Summer 2017 SBTS & TBTS Update

SUMMER 2017 UPDATE

It’s a World First! Multi-Country Single-Step BREEDPLAN analysis for the Hereford breed

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REEDPLAN is pleased to announce the release of a world first: a multi-country Single-Step BREEDPLAN analysis for the Hereford breed, released as the mid-October

2017 Hereford GROUP BREEDPLAN analysis. “This allows the Hereford breed in Australia, New Zealand and Namibia to take advantage of cutting-edge analytical software that now includes

important that breeders embrace genotyping if they are going to extract any benefit from Single-Step BREEDPLAN”.

Overall, the most important outcomes of introducing Single-Step BREEDPLAN are: n

EBVs calculated within the main multi-trait BREEDPLAN

genomics,” said Dr. Brad Crook, BREEDPLAN (ABRI).

The release of Single-Step BREEDPLAN heralds a new age in genetic evaluation technology available to the beef cattle industry, and specifically the Hereford breed in Australia, New Zealand and Namibia. This new genetic analysis combines pedigree,

analysis. n

fertility, carcase and feed intake traits. Genomic information now contributes to the EBV and accuracy calculations of genotyped animals and their relatives.

What is Single-Step BREEDPLAN? Single-Step BREEDPLAN is genetic analysis software developed by the Animal Genetics and Breeding Unit, a joint venture of NSW Department of Primary Industries and the University of New England, which receives funding for this purpose from Meat and Livestock Australia Limited. The single step analysis utilises pedigree, performance and genomic information simultaneously. The analysis takes account of each animal’s actual genetic relationship based on its genotype with all other

Unknown parents may be identified (providing animals have genomic information available).

n Genomic

information contributes not only to EBVs of

genotyped animals but also contributes to EBVs of their

performance and genomic (DNA) information together in a complete multi-trait BREEDPLAN analysis of birth, growth,

Genomic information will contribute to all traits that have

relatives (e.g. parents, progeny). n

With a traditional pedigree based approach, the relationships between animals within Hereford BREEDPLAN are determined by pedigree alone. For example, pedigree would predict that the genetic relationship between full siblings (i.e. animals with the same sire and dam) is 0.5. This means that full siblings are predicted to have 50% of genes in common when calculating traditional pedigree-based breeding values.

In Single-Step BREEDPLAN, however, SNP genotypes are used to determine the actual degree of relationship between individuals. In the case of full siblings, this may now vary from 0.35 to 0.65 – rather than 0.5 as would be assumed in a traditional approach to genetic evaluation. This will allow for improved accuracy in the EBVs calculated.

genotyped animals, including those in the reference population.

Summary

The reference population is the set of Hereford animals within the

With the release of the mid-October 2017 BREEDPLAN results,

Hereford BREEDPLAN analysis that have both genotypes (SNP data) and phenotypes (performance records) for a particular trait.

“Single-Step BREEDPLAN doesn’t remove the need for ongoing

the Hereford breed in Australia, New Zealand and Namibia became the first breed world-wide to implement a multi-country Single-Step BREEDPLAN analysis. Genomic information as well

collection of accurate phenotypes”, said Dr. Alex Ball, formerly

as pedigree and performance data is now being used to calculate

Strategic and Innovation Manager at Herefords Australia. “It is

Hereford BREEDPLAN EBVs and accuracies.

SBTS & TBTS provide a national extension network for genetic technologies for the Australian beef seedstock industry 1

Northern BIN Steer Project Update

IN THIS ISSUE

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It’s a World First! MultiCountry Single-Step BREEDPLAN analysis for the Hereford breed

he Droughtmasters Stud Breeders Society (DSBS), Australian Brahman Breeders’ Association (ABBA) and a consortium of Santa Gertrudis breeders are currently conducting a joint progeny test project with funding assistance from the Meat

& Livestock Australia Donor Company under the Beef Information Nucleus (BIN)

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program. This joint Northern BIN Steer Project has utilised the steer progeny from a second MLA funded project ‘Enabling genetic improvement of reproduction in tropical beef breeds (Repronomics)’ outlined below. The project has currently purchased five

Northern BIN Steer Project Update

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cohorts of steers from Spyglass and three cohorts of steers from Brian Pastures Research Stations. The Northern BIN Steer Project will provide data which will assist in the implementation of a Multi-Breed database and a future Tropical crossbred analysis. This is possible as the Brahman and Droughtmaster steers (at Spyglass and Brian Pastures)

Get Social With SBTS & TBTS

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and also Santa Gertrudis steers at Brian Pastures have been run together since birth, having only been split during the joining period of their dams in the Northern BIN Steer Project.

Where Does This Animal

Overview of the Repronomics Project

Rank? Introducing The EBV Percentile Graph

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This collaborative, five-year Meat & Livestock Australia funded project aims to improve the evaluation of animals within industry for a number of economically important performance traits, in particular female fertility. The collaborative partners are the Department of Agriculture and Fisheries’ Agri-Science Queensland, University of New

Optimise Joining Using MateSel

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England’s Animal Genetics and Breeding Unit (AGBU) and the Northern Territory Department of Primary Industry and Fisheries (NTDPIF).

The key component in the evaluation is the combination of strategic phenotypic

Artificial Breeding in Beef Cattle

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recording and new, high density SNP (Single Nucleotide Polymorphism) genotyping of well controlled, specifically managed cattle to rapidly increase the accuracy of genetically describing the reproductive merit of tropically adapted beef cattle. The data collected through this study will also be used to seed the new genetic analysis methodology of

Upskilling the Northern Industry about EBVs

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calculating estimated breeding values for all traits.

