Dairy Cattle Genome Project

Marijke Boerefyn

1058919

November 27, 2018

AGR 1110
Introduction

Introducing a dairy cattle genome project to the Canadian Agricultural industry would be

an innovation improving on the sustainability and economic viability of Canadian dairy herds.

Expanding our national database beyond Holsteins to include breeds such as Jersey, Brown

Swiss, and Ayrshire would increase the genetic merit across all herds assisting in breeding

calculations, the proving of young bulls, and aiding in disease resistance.

Product/Technology Description

A dairy cattle genome innovation would utilize genomics to provide accurate data for the

analysis of specific traits and genetic markers throughout herds and breeds across Canada.

Genomics is the examination of nucleic acid sequences in cellular DNA investigating

how single nucleotide polymorphisms (SNPs) influence traits or performance in animals. A

Genome is a complete set of DNA in an organism, genomics is the study of the effects, complete

sets of genes, have on a living organism. Unlike genetics which only looks at a single trait or

gene, genomics studies all the genes and how they interact and influence the growth and

development of a living organism (Monke,2017). At any one time animals can be genotyped for

1000s of single nucleotide polymorphisms. These SNPs are approximately found in 1-cM

(centimorgan – a distance for measuring genetic linkage) intervals throughout the genome

(Schaeffer,2006). In dairy herds a vital and ongoing practice of genome sequences is the ability

to anticipate the genetic value of dairy cattle for economically significant traits. One important

benefit is the ability to recognize mendelian or inherited traits, such as polled-horned, coat color,

and other genetic traits previously discovered through pedigree relationships. SNP sequences are

available at a very young age for traits including milk yield and conformation, allowing accurate
decisions to be made about the selection of males to use as sires. Genomic testing makes a

fundamental change in long held beliefs about the breeding of dairy cattle, giving producers the

ability to make significantly more accurate decisions without waiting for progeny test results.

Genetic information is retrieved from tissue samples taken from cattle for testing. Genomic

testing examines for specific nucleic acids at uniformly distributed sites across twenty-nine

autosomal chromosomes in dairy cattle as well as investigates sex chromosomes. The 50K test is

an example of testing available which looks at over 50,000 individual sites (Cassell,

Emeritus,2012).

An investigation was performed by the Animal Improvement Programs Laboratory

(AIPL) in the United States which used progeny testing and the genomic testing on old AI bulls

to create prediction equations, allowing the AIPL scientist to develop a test to prove if the

genomics predictions were correct. The accuracy of genomic testing was compared to progeny

testing using Holsteins as the animals for the experiment, collecting data from twenty daughters

from different herds of various AI bulls. Accuracy is lower in breeds such as Jersey and Brown

Swiss breeds because fewer AI bulls exist. With larger progeny groups such as Holsteins, there is

greater opportunity to create prediction equations, it proves to be more difficult with breeds such

as Jersey or Brown Swiss. Instead of choosing young bulls and waiting five years to see the

results, the AIPL scientists found over 2000 genomically tested Holsteins with “first crop”

daughters born in 2009. Genetic evaluations were calculated using the data from 2009 and used

on a larger population which included the young bulls and over 4000 older bulls with “second

crop” daughters. The scientists then reviewed performance records and calving dates five years

previous from 2004 daughters. Genetic evaluations were calculated on the data set and were

named the discovery population. Prediction equations from 2004 were made from the collected
data and predictions on the genetic merit of 2000 young bulls were made. The results show that

Holsteins increase to 59% Net Merit $ (NM$ -- lifetime net merit index ranking dairy animals

based on their combined genetic merit for economically important traits) compared to a

reliability of about 25% on traditional parent average bulls. This was a critical advancement in

the accuracy in the selection of young animals. Today improvements in predictions in the

reliability of the Holstein gNM$ (reliability of combined genomic/traditional genetic

evaluations) has increased by over 70% (Cassell, Emeritus,2012).

An Australian study was done to estimate the net benefit from genotyping heifer selection

in commercial dairy herds. Three scenarios in total were investigated, as shown in table one.

