2002 Curt Van Tassell Gene Evaluation and Mapping Laboratory and Animal Improvement Programs...

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200 2 Curt Van Tassell Curt Van Tassell Gene Evaluation and Mapping Laboratory and Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD [email protected] Application of Application of Genetic Markers Genetic Markers to Dairy Cattle to Dairy Cattle

Transcript of 2002 Curt Van Tassell Gene Evaluation and Mapping Laboratory and Animal Improvement Programs...

Page 1: 2002 Curt Van Tassell Gene Evaluation and Mapping Laboratory and Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville,

2002

Curt Van TassellCurt Van TassellGene Evaluation and Mapping Laboratory andAnimal Improvement Programs LaboratoryAgricultural Research Service, USDA, Beltsville, [email protected]

Application of Application of Genetic Markers to Genetic Markers to

Dairy CattleDairy Cattle

mailto:[email protected]
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OverviewOverview

Traditional selection

Genetic markers

Granddaughter design

Resource populations

QTL identification

EST sequencing

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IntroductionIntroduction

Traditional dairy cattle breeding has assumed that an infinite number of genes each with very small effect control most traits of interest

Logical to expect some “major” genes with large effect; these genes are usually called quantitative trait loci (QTL)

The QTL locations are unknown! Genetic markers can provide information

about QTL

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Traditional Selection ProgramsTraditional Selection Programs

Estimate genetic merit for animals in a population

Select superior animals as parents of future generations

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Genetic Improvement: Genetic Improvement: Challenges and TechnologiesChallenges and Technologies

Traditional selectionTraditional selection

Gene mapping and Gene mapping and marker assisted selectionmarker assisted selection

TransgenicsTransgenics

Abundant Genetic variationAbundant Genetic variation

Limited genetic variationLimited genetic variation

Little or no genetic variationLittle or no genetic variation

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Application of Genetic MarkersApplication of Genetic Markers

Identify genetic markers that are associated with changes in genetic merit

Use marker assisted selection (MAS) to make selection decisions before phenotypes are available

Adjust genetic merit for genetic markers

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Useful Genetic Markers:Useful Genetic Markers:

Allow marker inheritance to be followed across generations

Many different types of marker alleles well represented in the population

Marker and QTL are close together so that recombination between marker and QTL is rare

Best case is when we know the QTL - then it is the marker!

Page 8: 2002 Curt Van Tassell Gene Evaluation and Mapping Laboratory and Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville,

m q

M Q

MarkerLocus

QuantitativeTrait Locus

{ {

LinkageDistance

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Page 9: 2002 Curt Van Tassell Gene Evaluation and Mapping Laboratory and Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville,

ParentalChromosomes

RecombinantChromosomes

MarkerLocus

QuantitativeTrait Locus

{ {

m q

M q

m Q

M Q

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Page 10: 2002 Curt Van Tassell Gene Evaluation and Mapping Laboratory and Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville,

ParentalChromosomes

A B C D E F

a b c d e f

RecombinantChromosomes

*******

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Genetic MarkersGenetic Markers

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Genetic Markers!!Genetic Markers!!

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Genetic MarkersGenetic Markers

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Bull

Granddaughter DesignGranddaughter Design

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Granddaughter DesignGranddaughter Design

Sons

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Granddaughter DesignGranddaughter Design

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Page 17: 2002 Curt Van Tassell Gene Evaluation and Mapping Laboratory and Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville,

Granddaughter DesignGranddaughter Design

DNA

Genetic

Merit

Data

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Resource Populations:Resource Populations: Cooperative Dairy DNA Repository (CDDR)Cooperative Dairy DNA Repository (CDDR) The CDDR is an ongoing collection of all

bulls entering progeny tests Includes all breeds Useful for QTL mapping in dairy cattle using

a granddaughter design and for complex pedigree analysis

Currently (6/01): Six North American studs contributing semen 9789 bulls in the collection 128 families with at least 25 sons

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Compare GeneticMerit

QTL IdentificationQTL Identification

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3.51.7 -0.1 -2.5 -6.20.7

QTL IdentificationQTL Identification

Bull

Sons

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USDA-ARS ProgressUSDA-ARS Progress