Australian Wagyu Association Genetics and Genomics Technical Workshop

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Moving Towards SNP Parentage Verification

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Accessing Support in Application of Genetic Technologies 16

Spyglass 2017 Brahman steers at Tawarri in January 2018.

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Table 1. Breakdown of steers origin and number per year.

Santa Gertrudis

Total

Cohort

Year

Brahmans

Droughtmaster

Spyglass

2013

59

47

106

Spyglass

2014

95

66

161

Spyglass

2015

98

107

205

Spyglass

2016

135

128

263

Spyglass

2017

111

105

216

Brian Pastures

2015

55

37

63

155

Brian Pastures

2016

45

53

65

163

Brian Pastures

2017

50

42

54

146

Total

648

585

128

1361

The 2013 Spyglass steer drop was purchased by and finished

Northern BIN Project

at Smithfield Feedlot (Proston) in February 2015. The 2014

To date the Northern BIN Steer Project has purchased 1,361

Spyglass steer drop was backgrounded at Banana Station,

steers, with a breakdown of breed and calving year shown in

while the 2015 drop steers were backgrounded at Tawarri near

Table 1. The sires of the project steers are either proven sires

Middlemount. The 2014 and 2015 drop steers were transferred

with a large number of registered progeny (few of which have

to Smithfield Feedlot for finishing for around 105 day prior to

been performance recorded with BREEDPLAN) or young up

slaughter. All steers were slaughtered at John Dee Abattoir in

and coming bulls.

Warwick. The 2016 and 2017 steers are currently at Tawarri for

The steers are by AI or natural matings out of highly recorded

backgrounding with the 2016 steers to go to the feedlot at the

cows from Spyglass Research Station and Brian Pastures. The

end of February 2018.

first steers to be purchased by the Northern BIN Steer Project

The 2015 Brian Pastures steers were sent to Sandstone Park at

were from the Spyglass 2013 drop, with steers from the 2014, 2015, 2016 and 2017 Spyglass drops subsequently purchased.

Taroom at 18 months of age for back grounding before being

The first steers purchased from Brian Pastures were the 2015

sent to Smithfield Feedlot for finishing on grain. The 2016

drop, and the 2016 and 2017 drops have since been purchased.

Brian Pastures steers were sent directly to Smithfield feedlot

To date the Northern BIN Steer Project includes 585

from Brian Pastures for finishing. All steers were slaughtered at

Droughtmaster steers by 52 Droughtmaster sires (representing

John Dee abattoir. The 2017 steers were purchased in July and

26 different stud prefixes), 648 Brahman steers by 53 Brahman sires (representing 26 different stud prefixes) and 128 Santa Gertrudis steers by 17 sires (representing 10 different stud prefixes).

Both 400 and 600 day weights have been or will be collected for all steers. Steers are scanned for rib fat, rump fat, intramuscular fat measurement (IMF) and eye muscle area (EMA) at the 600 day weight measurement as is a structural soundness assessment. Full MSA chiller assessments will be conducted on the steer carcases, and meat samples from all steer carcases will be analysed by the UNE Meat Science Lab for tenderness, cooking loss, meat colour and intramuscular fat (IMF). All data collected as part of the Northern BIN Steer Project will be submitted to BREEDPLAN. Tail hairs and blood samples were collected from all steers as a source of DNA information for future development and validation of genomic based technologies.

Figure 1. Locations of interest for the Northern BIN Steer Project.

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transferred to Berrigurra (Blackwater) for backgrounding. The property locations are shown in Figure 1.

The Northern BIN Steer Project will also purchase the 2018 drop steers from Spyglass and Brian Pastures. As these steers are currently on the dams they will be purchased following weaning later in 2018. A major change to the project is a change in the finishing of the animals from grain to pasture.

This is seen as a more industry relevant finishing method for the Brahman, Droughtmaster and Santa Gertrudis steers in Northern Australia. This will start with 2017 steers being finished on grass with the aim to turning these steers of by 30 months.

The Northern BIN Steer Project will provide vital data that will assist in the rapidly increase the accuracy of genetically describing carcase and growth traits for Droughtmaster, Brahman and Santa Gertrudis cattle. Along with fertility data being collected from the Repronomics project, the Northern BIN Steer Project will help the breeds drive genetic progress for the important traits in the future.

For more information on the Northern BIN Steer Project please contact Paul Williams from Tropical Beef Technology Services on 0427 018 982 or via email paul@tbts.une.edu.au.

600 day weight and carcase scanning at Tawarri on the Spyglass 2016 steers.

Get Social With SBTS & TBTS SOCIAL MEDIA

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eef producers can keep up to date with the latest developments in genetic technologies and the activities of SBTS and TBTS by following SBTS and TBTS on Facebook, Twitter and YouTube. Articles and information on upcoming events (e.g. webinar series, BullSELECT workshops) are routinely posted on Facebook and Twitter. The YouTube channel contains video presentations from past webinar series and short ‘Understanding BREEDPLAN EBVs’ video clips.

TO FOLLOW > SBTS and TBTS on Twitter, Facebook or YouTube simply go to the SBTS or TBTS website and click on the relevant icon, or go directly to the SBTS & TBTS Facebook account at http://facebook.com/SBTSTBTS, Twitter account at http://twitter.com/SBTSTBTS or YouTube Channel at http://youtube.com/user/sbtstbts.

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http://facebook.com/SBTSTBTS

http://twitter.com/SBTSTBTS

http://youtube.com/user/sbtstbts

Where Does This Animal Rank?

Introducing The EBV Percentile Graph

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shown in Figure 1. This will display the EBV Percentile Graph

hile comparing an individual animal to the breed average (calculated from the two year old animals) allows producers to identify whether the animal

for the animal.

