Autumn 2021 SBTS & TBTS Update

AUTUMN 2021 UPDATE

Santa Gertrudis Implement Single-Step BREEDPLAN

T

he Santa Gertrudis Breeders` (Australia) Association (SGBAA) has worked collaboratively with staff at the Animal Genetics & Breeding Unit (AGBU) and

the Agricultural Business Research Institute (ABRI) to incorporate genomic information into the calculation of Estimated Breeding Values (EBVs) within Santa Gertrudis BREEDPLAN, known as Single-Step. This major upgrade will be implemented in the March 2021 Santa Gertrudis BREEDPLAN analysis.

What is Single-Step BREEDPLAN? Single-Step BREEDPLAN is new analysis software developed by AGBU, a joint venture of NSW Department of Primary Industries (NSW DPI) and the University of New England (UNE), funded

by Meat and Livestock Australia Limited (MLA). The SingleStep BREEDPLAN analysis utilises pedigree, performance and genomic information simultaneously. The analysis takes account of each animal’s actual genetic relationship with all other genotyped animals, including those in the reference population.

The reference population is the set of Australian Santa Gertrudis animals that have genotypes (SNP data) and phenotypes (performance records) for each particular trait. Currently the

n Genomic

information contributes to all EBVs that are

reference population for Australian Santa Gertrudis includes

calculated within the main multi-trait BREEDPLAN

animals measured and genotyped in the CRC, along with animals

analysis, resulting in an increased spread in the EBVs and an

genotyped and recorded in the Santa Gertrudis BIN program

improvement in the accuracy in the EBVs. The amount of

and current R&D projects (Repronomics) and several industry

change depends on the size of the reference population for a

herds.

given trait, and the relatedness of a genotyped individual to the existing reference population.

Overall, the most important effects of the implementation of n

Single-Step BREEDPLAN are that: n

The Days to Calving EBV now incorporates information from research data on two highly heritable, genetically correlated

The evaluation requires high density SNP genotyping and

traits – heifer age at puberty and first-calf cow anoestrous

those profiles are submitted to the BREEDPLAN genomic

interval.

pipeline where they undergo extensive QA checking before being eligible for inclusion in the Single-Step run.

n

Single-Step may identify previously unknown pedigree (or

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

multiple sire mated) of genotyped individuals, if their parent(s) have been genotyped. n

but does also contribute to the EBVs of their ungenotyped relatives (e.g. parents,

IN THIS ISSUE

progeny).

Prior to Single-Step, the evaluation used relationships between animals within Santa

Santa Gertrudis Implement Single-Step BREEDPLAN

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How Do Genetic Evaluations of Genotypes

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See You at Beef Australia 2021

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the evaluation modelled a genetic relationship between full siblings (i.e. animals with the 50% of their genes in common. Whereas in Single-Step BREEDPLAN, high density SNP genotypes are used to determine the actual degree of relationship between individuals.

In the case of full siblings, their relationship may vary from 0.35 to 0.65 depending on the number of SNP they share in common. Similarly, while pedigree may indicate that two

Flood Support Resources 5

A Seedstock Producer's Perspective On: Breeding for Fertility

Gertrudis BREEDPLAN that were determined by the pedigree provided. For example, same sire and dam) of 0.5. This means that full siblings are predicted to share on average

Handle Large Numbers

for Beef Producers

Genomic information contributes mostly to the EBVs of animals with genotypes,

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animals are unrelated, they may actually share common genes and if genotyped, they will have a genomic relationship greater than 0.

The Single-Step analysis relies on the construction of the genomic relationship matrix (GRM) for a given breed. Important to this step is ensuring the animals entering the

TBTS Technical Officer Tim

evaluation are from the given breed. Therefore, as part of the genomic pipeline QA

Emery a 2021 Zanda McDonald

checking, the genomic breed composition of an individual is determined. The GRM

Award Finalist

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of genotyped animals in the breed. The software also identifies possible discrepancies

BREEDPLAN Top Tips: Understanding Milk EBVs

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Ahead of Time: A Sale Catalogue 10

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BREEDPLAN Top Tips: Checking Your Scales

these discrepancies and encouraged to re-sample animals to ensure DNA integrity and Other Changes to the Santa Gertrudis Analysis In addition to the implementation of the single step method, a Shear Force EBV will be

Genotyping the Keepers: It’s All in the Timing

in the society recorded pedigrees for genotyped animals. Breeders will be notified of in some cases, pedigrees may need to be corrected by the SGBAA.

No Crime in Submitting Data Preparation Timeline

is only constructed for those animals that are ≥80% related to the existing population

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switched on in the March Santa Gertrudis BREEDPLAN analysis.

Shear Force EBVs are estimates of genetic differences between animals in meat tenderness.

Shear force is measured as the force required (in kilograms) to pull a mechanical blade through a piece of cooked meat. It is based upon direct carcase measurements recorded

Australia Limousin Breeders'

in research projects. Shear force EBVs are expressed in kg, with lower (more negative)

Society Releases New

EBVs predicting lower shear force i.e. more tender meat.

Selection Indexes

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Summary

Talks, Reports & Paddock Walks 16

The March 2021 Santa Gertrudis BREEDPLAN analysis included a major upgrade.

New SBTS & TBTS Technical

Single-Step software has been introduced, meaning that genomic information, along

Notes Now Available

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EBVs for Australian Santa Gertrudis animals. Additionally, Shear Force EBVs have also

Breeding for Efficiency Webinar Now Available

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MateSel 18 18

Step BREEDPLAN analysis must submit DNA samples for genotyping via the SGBBA office. If DNA samples are not processed through the SGBBA office, then resulting genotypes cannot be included in the Santa Gertrudis Single-Step BREEDPLAN analysis.