Scenario one considered the implication of genomic testing. Scenarios two and three increased

the number of selection heifers from both sexed semen and genomic testing. In scenario two,

only the cost of genomic testing and the additional cost of sexed semen were considered.

Scenario three considered the cost of genomic testing plus additional costs, losses, and benefits

likely to be associated with the adoption of sexed semen (Newton,2017). The study discovered a

positive net benefit even if genomic testing is used only once in an animal's lifespan and that

recommends genomic testing of heifers as a profitable investment.

Table 1. Overview of the 3 scenarios tested, the benefits and costs (and losses) considered, and the parameters that

were varied for the 3 scenarios considered

(https://www.sciencedirect.com/science/article/pii/S0022030218303758)

Technology

A genome is the entire sector of an organism’s DNA, containing the complete set of

genes. Each genome consists of all the data required to construct and manage that organism.

There are three billion DNA base pairs and of which there are 25,000 - 30,000 known genes

contributing to desired traits or characteristics. In genomic selection, scientists search for single
nucleotide polymorphisms (SNPs). A SNP is a location in the chromosome where the DNA

arrangements may diverge among organisms. When SNPs occur on a gene that adds or interacts

with a certain trait or genome they are exceptionally useful in genomic testing. Illumina, a

developer of products assisting in mapping gene variations, created the Illumina 50K test chip to

evaluate approximately 54,000 SNPs valuable to the bovine cattle genome. This test has

developed into the accepted method for genomic testing of artificial insemination cattle sires and

is most often used on high-end or elite breeding stock. Holstein Canada and Semex partnered to

launch GenoTest in 2010 creating the 6K test, a more economical and simpler test which

classifies 6000 carefully chosen key SNPs that are most useful in identify economically

significant dairy traits. (Murray,2013).

Global Projects

The 10,000 Holstein Cow Genome Project was an extraordinary cooperation between

farmers, genetic companies, government and scientists in Australia dairy industry. It was based

on genomics, an innovation that uses DNA data to assist in computations for breeding standards

in dairy animals. This project aimed to advance the standard of genetic gain for financial

advantage by one hundred percent by expanding the veracity of genomic selection. By

introducing this style of project to the Canadian dairy industry, like Australia, Canada could

double the content of their national database for genetic data giving more dependable estimates

of genetic quality for dairy animals, creating a stronger economic basis for the dairy industry.
 Dairy Futures Cooperative Research Centre funded the 10,000 Holstein Cow Genome

Project in partnership with a one point two million dollar grant from the Regional Development

of Victoria, Australia. The project aimed to use genomic information to increase the

dependability of Australian Breeding Values (ABVs) for adolescent Holstein bulls that are

unproven by ten to twenty-eight percent over parent averages for Australian breeding values. The

goal was to increase the reliability of ABVs through collection of genomic data from animal’s

suitable herd records. This ambitious project aimed to improve the genetic gain rate for cost-

effectiveness Australian Dairy herd by 100% through the increase in accuracy of genomic

selection. A substantial productivity driver for dairy herds is genetic gain (quantity of increase in

performance gained through artificial genetic advancement programs) and the outputs of the

gains which through greater accuracy of selection would have a greater impact. The impact

would be approximately $54 million which would contribute to a reduced generation interval

(median lifespan of a bovine animal when their calf is born) of cows or bulls (impact $8 million).

Achieving this goal, the project used sequencing science called next generation sequencing

technology which analyzed pivotal ancestor bulls, combining with 10,000 cows with high quality

phenotypes correlating with fertility and more key influencers in economic traits. The 10,000

cow genome project improved SNP-based marker sets for economically important traits for the

Australian Dairy Industry. The project improved the effectiveness of DNA markers and

predicted financial gain of cow and bull genetics for forty essential traits inclusive of protein,

resistance to mastitis, milk yield, and Australian Profit Ranking. By using genomics to enhance

ABVs there was a great genetic advancement over time that lead to enhanced genetic value and

eventually improved the profitability and productivity in that dairy industry. The collection of the

DNA information by the Department of Environment and Primary Industries (DEPI), Victoria,
Australia, within the Dairy Futures Cooperative Research Centre, Australia, has allowed the

national database for DNA information to double, resulting in more reliable estimates for genetic

merit in dairy cattle and has significantly increased the reliability for genomic breeding values.

