October 2013

One of the Least Studied Ruminants Finally Gets
Its Time in the Genomics Spotlight
The USDA is employing Illumina sequencing to uncover the genetic differences between theworld’s goat breeds, identifying mutations that enable goats to thrive in harsh environments.

Recognizing that its technology could
play a critical role in alleviating global
hunger, malnutrition, and poverty, Illumina
created the Agricultural Greater Goodinitiative. Each year, Illumina awards
Greater Good grants to agriculturalresearch organizations that are focusedon identifying and breeding plants and animals that will increase
the sustainability, productivity, and nutritional density of crop andlivestock species. Under the grants, Illumina sequencing andgenotyping reagents are provided free of charge.

U.S. Department of Agriculture
2012 Illumina Greater Good
Initiative Award Winner

Introduction
In 2007, the U.S. Department of Agriculture (USDA) substantiallyexpanded its mandate beyond providing safe, healthy food forAmericans to supporting global food security initiatives. Ensuring foodsecurity for nations with emerging economies is now one of the fivepillars of research for scientists in the USDA. “Our team was charged
with finding an area where we could make a contribution,” said Tad
Sonstegard, Ph.D., Research Scientist at the Agricultural ResearchService (ARS)1, the research arm of the USDA. “We chose goats
because when you look at the United Nation’s Food and Agriculture

Tad Sonstegard, Ph.D., is a Research Scientist at the Agricultural ResearchService (ARS), the research arm of the USDA.

Organization (FAO) statistics on livestock numbers2, you see that goats
are important in Africa and Asia. Scientists predict that Africa will facea shortage of food because the population is growing so quickly.
Countries on the African continent are already on the threshold ofnot producing enough food for their inhabitants3, with many people
suffering from malnutrition.”
Through their meat and milk, goats provide protein essential for earlychildhood development. Many African households have at least one
goat, with women responsible for tending to their care. From a protein
output, these goats can’t compare to their European cousins. “Dairyproduction of African goats is about half per annum of those found inEurope,” said Dr. Sonstegard. “If you could close that milk production
yield gap by half, imagine how much additional animal protein would
be available for children’s diets, for selling to generate income, etc. The
same is true for meat yield, with meat production critical for the largecommercial ventures that raise goats for sale to Middle East buyers.”
The lower protein yield is in part influenced by years of negative
selection. “Unfortunately, the biggest and best producing goats are
killed for family celebrations, such as weddings,” Dr. Sonstegard said.
“What remains is a gene pool lacking contribution from some of thesuperior goats.”

Tapping Into the Goat Genome
Genomic analysis is enabling researchers to determine the differences
between the goats found in Africa and elsewhere in the world. “Itbegan with mitochondrial DNA research that indicated goats weredomesticated somewhere in Northern Iran,” Dr. Sonstegard said.

Native to San Clemente island off the coast of California, the inbred San
Clemente goat provided an ideal genome for sequencing with Illumina
HiSeq and MiSeq systems.

October 2013
“They were derived from the Bezoar goat, which can still be found inthe Middle East. From there, goats radiated out everywhere acrossthe globe.”
When the USDA originally drafted the project in 2010, there had been
little research into the goat genome. In 2012, the International Goat
Genome Consortium sequenced the first goat genome and worked
with Illumina to develop a goat SNP array, the Caprine53K BeadChip.
“We need to understand genetic differences among the world’s
goat populations, the differences that make them unique and which
differences are adaptive,” Dr. Sonstegard said. “We initiated ourproject by collecting samples from 96 goats, representing different
U.S. breeds and used the Caprine 53K BeadChip to identify whichanimal was the most inbred,” said Dr. Sonstegard. “The most inbred
animal would be the best animal to sequence, because it’s easier toassemble. We found that the San Clemente goat was the most inbred,and have generated sequence from this animal on a number of next
generation platforms including short paired-end reads and fosmid
ends using both the MiSeq® and HiSeq®.”
The data from these runs will enable Dr. Sonstegard’s team to builda genome assembly as a resource for future BeadChip development.
“We’ll use them to continue characterizing goat populations acrossthe globe,” Dr. Sonstegard said. “We’re already performing agenetic survey of unique populations of goats in Africa that possess
special traits, looking for genomic regions where there’s complete
homozygosity that could reflect positive selection and the location ofgenes that contribute to survivability.”

Taking a World View with Big Data
While it’s important to conduct this survey in African goat populations,it’s equally important to look at populations in other parts of the world
where goats are in similar environments and undergoing droughtor parasite stress. “If we’re going to suggest goats for families andranchers to breed, we want to be sure the progeny can survive
and thrive in harsh environments and against endemic disease,” Dr.
Sonstegard said.
As Dr. Sonstegard and his team identify SNPs that are segregating in
African goats, they’ll be added to the Caprine BeadChip to support
continued research and breeding of goats worldwide. “Bringing inscientists from all over the world to work on this project builds astronger community where people can share ideas,” Dr. Sonstegard
added. “It also allows everybody to access each other’s resources.
Funds are limited for goat research—they’re probably the least studied
domesticated ruminant to date as far as genomics goes.”

Researchers worldwide are jumping on the goat sequencing bandwagon. “People want to participate in this project,” Dr. Sonstegard
said. “To name a few, we have the Brazilians from Embrapa and theUniversity of Sao Paulo State wanting to collaborate. The FAO has
goats in Chile that they would like to be included. We’re trying tocontact people in St. Croix where goats are reported to be resistant toparasites found in the Caribbean. We also have a partner in Australia
who has been looking at feral goats. They all want to apply genomic
technologies in goat breeding.”
The ADAPTMap4 project is an international effort initiated by Dr.
Alessandra Stella of Parco Tecnologico Padano (Lodi, Italy) designed
to coordinate the disparate goat breed genotyping and resequencing
efforts of organizations worldwide. “We’re putting our data into thepool so we can make more comparisons, Dr. Sonstegard said. “3SR,a small ruminant EU project, as well as INRA, the French National
Institute for Agricultural Research, are also a part of the ADAPTMap
project. It’s all about big data being shared, people looking at results,
and identifying new breeding paradigms.”

Greater Good Award Expands Goat Research“The Greater Good award enabled us to double the size of oursampling budget,” Dr. Sonstegard stated. “In the future, we’ll beobtaining samples from goat populations along the eastern side ofAfrica, from Kenya to South Africa. The larger sample size means we’llhave a much larger impact and a better chance of finding survivability
genes that will positively impact goat breeding. In turn, the expanded
sampling has attracted other groups to the project and leverages
additional researchers and resources. If it hadn’t been for receiving
Illumina’s Greater Good award, this would have been a relatively
small project.”
Dr. Sonstegard believes that global food security is going to be a big
focus area in agriculture research, especially in animals. “It’s an areathat scientists have been ignoring, because most have been focusedon national interests. It’s become a smaller world and everyone isstarting to look outside of their own country.”

References1.

http://www.ars.usda.gov/main/main.htm

2.

http://www.fao.org/ag/againfo/resources/en/glw/GLW_dens.html

3.

http://www.fao.org/economic/ess/ess-fs/en/4.

http://www.goatadaptmap.org/

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Pub. No. 1370-2013-005 Current as of 18 October 2013