If you have any questions regarding the changes to Santa Gertrudis BREEDPLAN, please

BREEDPLAN Performance Recording Timeline

been made available.

Any Santa Gertrudis breeder wishing to include genotypes in the Santa Gertrudis Single-

Optimise Joining Using

Get Social With SBTS & TBTS

with pedigree and performance data, will now be used in the calculation of BREEDPLAN

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Accessing Support in Application of Genetic Technologies 20

contact Paul Williams or Tim Emery, TBTS Technical Officers for Santa Gertrudis. Paul can be contacted on 0427 018 982 or via email paul@tbts.une.edu.au, while Tim can be reached on 0408 707 155 or via email tim@tbts.une.edu.au. You can also contact staff at Santa Gertrudis BREEDPLAN on (02) 6773 3555 or via email santagertrudis@ breedplan.une.edu.au.

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How Do Genetic Evaluations Handle Large Numbers of Genotypes

C

onsiderable computing power and time is required to run each BREEDPLAN analysis, particularly for the larger runs and/or those that include genomic

information. To accurately include genomic information into a genetic evaluation requires multiple thousands of animals with both genotypic and performance data (the reference population). Of the data required, the genomic test data takes up the largest amount of space, with each 50K genomic test taking up approximately 3.2 megabytes, with larger tests now routinely offered by most gene test providers. Thus for an analysis that includes 5000 50K genotypes there is 16 gigabytes (GB) of genotypes before considering the pedigree and performance data, or the software required for the analysis.

To put this in perspective, the average laptop RAM currently advertised on a prominent retailer’s website is 11 GB. Compounding this issue is a limitation of the previously available methods of incorporating genomic information into genetic evaluations which had an upper limit of the same number of animals with genotypes as there are markers on the SNP chip (i.e a maximum of 50,000 animals with 50K SNP chips). While this limit was not breached in any BREEDPLAN

are greatly reduced. However, this fails to make use of all of

analysis, preparations had to be made for when it would occur

the available genetic relationships that exist between traits.

in the future as the number of genotypes submitted continues

The BREEDPLAN analysis has committed to maintaining the

to increase within each analysis. This issue is not exclusive

majority of the traits in a single analysis (exceptions are calving

to BREEDPLAN, rather an industry/world-wide problem,

ease and docility where available) as this allows data on one

regardless of service provider. This article will discuss different approaches to overcome this issue.

trait to inform others. The most extreme example of traits

Methods of incorporating genotypes into genetic evaluations

have an EBV reported based on known relations with other

informing others is where a trait is not recorded but is able to traits, for example the reporting of the Retail Beef Yield EBV

There are a number of different ways in which genetic

from the recording of carcase scan traits.

evaluations such as BREEDPLAN can handle large amounts

Another method of reducing the computational requirements

of genomic information within their analyses. Some genetic

is to utilise a subset of the available SNP markers (genomic

evaluation services compensate for the extreme size of the

data) in the analysis rather than all of the information that is

datasets by (a) breaking their analyses down into multiple

available. As an example, an evaluation might use as few as

subsets, (b) only using a small subset of the available SNP

2000 of the SNPs available on the 50K or 100K SNP chips,

markers and/or (c) prioritising a subset of animals from which

these being SNPs expected to account for some of the genetic

the genomic information is used in specific critical steps in the

variation present in the traits of importance in the population.

evaluation. None of these approaches are ideal.

While this keeps things simple to implement, it also means

By analysing trait groups in different analyses (e.g. weights

most of the genomic information available is not used in the

in one, carcase in another etc) before presenting them as the

evaluation. Other providers have chosen to prioritise which

result of a single analysis, the computational requirements

animals have the genomic information used in all parts of their 3

analysis and which animals have their genotype used in only

testing, AGBU found that the GTBLUP methodology was able

some stages of the analysis. This can mean that the animals that

to process a test dataset including ~400,000 genotypes, with 50K

have the full influence of their genomic data included in the

SNPs per genotype. The processing times and computational

calculation of their breeding values can change between runs

costs for this test case were lower using GTBLUP than for other

and thus individual animals may not receive the full benefit of

single step genomic approaches. As a consequence, GTBLUP

the genomic tests that the breeders have paid for.

gives BREEDPLAN the capability of keeping all the SNPs and all the genotyped animals in the analysis for even the largest of

The Solution: GTBLUP

its clients and will be able to continue doing so in the future

To overcome the computational requirement issues and avoid

regardless of the growth in the population.

the drawbacks identified in the methodology discussed in the

ABRI’s managing director, Hugh Nivison, said that ABRI’s

previous section, BREEDPLAN has invested in upgrading its

decision to embrace GTBLUP, is a conscious effort to maintain

computer systems and a new genetic evaluation methodology called GTBLUP. With GTBLUP, BREEDPLAN is believed to be

position at the forefront of providers for genetic evaluations.

the first multi trait commercial beef genetic evaluation that can

“This is an exciting opportunity for the inclusion of substantial

make use of all available genotypes in a multi country genetic

amounts of genomic data in BREEDPLAN multi-trait

evaluation.

evaluations. This unlimited capacity provides BREEDPLAN

The implementation of GTBLUP was made possible by

users with an enormous amount of flexibility to submit as

developments at the Animal Genetics and Breeding Unit

much genomic data as they want, without limitation” said Mr

(AGBU) led by Principal Scientist Dr. Vinzent Boerner. In

Nivison.

See You at Beef Australia 2021 The SBTS & TBTS team are heading to Rockhampton in May for Beef Australia 2021.

Come and visit us in the Durack Pavilion at sites D9 and D10.

