Sequencing a North American yak...

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Sequencing a North American

yak genome Presentation for the annual meeting of the International Yak association

Denver Colorado, January 24, 2014

Mike Heaton, Ph.D. USDA Meat Animal Research Center (USMARC), Clay Center, Nebraska

An equal opportunity provider and employer

• Introduction to USMARC, aims, and role

• Answering cattle questions with Yak DNA

• Publication of the Chinese yak genome sequence

• Opportunities to improve herds with DNA testing

Topics

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USDA Meat Animal Research Center

35,000 acres

54 scientists

250 employees

4000 ewes

7000 lambs

6300 cows

5000 calves

720 litters

USDA Meat Animal Research Center Federal appropriation: $18.1 M

Sale of animals: $6.5 M

2013 operating budget: $24.6 M

Federally approved 6000-head capacity feedlot

We host about 1700 visitors from 40

states and 28 countries per year

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USMARC Aim

To deliver timely research for solving

problems facing our stakeholders

Michael P. Heaton, PhD

Interest: reducing the impact of infectious disease

Bacteria cell wall assembly:

targets for antibiotics

University of Nebraska-Lincoln, NE

Northwestern University, Evanston, IL

“Super bugs” antibiotic resistance

mating and gene transfer

Donor

(Vancomycin resistant)

Recipient

(Vancomycin susceptible)

Rockefeller University, New York, NY

M. H

ea

ton

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USMARC Animal Health Research (since 1996)

Michael P. Heaton, PhD

Identify genetic resistance to infectious disease

• Bovine respiratory disease complex

• Ovine progressive pneumonia in sheep

• Genetics of prion disease

• Failure of passive transfer in neonatal calves

Develop efficient DNA marker systems for cattle and sheep:

• disease traceback and animal identification

• parentage testing

• disease testing in sheep

What is the goal?

To read an animal’s DNA sequence and

predict its risk for disease.

DNA tests to improve herds Outcome:

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Who benefits from the research?

• DNA testing companies

• Agencies that use or perform DNA testing services

• Livestock breed associations and producers

• Researchers

USDA

firewall

Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply

recommendation or endorsement by the U.S. Department of Agriculture.

What is DNA and how can we use it?

A calf has about 10 trillion cells

nucleus

30 chromosome

pairs

A T “A” allele from one

parent, “T” allele

from other

Bovine pulmonary endothelial cell-Invitrogen

from

sire

from

dam

Phoebe, Grunniens Ranch

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Two important concepts for

understanding the genome

Proteins do the work in cells and

regulate the body’s tissues and organs.

Genes have DNA sequences encoding proteins.

For more information, click to play short videos:

http://www.dnatube.com/video/2933/The-Human-Genome-Project-Video--3D-Animation-Introduction

https://www.23andme.com/gen101/genes/

Genes are encoded by sequences of DNA

exon 3 exon 1 exon 2 exon 4

intron 3 intron 1 Intron 2

Most of the genetic diversity in livestock occurs at this level

nucleotides: A, C, G, T




















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…aatggtataAattaatgctt…

…aatggtataTattaatgctt…

What are SNPs? Single Nucleotide Polymorphisms

Sites in the genome where two different nucleotides occur

paternal chromosome

maternal chromosome individual #1:

paternal chromosome

maternal chromosome …aatggtataTattaatgctt…

…aatggtataTattaatgctt…

individual #3:

individual #2:

paternal chromosome

maternal chromosome …aatggtataAattaatgctt…

…aatggtataAattaatgctt…

A/A

T/T

A/T

DNA trace file

DNA markers in cattle for parentage

…aatggtatcaTattaatgctt…

…aatggtatcaTattaatgctt…

…aatggtatcaAattaatgctt…


A/A

T/T

…aatggtatcAattaatgctt…

…aatggtatcTattaatgctt…

A/T


With 50 informative SNPs, the

probability that a randomly

chosen sire will be excluded

from paternity >99% The calf must share an

allele with each parent

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Why not use “microsatellite” markers instead?

(also known as variable number tandem repeats: VNTRs)

• A good microsatellite marker is five times more powerful

than a good SNP allele.

