SUMMER 2016 UPDATE
An Introduction to Genomics
ith several breed societies already incorporating genomic information into their BREEDPLAN analyses, and several more aiming to move to
genomic evaluations in the not-too-distant future, this Technical Note has been developed to give beef producers an introduction to genomic technology. This Technical Note outlines what genomics is, how genomics works, and how the inclusion of genomic information into the BREEDPLAN analysis can benefit beef producers. What Is Genomics? The genome is the genetic material of an organism; that is, all of an organismâ&#x20AC;&#x2122;s DNA. Genomics is the study of the genome, while genomic selection refers to the inclusion of DNA information into a genetic evaluation and selection program (such as BREEDPLAN). The DNA information (or genotypes) used for genomic selection
is in the form of thousands of genetic markers,
as Single Nucleotide Polymorphisms (SNPs).
How Does Genomic Selection Work? When genomic information is not included in the
Genotypes containing these thousands of SNP markers are
BREEDPLAN analysis (the current situation for
generated by analysing a DNA sample from the animal on a
Australian breeds), the BREEDPLAN analysis uses pedigree
SNP chip. SNP chips are available in different densities; for
information and performance data (both on the individual
example the SNP chip might have 20,000 SNP markers (20K), 50,000 SNP markers (50K) or 800,000 SNP markers (800K).
and the related animals) to generate EBVs.
To generate genomic information on their animals, breeders
When genomic information is implemented for a breed specific GROUP BREEDPLAN analysis, breeders will be
take a hair sample from their animals and request the breed
able to take a hair sample on an individual animal, send the
society or a laboratory to do a genomic test on the sample.
sample to the lab, and have the sample genotyped on one of
The DNA gets extracted from the hair sample, and the DNA is run on a SNP chip (density specified by the breeder,
the available SNP chips.
with the denser chips being more expensive). The resulting
The genotype information needs to be supplied to the breed
SNP genotypes can then be used, along with pedigree
to be included in the BREEDPLAN analysis and used, in
information and performance information, in the calculation
conjunction with pedigree and performance information, to
of BREEDPLAN EBVs.
SBTS & TBTS provide a national extension network for genetic technologies for the Australian beef seedstock industry 1
For genomic selection to work, a reference population is required. The reference population consists of thousands of animals which have both phenotypes
IN THIS ISSUE
(performance data) and genotypes (Figure 1). Setting up a reference population has been one of the challenges in implementing genomics in many breeds of
An Introduction to Genomics 1 2017 Regional Forums
population. The ideal reference population has phenotypes collected on all traits of economic importance and interest to the breed. not yet have phenotypes collected. Typically these are young animals which have not yet reached an age where they can be performance recorded. However; any
Do Estimated Breeding Values (EBVs) Really Work?
with both phenotypes and genotypes available to form an effective reference
The second group of animals in Figure 1 are those which have genotypes, but do
Scan Data for Heifers is Valuable
beef cattle; for most breeds to date, there simply have not been enough animals
animal with a genotype but no performance data fits into this second group. 11
Genomic selection uses the known relationships between the phenotypes and genotypes of the animals in the reference population to calculate genomic EBVs
SBTS &TBTS Technical Notes
for young animals (Figure 1).
on Genomic Technology Available 11 2016 Wagyu Genetics & Genomics Field Day & Workshop
Australian Wagyu Association - Crossbred Wagyu Test (CWT)
Brahman BIN Projects Update
Understanding Why & How to Measure Scrotal Size
2016 SBTS & TBTS Webinars Presentations Now Available
There are several factors that will influence how well genomic selection works.
Monthly GROUP BREEDPLAN Analyses for Australian Salers
Figure 1. A reference population is critical to the implementation and ongoing success of genomic evaluations. The reference population consists of animals which have phenotypes (performance data for economically important traits) and genotypes available. The relationship between the genotypes and phenotypes of the reference population can be used to calculate genomic EBVs for young animals which have genotypes but do not have phenotypes (performance data).
Firstly, the size of the reference population is critical. For genomic selection to work successfully in Australian beef cattle, a reference population with a minimum
of three to five thousand animals with both phenotypes (performance data) and
genotypes will be needed. Secondly, genomic selection works best when the reference population is closely related to the young animal population for which
New Protocols for Feed
genomic EBVs are being calculated. For this reason, the reference population
should be designed to represent the whole genetic pool of a breed, rather than
& Data Submission
Accessing Support in Application of Genetic Technologies 28
just a subset of genetics within a breed. This is also one of the reasons why genomics will not replace performance recording â&#x20AC;&#x201C; there is a requirement that animals from the next generation have both genotypes and phenotypes coming into the reference population over time. It is important that seedstock producers understand genomics will not replace performance recording; the work that you as seedstock producers do to performance record your animals will be critical for
Cover photo by Kjpargeter, Freepik.com
the success of genomics in the future. 2
What Benefits Can Beef Producers Expect from Genomics?