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Flood Support Resources for Beef Producers

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ith the recent floods across parts of New South Wales and southern Queensland impacting many beef producers, Meat and Livestock Australia

As affected herds move into a recovery and re-building phase

(MLA) have put together a directory of flood recovery

the SBTS & TBTS websites. This article outlines a number of

over the coming months, a reminder that the ‘Re-Building Herds After Adversity’ Technical Note is also available on both artificial breeding techniques that can assist during the herd

resources to provide immediate support for flood affected

rebuilding stage, options to managing breeding objectives and

producers. This flood directory contains a list of alert services,

genetic diversity, and considerations for performance recording

contacts and support as well as resources for managing and

following an adverse event. Please feel free to contact staff at

recovering from flood. This directory can be found at: www.

SBTS, TBTS or your BREEDPLAN processing centre, should

mla.com.au/research-and-development/dealing-with-natural-

you wish to discuss any of these topics in more detail or for your specific situation.

disasters/flood-information-for-livestock-producers

We are aware that there are a number of BREEDPLAN herds currently affected by the flood situation, and our thoughts are with you and all that have been impacted during this difficult time.

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A Seedstock Producer's Perspective On: Breeding for Fertility

B

sending heifers to the meat works who couldn’t deliver a calf

reeding for improved fertility has been a key focus for Lyn and Brett Coombe, the owners of Roxborough Brahman stud based in the Moura district, Queensland.

by the age of three and cows that weren’t rebreeding while lactating or raising a calf annually.

TBTS Technical Officer, Paul Williams, recently caught up with

We started to put pressure on our females to deliver along

Lyn to discuss how she and Brett have utilised BREEDPLAN to

these parameters but were using bulls not produced under the

improve the fertility of their breeding herd.

same or similar management program. We were seeing the negative effects of using bulls selected purely on growth with

Q: Could you tell us a little about the Roxborough Brahman herd?

their daughters being later maturing, high maintenance type females unable to produce a calf by three and rebreed while

Roxborough Brahman Stud was started back in 1977 by Brett

lactating. This was backed up by the research being done in the

and his three brothers at the family property Roxborough

northern beef industry.

north of Rockhampton. Now based in Moura, still in the Central QLD area, we run and calve out 200 registered cows

Q: Which fertility traits are you collecting for BREEDPLAN?

and market between 50 – 70 grassfed bulls per year.

Scrotal measurements are collected at 400 days on the bulls

Q: What are the key traits that you focus on in your herd?

and every year we submit bull in & bull out dates for DTC. We also weigh cows at weaning each year to monitor the mature

Adaptability, fertility, moderate growth & docility. With our

cow weight of the herd which we think is an integral part of the

grazing management focussed on optimising stocking rates,

profitability equation.

the ability to maintain body condition will be very important going forward.

We are also part of the “Commercial cow fertility” project

Q: What was it that prompted you to focus more on the fertility of your herd?

CSIRO looking at more DNA markers for female fertility and

supported by MLA Donor Company in conjunction with have been part of the Repronomics project run by AGBU

Within our herd we had some females who were able to get

which is also an MLA Donor Company project concentrating

in calf every year regardless of the season but we were also

on cow fertility in the North.

Lyn and Brett Coombe, Roxborough Brahman stud, have used BREEDPLAN EBVs as a tool to improve the fertility of their breeding herd.

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Q: Do you have any additional herd management practices that you utilise to help identify more fertile animals?

We use multiple sire mating to avoid failings of single sires, and all calves are sire verified through DNA. Our older cows have a 90 day joining period which traditionally started 1 December each year (normal practice in our part of Queensland). Over the past four years, we have crept the 90 day joining forward by two weeks each year. Our older cows are now joined from 1 October. This means the cows calve out from the middle of July, and this puts them under pressure nutritionally because this is well before the season ever breaks.

The Roxborough Brahman Days to Calving (DTC) genetic trend for the 2001 to 2020 calving years. Rapid progress has been made since 2012, with the 2020 calving drop averaging -9 (Top 25% of the breed).

We now join yearling heifers and have done so for the last seven years. The yearling heifers have a shorter 45 day mating period from November 1 til December 12, and are joined regardless of live weight (this year they averaged 191 kg into mating). This challenges the heifers, and while success has been variable due to joining weight and season, it amazes us that it is not necessarily the heaviest that gets in calf.

We have also made genetic progress with the herd, and this is reflected in our Fertility EBV trends. Our trend for DTC was slowly improving until 2012, where a single bull pushed us in the wrong direction. Since then, following the introduction of Alf Collins Snr genetics (Belah Valley), we have made rapid progress in DTC. Our 2020 calving drop averaged -9 for DTC EBV (Top

Of our Brahman females that calf as two year olds, we allow only one miss in the next three years. Heifers that don’t calve

25% of the breed). We have also made progress for Scrotal Size, and this reflects our observation that our bulls are maturing at

until 3 years old are never allowed to miss and, as with any other empties, these are culled. We value longevity in our herd. If a cow has been around this long with that kind of production record there are many characteristics where the boxes are ticked e.g. structural correctness, udders etc. The oldest cows in our herd who have calved every year without a miss, regardless of what they look like, are the very best cows in the herd in our opinion.

a younger age.

Interestingly our mature cow weight (MCW) has become lower which has in turn allowed us to run more cows and produce more kgs per hectare than previously. Those cows with the lower MCWs can maintain body condition and seem to be able to rebreed quicker regardless of the season.

Q: What would you say to those that struggle to collect Days to Calving information in their own herds?

Q: Do you have any other advice for those that are looking to improve fertility in their herds?

Within all herds, there are cows that calve every year on time

Most people keep diaries or have a calendar or whiteboard on the wall therefore it’s very easy to record bull in & bull out dates. We

and deliver a weaner despite the seasonal conditions. Everyone has them. As previously mentioned, the management program

find it doesn’t take much time or effort to record this information.

