1 The Promise of Animal Genomics Max Rothschild Department of Animal Science and Center for Integrated Animal Genomics Iowa State University The building blocks of life… Definitions Genetics • the science of heredity • transmission of genetic information from one generation to the next • interactions of genes with each other and with the environment to produce phenotypes Definitions Genomics • the science of sequencing data • discovery of new genes, gene mapping • new genetic technologies • gene regulation and genome expression In many parts of the world, animals are crucial to people’s economic survival Meat consumption, million tons Region 1997 2020 Developed 98 114 EU 32 35 USA 32 40 Developing 111 212 China & SE Asia 64 127 South Asia 7 16 Latin America 26 47 Sub-Saharan Africa 7 11
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The Promise of Animal GenomicsMax Rothschild
Department of Animal Science and
Center for Integrated Animal GenomicsIowa State University
The building blocks of life…
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Definitions
Genetics• the science of heredity• transmission of genetic information from
one generation to the next• interactions of genes with each other and
with the environment to produce phenotypes
Definitions
Genomics • the science of sequencing data• discovery of new genes, gene mapping• new genetic technologies • gene regulation and genome expression
In many parts of the world, animals arecrucial to people’s economic survival
Meat consumption, million tons
Region 1997 2020Developed 98 114
EU 32 35USA 32 40
Developing 111 212China & SE Asia 64 127South Asia 7 16Latin America 26 47Sub-Saharan Africa 7 11
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Challenges for Animal Genomics Research
How do we improve production of meat, milk and fiber while minimizing environmental impacts?How do we reduce animal disease and improve welfare?How do we use animals as models to improve animal and human health?
Find genes controlling major variation and then use DNA tests to select best animals for breeding.
We can employ modern methods of molecular biology and molecular genetics to unlock the secrets of animal genomes.
Opening the Black Box of Phenotype
How many genes?Size of gene effects?Which genes are most important?
Finding a Gene – An Analogy
The genome
The chromosome
The general location
The gene
The mutation
Approaches to Finding Trait Genes
Use several approaches:Candidate gene search QTL or genome scan projectMajor gene identificationExpression studiesWhole genome SNP associations
Candidate Genes
Candidate genes are those believed to control a specific physiological process.We can examine:
Estrogen plays a central role in many reproductive functions: embryo survivalfetal developmentfertility maintenance of fertility secondary sexual characteristics
ESTROGEN Estrogen Receptor (ESR)A candidate gene for litter size?
Estrogen receptor is crucial since it binds the estrogen.
We used the human ESR gene to develop a genetic test for a rare genetic difference in the pig ESR gene.
Meishan Pig from China Effect of ESR on Litter Size Meishan Synthetics
ESR First ParityGenotype N TNB NBA
AA 75 11.2a 10.0a
AB 94 12.5b 11.1b
BB 38 13.5b 12.3b
TNB = Total Number Born NBA = Number Born Alive**P<.01. a,b Means in the same column with different superscripts significantly differ P<.01.
Rothschild et al., 1996. Proc. Nat. Acad. Sci. (USA) 93:201-205.
ESR Means for Reproduction Traits~5,000 Commercial Females
ESR 1st Parity Genotype TNB NBA
AA 10.14a 9.42a
AB 10.59b 9.87b
BB 10.97c 10.22c
TNB = Total Number Born NBA = Number Born Alivea,b,c,d Means within a column without a common
superscript differ (P<.01).
Short et al., 1997. J. Anim. Sci. 75:3138-3143.
ESR effect is 5 X greater than normal response to selection.
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Gene Identification for Feed Intake and Growth Traits:
MC4R
Mutant mouse Does a MC4R mutation and fullsib exist in this pig?
