March 2014

Using SNP-Based Genotyping to Select for
Climate-Resilient Livestock
Illumina sheep and goat BeadChips help Iowa State University researchers identify selection
signatures associated with heat and drought tolerance.

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.

2014 Illumina Greater Good
Initiative Award WinnerIntroduction
Temperature fluctuations put real stress on livestock. For instance,
the Midwestern United States has experienced several very hot anddry seasons over the last 10 years that have led to phenomenal
losses of livestock, subjecting some farms to financial risk. While thepublic debate continues about whether these temperature extremes
are the result of global warming, most people would agree that thetemperature fluctuations worldwide are more severe than they used
to be. Climate change is of particular concern for smallholders, poor

Max Rothschild with a goat and sheep herder in the arid region ofJordan in 2012.

farmers that depend on livestock for their very existence. More broadly
it could impact sustainable food production worldwide.
In the developed world, farmers moderate temperature by constructing
shade structures and using fans and water spray to ameliorate heatstress in livestock. However, these materials are not widely accessible
in the developing world. In perennially hot and dry regions, such as
the Middle East, natural selection may provide clues in solving theproblem. Sheep and goats in these regions demonstrate far higher
heat tolerance than breeds found in more temperate climates.
Natural selection in Middle Eastern herds has occurred over centuries.
Archaeological evidence indicates that the earliest domestication of
sheep and goats occurred in the Middle East about 10,000 years
ago. These herds provide communities with meat and milk for food,animal skins and fiber for clothing, and manure for fertilizing crops.
They are also the sole source of livelihood for large numbers of small
and marginal farmers and are an important source of export earnings,
especially of skins and hand-knotted carpets.1,2Max F. Rothschild, Ph.D., Distinguished Professor in animal scienceat Iowa State University, Ahmed R. Elbeltagy, Ph.D. from the Animal
Production Research Institute in Egypt, and their colleagues at theInternational Center for Agricultural Research in the Dry Areas areseeking to understand how certain breeds of sheep and goats havedeveloped over thousands of years, and how they thrive in very hotand dry climates. Illumina sheep and goat BeadChips, containing
SNPs that represent the genetic diversity of these animals, are helping
them look for genes that are associated with resilience to heat stressand drought conditions.

Max F. Rothschild, Ph.D., is a Distinguished Professor of animal science at
Iowa State University.

March 2014

The Genomics of Climate-Resilient Sheepand Goats

Broader Applications to Global Food Security“As a geneticist by training, I’m interested in finding genes in avariety of species that are associated with production traits,” saidDr. Rothschild. “In this project, we are specifically interested in studyingclimate-resilient sheep and goats.” Dr. Rothschild met Dr. Elbeltagy
while on a USAID* mission in Egypt. They had similar interests ingenetics and began collaborating to study genes that underlie heatstress and drought resistance. “Understanding the genomics ofclimate-resilient sheep and goats will help us select livestock that
could be further adapted to hot, dry weather” Dr. Rothschild added.

Sheep and goats have similar chromosomal gene arrangements
and, according to Dr. Rothschild, they essentially found one selection
signature that was the same in both species. This suggests there
is something going on in this region that has helped push natural
selection for heat resilience. “We’re in the process of furtherinvestigating these regions,” said Dr. Rothschild. “We’re using theseanimals as indicators for what genes are involved in heat and stress
tolerance. Next, we’ll look for these regions in breeds that live in moretemperate climates. If we can increase the frequency of these alleles,
it may help those animals be more heat and stress resilient as theclimate changes.”

Dr. Elbeltagy and his colleagues in Egypt identified the most climateresilient animals in herds from hot and dry regions. They measured
respiration rate and rectal temperatures of animals exercised in
the hottest part of the day during the driest climate. “The internal
temperatures of heat-tolerant animals may go up for a while, butthey don’t stay elevated for long,” said Dr. Rothschild. “Extendedtemperature elevation would show an animal under stress. We wanted
to identify animals whose temperature and respiration rates returned tonormal quickly.”

According to the World Bank, supporting smallholders is the mosteffective way of stimulating economic growth and poverty reduction.
Helping smallholders improve their herds will ultimately help provide
a better standard of living for them and their families.3 “We’re offering
training and development to Egyptian scientists to ensure our findings
can be implemented to improve farming practices in the region. Our
hope is that this research can be translated into improved productivity
and food availability for people around the world.”

SNP-Based Genotyping Reveals
a Selection Signature
Dr. Rothschild used the Illumina sheep and goat SNP BeadChips toconduct an initial survey of Dr. Elbeltagy’s samples from the region.
They looked for a genotypic signature, a fixed region or regions of thegenome specific to the climate-resilient animals. “At the beginning ofa project, we never know what that genotype is. We’re looking for thedata to tell us something,” said Dr. Rothschild. “In the small sheep andgoat genotyping samples we’ve completed so far, we identified four orfive regions in the genome that appear to have selection signatures.”

References1.

http://www.penn.museum/documents/publications/expedition/PDFs/22-4/Nyerges.pdf

2.

http://www.fao.org/docrep/009/ah221e/ah221e14.htm

3.

http://www.worldbank.org/

The Greater Good Initiative award will provide the team with more
BeadChips and allow Dr. Rothschild to triple the number of animals
they genotype. “We can further study the genes that control theresponse to heat stress and drought tolerance,” Dr. Rothschild said.
“We’re trying to understand what metabolic pathways are involved in
the animals’ ability to withstand these types of stresses. At least wehave some indication of that looking at the selection signatures.”*U.S. Agency for International Development that works to end extreme global
poverty.

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Pub. No. 1370-2014-001 Current as of 02 April 2014