Interpreting the EBV Percentile Graph

is better or worse for the trait than the average animal in the

The EBV Percentile Graph allows beef producers to compare

breed, it does not allow producers to quantify how much better or worse the individual is.

how the EBVs of an individual animal rank against the two year

To do this, BREEDPLAN publishes percentile bands, which

evaluation.

old animals that have been evaluated within the same genetic

allows beef producers to rank animals from the Top 1% of the

On the vertical axis, a separate bar is provided in the graph for

breed (1st percentile) down to the Bottom 1% of the breed (99th

each individual trait. The bars are coloured depending on the

percentile). While the more traditional Percentile Band table is

trait type, where:

still available, more recently BREEDPLAN has published the EBV Percentile Graph. This provides producers with a visual

n

Calving traits = yellow

representation of how the EBVs of an individual animal rank

in comparison to the rest of the breed. This article will outline

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Growth traits = green

how to find, interpret and use the EBV Percentile Graph.

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Fertility traits = red

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Carcase traits = light blue

Finding the EBV Percentile Graph

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Other traits = dark blue

The EBV Percentile Graph is available from the Animal Details

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Selection Indexes = pink

page on Internet Solutions for each individual animal. Firstly,

It should be noted that while for the majority of traits it is

to find the animal, enter the animal name and/or identifier into

usually more desirable to be on the right hand side of the graph

the EBV Search area on Internet Solutions, and click search.

(e.g. in the 0-50th percentiles), this is not always the case.

Select the relevant animal to bring up the Animal Details page

The optimum EBVs will depend on the individual producer’s

for that individual. Once on the Animal Details page, scroll

breeding objective(s), and the direction in which the producer

down until you see the EBVs, and click on the graph icon, as

is trying to move the herd.

Figure 1. To find the EBV Percentile Graph, open the Animal Details page on Internet Solutions for the individual animal of interest.

From the Animal Details page, click on the graph icon (circled) above the individual’s EBVs to bring up the EBV Percentile Graph.

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For example, a higher percentile for Mature Cow Weight indicates a heavier Mature Cow Weight EBV, which, for those producers trying to limit the mature cow size of their herd, may be undesirable. Similarly, depending on the environment their cattle are running in (e.g. scrubby rangelands), some beef producers do not want cows with a lot of milk. In these cases, producers may decide that they want a sire with a more moderate Milk EBV. Equally, in situations where beef producers are trying to limit or actively decrease the Rib and Rump Fat of their herd, a sire with more moderate Rib and Rump Fat EBVs may be more desirable.

When the EBV Percentile Graph in Figure 2 is examined, it can be quickly seen that the individual animal is below breed average for four traits (Calving Ease Direct, Calving Ease Daughters, Birth Weight and Retail Beef Yield) and above breed average for all other traits. Furthermore, the percentile band rankings can be determined by identifying where the end

Figure 2. The EBV Percentile Graph allows beef producers to compare how the EBVs of an individual animal rank against those of the two year old animals that have been evaluated within the same genetic evaluation; thus allowing the strengths and weaknesses of an individual animal to be assessed.

of the trait bar lines up along the horizontal axis. For example, the animal represented in the EBV Percentile Graph shown in Figure 2 is in the 58th percentile for Retail Beef Yield, and in the 3rd percentile for 200, 400 and 600 Day Weight.

Milk, and above breed average for the fertility traits (Scrotal

Using the EBV Percentile Graph

Size and Days to Calving), the carcase traits (EMA, Rib Fat,

As seen in the above section, the EBV Percentile Graph can

Rump Fat, Retail Beef Yield and IMF) and the four selection

be utilised as a visual tool to understand the strengths and

indexes (Supermarket, Grass Fed Steer, Grain Fed Steer and

weaknesses of an individual animal. It can also be used to

EU).

compare the attributes of different animals, and to identify

The biggest differences between these three bulls are seen for

which has the best combination of genetics for a given scenario.

the calving traits (Calving Ease Direct, Calving Ease Daughters,

Consider the three bulls in Figure 3, and their potential to be

Gestation Length and Birth Weight) and the weight traits (200

used as heifer bulls (i.e. joined to heifers which will calve at 2 year old). While the percentile band ranking for each trait does

Day Weight, 400 Day Weight, 600 Day Weight and Mature

vary across the bulls, all three bulls are below breed average for

Cow Weight).

Figure 3. The EBV Percentile graphs for three bulls, which, when compared, allow beef producers to quickly compare the genetic potential of each as a sire, and identify which would best suit a certain scenario (in this case, a heifer bull).

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Bull 1 is a high growth bull, being in the 10th percentile (Top

weight and which require less assistance at calving than those

10% of the breed) for 200, 600 and Mature Cow Weight, and in

sired by Bull 1.

the 20th percentile for 400 Day Weight. However, this bull is

So which of these three bulls would make the best heifer bull?

also likely to have heavy calves which may require assistance at

Given the potential for calving difficulty, Bull 1, despite his high

calving, being in the 90th percentile (Bottom 10% of the breed)

growth, is not the best choice (dead calves don’t grow). Bull

for Calving Ease Direct, Calving Ease Daughters and Birth

2 should sire calves that are more likely to be born without

Weight and the 60th percentile for Gestation Length.

assistance, but these calves are unlikely to have the genetic

In contrast, Bull 2 would be expected to produce calves with

potential for growth. Therefore, Bull 3, which should sire calves

low growth, being in the 80th percentile or lower for 200, 400

that are likely to be born without assistance and which will also

and 600 Day Weight and Mature Cow Weight. However, with

have the genetic potential for high growth, is the best choice

Bull 2 being in the 10th percentile or higher for Calving Ease

for a heifer bull.