MC4R mutation and TestKim et al., 2000. Mammalian Genome 11:131-135
Comparison Between Comparison Between GenotypesGenotypes
Backfat 1.1 mm lessFeed intake -.17 kg/dayFeed efficiency -.09Days to market 2.8 moreBenefits Producer
Consumer2/2 1/1 1/2
Environmental benefit:Reduced waste
Use of this genetic marker in a sire’s lifetime results in:28 tons less feed needed to raise 6000 progenyA reduction of 33,600 gallons of manure
Per 10,000 sows per year:930 tons less feed1,100,000 fewer gallons of manure
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What do We Eat? Consumer Attitudes
South Beach
Diet
“The fundamental trends driving how America eats are convenience and health, but even more central is taste. People are not willing to sacrifice taste. They want to provide quality, good-tasting meals to their families at home, but they want to get them on the table in 30 minutes or less.”
Betsy Holden, president & co-CEO, Kraft Foods, North America
Consumers Want Tasty Food
Meat Quality
MUSCLE
NERVE
CONNECTIVE TISSUE
NUCLEI
MEMBRANE
BUNDLE OF FIBERS
MUSCLE CELL (FIBER)
MYOFIBRIL
FILAMENTS
MYOSIN FILAMENT
ACTIN FILAMENTSARCOMERE
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F0 2 Berkshire sires 9 Yorkshire dams BB x YY F1 8 sires BY x BY 26 dams F2 525 BB BY YB YY
Genome Scan for Meat QualityMalek et al., 2001. Mammalian Genome 12:637-652.
DGtBW
BW
DGt
DGp
DGt
DGp
DGt
DGsWW
WtDGt
WpBWDGt
BWWT
DGpDGt
DGp
DGtWt
DGp
Wp
DGp
DGt
DGp
DGtDGt
BW
DGt BWDGt
Wt
DGp
DGt
DGp
BW
DGs
DGp
DGp
DGt
DGt
FE
Wp
BW
DGp
FI
DGt
DGt
DGt
DGpWt
Wt
DGt
DGtWt
DGs
DGt
DGp
DGt
DGt
BW
BW
DGt BW
WtDGt
Wt
DGt
DGt
DGp
DG
WtDGp
FI
WtDGt
DGp
MC4RRN
PIT1RYR1
SLA
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20
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60
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120
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 X
Leng
th (c
M)
SSC
Current Status of Quantitative Trait Locus Mapping in Pigs – Growth and
Meat Quality
Higher pH and more moisture meansAppearance ++Color ++Tenderness ++Aroma +Juiciness ++Flavor ++
PRKAG3 and CASTCiobanu et al., 2001, Genetics; Ciobanu et al., 2004, JAS
Swine Gene Mapping:A Record of Progress
Genetic Parameters 1990 1995 2000 2005
Mapped genetic markers 100 1,200 4,000 8,000
Physically mapped markers
50 500 1,300 15,000
Mapped QTL 2 10 > 50 >1,400
Number of ESTs 0 < 2,000 >70,000 >1.5M
BAC, YAC libraries 0 3 4 4
Number of RH Panels 0 0 3 3
Resource Populations 1-3 10 > 20 >25
Where we are today?Table 1. Candidate genes and gene tests identified and used in the industry
Candidate genes Traits Industry useHAL meat quality/stress yesKIT white color yesMC1R red/black color yesMC4R growth and fatness yesRN, PRKAG3 meat quality yesAFABP, HFABP intramuscular fat ?? CAST tenderness yesIGF2 carcass composition yesESR, PRLR, RBP4 litter size yesFSHB reproduction unknownNRAMP, SLA disease susceptibility unknownFUT1 disease susceptibility yesTrade secret tests several traits yes
Efficient Agriculture Gives More People Richer Lives
In the 1950s:10 million cooked breakfasts required more than 15,000 acres.Today:If you want 10 million cooked breakfasts it requires ~5,000 acres of crops to feed animals
Which would mean less land for all of us to enjoy in other ways
Rainforest Rainforest Destruction Destruction
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Complexity of disease
requires the use of many approaches
Human Health
Complexity of disease requires the use of many approaches
Comparative Approaches
Companion Animals
Dogs and cats were among the first animals domesticated – companions to humans.They have been inbred to form hundreds of breeds which has resulted in many associated diseases.Animal genomics offers opportunities to improve companion animal health.In addition, both the dog and the cat serve as excellent animal models for human health.
