avenues as
well: identifying genetic markers to speed breeding of bees, such as for
better winter survival; modeling host-pathogen interactions to better
control honeybee disease organisms; and conducting genome-driven studies
to fine-tune honey bee nutrition and pollination.

For example, by locating honeybees' olfactory genes, researchers may be
able to improve the insect's diet through supplementation or improve its
ability to forage for nectar longer.

                                  PART II
-------------------------------- GENET-news -------------------------------

TITLE:  An Agency Effort To Sequence Genomes
SOURCE: Agricultural Research magazine, U.S. Department of Agriculture
DATE:   Jan 2005

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An Agency Effort To Sequence Genomes

Though mapping the human genome received a lot of media attention,
scientists have been performing the same studies in other animals--with
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 research.

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.

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 years--
rare 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 Oncology Laboratory.

Dodgson created a physical map with Female #256's DNA. Cheng created a
genetic map using DNA from progeny of Male #10394--a member of the same
Red Jungle Fowl line--and 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.

At East Lansing, ARS maintains more than 50 inbred lines of chickens
ideally suited for genetic studies. The collection--begun in the 1930s--is
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 genes--especially 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 chicken."

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."

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."

Sweet Research

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
important insect.

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 insect--and 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.

"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 scientists--led by Baylor College
of Medicine in Houston--about 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.

"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 forage--with 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 losses.

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 pathogens.

"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."

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 microorganisms--
what'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 chromosome--BAC--map of the cow.

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 Kingdom.

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 encephalopathy--or mad cow disease--by
knowing what DNA changes are responsible for the resistance. Then
scientists would be able to breed cows naturally immune to the disease.

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

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 sequencing work.

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, Don Comis, Jan Suszkiw, and Alfredo 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.

Katherine 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.

Gary A. 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 the January 2005
issue of Agricultural Research magazine.


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