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Livestock Epigenetics
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Livestock Epigenetics
Edited by
Hasan Khatib
DepartmentofAnimalSciences
UniversityofWisconsin
Madison,Wisconsin,USA
A John Wiley & Sons, Ltd., Publication
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ISBN978-0-470-95859-9(hardcover:alk.paper) 1.Livestock–Genetics.
2.Livestock–Embryology. 3.Epigenesis. I.Khatib,Hasan.
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Contents
Contributors vii
Preface xi
1. EpigeneticsofMammalianGameteandEmbryoDevelopment 3
NelidaRodriguez-Osorio,SuleDogan,andErdoganMemili
2. EpigeneticsofClonedPreimplantationEmbryosofDomesticAnimals 27
X.CindyTianandSadieL.Marjani
3. RolesofImprintedGenesinFertilityandPromisesoftheGenome-Wide
Technologies 43
AshleyDriver,WenHuang,andHasanKhatib
4. SheepasanExperimentalModelforHumanART:NovelInsightsonPhenotypic
AlterationsinART-DerivedSheepConceptuses 59
PasqualinoLoi,AntonellaD’Agostino,MartaCzernik,FedericaZacchini,PaolaToschi,
AntonellaFidanza,andGrazynaPtak
5. TheDLK1-DIO3ImprintedGeneClusterandtheCallipygePhenotype
inSheep 73
ChristopherA.Bidwell,RossL.Tellam,JolenaN.Waddell,TonyVuocolo,
TracyS.Hadfield,andNoelleE.Cockett
6. GenomicImprintingandImprintedGeneClustersintheBovineGenome 89
IkhideG.Imumorin,SundayO.Peters,andMarcosDeDonato
7. ImprintinginGenomeAnalysis:ModelingParent-of-OriginEffectsin
QTLStudies 113
SuzanneRowe,StephenBishop,andD.J.deKoning
8. EpigeneticsandAnimalHealth 131
JuanLuo,YingYu,andJiuzhouSong
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vi Contents
9. EpigeneticsandmicroRNAsinAnimalHealth 147
FeiTianandJiuzhouSong
10. NutrientsandEpigeneticsinBovineCells 161
Cong-junLi,RobertW.Li,andTedH.Elsasser
Index 179
Colorplatesappearbetweenpages148and149.
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Contributors
ChristopherA.Bidwell
DepartmentofAnimalSciences
PurdueUniversity
Indiana,USA
StephenBishop
TheRoslinInstituteandR(D)SVS
UniversityofEdinburghRoslinMidlothian
Scotland,UK
NoelleE.Cockett
DepartmentofAnimal
DairyandVeterinarySciences
UtahStateUniversity
Utah,USA
MartaCzernik
DepartmentofComparativeBiomedicalSciences
UniversityofTeramo
Teramo,Italy
AntonellaD’Agostino
DepartmentofComparativeBiomedicalSciences
UniversityofTeramo
Teramo,Italy
SuleDogan
DepartmentofAnimalandDairySciences
MississippiStateUniversity
Mississippi,USA
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viii Contributors
MarcosDeDonato
DepartmentofAnimalScience
CornellUniversity
NewYork,USAand
LaboratorioGeneticaMolecular
IIBCA
UniversidaddeOriente
Cumana,Venezuela
AshleyDriver
DepartmentofDairyScience
UniversityofWisconsin-Madison
Wisconsin,USA
TedH.Elsasser
BovineFunctionalGenomicsLaboratory
Animal&NaturalResourcesInstitute,ARS,USDA
Washington,DC
AntonellaFidanza
DepartmentofComparativeBiomedicalSciences
UniversityofTeramo
Teramo,Italy
TracyS.Hadfield
DepartmentofAnimal
DairyandVeterinarySciences
UtahStateUniversity
Utah,USA
WenHuang
DepartmentofDairyScience
UniversityofWisconsin-Madison
Wisconsin,USA
IkhideG.Imumorin
DepartmentofAnimalScience
CornellUniversity
NewYork,USA
HasanKhatib
DepartmentofAnimalSciences
UniversityofWisconsin-Madison
Wisconsin,USA
D.J.deKoning
DepartmentofAnimalBreedingandGenetics
SwedishUniversityofAgriculturalSciences
Uppsala,Sweden
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Contributors ix
Cong-junLi
BovineFunctionalGenomicsLaboratory
Animal&NaturalResourcesInstitute,ARS,USDA
Washington,DC
RobertW.Li
BovineFunctionalGenomicsLaboratory
Animal&NaturalResourcesInstitute,ARS,USDA
Washington,DC
PasqualinoLoi
DepartmentofComparativeBiomedicalSciences
UniversityofTeramo
Teramo,Italy
JuanLuo
DepartmentofAnimalandAvianSciences
UniversityofMaryland
Maryland,USA
SadieL.Marjani