Everyone has got fertile females in their herd, but we need to be able to identify them and in doing so identify those genetics producing the most profitable animals by using the DTC EBV.

put in place by breeders is equally as important as BREEDPLAN EBVs. We get rid of the free loaders - the cows that are lazy and don’t deliver a calf on time every year.

If a strict culling program is implemented with this

Q: Has there been a noticeable response to the collection of fertility data and use of Fertility EBVs in the Roxborough herd?

management strategy in place then the most fertile females will select themselves. By recording each cow’s performance and collecting this information it is then on hand for bull buyers

Even though we have been putting more pressure on our breeding herd by joining earlier and calving further ahead of the wet season break, we have noticed that our pregnancy rates have improved.

Around seven years ago we were averaging a pregnancy rate of ~80%, and in the last three years, have averaged ~90%. This is despite the last three years being well below average rainfall. We credit the improvement in our pregnancy rates to the increased re-breed rates of our first calf heifers and second calf cows. We are continually surprised at how many of the two year old calvers are pregnant following their second and third matings.

to access.

I see our role as seedstock producers to combine all of the objective measurements, to look at the temperament, market suitability and the whole package. The colour and shape of the package may not be perfect to some peoples’ eyes, but for us if we tick most of the boxes, produce more kilograms per hectare and provide the industry with well described, predictable, profitable genetics then we are doing our job. You can’t manage what you don’t measure!!

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TBTS Technical Officer Tim Emery a 2021 Zanda McDonald Award Finalist

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amed in honour of the late Queensland beef producer, the prestigious Zanda McDonald Award celebrates the contributions of talented, passionate

n

Founder of Humans in Agriculture.

“Our four Aussie finalists are an impressive bunch, and we’re

young professionals working in agriculture across Australia

committed to providing opportunities for them all,” said Richard

and New Zealand. With COVID-19 making TransTasman

Rains, Award Chairman. “They’re ambitious, passionate, and

travel difficult, the award organisers opted to recognise two

making huge contributions to the primary sector already.”

winners – one from each side of the Tasman – in 2021.

All four Australian finalists travelled to Orange in February,

Four finalists were in the running for the 2021 Australian

where they spent several days completing final interviews,

Zanda McDonald Award: n

receiving media training and networking with agricultural

Our very own TBTS Technical Officer, Tim Emery, from

industry leaders. They also toured Sparklabs Cultiv8 where they

Roma, Queensland. n

were inspired to hear about a range of Agri-Tech and Food-

Hugh Dawson, Head Stockman at Barkly Pastoral Company

Tech startups. This was followed by the award dinner, where

in the Northern Territory. n

Oli Le Lievre, Consultant at KPMG in Melbourne and

Rozzie O’Reilly was announced as the 2021 Australian Zanda

Rozzie O’Reilly, Breeding Manager at Lambpro, Holbrook,

McDonald Award winner. The SBTS & TBTS team extend our

New South Wales.

congratulations to Rozzie on her well-deserved win.

2021 Australian Zanda McDonald Award winner Rozzie O’Reilly, with finalists TBTS Technical Officer Tim Emery, Hugh Dawson and Oli Le Lievre. Image Credit: Zanda McDonald Award.

Are you passionate about agriculture, making a difference, and wanting to take it to the next level? Apply for the 2022 Zanda McDonald Award. There’s a significant prize package up for grabs, which includes an all-expenses paid trans-Tasman mentoring trip, $10,000 for further education, expert media training, and incredible networking opportunities with some of the biggest and best agriculture operators in Australasia. Applications are open from 1 – 31 August 2021 to Kiwis and Aussies aged 21 – 35 years old, working and living in Australia or New Zealand. Find out more at www.zandamcdonaldaward.com 8

BREEDPLAN Top Tips: Understanding Milk EBVs

T

he influence a cow has on the pre-weaning growth of her calf is two-fold; her direct growth genetics (i.e.

200 Day Weight EBV) and the maternal environment

the 200 day weight of their calves than the daughters of Sire B.

she provides (i.e. Milk EBV). The BREEDPLAN Milk EBV, by

daughters will lead to a 5 kg average increase in the 200 day

With all other factors (e.g. the 200 Day Growth EBVs of calves) being equal, the greater maternal contribution from Sire A’s

describing the genetics of a cow’s maternal contribution to the

weight of their calves (grand progeny of Sire A).

200 day weight of her calf, captures the mothering ability of a

The production system and environment in which cows will run

cow and the amount and quality of milk received by her calf.

should also be considered when considering the optimum level

For a sire, the Milk EBV describes the maternal contribution

of Milk EBVs for your herd. Selection for increased Milk EBVs

that his daughters will have on the 200 day weight of their

may be warranted when cows are run under good nutritional

calves. The Milk EBV is expressed in kilograms.

conditions and/or calves are sold as weaners. However, some

The context of how the Milk EBV is reported should be

environments may not support high Milk EBVs. For example,

considered when comparing different animals. For example, if

under suboptimal conditions, high Milk EBV cows may not get

we consider Sire A with a Milk EBV of +20 and Sire B with a

back in calf as easily as lower Milk EBV cows in the following

Milk EBV of +10, we can see that the difference between the

year. Therefore, when considering Milk EBVs in animal

two bulls is 10 kg. As only half of the genetics come from the sire, we would expect that, on average, the daughters of Sire

selection, ensure you select animals with appropriate Milk

A would contribute 5 kg more (via maternal contribution) to

EBVs for your production system and environment.