Timothy M. Frayling. 2007. Nature Reviews Genetics.
T2D and Obesity T2D Genes and Pig Fatness
T2D Genes:
TCF7L2FTOSLC30A8WFS1IGF2BP2KCNJ11GCKR
Animals: BY Resource family (F2 design) (Berkshire and Yorkshire)
SNP Genotyping: PCR-RFLPStatistical Analysis: SAS proc mixed Genetic Mapping: CRIMAP
Malek M. et al. 2001. Mammalian Genome
Timothy M. Frayling. 2007. Nature Reviews Genetics.
Zhiliang Hu, Svetlana Dracheva, Wonhee Jang, Donna Maglott, John Bastiaansen, Max F. Rothschild and James M. Reecy (2005). A QTL resource and comparison tool for pigs: PigQTLDB. Mammalian Genome. Volume 16(10):792-800.
QTL on Pig Chromosome 14
Pig QTL for Fat-related Traits T2D Genes and Pig Fatness
0
0.5
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TCF7
L2-3UTR
INSI
G2pse
udo
WFS
1
KCNJ1
1
SLC30
A8FT
OGCKR
-logP
AVBFAT
LASTRIB
LUMBAR
TENTHRIB
MARB
CHOLES
TOTLIPPR
LEA
BIRTHWT
CARCWT
SIXTHEWT
LENGTH
ADGWT
AGDTEST
AVGGG
AVGP
AVLAC
AVDRIPPR
FTYPI
FTYPIIR
HAMH
HAMM
HAMPH
HORMLH
HORMLM
HORMLPH
LABLH
LABLM
LABLPH
COLOR
WHC
FIRM
AVINSFOR
CHEWSCR
FLAVSCR
JUICSCR
OFFLAVSC
PCCOKLOS
Carcass Traits
Meat QualityTraits
P=0.05
P=0.01
Only TCF7L2 is associated with all the fat traits.
Fat traits
Mutation testing -BRCA1, BRCA2Differential drug treatment – gene chips to identify problemsMicrobial genetics leading to new vaccinesGenetic susceptibility –Genetic Information Non Discrimination Act of 2003
Genomic Medicine Personal Genomics
Many to choose from:
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Sequencing the Genome
Unlocking the secrets of the genetic code
Adapted from
Genome Sequencing
Humans have an excellent, nearly complete genomic sequence for study
Attention turned to other organisms and species:
Microbes
Animals: chicken, cow, dog, and honey bee
Great value in comparative genomics
Pig genome sequencing will cost about $30,000,000.
Efforts to start a sequencing consortium are well underway.
14805 clones selected and sent for sequencing covering 90.5% of the map.Total sequence = 1888 Mb (61.9 Mb Finished quality) from 11131 sequenced clones with 6357 at Improved status.
Understand the genetic basis for trait differencesFind mutations associated with traits of real interest – growth, FE, obesity, disease associations
**HUMANSDevelop new pharmaceuticals to combat disease.Create genomic medicine
**PIGS
Genome sequence provides Genome sequence provides a template to:a template to:
Locate genes and link them to functionLocate genes and link them to function
Functional and applied genomicsFunctional and applied genomics
Find Find SNPsSNPs -- positions in the genome wherepositions in the genome wherethe genetic code differsthe genetic code differsbetween breeds or individualsbetween breeds or individuals
Some are causative mutations for traits Some are causative mutations for traits
Most will be linked markersMost will be linked markers
HighHigh--throughthrough--put SNP genotypingput SNP genotyping
60K SNP Chip ready by December 2008
What will we do with 60K SNP markers?
Perform genome wide associations
Use ALL marker associations to estimate breeding value – genomic selection
Goal: collect useful phenotypes!