The genetic samplings were selected from 91 Australian dairy farms who kept pristine records

over many years. The samplings were taken through a collection of tail hairs from selected

individual Holstein cattle. The 10,000 cows were then analyzed for 50, 000 DNA markers. The

combination of trait evidence and data from the DNA markers proved it was possible to make

improved predictions for young bulls and heifers in breeding merit, impacting the genetics for

fertility, production, and other traits affecting profitability on a dairy farm. Since the 10,000

Holstein Cow Genome Project, DNA markers have become utilized widely in dairy herds aiding

in the global selection of prime bulls and heifers to breed and improving the management and

financial gain of farms. Many advantages of the program have impacted the industry including

how dairy bulls marketed by AI companies can now be selected for with significant increase in

reliability and at a younger age. Subsequent to the 10,000 cows research project, genetic markers

proved to be more accurate, allowing farmers to have greater reliability in the bulls and their

breeding decisions. There is an industry wide genetic advancement of up to fifty percent

increased production and improved financial gain. Australia predicted an estimated $100 million

potential economic value for this genomic technology in the twelve years following the study.

The research is available to dairy farmers through the Australian Dairy Herd Improvement

Scheme, making the information for this technology readily accessible (Hayes, 2017).
Where to use to Project

The dairy cattle genome project could become proactively engaged with dairy operations

across Canada. It would be vital to include AI companies such as Semex which actively engages

in advancing and developing genetic solutions for the dairy industry. Holstein Canada would also

be a viable partner as they have an extensive data base of herd records and genetic information of

registered dairy cattle throughout Canada.

Market Opportunities

The most powerful marketing tool would be educating the personnel who interact closely

with farmers. This would include classifiers from Holstein Canada, breeders from AI companies,

and veterinarians. These would be people who have standing relationships and a foundation of

trust with farmers. Utilizing agricultural print media such as local papers and provincial

magazines would also be excellent resources for providing information and scientific material.

Canadian Programs

Canada already has the Canadian Cattle Genome Project which is an extensive global

project including scientists from Ontario, Alberta, Australia, Ireland, USA, Scotland, and New

Zealand. The Canadian Genome Project’s purpose is to promote genomic-based devices to

improve the performance and sustainability of the beef and dairy industry (Stothard,et al, 2015).

The Canadian Cattle Project has completed sequencing three hundred and fifteen animals and

genotyping (770K and 50K) of over ten thousand animals. Many of the animals sequenced and
genotyped are prime historic bulls that have had a significant impact on our existing Canadian

herds. Rulings on which animal to sequence and genotype were based on an investigation of the

breed structure and pedigree for each breed. The Canadian Cattle Genome Project is in its final

year of its three-year project and all of the sequence and genotype information will be used in the

advancement of improving calculations to convey imputed genotypes. The collected genotypes

will create the reference data sets for future distribution and selection of genomic preferences, as

well as give suitable techniques for applying a genome-wide choice, relating imputed high

density and sequence genotypes (Canadian Cattle Genome Project, 2017).

The Canadian Cattle Genome Project works in partnership with the 1000 Bull Genome

Project. The Bull Genome Project planned to combine sequencing data for 1000 bulls.