Direct, Calving Ease Daughters, Gestation Length and Birth Weight, his calves are also likely to be lighter than the calves

Conclusion

Bull 1 would produce, with a shorter gestation length and less

The EBV Percentile Graph can be used to quickly get a feel

assistance required at calving.

for the strengths and weaknesses of individual bulls, and to

Bull 3, like Bull 1, is a high growth bull, being in the 5th

compare the attributes of different bulls. This makes it a great

percentile or higher for 200, 400 and 600 Day Weight, and the

tool for beef producers looking to use BREEDPLAN EBVs and

10th percentile for Mature Cow Weight. However, Bull 3 is

Selection Indexes as a part of their bull selection decisions.

also in the 10th percentile or higher for Calving Ease Direct,

For further information on interpreting or using the EBV

Calving Ease Daughters and Gestation Length, and in the 35th percentile for Birth Weight. Therefore, Bull 3 is likely to

Percentile Graph, please contact staff at Southern Beef

produce heavier calves at 200, 400 and 600 days than Bulls 1

Technology Services (SBTS) or Tropical Beef Technology

and 2, and also likely to produce calves of more moderate birth

Services (TBTS).

Optimise Joining Using MateSel

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eedstock producers in Australia who are members of a breed society with a published Selection Index are encouraged to consider using the MateSel mating

optimisation tool when planning their upcoming joinings.

MateSel creates additional genetic progress within a breeding program by generating a suggested mating list from a list of sires and dams that a seedstock producer nominates as being available for use within their upcoming joining program.

objective. Results from the MateSel analysis are returned promptly, usually within one working day.

MateSel not only allows seedstock producers to maximise genetic progress whilst managing inbreeding, but will also save

MateSel is a valuable addition to the BREEDPLAN suite of tools that are offered by the Agricultural Business Research Institute (ABRI) in Armidale, NSW.

significant time previously spent compiling mating lists.

MateSel is fully customised to the breeding program of each individual seedstock operation with the seedstock producer

Seedstock members interested in learning more about MateSel should visit the BREEDPLAN website (http://breedplan.une. edu.au) and click on the MateSel icon on the right hand side, or contact staff at SBTS or TBTS.

choosing acceptable inbreeding limits by selecting one of three breeding strategies, “Genetic Diversity”, “Balanced” or “High Genetic Gain” and providing details of their desired breeding 7

Artificial Breeding in Beef Cattle

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rtificial insemination (AI) has accounted for 18% of all calves born and registered with SBTS & TBTS stakeholder breed societies in the last 5 years and

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this proportion is increasing (Figure 1). Meanwhile, embryo

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natural mating. This can be used to reduce the number of bulls required to be physically on farm.

transfer (ET) accounts for 5% of the calves registered and it has

Reducing the age restrictions on breeding and allowing younger animals to have more progeny than is possible

been recently reported that commercial cloning of beef cattle

naturally at their age. In turn, this reduces the generation

is now being offered around the world, including in Australia.

interval (average age of sires and dams) and allows faster genetic progress.

Advantages of using Artificial Breeding Techniques

4. The opportunity to use sexed semen in either AI or ET to

There are many reasons why cattle breeders may choose to

produce offspring of the desired gender. While both males

utilise artificial breeding. Some of the major benefits include:

(sale) and females (herd replacements) are both valuable

1. A larger gene pool to select from. This is could be achieved n

AI allowing more matings per bull than possible with

in seedstock operations, it gives the option of using sexed

by:

semen in heifers to produce female calves which are on

Using the best bulls/cows regardless of their physical

average lighter and thus easier born than male calves. This approach is also beneficial if a breeder struggles to grow

location, e.g. an overseas bull. n

Using an expensive bull via cheaper semen straws.

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Continued use of a bull or cow after he/she has been sold or

bulls to suitable sale weights if they are born out of heifers.

By using sexed semen, these breeders can generate high genetic merit herd replacement daughters without the

died.

concern of their young mothers not growing them as fast

2. The opportunity to mate specific sires to individual cows.

as their contemporaries out of older cows.

This can be used to:

5. Reduced infection risk. This could be from venereal

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Avoid inbreeding.

diseases or just from a disease that could be introduced via

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Target specific trait characteristics in particular matings,

animals bought in from other farms.

e.g. a bull with desirable calving ease over heifers.

Considerations when using Artificial Breeding Techniques

3. The ability to produce larger amounts of progeny than n

would be possible via natural mating. This can achieved by:

With the ability to make genetic change faster using artificial

ET allowing multiple progeny per cow to be produced per

breeding, it places a greater importance on accurately selecting

year.

the correct parents. For example if there are negatives in

Figure 1. Use of Artificial Insemination and Embryo Transfer in SBTS and TBTS stakeholder breed societies since 2003.

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can be mitigated by using multiple sires (and dams for ET)

Artificial Breeding Terminology

Artificial Insemination (AI)

within each program and by using mate selection software

The deliberate introduction of sperm into a cow’s reproductive tract for the purpose of achieving a pregnancy by means other than sexual intercourse.

Cloning

Artificial production of genetically identical calves.

Embryo Transfer (ET)

The process of removing one or more embryos (fertilized eggs) from the reproductive tract of a donor female and transferring them to one or more recipient female.

like MateSel to balance genetic gain against the reduction in genetic diversity and increased inbreeding.

One of the main considerations that discourage breeders from utilising artificial breeding is the cost, both in financial and in animal management terms. All three techniques discussed in this article require specialist personal, equipment and drug treatments to perform which all come with associated financial costs. The amount of yarding required is also greatly increased which takes planning and labour to achieve.