animal is placed in a single animal contemporary group,
When genomics is implemented, a breeder will be able to
BREEDPLAN analysis to calculate EBVs. As a result,
its performance information cannot be used by the most animals in single animal contemporary groups have
take a hair sample on an individual animal, send the sample
mid-parent EBVs until performance information can be
away for genotyping, and the genotype information will be
collected on their own progeny or other relatives.
included in the BREEDPLAN analysis and used to generate EBVs. This will have two main applications for seedstock
Whatever the reason an animal does not have performance
information; the animal will either not have EBVs for the trait in question, or have mid-parent EBVs of fairly low
1. EBVs can be generated for animals which do not have performance data
accuracy. With genomics, such animals could be genotyped and get EBVS for a range of traits (provided that the
Within any breed, there will be a number of animals
inclusion of the genomic information into the BREEDPLAN
which do not have performance information as they are
analysis means that the EBVs reach the minimum accuracy
from herds which do not record performance data. In the
threshold required to report). Animals which are too young
future, with the inclusion of genomic information into the
to be performance recorded for a trait could be genotyped
BREEDPLAN analysis, these animals could be genotyped
at a young age (e.g. at birth) and get EBVs that normally they
and get BREEDPLAN EBVs. These animals could be from
would not receive until they were much older (e.g. rising
both seedstock and commercial herds.
2 year olds with scan data). Similarly, where a seedstock producer wanted EBVs on stud animals for hard to measure
There are also a number of animals which are in BREEDPLAN
traits, genomics would mean that relevant animals could
herds, but do not have performance information for some
be genotyped and EBVs generated using the genomic
traits. This may be because: n
The animal is too young to have been measured for that
trait. For example, a 200 day old calf will not have been
2. More accurate EBVs can be generated for animals with limited performance information
ultrasound scanned, so is unlikely to have EMA, Rib Fat, Rump Fat or IMF EBVs. Where the 200 day old calf does
Currently, a young animal with no performance data
have carcase EBVs, these are likely to be mid-parent EBVs
(either of its own or its progeny) will have mid-parent
of fairly low accuracy. n
EBVs with quite low accuracy. With the addition of its own
The trait is hard and/or expensive to measure. For example,
performance data and performance data of its progeny, the
Net Feed Intake (NFI) is measured in feedlot trials where
EBVs will change (depending on how well the individual
the animals are on ad libitum feed for nearly 100 days
and its progeny perform within their contemporary groups)
(including the pre-trial adjustment period). This makes NFI
and the accuracy associated with the EBVs will increase.
very expensive to measure, and thus NFI measurements are
Genomics will â&#x20AC;&#x153;boostâ&#x20AC;? the accuracy of BREEDPLAN EBVs;
usually only collected on animals in progeny test programs.
this benefit is most pronounced when the animal has EBVs
Retail Beef Yield is another good example; measuring
with low accuracies. For example, a young animal may have
Retail Beef Yield is very expensive because the carcase has
an accuracy of 30% for one EBV; with the inclusion of a
to be completely boned out and the individual retail cuts
genomic test, the accuracy for that EBV might become 40%.
trimmed and weighed. n
However, an older animal, which might have an accuracy of
The trait is only able to be measured in one sex. For
90% for the same EBV, would likely only have an increase
example, Mature Cow Weight is only recorded for females. n
to 92% accuracy for that EBV with the inclusion of genomic
The trait can only be measured once the animal is dead.
For example, abattoir carcase information, including Retail
In this way genomics can be considered similar to the
Beef Yield and Marbling, is only measured on carcases, and
addition of progeny performance data into the BREEDPLAN
not from live animals. The beef industry utilises live animal
analysis; when the accuracy of an EBV is low additional
ultrasound scanning measurements as a way around this
data has a large effect, and when the accuracy of an EBV is
problem, but the actual carcase measurements can only be n
done on dead animals.
high, additional data has a small effect.
Even when an animal does have performance information,
Of course, the improvement in the accuracy of an EBV due
this information may not be able to be used effectively
to the inclusion of genomic information will vary for each
by the BREEDPLAN analysis. For example, when an
trait (depending on the size of the reference population and 3
the heritability of the trait) and for each animal (depending
illustrative purposes only; in reality the breeder would need
on how closely the animal is related to the reference
to consider both Selection Indexes and individual EBVs of
importance, and do a visual assessment for structure, when making selection decisions.