DepartmentofGenetics
YaleUniversitySchoolofMedicine
Connecticut,USA
ErdoganMemili
DepartmentofAnimalandDairySciences
MississippiStateUniversity
Mississippi,USA
SundayO.Peters
DepartmentofAnimalScience
CornellUniversity
NewYork,USA
GrazynaPtak
DepartmentofComparativeBiomedicalSciences
UniversityofTeramo
Teramo,Italy
NelidaRodriguez-Osorio
GrupoCentauro
UniversidaddeAntioquia
Colombia
SuzanneRowe
TheRoslinInstituteandR(D)SVS
UniversityofEdinburghRoslinMidlothian
Scotland,UK
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x Contributors
JiuzhouSong
DepartmentofAnimalandAvianSciences
UniversityofMaryland
Maryland,USA
RossL.Tellam
CSIROLivestockIndustries
St.Lucia,Queensland
Australia
X.CindyTian
DepartmentofAnimalScience
CenterforRegenerativeBiology
UniversityofConnecticut
Connecticut,USA
FeiTian
DepartmentofAnimalandAvianSciences
UniversityofMaryland
Maryland,USA
PaolaToschi
DepartmentofComparativeBiomedicalSciences
UniversityofTeramo
Teramo,Italy
TonyVuocolo
CSIROLivestockIndustries
St.Lucia,Queensland
Australia
JolenaN.Waddell
DepartmentofAnimalSciences
PurdueUniversity
Indiana,USA
YingYu
DepartmentofAnimalandAvianSciences
UniversityofMaryland
Maryland,USA
FedericaZacchini
DepartmentofComparativeBiomedicalSciences
UniversityofTeramo
Teramo,Italy
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Preface
Inrecentyears,wehavewitnessedremarkablepositivechangesintheperceptionofthevalue
oflivestockgeneticandepigeneticresearchamongfederalandnonfederalagenciesandinthe
scientificcommunitymoregenerally.First,itisbecomingwidelyacceptedthathumanhealth
benefitsfromthepromotionofanimalhealth.Humanconsumptionofhealthymeat,eggs,dairy,
andotheranimalproductsnecessitateshealthyanimals.Second,thewiderangeofphenotypic
andgenotypicdiversityinlivestockpopulationsfacilitatestheuseofthesespeciesasmodels
forcertainhumandiseasesandhealthtraits.Thereareplentifulhistoricandcontemporaryex-
amplesofdomesticanimalsbeingusedinbiomedicalresearch,includingvaccinations(cowpox
virus),xenotransplantations(heartvalvesofpigs),reproductivebiologyandcloning(Dolly,the
firstclonedmammal),developmentalbiology(limbpatterninginchicken),metabolicdiseases
(malignanthyperthermiainthepig),andneurodegenerativediseases(prionswerefirstisolated
fromsheepandgoat)(http://www.adsbm.msu.edu/).
At present, epigenetic studies are focused on understanding the mechanisms of actions of
chromatinmodificationsthatregulatethemachineryofgeneexpression.AlthoughDNAmuta-
tionsarecrucialinthedevelopmentofdiseasesandotherphenotypes,itisbecomingincreasingly
evidentthatthesemutationsarenotsufficienttofullyexplaindiseaserisksandthat“additional”
factorsareequallyimportant.Amajorelementofthe“additional”factorsisepigenetics,which
playsakeyroleinphenotypicvariations,someofwhichappeartobetransgenerationallyinher-
itedinalmostallorganisms.Theaccelerationofepigeneticresearchoverthelastfewyearsis
impressive.Indeed,itisnoteasytofindabiologicalquestionthatdoesnotengageanepigenetic
component.
Thereisampleandaccumulatingevidenceoftheinfluenceofenvironment,includingdiet,
ongeneactionsthroughthemanipulationoftheepigenome.Currently,thebestknownexample
ofanepigeneticallysensitivegeneaffectedbyanenvironmentalfactorisAgoutiviableyellow
and the maternal diet in the mouse. Interestingly, it was found that methyl supplements in
the diet of pregnant mice increased the methylation level of the Agouti gene, consequently
causingcoatcolorchangesintheoffspring(Cooneyetal.,2002;Waterlandetal.,2008).Further
studies in rats showed that high-fat diet consumption by sires induced increased body and
bodyfatweightsandhigherglucosetoleranceandinsulinresistanceintheirfemaleoffspring
(Ngetal.,2010).AnotherfascinatingexampleofnutritionaleffectsonDNAmethylationand
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