Over 160 markers studied in over 1000 animals from 8 families

Evaluated all available traits: Conformation traits, M, F, P, SCS, PL, and calving ease

Genome-wide scan across all families was recently completed

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Marker Association ResultsMarker Association ResultsChromosome Trait

3 Protein Percentage4 Strength

Body Depth5 Dairy Form6 Protein PercentageProtein Percentage7 Somatic Cell Score

12 Foot AngleRear Legs (Rear View)

14 Fat PercentageProtein PercentatgeFore Udder AttachmentFront Teat Placement

16 Udder Depth18 Rump Angle20 Protein Percentatge22 Rump Angle27 Dairy FormDairy Form

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0

4

8

12

16

20

0 20 40 60

DF M F PF% P% PL SCS

Family 8 interval analysis resultsFamily 8 interval analysis results

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Page 24: 2002 Curt Van Tassell Gene Evaluation and Mapping Laboratory and Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville,

What is an EST?What is an EST?

ATG TAAmRNA

ESTs

AAAAAAAAA

5’ AAAAAAAAATTTTTTTTTT3’

5’ 3’

5’3’

cDNA

Tissue Biopsy

mRNA isolation

RT-PCR

Sequencing of cDNA clones

Bioinformatics

Bovine Sequence database

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USDA-ARS Bovine EST ProjectsUSDA-ARS Bovine EST Projects

Initial goal: Single pass sequencing of 5 bovine cDNA libraries

4 axis libraries @ MARC = 80,000 EST 1 mammary library @ BARC = 10,000 EST

Mammary cDNA library has stages from prepubertal, mid-gestation, late gestation, cholostrogenesis, lactation, infected lactation, and early and late involution.

Sample diverse developmental stages and morphological cell types to maximize diversity and minimize redundancy

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Status ARS EST sequencingStatus ARS EST sequencing

GenBank dbEST database submissions: 231,577 total cattle gene-related

sequences >150,000 cattle ESTs generated by USDA 120,745 cattle sequences 1-4BOV cDNA

libraries (MARC) 23,202 cattle sequences 5BOV cDNA

library (BARC)

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EST Sequence Analysis & AssemblyEST Sequence Analysis & Assembly

AGCTTTAAGCCATACCTTAGGACATTACCTAGGAGCTTTAAGCCATACCTTAGGGTCAGCTTTAAGCCATACCTTAGGACATTACCTAGG

AGCTTTAAGCCATACCTTAGGACATTACCTAGG

GCCATACCTTAGGACATTACCTAGGAGCTTTAAGCCATACCTTAGGGTC

AGCTTTAAGCCATACCTTAGGACATTACCTAGGAGCTTTAAGCCATACCTTAGGGTCAGCTTTAAGCCATACCTTAGGAC

AGCTTTAAGCCATACCTTAGGGTCAGCTTTAAGCCATACCTTAGGACATTACCTAGG

TC

EST1EST2EST3EST4

TIGR Bovine Gene Index:TIGR Bovine Gene Index:

Over 67,000 unique sequence elementsOver 67,000 unique sequence elements

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Page 28: 2002 Curt Van Tassell Gene Evaluation and Mapping Laboratory and Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville,

Unique Cattle SequencesUnique Cattle Sequences

Rat Gene Index

11,077

28,61718,292

36,7

34

10,1

75

44,367

2,542

31,67115,238

22,760

24,149

Human Gene Index

Mouse Gene Index

Human Golden Path

TOGA

Over 17,000 “no hit” bovine sequence elements.

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ConclusionsConclusions

Marker assisted selection is an evolutionary improvement over traditional selection methods. It allows more accurate estimation genetic merit of animals

Evidence of important QTL has been found

EST sequencing has been very successful

Lots of interesting findings from EST project that will need additional research


42960 Signalman John Darrell TASSELL (1944-1966)...orneo Veterans’ Day on 31 August. Among the fallen from Confrontation honoured each year is Signalman John Tassell. John Tassell

42960 Signalman John Darrell TASSELL (1944-1966)...orneo Veterans’ Day on 31 August. Among the fallen from Confrontation honoured each year is Signalman John Tassell. John Tassell

2003 P.M. VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD paul@aipl.arsusda.gov Genetic Evaluations.

2003 P.M. VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD [email protected] Genetic Evaluations.

Dr. George R. Wiggans, Ph.D. Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD, USA george.wiggans@ars.usda.gov.