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No Crime in Submitting Data Ahead of Time: A Sale Catalogue Preparation Timeline

W

ith sale bulls being the main source of income for seedstock producers, it makes sense to ensure that sale catalogues include BREEDPLAN EBVs

on their sale animals to their BREEDPLAN processing centre

calculated from all available sources of information. To achieve

For those in breed societies/associations running monthly

this, seedstock producers are encouraged to complete their

BREEDPLAN analyses, planning to use the July EBVs in your

data collection well in advance of the BREEDPLAN analysis

sale catalogue would mean that all performance data for sale

from which sale catalogue extracts are done.

animals should be submitted to your BREEDPLAN processing

at least two analyses in advance of the BREEDPLAN analysis in which they intend to extract sale catalogue information.

centre prior to the performance submission deadline for the

Performance Data

May analysis.

While best practice is to always submit performance data

By submitting performance data on sale animals well in

to your BREEDPLAN processing centre as soon as possible

advance of the analysis you are using for your sale catalogue,

after collection, not all performance data is submitted to

you have given yourself sufficient time to deal with any issues

BREEDPLAN promptly. Instead, some breeders will wait until

or problems that may arise. These include animal registration

they have collected a complete set of performance data on an

issues (e.g. animal “pending” registration, wrong sex, wrong

animal and do a bulk submission of this data to BREEDPLAN.

ident), which can then be followed up with your breed society/

There are several dangers to this approach; firstly, some

association, and the ability to correct or verify any outliers

performance data (particularly that stored in hard copy format)

that arise once the sale animals’ performance data has been

may be mislaid, and secondly, if submission is delayed for too

through a BREEDPLAN analysis. After all, no one wants to

long, this may mean that EBVs published in the sale catalogue

have the EBVs printed in their sale catalogue to not include the

do not include the performance information collected on the

performance data of a genetically outstanding animal simply

animal.

because they had run out of time to verify an outlier record.

To ensure that the BREEDPLAN EBVs used in the sale catalogue

An additional advantage to ensuring that all performance data

include performance data collected on each animal, breeders

on sale animals is included in the BREEDPLAN analysis well

should ensure that they have submitted all performance data

ahead of the sale catalogue extract is that this helps to avoid

An example sale catalogue preparation timeline for a September sale, showing the deadlines for each required task.

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large EBV changes between the sale catalogue being printed and

for a variety of reasons, including sample mix-ups, sample

the day of sale (i.e. current EBVs supplied in a supplementary

contamination or insufficient DNA. Therefore, seedstock

sheet). This assists your commercial clients, as they can then

producers should ensure that DNA samples are submitted for

identify sale bulls which meet their genetic requirements well

genotyping at least six months in advance of the analysis for

in advance of sale day. With a subset of genetically suitable bulls

which they plan to extract sale catalogue information. This

identified prior to the sale, commercial clients can concentrate

will give you some leeway in case re-sampling is required, or if

on completing visual inspections (e.g. for structure) on sale day.

there are other issues (e.g. parentage) that need to be resolved.

Genomic Information (Single-Step BREEDPLAN)

Continuing with the earlier example of using July EBVs in the

For those in breeds with Single-Step BREEDPLAN (currently

genotyping by the preceding January.

sale catalogue, this means that DNA samples should be sent for

Angus, Brahman, Hereford, Santa Gertrudis and Wagyu), one

Seedstock producers should also consider collecting a spare

consideration is when to submit DNA samples for genotyping

DNA sample (hair) for home storage when collecting samples.

purposes. While those that are keen to use genomically

Hair samples should be stored at room temperature, in labelled

enhanced EBVs to make selection decisions (for sale and/or

envelopes. Avoid storing in plastic as this will cause the hair

breeding purposes) are encouraged to collect DNA samples at

to sweat, which can allow mould and other contaminants to

birth (TSU only) or marking (TSU and/or hair), some breeders

flourish. While collection of a new sample is recommended if

may wish to simply include genomically enhanced EBVs in

the lab does require re-sampling, a backup sample may also

their sale catalogues. In this situation, breeders need to allow

come in useful in the future (e.g. if a genotype is required once

sufficient time for the genotyping process to occur, including time to resolve any issues that may arise.

a bull is sold/deceased).

The process from DNA sampling to genotypes being included

Conclusion

in the BREEDPLAN analysis is not a quick one; once samples

Ensuring that all available information has been included in the

are received by the genotype service provider, they need to be

calculation of BREEDPLAN EBVs included in sale catalogues

processed (processing alone typically averages three to four

is beneficial for seedstock producers and their commercial

weeks) before genotypes are returned to the breed society/

clients. Seedstock producers should aim to have DNA samples

association. From here, the genotypes will need to wait for the

for all sale bulls sent off for genotyping at least six months

next BREEDPLAN analysis (this can be up to four weeks if they

ahead of the BREEDPLAN analysis used for sale catalogue

are received shortly after the data submission deadline).

compilation, and all sale bull performance data submitted at

While a three to four month turnaround should be sufficient

least two months ahead of sale catalogue compilation. Doing

for the majority of your DNA samples to be genotyped and

so will ensure you have sufficient time to deal with any arising

these genotypes included in the BREEDPLAN analysis, a small

outliers (performance data), re-sampling requirements (DNA)

subset of animals may require re-sampling. This can occur

and/or animal registration issues.

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Genotyping the Keepers: It’s All in the Timing

T

hose in breeds with access to genomically enhanced breeding values via a Single-Step BREEDPLAN analysis (currently Angus, Brahman, Hereford, Santa Gertrudis

of Single-Step BREEDPLAN EBVs) can be utilised when the

and Wagyu) may be considering when the best time to genotype

pedigree and the animal’s own performance, genomics

cattle breeder is making selection decisions. While traditional BREEDPLAN EBVs for young animals are calculated from

their young animals is. Additionally, consideration may be given

provides an additional source of information for the Single-Step

to whether all animals should be genotyped or just those that

BREEDPLAN analysis to use. This offers several advantages.

are to be kept (e.g. replacement heifers and/or sale bulls). This

Firstly, genomic information typically increases the variation

article will explore these considerations in more detail.