• Tradition (legacy data), genotyping infrastructure

However, SNP platforms now routinely use 50 to 700,000 markers

10-50

50-100

3,000

8,000

50,000

700,000

Whole genome

SNPs Use

Traits/Traceback

Parentage/Inbreeding

Genomic Selection

Genomic Selection

Gene Mapping

Gene Mapping

Causative Mutations

Genomic advances in yak research

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History of USMARC with IYAK research

2006, Sep: The late Jerry McRoberts visited USMARC in 2006 to discuss yaks.

2008, Jan: Planned for collecting 24 yaks across N. American population.

2008, Apr: Received 2 yak livers from Jim Watson.

2008, Dec: Received hair follicles from 11 yak from Jim Watson.

2009, Jan: 15 IYAK samples run on bovine 50k SNP chip by collaborator.

2009, Apr: Received 2 yak livers from Jim Watson (cattle genome published)

2009, Jul: Received 9 blood samples from Jim Watson Bulls

2009, Oct: IYAK DNA used in National Academy of Sciences paper (PNAS)

2012, Jan: IYAK DNA used in PLOS Genetics paper (sheep research)

2010, Jan: Queen Allante passes away, tissue saved, sent to USMARC

2011, Jan: Received about 10 blood samples from Lawrence Richards

2012, Jul: Chinese yak genome sequence published

2014, Jan: Present results at annual IYAK meeting in Denver

2013, Dec: USMARC-Intrepid map Chinese yak genome to cattle genome--makes public

2006 2007 2008 2010 2011 2012 2013 2014 2009

2007, Mar: IYAK board contacted for help in getting yak tissues for DNA.

2013, Dec: USMARC extracts good quality DNA from Queen Allante

2007, May: Received 2 yak steer livers from Mike Swartz.

Research articles published with IYAK DNA

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Research articles published with IYAK DNA

Why am I here today?

There is an opportunity to sequence the genome of a North American yak

Minke whale

http://server1.intrepidbio.com/FeatureBrowser/customlist/record?listid=7646266992



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Genome Sequencing costs

cattle

pig

sheep

yak

anything

Today: any animal sequenced (10X) for <$3000

What can you do with 10x whole genome

sequence of a N. American yak?

Parentage determination and pedigree analysis

Traceback (forensics)

Animal identification

Manage inbreeding (conservation genetics)

Design custom N. American yak-specific DNA tests for:

Genotype yak for newly discovered genes

Disease resistance

Wool

Monogenic traits

Estimating percent Bos taurus DNA in an animal

Map royal, trim solid coat color

Learn how to use genomics to advance the IYAK mission

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How does it work?

L1 Dominette 01449

Chinese yak Huangyuan County of Qinghai Province

Dr. Ted Kalbfleisch

Map 350M Chinese yak reads to cattle reference genome


Yak

SNP

A G

C C

G

G,A

nucleotide

difference

compared to

cattle

Yak reads mapped to cattle red-black gene (MC1R)



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Yak sequence differences in MC1R gene

Yak-specific SNPs in the MC1R gene

C/G

yak

SNP

C = yak

T = cattle

nucleotide

difference

compared to cattle

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Mapping a N. American yak genome

L1 Dominette 01449

Chinese yak Huangyuan County of Qinghai Province

Queen Allante D171

A G

C C

G

G,A

C

G,T IYAK

SNP

Map 350M Chinese yak reads to cattle reference genome

Map 350M Queen Allante reads to cattle reference genome

How to turn IYAK DNA into IYAK tests

IYAK DNA

Validation and use

SNP tests in

sets of 50

markers

each Commercial

genotyping

outfit

Genetic test design

~300 SNPs

For each

test design

Identify > 100,000 SNPs

Contract sequencing outfit Bioinformatics, storage and

web access outfit

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What can you do with 10x whole genome

sequence of a N. American yak?

Parentage determination and pedigree analysis

Traceback (forensics)

Animal identification

Manage inbreeding (conservation genetics)

Design custom N. American yak-specific DNA tests for:

Genotype yak for “new” genes discovered in cattle or sheep:

Disease resistance

Wool

Monogenic traits

Estimating percent Bos taurus DNA in an animal

Map royal, trim solid coat color

Sequencing a North American yak...

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