Surpassing their goal, they currently have 1147 whole genomes sequenced with the numbers still

increasing. This project information and sequences are available to any research team worldwide

who would then be required to contribute a certain amount of data to the project, so everyone is

benefited. The Canadian Cattle Genome Project contributed 315 sequences from key ancestors,

being the largest contributor to the project so far. In return for their contributions the Canadian

Genome Project has gained access to over 1147 sequences (Canadian Cattle Genome Project,

2017).
Figure 2: Canadian Cattle Genome Project

Figure two shows the Canadian Genome Project consists of three interconnected research

streams, the population and pedigree characterization, the genome imputation, and the

technology platforms. The research identifies economic and social benefits as well as costs

associated with the usage of genomic testing in livestock improvement. It provides accurate and

low-cost genome-wide selection methods for breeders in the cattle industry. The goal of the

project is to have genome-wide selection research available to all Canadian herds. First comes

the development of a program infrastructure and other necessities, enabling the industry to utilize

Canada wide genome selection. Breeders will benefit from this project and help with laying the

cornerstone for subsequent generations of technology, including enhanced capacities for

guaranteeing a stable environment of dairy and beef production (Canadian Cattle Genome

Project,2017)

Novelty to Canada

Canada already has the Canadian Genome Project set in place, but the Canadian Genome

project only focuses on Holsteins for dairy breeds. By introducing genomics for not just

Holsteins but various dairy breeds in the Canadian dairy industry, including Jersey, Guernsey,

Brown Swiss and Ayrshire, we can improve the genetic merit and expand the national data base

for each breed. By improving the genetic merit for each breed, we will see an economic gain in

the Canadian Dairy Industry.

Costs

The original Illumina 50K test originally costed out at approximately two hundred and

fifty dollars per animal, which, for the average farmer, was too hefty a price tag to use on a large

herd for the 35 – 70% benefit in a cow. This resulted in the original test only being used on elite

cattle. Costs have continued to decrease over time, by 2012 the 50K test was available for one

hundred and fifty dollars. A less expensive 3K test was introduced but did not come close to the

increase in reliability as significantly as the 50K test. Shortly after the 3K test was introduced a

6K test was developed. This test was less expensive, costing around $30-$40 per cow, and was

within 2% of reliability of the 50K test for various traits (Cassell, Emeritus,2012), The 6K test is

currently the most popular test in Canada and allows genomic testing to be widely used as it
provides farmers with an economical option and the ability to make more accurate estimates of

genetic value for bulls and heifers earlier in life.

Challenges or Barriers

Gaining precise genomic breeding merits requires an extensive population of previously

genotyped and phenotyped dairy cattle. Creating a significant reference population can be

achieved for Holsteins because of the size of herd populations in Canada. For other breeds such

as Jersey or Brown Swiss this proves to be difficult because of the fewer individuals, making it

harder to start creating prediction equations (Biochard,et all, 2016).

The cost of the testing has been a barrier to most farmers, but the cost of the testing only

has a small implication on the net benefit. With the Australian project the net benefit over the life

time of genotyped heifers for genomic testing ranged from approximately two hundred and four

dollars to approximately $1,124 per one hundred cows in a herd with average reproductive

performance. Genomic testing has proved itself to be more profitable than sexed semen, as well

as an increased genetic gain in heifers (Newton, 2017).

Challenges facing genomic selection and being able to implement genomic selection into

our dairy herds, include further advancing the veracity of genomic breeding values and

assimilating genomic data into global data bases for creating accurate genetic evaluations as well

as managing long-term genetic gain for dairy herds across the world (Hayes,et al, 2008).
Benefits to Canada

Genomic testing gives dairy farmers the ability to make accurate and sustainable breeding

decisions in both breeding goals and genetic variability. Genomics offers a decreased generation

interval, a gain in selection intensity, and an improvement in reliability for bovine cows and for

decreased heritability traits (Biochard,et all, 2016). Another benefit genomic testing will have on

the Canadian dairy industry is a reversal of the increase in subfertility and infertility. Currently

there has been a decrease in fertility as seen with the American dairy pregnancy rate down by