Dr. George R. Wiggans, Ph.D. Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD, USA [email protected].

John B. Cole Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350 john.cole@ars.usda.gov 2014 Phenotypes.

John B. Cole Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350 [email protected] 2014 Phenotypes.

Curt Van Tassell USDA Agricultural Research Service AIPL – Animal Improvement Programs Laboratory BFGL – Bovine Functional Genomics Laboratory Recent Developments.

Curt Van Tassell USDA Agricultural Research Service AIPL – Animal Improvement Programs Laboratory BFGL – Bovine Functional Genomics Laboratory Recent Developments.

H. Duane Norman Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD duane.norman@ars.usda.gov NDHIA San Antonio.

H. Duane Norman Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD [email protected] NDHIA San Antonio.

2007 Paul VanRaden, George Wiggans, Jeff O’Connell, John Cole, Animal Improvement Programs Laboratory Tad Sonstegard, and Curt Van Tassell Bovine Functional.

2007 Paul VanRaden, George Wiggans, Jeff O’Connell, John Cole, Animal Improvement Programs Laboratory Tad Sonstegard, and Curt Van Tassell Bovine Functional.

Curt Van Tassell Bovine Functional Genomics Laboratory Agricultural Research Service, USDA Beltsville, MD curtvt@ars.usda.gov Applied Genomics for Sustainable.

Curt Van Tassell Bovine Functional Genomics Laboratory Agricultural Research Service, USDA Beltsville, MD [email protected] Applied Genomics for Sustainable.

2007 Paul VanRaden, George Wiggans, Animal Improvement Programs Laboratory Curt Van Tassell, Tad Sonstegard, Bovine Functional Genomics Laboratory USDA.

2007 Paul VanRaden, George Wiggans, Animal Improvement Programs Laboratory Curt Van Tassell, Tad Sonstegard, Bovine Functional Genomics Laboratory USDA.

2014 John B. Cole Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD john.cole@ars.usda.gov Genetic improvement.

2014 John B. Cole Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD [email protected] Genetic improvement.

George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD george.wiggans@ars.usda.gov 2008 Genetic trends.

George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD [email protected] 2008 Genetic trends.

G. R. Wiggans, wiggans@aipl.arsusda.gov Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD M. A. Faust ABS Global,

G. R. Wiggans, [email protected] Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD M. A. Faust ABS Global,

2004 2006 John B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD jcole@aipl.arsusda.gov Dairy Cattle Breeding.

2004 2006 John B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD [email protected] Dairy Cattle Breeding.

WiggansBritish Cattle Conference 2015 (1) Dr. George R. Wiggans Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville,

WiggansBritish Cattle Conference 2015 (1) Dr. George R. Wiggans Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville,

V. R. Reddy Crop Systems and Global Change Laboratory, Beltsville Agricultural Research Center, USDA- ARS, 10300 Baltimore Ave. Beltsville, MD 20705, USA.

V. R. Reddy Crop Systems and Global Change Laboratory, Beltsville Agricultural Research Center, USDA- ARS, 10300 Baltimore Ave. Beltsville, MD 20705, USA.

Recipes From the kitchen of Jean Van Tassell

Recipes From the kitchen of Jean Van Tassell

WiggansARS Big Data Computing Workshop (1) 2013 George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville,

WiggansARS Big Data Computing Workshop (1) 2013 George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville,

G.R. Wiggans* and P.M. VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD *george.wiggans@ars.usda.gov.

G.R. Wiggans* and P.M. VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD *[email protected].

Genetic Selection Tools in the Genomics Era Curt Van Tassell, PhD Bovine Functional Genomics Laboratory & Animal Improvement Programs Laboratory Beltsville,

Genetic Selection Tools in the Genomics Era Curt Van Tassell, PhD Bovine Functional Genomics Laboratory & Animal Improvement Programs Laboratory Beltsville,

Paul VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD paul@aipl.arsusda.gov 2007 Improving Animals Each.

Paul VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD [email protected] 2007 Improving Animals Each.