got genomics?

Joseph C. Dalton, PhD

Definitions

• Genome: complete collection of hereditary information (DNA)

• DNA: material that carries genetic information

(The Wellcome Project)

Definitions

• DNA is made up of two chains of nucleotide base subunits.

• Nucleotide bases link together:–Adenine: Thymine

–Cytosine: Guanine

(The Wellcome Project)

~3 billion base pair sites in the bovine genome!

Definitions

Gene: Basic unit of inheritance A specific section

(sequence of DNA) required to encode a particular proteinProteins determine

form and function

(The Wellcome Project)

Definitions

Chromosome: A threadlike strand of DNA and associated proteins in the nucleus of cells that carries the genes and functions in the transmission of hereditary information.

DNA and genotyping

• DNA can be collected from a blood, tissue, hair, or semen sample.

• From a DNA sample it can be determined which of the four bases are located at ~ 40,000 sites (genotyping).

(ABS Global, 2008)

Single nucleotide polymorphism

• A single nucleotide polymorphism (AAGCCTA to AAGCTTA ) may produce a variation in an important trait.

• Single nucleotide polymorphisms are also called SNP or SNIP.

What is a “SNP-CHIP?”

A tool to identify DNA markers for economically important traits in livestock.

A snip (SNP) is a change in a single location in the DNA structure (AAGCCTA to AAGCTTA ).

(Illumina, Inc.)

How does a SNP-CHIP help estimate the breeding value of an animal?

Progeny tested sires were genotyped and associations were made between genotypes and traits (proofs).

Associations between key traits (proofs) and genotypes at the 40,000 base pair sites are used to define information in a bull’s genomic proof.

(ABS Global, 2008)

How does a SNP-CHIP help estimate the breeding value of an animal?

• In young animals, associations between key traits and marker genotypes are estimated using data from the animal's ancestors (progeny tested bulls).

Which traits?

Genomic traits that are estimated:

• Production traits: milk, fat, protein, fat (%) and protein (%)

• Health and fitness traits: PL, SCS, DPR, calving ease and stillbirth, type and linear conformation traits

(ABS Global, 2008)

What does all this mean?

Genomic evaluation

Past: A young animal's genetic potential was based on parent average (PA).• PA = average of the predicted transmitting abilities

(PTA’s) of its parents; reliability = 30-40%

• Flaws:• No way to determine the sample of genes the young

animal inherited from its parents.

• Must wait 2 yr to measure performance of females, and five years (in the case of males) to measure the performance of its progeny.

(Weigel, 2008)

Genomic evaluation

Present: Because of the relationships between SNP markers and important genes observed in an animal's ancestors, we can see what the future may hold for that animal. For a young Holstein bull and heifer, a

combination of the animal's PA with information from the SNP Chip = a “genomic PTA” with a reliability of 60 to 70%. 

(Weigel, 2008)

Genomic PTA

Heifers: Reliability ~ = to measuring several lactation records on the animal and its daughters.

Young cow: Information from the SNP Chip can be combined with its lactation records to obtain a more accurate estimate of its genetic merit.

(Weigel, 2008)

Genomic PTA

Bull calf: Reliability = to that obtained by measuring performance on about a dozen daughters.• After performance data from 80 to 100

daughters is available (through progeny testing), information from the SNP Chip has relatively little value.

(Weigel, 2008)

So what’s going on now?

Most young bulls entering N. American AI centers (and many potential bull dams) are tested with the SNP Chip.•Result: A higher success rate from progeny

testing in the future, as we know prior to entry into an AI center that each young bull has received a good sample of genes from its parents. 

(Weigel, 2008)

Genomic-enhanced evaluations

Published by USDA-AIPL (beginning with the January 2009 Sire Summary)

• unproven and proven sires

• Holstein and Jersey breeds Incorporate daughter information,

genomic information, and traditional pedigree contributions.

Evaluation differences in a full brother group

Bull Evaluation type Milk Fat Prot PTAT

PL

Litter Traditional PA 1151 46 45 2.4 3.8

A Genomic-enhanced 1176 27 34 1.5 3.6

B Genomic-enhanced 1395 43 42 2.1 1.6

C Genomic-enhanced 1230 73 56 2.8 3.3

Which young bull would you select?

(Adapted from ABS Global, 2008)

Benefits of genomics

Earlier information about genetic merit and fitness traits of young sires

Assists in parentage validation More accurate inbreeding calculations Testing of potential bull dams Testing of animals in consignment sales “First choice of flush” from embryo

transfer

(ABS Global, 2008; Weigel, 2008)

Will there be a need for progeny testing in the future?

Yes. Lactating cows are the true measure of a bull’s transmitting ability.

Progeny test information is required to generate genomic information.

What about genomic evaluation of other breeds (Brown Swiss)?

Gains in reliability for Brown Swiss have been negligible. Why? Small population size (not as many progeny tested

bulls are available for estimating the associations between SNP markers and important traits)

Is anything being done to increase the population size? Yes. Through a combination of information from North

American sires with key international sires.

(Weigel, 2008)

Questions?

For more information

http://www.absglobal.com/dairy/genomics/

http://www.selectsires.com/genomics_menu.aspx

http://agteamdirect.com/Genomics.aspx

http://genex.crinet.com/page1973/Genomics

(Photo on title slide courtesy of ABS Global)