The Importance of Recording of Artificial Breeding Information with Breed Societies and BREEDPLAN The recording of artificial breeding information with your

a parents genetic makeup (e.g. the presence of a genetic

breed society and/or BREEDPLAN is important for the

condition), artificial breeding has the potential to quickly

estimation of the Gestation Length EBV and for the formation

magnify the problem. The utilisation of genetic technologies

of BREEDPLAN contemporary groups.

can reduce this risk by testing for known genetic conditions

Only data from calves conceived by AI or hand matings are

or by increasing the accuracy of EBVs via genomic selection.

used in the calculation of the Gestation Length EBV due to the

This testing could potentially extend in the future to the testing

need for an accurate conception date. The resulting calves’ date

of individual embryos before implantation in embryo transfer

of birth is also used to calculate this trait. More information

programs (this technique is currently being researched).

on Gestation Length EBVs can be found in the ‘Understanding

The genetic diversity and inbreeding levels of a herd can also be

Gestation Length EBVs’ tip sheet while more information on

adversely affected by using artificial breeding to generate larger

how to record gestation length can be found in the ‘Recording

numbers of genetically similar progeny. The artificial breeding

Gestation Length’ tip sheet. Both are available in the Technical

technique(s) utilised will affect how quickly this will occur as AI

area on the BREEDPLAN website (http://breedplan.une.edu.

can produce large amounts of half siblings (common sire), ET

au).

will produce large amounts of full siblings (common sire and

Due to the involvement of a recipient dam in ET, ET calves get

dam) and cloning large amounts of full siblings with identical

placed in separate contemporary group(s) to their naturally or

genetic makeup. By reducing the genetic diversity of a herd,

AI conceived peers. This is to allow for variation in the maternal

there will be a smaller range of performance from which to

environment provided by the recipient dams to be taken into

select the top animals, an increased chance of inbreeding when

consideration as it is not a genetic effect. For example, two

the progeny are mated and an increased chance of recessive

identical embryos are implanted into a dairy cow recipient and

genetic conditions being expressed. In the extreme example of

a beef cow recipient. These recipients are run together in the

cloning, there would be no genetic diversity in the resulting

same paddock from the day of implantation, over calving and

progeny from which to select better replacements and make

through to weaning. At weaning, the ET calves are weighed and

genetic improvement.

the calf reared by the dairy recipient is considerably heavier

This is in addition to the cloning process replicating a set of

than the calf reared by the beef recipient. As these calves are

genes that already exist in the herd, thus the progeny will have

of similar genetic merit (full siblings), the difference in their

the same genetic merit as the animal being cloned (thus no

weights is not due to differences in their genetic potential for

genetic improvement occurs from the cloning process). That

growth but can be attributed to the greater milking ability (i.e.

said, cloning can be used to aid genetic linkage (clones used for

maternal effect) of the dairy recipient. To account for variation

breeding in multiple mobs/farms etc.), to compare the same

in the maternal effects of the recipient dams, BREEDPLAN

genetics in different production systems (e.g. in vealer and

requires information about the recipient dam to have been

heavy steer production systems) and the ability to breed from

recorded. For more information on recording ET calves, please

a set of genetics that have been recorded for slaughter traits

refer to the “Recording ET calves with BREEDPLAN” tip sheet,

(this is also possible via semen and embryos). In AI and ET

which is available in the Technical area on the BREEDPLAN

programs, the risks of low genetic diversity and high inbreeding

website (http://breedplan.une.edu.au).

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Upskilling the Northern Industry About EBVs

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he second half of 2017 once again saw TBTS personnel, Paul Williams and Tim Emery, clock up the kilometres both on the bitumen and in the sky to engage and

deliver technical presentations to the northern beef industry.

On 18th July, TBTS and SBTS staff teamed up to hold a TBTS Regional Forum in Toowoomba, where 15 seedstock producers were in attendance. Topics discussed included: BREEDPLAN 101, contemporary groups & genetic linkage, common performance recording problems, interpreting Completeness of Performance and Genetic Progress reports, and genomics.

A week later Tim headed out to far western Queensland to codeliver a Breeding EDGE workshop with nine managers/head stockmen, along with present breeding and genetics content at a Jundah weigh day (11 commercial producers) and Blackall OBE Grazing BMP event (10 commercial producers).

In mid-August, Gyranda Santa Gertrudis Stud at Theodore played host to 70 guests at their annual open day. The event involved an array of guest speakers, including Tim and Paul, Tim Emery (TBTS) presents to beef producers at the Richmond Grazing BMP event.

who discussed breeding objectives, EBVs 101 and used real EBV figures and animals as part of a practical yard discussion.

conference, Tim briefly travelled across into the Northern

On 14th September, Paul headed south from Rocky to the

Territory and met with producers and agri-service providers,

Ubobo landcare field day and presented to the 60-strong crowd

before flying onto the Atherton Tablelands. Over a few days,

on BREEDPLAN and the BIN and Repronomics Projects. The next day Tim also presented along the coastline, this time in

Tim visited six commercial properties and one seedstock

Gympie at the MSA Excellence in Eating Quality Awards.

operation and presented at the Mt Surprise Grazing BMP

Seventy producers heard about ‘The role genetics plays in

event attended by 11 commercial producers. The following

achieving the perfect MSA index’.

week, Tim headed into the state’s North West and presented at

Late October saw Tim venture over to Northern WA to

another Grazing BMP event in Richmond (nine attendees) and

engage with pastoralists at two large-scale industry events; the

visited two properties.