(spread) observed between animals. This allows greater

When is the Best Time to Genotype a Calf?

differentiation between the top (keeper) and bottom (cull)

Beef producers now have the opportunity to collect DNA

response. Secondly, genomics typically causes increases in EBV

calves, allowing easier selection decisions and greater selection

samples for genotyping very early in a calf ’s life. Tissue

accuracy, which can cause re-ranking of animals. This increase

Sampling Units (TSUs) can be used to collect a tissue sample

in EBV accuracy is usually more pronounced for animals with

when tagging and/or weighing the calf soon after birth. While

a lower starting EBV accuracy, such as young animals with no

it is recommended that hair samples are not taken until the

progeny performance in the system. By lifting the EBV accuracy,

calf is at least 60 days of age (allowing time for the hair follicles

genomics is providing breeders with a better description of an

to develop), hair samples are commonly collected at marking/

animal’s genetic potential. This allows beef producers to be

weaning. Even allowing for the genotyping process (typically

more confident in their selection accuracy when identifying

3-4 months) beef producers can have genotype information

which animals to keep, and which to cull.

included in the Single-Step BREEDPLAN analysis by the time

An example of the effect of genomic data in animal selection

the calf is four to six months of age. For those who wish to

can be seen in Figure 1. This figure shows ten heifers from a

utilise genomically enhanced EBVs as part of their selection

real Australian herd, born in 2020, and their Selection Index

criteria, collecting DNA samples at birth or marking/weaning

values when a) their own genotypes are not included (i.e. just

is strongly encouraged.

pedigree and own performance) and b) their own genotypes

Why Genotype Young Calves?

were included (along with pedigree and own performance). Let

The major advantage to having genomic information on

us assume that the breeder plans to keep 60% of the heifers

animals at such a young age is that this information (in the form

as replacements, and, for simplicity, is using the Selection

12

Figure 1. Ten 2020 drop heifers with Selection Index values when a) their own genotypes were not included and b) their own genotypes were included. Assuming a 60% replacement rate and selection on the Selection Index value, the larger animals are those that would be retained, while the smaller animals would be culled.

Index values as the sole selection criteria. Without genomically

In situations where finances do not allow for all calves within

enhanced EBVs (which contribute to the Selection Index),

the calving drop to be genotyped, an alternative approach

the breeder would select heifers 1, 3, 5, 6, 7 and 8. However,

may be to genotype all calves but the definite culls (e.g. calves

a month later, with genomic information included, the heifers

to be culled for other reasons, such as structure). That is, all

have re-ranked and the breeder would now select heifers 1,

calves you intend to keep or are considering keeping should

2, 3, 4, 6 and 7. While not shown, the inclusion of genomic

be genotyped. This will ensure that you are not only able to

information is also lifting the EBV accuracy of these heifers.

use genomic information to make selection decisions for these

With the inclusion of genomic information, the beef breeder is

animals but will have genomic information on all of the keepers.

able to make a more informed selection decision.

This will have benefit for their future progeny, as genomic

There are several other benefits to genotyping calves prior to

information will flow through the pedigree from the parent to

animal selection. In addition to the ability to use genomically

the progeny. Indeed, one option for those looking to gradually

enhanced EBVs for identifying replacement heifers and/or sale

build the herd to the point that all cows are genotyped is to

bulls, many breed societies/associations offer DNA “bundles”

genotype the replacement heifers each year.

which allow breeders to do parentage verification and genetic condition testing of their animals. Both of these, in particular

Conclusion

genetic condition status, may also be important factors in the

Beef breeders who wish to utilise genomically enhanced EBVs

final selection of replacement animals.

in their animal selection decisions are strongly encouraged to collect DNA samples for genotyping at birth (TSUs only) or

Should I Genotype All of My Calves?

marking/weaning (TSUs or hair). By doing so, and sending

One of the barriers to genotyping the entire calf crop is cost,

samples off for genotyping straight away, beef producers

particularly for larger beef herds with several hundred calves

can have genotype information included in the Single-Step

born each year. Understandably, some beef producers may

BREEDPLAN analysis by the time the calf is four to six months

look to genotype just those animals that they plan to keep,

old. Genotyping young animals also allows beef producers to

rather than the entire calving drop. While this may make sense

consider parentage verification and genetic condition results

from a financial viewpoint, this does cause a trade off with

when making animal selection decisions. While the cost

selection accuracy. As the example in Figure 1 showed earlier,

to genotype the entire calf drop can be a large outlay, the

the addition of DNA information can lead you to identify

advantage of this investment is that beef breeders will have all

more suitable replacements than those that you identified initially (i.e. prior to having genomically enhanced EBVs). For

available information on all calves, allowing them to make the

this reason, in the ideal situation, all young animals should be

most informed selection decisions when deciding which calves

genotyped.

to keep, and which to cull.

13

BREEDPLAN Top Tips: Checking Your Scales

T

he collection of weights is critical for the calculation of BREEDPLAN Growth EBVs. As scale accuracy can deteriorate over time, weigh scales should be regularly

calibrated. Additionally, there can be variation between different sets of scales; this can be removed through the calibration process. This is particular important in situations where beef producers have multiple sets of scales, such as in different yards on their property(s). It is also common for different scales to be used for birth weight compared to postbirth weights, due to portability and weight range requirements.