15%. The fertility rate has decreased because of the focus on breeding for greater milk

production, which has been highly successful, but has resulted in an increase in subfertility and

infertility. Recent advances in genomics have created an integrated approached to improve the

reproductive performance and profit margins of dairy cattle, with advancements in the

understanding on animal fertility, there has been a substantial increase in the improvement of

animal genomics for fertility (Spencer et al, 2016). Implementing genomics in the Canadian

dairy industry we will further improve the sustainability and productivity of the Canadian dairy

industry. There will be economic increases as well as an increase in herd health, improving and

creating a stronger future for the Canadian dairy herds (Berry. et al. 2006). The Canadian Dairy

Network (CDN) has published genomic evaluations demonstrating the significant value of

genomics in the Canadian dairy industry. Figure 1 shows a remarkable trend with the arrival of

genomic evaluations. With the new ability of selecting young bulls with more accuracy, the

average GLPI (genetic lifetime profit index) of young bulls provided by A.I. in Canada between

2009 and the first half of 2012 increased by an average of 445 LPI (lifetime profit index) points

per year

(Van Doormaal, 2012).

https://www.cdn.ca/document.php?id=281
The CDN also provided a study “Analysis of Genetic Gains Realized Since Genomics”

comparing two five-year periods with animals born between 2004 – 2009, prior to the existence

of genomic testing, and with animals born between 2011 – 2016, after genomic research became

available to breeders. The chart below shows the lifetime profit index (LPI) and Pro$ (genetic

selection index for profit) of Holsteins in Canada before and after genomics.

http://www.thebullvine.com/category/genomics/
The following chart is a great indicator of genetic gains by traits realized over 5-year periods

before and after genomics as researched by the Canadian Dairy Network (CDN). There are

significant genetic gains across all dairy traits (Hunt.A, 2018).

http://www.thebullvine.com/category/genomics/
Future

Genomics testing has been proven to provide high accuracy. The advantages of

genomics testing compared with progeny testing strategies are too countless to disregard. The

overall genetic change can be two times greater than the current progeny testing methods, saving

in logistical costs, potentially 92% of today’s expenditures. Over time, the cost of genomic

testing will decrease, making genomic testing more affordable to implement in herds across

Canada. For breeds less numerous than Holsteins, with available funds, we could genotype these

breeds, increasing the accuracy of AI bulls and proving them at a younger age. Currently, it takes

six years to prove young AI bulls with progeny style testing, and only one or two bulls are

proven each year. Progeny testing has proven not to be effective in alternate dairy breeds. Bulls

selected on their GEBV (genetic evaluation) as calves, could meet the demand for an increase in

genetic merit (Schaeffer, 2006).

Conclusion

The Canadian Cattle Genome Project currently exists in Canada, which is a large-scale project

aiming to develop genomic tools helping to improve the efficiency and sustainability of the beef

and dairy industry (Canadian Cattle Genome Project, 2017). Canada already has a genome

project set in place, but its sole focus in on one breed of dairy cattle -Holsteins- with the rest

being a breed of beef cattle. By expanding our data base on not only Holstein genetics but

expanding into different breeds of dairy cattle including, for example, Jerseys and Brown Swiss,

we would be able to further improve the sustainability and productivity of the Canadian dairy

industry. Genome testing benefits farmers in providing the potential to learn more about their
animals’ genetics much sooner, it allows them to trace productivity, and be able to see how the

genetics of a calf will affect it later in life. Genomics is a once in a life time investment per

animal, allowing Canadian farmers to create a more profitable herd by understanding more about

the genetics in each of their animals. Benefits extend beyond individual farms to the national

level as the increase in value of each cow on each farm escalates the sustainability and economic

viability of the Canadian dairy industry. The Australian 10,000 Holstein Cow Genome Project

indicated the strong financial gain nationally, as their genomic research determined financial

benefits of 100 million dollars over twelve years. If Canada proactively accelerates their genome

projects with greater parameters beyond Holstein and beef cattle, they could increase their global

recognition as leaders in agriculture on the world’s stage.

Important Contacts

Dr. Ben Hayes

Research leader, Computational Biology

VABC

ben.hayes@ecodev.vic.gov.au

Holstein Canada

1-855-756-8300

Brantford ON Canada
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