Mowanjum irrigation trial field day near Derby (100 attendees)

Furthermore, in late November/early December, Tim was

and the Kimberley Pilbara Cattlemen’s Association Conference

asked to participate (& co-deliver) in the EDGE training

near Kununurra (200 attendees). Both events were extremely

event for industry service providers held in Rockhampton,

informative and thought provoking and provided an amazing

and he delivered technical content to a rural agency gathering

opportunity to engage with commercial producers. It was

which entailed 15 agents (predominantly young) based across

interesting to see and hear about the large-scale nature of

Queensland. TBTS also had a presence at the well-attended

properties in the Kimberley, which breeds and Queensland

industry events, the “Young Beef Producers’ Forum” in Roma

studs are well represented in the region, along with discuss the

and the “Calf Alive Symposium” in Capella.

current and future challenges and opportunities. High costs

If you’re interested in having either Tim or Paul speak at an

(infrastructure, transport, mustering, supplementation etc.)

upcoming event in your region, please feel free to get in touch

and red tape were a couple of the challenges echoed by many.

Opportunities mentioned included using drones and walk over

with us. Tim can be contacted on 0408 707 155 or via email

weighing, irrigation, and whole cottonseed as a supplement

tim@tbts.une.edu.au, while Paul can be contacted on 0427 018

(once the irrigated cotton crops ramp up). Following the

982 or via email paul@tbts.une.edu.au.

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Australian Wagyu Association Genetics and Genomics Technical Workshop

T

BREEDPLAN.

he 2017 Australian Wagyu Association (AWA) Genetics and Genomics Technical Workshop was held over two days at the University of Queensland

Rob highlighted that the goal of BREEDPLAN was to enable comparison of animals that are treated alike so that the

Gatton campus. 120 AWA members enjoyed some visionary

difference between animals that are due to genetics can be

presentations from internationally renowned researchers and

determined. A comparison of height in humans was used, in

key Australian Wagyu industry influencers.

which 2 brothers, full siblings but born 10 years apart, have very similar genetics (50% from mum and 50% from dad), but if measured at the same date (one being 7 years old and one being 17 years old), they will have different height. Hence, it

Professor Rob Banks Director of the Animal Genetics and Breeding Unit, University of New England

is important to take into account things such as age in genetic analysis.

Wagyu EBVs also take into account the performance of individuals relative to each other within a group of contemporaries. That is, a group of animals that have all shared similar management and treatment. This allows the ranking of individuals relative to each other once non-genetic effects such as age are accounted for as described above.

Rob presented an overview of how Wagyu BREEDPLAN

A particular characteristic of the Australian Wagyu industry

calculates Estimated Breeding Values for cattle performance

is that the genetics of extremely well known sires such as

traits and took the audience through how the technology has

Michifuku and Itoshigenami are used across the majority

developed to enable use of genomic information (from high

of contemporary groups and this can be used to link or

density SNP chip panels such as the 50k SNP test) within

benchmark the performance of contemporary groups to each

Figure 1. Demonstrates the improvement seen in accuracy of predicting the Marble Score EBV within testing of Single-Step Wagyu BREEDPLAN.

11

other. Wagyu BREEDPLAN uses all of this information, in addition to the pedigree information for registered animals in

Trait

Validation Accuracy

Hot Carcase Weight

0.71

Marbling Score

0.43

Fat Colour

0.15

Rib Fat

0.62

Eye Muscle Area

0.57

P8Fat

0.46

calculating EBVs for traits.

The future of Wagyu BREEDPLAN was described for the audience. This is the single step revolution. Single-Step BREEDPLAN refers to combining genomic information on individuals with their performance data, and pedigree information for non-genotyped animals, to more accurately estimate or determine the genetic merit of each animal in the analysis. Currently routine Wagyu BREEDPLAN does not use genomic information in this way. The improvement in accuracy of the EBVs comes from more precisely knowing the genetic relatedness of animals that have genotypes. The new analysis will produce genomically improved EBVs for all animals with 50k SNP tests completed, as well as distributing the extra accuracy that comes from using genomic information through the entire pedigree, according to the relationships amongst animals. Prof. Banks demonstrated the testing of Single-Step Wagyu BREEDPLAN on Marble Score (MS) EBVs in which including genomic information improved the accuracy in MS EBV by an average of 10%.

Figure 1 (taken from the presentation of Prof. Banks), plots the accuracy of the original EBV for MS on the bottom or x-axis vs. the new Single-Step MS EBV on the vertical or

scientific journal Genetics in 2001. The processed defined by

y-axis. This figure demonstrates the improvement seen in

Ben and his co-authors is now being used in livestock and crop

accuracy of predicting MS EBV within testing of Single-Step Wagyu BREEDPLAN. Any individuals above the red dotted

genetic improvement programs globally.

line that passes through 0 on both axes is gaining a benefit or

Ben presented to the AWA members the results of an analysis

lift in accuracy for MS EBV through the Single-Step process.

he has been conducting with the Australian Wagyu Industry

For animals with lower accuracies (below 50%), this lift is on

leader, Mr. David Blackmore and his daughter Danielle. This

average, greater than 10%. These are the animals that we have

powerful collaboration has resulted in a whole-of-herd

little performance data on (e.g. newly born bull calves) and

genomic analysis in which high density SNP information and

these animals will benefit the most from Single-Step.

accurately recorded carcase traits are being analysed using genomic prediction.

Prof. Hayes described the high degree of validation accuracy

Professor Ben Hayes Queensland Alliance for Agriculture and Food Innovation, University of Queensland

obtained through genomic prediction within the Blackmore herd for critical traits that underpin profitability of Wagyu Fullblood carcase production.