Regular calibration is required to ensure that all sets of scales give the same reading.

weight (light) or various combinations of multiple weights

The scale calibration process typically involves the test

(heavier). Additionally, multiple smaller weights are easier

weighing of multiple known or ‘standard’ weights. The scales

to move on and off the scales compared to a single large

are then adjusted until they report the known weights of the

weight.

standards. Some important things to consider when calibrating

2. The use of inert standard weights. Our own body weight

your scales include:

changes over time, as does the weight of containers filled

1. The use of multiple standard weights. This is required as

with liquid (e.g. through leaks, evaporation). For this

it is possible for scales to be accurate at a single weight

reason, using inert standards such as tractor weights or

point but inaccurate across a range. The use of multiple

buckets full of concrete is advised. To obtain a known

standard weights allows for scales to be tested with a single

weight for these inert standards, they should be weighed at a certified weigh scale like those found at your rural supply store for weighing seed and other produce.

3. The use of the same standard weight across all scales.

This ensures that the calibration of all scales used on your property(s) is equal. However, when collecting a particular weight (e.g. 200 day weight), the whole management group/ mob should be weighed using the one set of scales.

4. The re-calibration of scales when moved. The process of transporting scales can affect their accuracy. Therefore, scales should be re-calibrated if they have been transported between yards/properties etc. Birth-weight scales are an exception to this; as they are designed to be portable, they do not need to be re-calibrated every time they are moved.

5. Regularly clean under scales. Scales located in cattle yards are prone to the build up of mud, hair and other detritus underneath. This can prevent the load bars from compressing and accurately measuring the animal’s weight.

The frequency at which you should calibrate your scales will vary depending on how often you use them and the conditions they are operated under. Please refer to the manufacturer’s recommendations for further detail. More information on recording weights for BREEDPLAN can be found via the Help Centre on the BREEDPLAN website.

14

T

Australia Limousin Breeders' Society Releases New Selection Indexes hree new selection indexes have been released for the Australian Limousin Breeders’ Society. The three new selection indexes were created using BreedObject

n

12mm P8 fat) at 22 months of age. n

technology (www.breedobject.com) and were designed to

at 22 months of age.

as described in the index descriptions below. Producers are advised to use the selection index that most closely aligns to their production system.

The three new selection indexes are the:

Marketed at 450kg live weight (250kg carcase weight &

Positive emphasis on meeting MSA specifications.

Limousin bulls joined with Bos indicus cows in Northern

n

All progeny finished on grass.

n

Steers marketed at 580kg live weight (330kg carcase weight & 12mm P8 fat) at 27 months of age.

8mm P8 fat) at 15 months of age. n

n

Australia targeting the export trade.

specifications. n

Positive emphasis on maternal traits.

n

herd targeting domestic supermarket

Steers finished on grass or short-fed.

n

Northern Export Index

Domestic Maternal Index

n

Selected heifers are retained for breeding and the balance marketed at 525kg (290kg carcase weight & 14mm P8 fat)

select cattle suitable for three separate production systems

n Self-replacing

Marketed at 560kg live weight (330kg carcase weight &

n

Selected heifers are retained for breeding and the balance

Heifers marketed at 545kg live weight (300kg carcase weight & 14mm P8 fat) at 27 months of age.

marketed at 425kg (235kg carcase weight & 9mm P8 fat) at 15 months of age.

n

Positive emphasis placed on finishing ability.

n

Positive emphasis on maternal traits.

n

This index can also be used by producers in Temperate

n

Positive emphasis on meeting MSA specifications.

Australia that are targeting larger carcase weights.

Export Maternal Index

Further details are available in the Interpreting Australian

n

Self-replacing herd targeting export specifications.

Limousin Selection Indexes tip sheet, available in the Help

n

Steers finished on grass or short-fed.

Centre on the BREEDPLAN website.

15

Talks, Reports & Paddock Walks

A

s a result of discussions between TBTS personnel and Far North Queensland seedstock producers, the decision was made to organise a Regional Forum

Having a variety of breeds represented at both events, along with different levels of BREEDPLAN knowledge, made for valuable knowledge sharing and discussion.

on the Atherton Tablelands in late 2020. The purpose of

Over the next two and a half days, Paul and Tim ventured

Regional Forums is to provide both BREEDPLAN and aspiring

south from Malanda, visiting a further two seedstock and three

BREEDPLAN members with the opportunity to discuss all

commercial operations on their way through Charters Towers

things BREEDPLAN and DNA technology. To make the most

and Emerald. Whilst near Charters Towers, the opportunity

of a northern trip, it was decided to deliver a commercial

presented itself to spend some time visiting DAF’s Spyglass

focused presentation whilst in the region, as well as conduct

Research Station to meet with staff and see some of the cattle

property visits en route to and from the aforementioned events.

involved in the Repronomics Project. In Charters Towers

TBTS Technical Officers, Paul Williams and Tim Emery, set off

itself, a catch up was had with DAF office staff and breeders

from Rockhampton on 29 October and over the course of three

associated with the Gold City Brahman Sale.

days visited nine seedstock producers (Brahman, Belmont Red, Droughtmaster), a former research project herd, and popped

Whilst on farm, where applicable, the Completeness of

into see some of the no.19 steers involved in the Northern BIN

Performance and Genetic Improvement reports were provided

Steer Project near May Downs. On 2 November, 13 seedstock

to seedstock producers and time was dedicated to go through

producers (Brangus, Brahman, Charbray, Charolais, Senepol

them. As to be expected, a number of topics were raised by

and Limousin) participated in a full day Regional Forum to

producers upon visiting, with a few examples being an update

discuss the role of genetics in beef breeding, BREEDPLAN

on Multibreed EBVs, submitting Days to Calving information,

data collection, submission and reports and DNA technology.

selection indexes and genotyping strategies.