Genomic Selection: select on the markers
PotentialHigh accuracy over several generationsLess progeny or sib testing lower costsshorter generation intervals
RequirementsLinkage Disequilibrium (LD) between markers and QTL
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Genomic Selection GoalsGenomic Selection Goals
Predict young animals more accuratelyAvoid costly phenotypic measurementsCompare actual DNA inheritedUse exact relationship matrix G instead of expected values in ATrace chromosome segmentsLocate genes with large effects
Genomic RelationshipsGenomic RelationshipsMeasures of genetic similarity
A = Expected % genes identical by descent from pedigree (Wright, 1922)G = Actual % of DNA shared (using genotype data)T = % genes shared that affect a given trait (using genotype and phenotype)
Best measure depends on useAllows us to reconsider “unrelated individuals” – are they really unrelated?
Old fashioned animal pedigree Genomic PedigreeGenomic Pedigreeatagatcgatcg
ctgtagcttagg
agggcgcgcagt
cgatctagatcg
cggtagatcagt
agagatcgatct
atggcgcgaacg
ctatcgctcagg
ctgtagcgatcg
agatctagatcg
agagatcgcagt
atgtcgctcacg
ctgtctagatcg
atgtcgcgcagt
Reliability from Full SibsReliability from Full Sibs50,000 markers, 1000 50,000 markers, 1000 QTLsQTLs, sib REL = 99%, sib REL = 99%
A = traditional additive relationships,G = genomic relationships
Genomic SelectionGenomic Selection MeuwissenMeuwissen et al. (2001)et al. (2001)
MODELMODELto predict to predict
phenotype/BV phenotype/BV from SNP from SNP genotypesgenotypes
GenotypeGenotype>50,000 >50,000 SNPsSNPs
PhenotypePhenotype
GenotypeGenotype>5,000 >5,000 SNPsSNPs
PredictPredictBV or BV or
phenotypephenotype
GenotypeGenotype>5,000 >5,000 SNPsSNPs
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3 4 5 6 7 8Generation
Acc
urac
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Traits that Add to Profitability
Growth
ReproductionDisease Resistance
Feed Intake
Behavioral
Meat QualityLeanness
$$$$$$$
Longevity
Environmental Soundness
$100 million
$10 million
$20 million $50 million
unknown
unknown$100 million
$10 million$20 million
Impact of ‘omics’
Basic research:structure, mechanisms,
Bioinformatics emerged as a discipline to meet the data acquisition, management, analysis and visualizationneeds of high throughput genomics technologies.
Genomics and theassociated ‘omics’refers to HTP biotechnologies that generate large volumesof biological data
models
HO
O
HO
O
PPO
β-Amyrin synthase (AS
Squalene epoxidase (SE)
Squalene synthase (SS)
FPP
β-Amyrin
Mevalonic acid
2,3-Oxidosqualene
Squalene
Cycloartenol
Sesquiterpe
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89
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function
Assuring the application of Genomics to
Agricultural Research
Basic:structure, mechanisms,models,function
Applied: treatments,therapies,breeding,selection
Translational:diagnostics,statistical inference,decision support,methods development
Imagine the Future
Imagine sequencing the entire genome of a pig for $1000 or less.Imagine a catalog of mutant alleles for every gene in the pig genome.Imagine following the fate of every cell during development.Imagine predicting the behavior of complex biological systemsImagine managing animal production more efficiently
“Vertical” Genotypes or Designer Genotypes
Specific corn genotypesfed to
Designer pig genotypesto produce
Specific products for special markets
Designer Health Plansfor
Designer Genotypes
Specific vaccinations and treatment regimes for
Specific lines and genetic products to produce
Specific products for special environments.
Vaccine - Ready Pigs
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Advances in Animal Genomics
20-40% increases in productionDesigner Genetics – specialized crop and animal genomics to produce specialized productsImproved animal welfareImproved environmental conditionsCloned/transgenic Animals – produce proteins and organs for human medicineBright future for food production and
contributions to humans
Acknowledgements
The collaboration of colleagues both at Iowa State University and around the world is appreciated.A special thank you is extended to my host and his colleagues for hosting this visit.