Moderate to high levels of

prediction accuracy were possible within this herd for traits including carcase weight, MS, rib fat, eye muscle area and P8 fat. For example, for hot carcase weight, genomic prediction of carcase weight across a range of animals explained 71% of the variation in carcase weight in that group. In other words, Ben, David and Danielle can estimate final carcase weight with a high degree of precision based on a DNA sample of an animal

Professor Ben Hayes is one of the noted founders of the

from the Blackmore herd.

modern genomics era in livestock. Ben was a co-author on the seminal publication “Prediction of total genetic value using

Applications of this technology would be to take DNA samples

genome-wide dense marker maps�, that was published in the

on very young animals and to use genomic prediction of their 12

carcase traits to better identify elite animals for breeding and

which started in 2003 and completed in 2009. Since then,

manage variation in groups of animals for optimal market

genomic information and the study of it “genomics” has

outcomes.

revolutionised genetic improvement in livestock.

Stewart described the rapid increase in genomic testing activity globally, increasing from 138,000 daily genotypes being collected in 2007 to 200 million per day in 2016. With this

Stewart Bauck Vice President of Agrigenomics, Neogen, Michigan USA

increase in throughput, the costs of genotyping have reduced remarkably.

The audience heard that along with the increase in genomic testing throughput and speed, there was a need to increase the efficiency of tissue and hair sample receipt and processing.

Dr. Bauck described the development of robotics to handle tissue sampling units and how this had streamlined sample processing in the US labs.

Dr. Bauck said “We realize that AWA members have many

Dr. Stewart Bauck made the trip to present to the AWA Genetics and Genomic Technical Workshop audience all the

thousands of DNA samples stored at our facility on hair cards

way from Lincoln Nebraska in the USA. Stewart is the Vice

and that using hair cards is still the standard industry practice

President of agrigenomics with Neogen and is responsible

in Australia. Historical and future hair card samples will be

for management of Neogen’s subsidiary company GeneSeek.

able to be used for DNA extraction into the future.”

The GeneSeek laboratory in Nebraska is the largest animal genomic testing laboratory in the world.

However, since robotics are already being introduced into

GeneSeek have

GAA labs, sample processing efficiency will be increased with

recently established in Australia at the GeneSeek AustralAsia

samples received in tissue sample units, and costs for hair card

Laboratories at UQ Gatton.

processing in the future will reflect true costs for labour and

Dr. Bauck provided an overview of the development of

overhead. GAA predicts that over year or so, tissue sample

genomics within the livestock industries starting with the

units will become the new normal practice for taking samples

original genome sequencing project of the Cow “Dominette”

from animals for genomic testing.

13

Moving Towards SNP Parentage Verification

D

NA parentage verification offers beef producers a tool to accurately determine animal parentage and reduce pedigree errors which may otherwise occur. This

sire of the calf must have passed on ‘C’ – once again this rules

article will explore how parentage verification works, the DNA

the sire of the calf must have passed on ‘e’, which rules out Sires

markers that are used for parentage verification, and examine

1 and 5 as possible sires.

out Sire 4. Sires 2 and 4 are ruled out yet again at Marker D, where the sire of the calf must have passed on ‘d’. For Marker E,

the best way for beef producers to manage the transition from

At the end of this process, the only sire left as a potential sire

microsatellite to SNP parentage verification.

candidate is Sire 3. Note that this process does not “prove” that Sire 3 is the sire of the calf; rather, it does not eliminate him as

How Does Parentage Verification Work?

the sire. In this simple example, five markers were enough to

DNA parentage verification works by analysing a series of

eliminate four of the five sire candidates from contention. In

DNA markers in the progeny and in potential parents. For each

real life situations, many more markers are used for parentage

DNA marker, one of the two variants observed in the progeny

verification.

must have come from the dam and the other from the sire.

Therefore, potential parents can be ruled out if their DNA

DNA Markers Used for Parentage Verification

markers do not match those observed in the progeny.

The two types of DNA markers that have been used for DNA

In the example shown in Figure 1, the calf and dam have

parentage verification in cattle are microsatellites and Single

been genotyped, as have five candidate sires. For simplicity,

Nucleotide Polymorphisms (SNPs). A microsatellite is a

five different markers (Markers A, B, C, D and E) are being

repeat of a particular base pair sequence at a specific location

used. When we examine Marker A, we can see that the calf

in an animal’s DNA. The number of base pair repeats can

has the genotype ‘Aa’, and the dam has the genotype ‘aa’. In this

differ between animals. Figure 2 shows a CA microsatellite,

instance, the dam must have passed on ‘a’ to her calf. Therefore,

where animal 1 has three repeats and animal 2 has five. SNPs

the ‘A’ must have come from the sire. Sires 1, 2, 3 and 5 could

occur where there is a difference in a single base pair. This is

have passed on an ‘A’ to the calf, so are potential sires of the calf.

highlighted in Figure 2 where A is substituted for T between

Sire 4, having the genotype ‘aa’, could not have passed on an ‘A’

the animals.

to the calf, so can be ruled out as a potential sire.

Historically, microsatellites were the DNA marker used

We can then repeat this process for Markers B, C, D and E. For

for parentage verification. However, SNPs are replacing

Marker B, the calf has the genotype ‘BB’, so one ‘B’ allele must

microsatellites as the genetic marker of choice because of

have come from the dam and the other from the sire. Of the

their greater abundance and stability. The greater abundance

five sires, Sires 1, 3, 4 and 5 have a ‘B’ which they could have

of markers means more markers can be included in tests,

passed on to the calf. Sire 2 can be ruled out. For Marker C, the

allowing them to be more powerful and accurate, while the

Animal

Marker A

Marker B

Marker C

Marker D

Marker E

Calf

Aa

BB

CC

dd

Ee

Dam

aa

Bb

CC

Dd

EE

Sire 1

AA

3

Bb

Sire 2

Aa

3

bb

Sire 3

Aa

3

BB

Sire 4

aa

Sire 5

AA

3

Cc

3

dd

CC

3

DD

3

CC

3

Dd

Bb

3

cc

Bb

3

Cc

3

3 3

DD 3

dd

3

Figure 1. Parentage verification compares the genotype of a calf against the genotype of its dam and candidate sires.