Later that evening, 16 producers, predominantly commercial

The TBTS team would like to take this opportunity to once

and members of the Malanda Beef Plan Group, heard how

again thank all those producers who welcomed us into their

Estimated Breeding Values (EBVs) can be used as part of the bull buying process and were provided with an update on

homes and onto their properties. We hope that your businesses

genetics focused research projects in Northern Australia.

have been positively influenced by engaging with Paul and Tim.

16

New SBTS & TBTS Technical Notes Now Available

T

he following articles (originally published in SBTS & TBTS Update magazines) are now available as standalone Technical Notes on the SBTS and TBTS websites:

The ‘A Seedstock Producer’s Perspective’ articles have also been made available on the SBTS & TBTS websites as standalone documents. These include:

n

Re-Building Herds After Adversity

n

A Seedstock Producer’s Perspective: MateSel

n

Breeding for Production System Efficiency

n

A Seedstock Producer’s Perspective: Using BREEDPLAN

n

Breeding for Environmental Efficiency

n

The Maternal Female: What Makes a Good Cow

n

The Case for Genotyping Females

n

ET Flush Siblings are not Identical Twins

in a Smaller Herd n

A Seedstock Producer’s Perspective: Breeding for Fertility

You can find all of the articles mentioned above in the Seedstock: Breeding Better Cattle area of the SBTS & TBTS websites, under Resources.

Breeding for Efficiency Webinar Now Available

I

n October 2020, SBTS Technical Officer, Catriona Millen, was invited by the North West Beef Extension Network and the North West Local Land Services to present a webinar on

in a self-replacing herd, both in the breeding herd and for

Breeding for Efficiency. With many beef producers in this area

sire x maternal cow). Catriona also outlined how BREEDPLAN

sale/slaughter progeny, environmental efficiency and the opportunity to make use of biological efficiency (i.e. terminal

of NSW in a re-building phase, the underlying theme of the

EBVs and Selection Indexes can be used in conjunction with

webinar was how producers could make their investments in

visual appraisal to identify animals with genetics appropriate

new animals and genetics count by building a herd of efficient

for the production system.

animals for the future.

For those interested in viewing the webinar, it was recorded

With this in mind, Catriona outlined efficiency from a range

and can viewed via the SBTS & TBTS YouTube Channel, or via

of perspectives. This included production system efficiency

this link: bit.ly/3rFQ1B3

17

Optimise Joining Using MateSel

S

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.

MateSel not only allows seedstock producers to maximise genetic progress whilst managing inbreeding, but will also save significant time previously spent compiling mating lists.

MateSel is a valuable addition to the BREEDPLAN suite of

MateSel is fully customised to the breeding program of each

tools that are offered by the Agricultural Business Research

individual seedstock operation with the seedstock producer

Institute (ABRI) in Armidale, NSW.

choosing acceptable inbreeding limits by selecting one of three breeding strategies, “Genetic Diversity”, “Balanced” or “High

Seedstock members interested in learning more about MateSel

Genetic Gain” and providing details of their desired breeding

should visit the BREEDPLAN website (breedplan.une.edu.au)

objective. Results from the MateSel analysis are returned

and click on the MateSel icon on the right hand side, or contact

promptly, usually within one working day.

staff at SBTS or TBTS.

Get Social With SBTS & TBTS SOCIAL MEDIA

B

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.

facebook.com/SBTSTBTS

twitter.com/SBTSTBTS

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 facebook.com/SBTSTBTS, Twitter account at twitter.com/SBTSTBTS or YouTube Channel at youtube.com/user/sbtstbts.

18

youtube.com/user/sbtstbts

19

Birth

Birth

Calving Difficulty Score

Preg Test Results

Flight Time

Docility Score

Mature Cow Weight (on dams)

200 Day Weight

Weaning

Weaning

600 Day Weight

18 months

Structural Score Information

Abattoir Carcase Data

Scanning Measurements (EMA, Fats, IMF%)

Scrotal Circumference

400 Day Weight

Yearling

Yearling

18 Months

Mature Cow Weight

Cow Disposal Code (Heifers and Cows)

Maturity

Maturity

BREEDPLAN results are calculated by the Agricultural Business Research Institute using beef genetic evaluation analytical software developed by AGBU and Meat & Livestock Australia Limited.

For more information visit breedplan.une.edu.au

Members of BREEDPLAN are not required to record all the above information for every animal. Members should aim to record the traits that are important to their breeding objective/s or that of their clients (at a minimum).

Recipient Dam Details

Birth Weight

AI Dates

Mating Program Details Date of Birth

Joining

Joining

The following table details the performance information that currently contributes to the calculation of BREEDPLAN EBVs and outlines the stage of the production cycle that each set of information should be recorded.

Performance Recording Timeline

Accessing Support in Application of Genetic Technologies

F

or support and assistance in the use and understanding of the different genetic technologies that are available, such as BREEDPLAN, BreedObject Selection Indexes, Internet Solutions, Completeness of Performance, 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

Gelbvieh Limousin Murray Grey

Red Angus Red Poll Simmental

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

Catriona Millen

Blonde d’Aquitaine Charolais Devon

Hereford Salers Speckle Park

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

Paul Williams

Belmont Red Brahman Brangus Droughtmaster

Santa Gertrudis Senepol Simbrah

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

Tim Emery

Belmont Red Brahman Brangus Droughtmaster

Santa Gertrudis Senepol Simbrah

Carel Teseling

Wagyu

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

carel@wagyu.org.au T (02) 8880 7703 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: tbts.une.edu.au

Southern Beef Technology Services Telephone: (02) 6773 3555 Email: office@sbts.une.edu.au Web: sbts.une.edu.au 20