Here, five markers are used to eliminate four of the five sire candidates as the potential sire of the calf.

14

EE ee

3

Ee

3

ee

3

EE

Their calves could then be parent verified using SNP. In Year 2, Microsatellite

SNP

Animal 1: ATGCCACACAATGC CACACA

Animal 1: A ATGCCACCATGCCAT

Animal 2: CACACACACA ATGCCACACACACAATGC

Animal 2: T ATGCCTCCATGCCAT

the only parents requiring a SNP profile are the new sires and dams coming into the herd (in this case, 2 year old bulls and 2 year old replacement heifers). The calves born in Year 2 can then be parent verified using SNP, as their parents would either have a SNP profile on file from Year 1 or have been tested in Year 2. In Year 3, the 2 year old sires and replacement heifers coming into the herd were born in Year 1, and so already have a SNP profile from when they were parent verified as calves.

Figure 2. There are two types of DNA markers; microsatellites (shown here as a CA repeat) and SNP (shown here as an A/T SNP).

Therefore, in Year 3 and beyond, only the new calves would need to have a SNP profile done.

greater stability means the test will remain accurate over many

Of course, not all breed societies require full parentage

generations.

verification. Where only sire verification is required, a similar strategy should be employed. The only difference would be that

Transitioning from Microsatellite to SNP Parentage Verification

the dams would not need to have a SNP profile taken (i.e. only sires and calves would require a SNP profile).

While many beef cattle societies are moving away from microsatellite parentage verification tests to the newer SNP

Summary

parentage verification test, one limitation to this upgrade is

The process of parentage verification, where a series of DNA

that microsatellites and SNPs are incompatible. Unfortunately,

markers are analysed in the progeny and potential parents,

microsatellite profiles cannot be converted to a SNP profile

allows breeders to identify the most likely sire and/or dam

equivalent. Therefore, animals which require parent verification

of the animal being tested. While traditionally microsatellite

via DNA need to have the same type of DNA profile as their

markers have been used for parentage verification, the newer

parents. In situations where the calf is to be parent verified

SNP parentage verification method provides improved

using a SNP profile, and the parents only have a microsatellite

accuracy and stability. In the upgrade from microsatellite to

profile, then the parents would need to be re-genotyped to

SNP parentage verification, some animals that have previously

have a SNP profile.

been tested via a microsatellite profile will need to be re-tested using a SNP profile. However, this can be managed effectively to

Let us consider the best way to manage the upgrade from

reduce the number of animals that already have a microsatellite

microsatellite to SNP parentage verification when full parentage verification is required (both sire and dam), as outlined in

profile and require re-testing to get a SNP profile.

Figure 3. In Year 1, all sires and dams that have calves born in

Should you have any questions on parentage verification,

the Year 1 calving drop should be re-tested using SNP, as their

or wish to discuss transitioning from microsatellite to SNP

microsatellite profile will not be compatible with a SNP profile.

parentage verification, please contact staff at SBTS or TBTS.

YEAR 1

YEAR 2 All Sires (all ages)

2 y.o Sires (1 y.o in Yr 1)

Dams (all ages)

2 y.oHeifers (1 y.o in Yr 1)

Calves (born Yr 1)

Calves (born Yr 2)

YEAR 3 2 y.o Sires & heifers (born in Yr 1) Already tested

Calves (born Yr 3)

Figure 3. The upgrade from microsatellite to SNP parentage verification can be managed to reduce the number of animals that already have a microsatellite profile and will require re-testing to get a SNP profile. In this full parentage verification example, all sires and dams of the Year 1 calves are re-tested using a SNP profile, allowing the calves to be parent verified using SNP. In Year 2, the calves will have a SNP parentage verification test done, with only new sires and heifers entering the herd requiring re-testing to get a SNP profile. From Year 3 onwards, all new sires and heifers entering the herd should already have a SNP profile, so only the current drop of calves will require a SNP parentage verification test.

15

Accessing Support in Application of Genetic Technologies For support and assistance in the use and understanding of the different genetic technologies that are available, such as BREEDPLAN, BreedObject Selection Indexes, Internet Solutions, TakeStock, GeneProb, Mate Selection Software & DNA based tools or to discuss any of the information included in this edition of the SBTS & TBTS Update, please contact:

TECHNICAL CONSULTANT

BREEDS

CONTACT DETAILS

Boyd Gudex

Limousin Simmental

boyd@sbts.une.edu.au T (02) 6773 1711 M 0437 468 159

Catriona Millen

Blonde d’Aquitaine Charolais Devon Gelbvieh Hereford Murray Grey

Red Angus Red Poll Salers Shorthorn Speckle Park

Paul Williams

Belmont Red Brahman Brangus Droughtmaster

Santa Gertrudis Senepol Simbrah

Tim Emery

Belmont Red Brahman Brangus Droughtmaster

Santa Gertrudis Senepol Simbrah

Carel Teseling

Wagyu

catriona@sbts.une.edu.au T (02) 6773 3357 M 0409 102 644

paul@tbts.une.edu.au T (07) 4927 6066 M 0427 018 982

tim@tbts.une.edu.au M 0408 707 155

carel@wagyu.org.au T (02) 6773 4222 M 0439 368 283

IF YOU WOULD LIKE ANY FURTHER INFORMATION ON SBTS AND TBTS PLEASE CONTACT: Tropical Beef Technology Services Telephone: (07) 4927 6066 Email: office@tbts.une.edu.au Web: http://tbts.une.edu.au

Southern Beef Technology Services Telephone: (02) 6773 3555 Email: office@sbts.une.edu.au Web: http://sbts.une.edu.au 16