The applications of genomics as discussed above will allow seedstock producers to identify elite bulls and heifers
As the Figure 2 example shows, the power of genomics is
at younger ages than is currently possible. For example,
the identification of elite bulls and heifers at a young age. This allows cattle breeders to make selection decisions at
consider an ET program where 10 full sibling bulls have
younger ages than are currently possible, and thus shorten
been born (Figure 2). As full siblings, these ET calves
the generation interval. In turn, shortening the generation
will share on average 50% of their DNA (e.g. full sibling
interval should increase the rate of genetic improvement,
ET calves are not genetically identical). These young bull calves, at marking time, will have identical mid-parent
both for individual breeders and the breed as a whole.
EBVs with low accuracy. This is illustrated in Figure 2A,
where all 10 bull calves have a mid-parent Selection Index
Several breed societies are already incorporating genomic
value of $100. Which one(s) should be kept as bull(s) for
information into their BREEDPLAN analyses, and several
breeding purposes, and which ones should be steered?
more are aiming to move to genomic evaluations in the
This is a difficult decision, because the breeder has limited knowledge of the genetic potential of these young bull
calves, and thus has no way of differentiating these calves
The introduction of genomic evaluations will have several
based on their genetic potential.
benefits to Australian cattle producers, including the potential to calculate EBVs on animals that cannot or have
Figure 2B shows the Selection Indexes generated after the inclusion of genomic information into the BREEDPLAN
not been measured for particular traits.
analysis. As illustrated in Figure 2B, following the inclusion
In addition, the inclusion of genomic data in the
of genomic data into the BREEDPLAN analysis, the
BREEDPLAN analysis is likely to increase the accuracy of
Selection Index values for these 10 full-sibling bull calves
EBVs for young animals with limited performance data.
now range from $89 to $114. As the breeder can now
Therefore, genomics looks set to be an important tool for
differentiate between calves on their genetic potential, the
Australian beef producers who wish to continue making
breeder can identify which of these young full-sibling bull
genetic improvement into the future.
calves has the desired genetics for their breeding program.
For further information on genomics, please contact staff
The breeder can now use the best young bulls for yearling
at Southern Beef Technology Services (SBTS) or Tropical
mating. Of course, the use of one Selection Index is for
Beef Technology Services (TBTS).
Figure 2. An ET breeding program results in 10 full sibling bull calves. In A) these 10 calves are too young to have performance information recorded, and so have identical mid-parent EBVs and Selection Index values. In this instance, all 10 calves have a Selection Index value of $100. In B) each of the 10 calves has had a genomic test done, and the genomic information has been included in the BREEDPLAN analysis. Here, due to the inclusion of genomic information, the Selection Index values range from $89 to $114.
2017 REGIONAL FORUMS In 2017, SBTS will be running 14 regional forums. These will be spread around the country, with regional forums to be held at a number of locations across New South Wales, South Australia, Tasmania, Victoria and Western Australia. In addition, SBTS, in conjunction with TBTS, will hold a regional forum in Toowoomba, QLD.
THE COST TO ATTEND A REGIONAL FORUM IS:
The regional forums will cover a number of important topics, including an update on the inclusion of genomic information in BREEDPLAN. There will also be several interactive sessions, where attendees will have the opportunity to reflect upon the amount of performance recording achieved for their own herd, and also to investigate whether they are making genetic progress and meeting their own breeding objectives.
$35 for members of an SBTS or TBTS Stakeholder Breed Society SBTS = Blonde dâ&#x20AC;&#x2122;Aquitaine, Charolais, Devon, Hereford, Limousin, Murray Grey, Red Angus, Red Poll, Salers, Shorthorn, Simmental, Speckle Park & Wagyu. TBTS = Brahman, Brangus, Droughtmaster, Santa Gertrudis, Senepol & Simbrah.
$70 for those that are not members of an SBTS or TBTS Stakeholder Breed Society This includes members of other Breed Societies and other industry representatives.
Numbers for each regional forum are limited, so be quick to ensure that you secure a place.
A draft program is provided on the following page and gives an overview of the sessions to be presented at the regional forums.
To register, please fill out the Registration Form and return it to the SBTS Office. Registration forms are also available from the SBTS (http://sbts.une.edu.au/) and TBTS (http:// tbts.une.edu.au/) websites.
Morning tea and lunch will be provided
8.45 am - 3.30 pm
Armidale Bowling Club
8.45 am - 3.30 pm
Commercial Club Albury
8.45 am - 3.30 pm
The Seymour Club
8.45 am - 3.30 pm
Warragul Sporting & Social Club
8.45 am - 3.30 pm
Comfort Inn Grange Burn
8.45 am - 3.30 pm
The Tramsheds Function Centre
8.45 am - 3.30 pm
Naracoorte Hotel Motel
8.45 am - 3.30 pm
The Haus Hahndorf
8.45 am - 3.30 pm
Best Western Albany Motel & Apartments
8.45 am - 3.30 pm
Comfort Inn Admiral
8.45 am - 3.30 pm
Dubbo RSL Club Resort
8.45 am - 3.30 pm
Orange Ex-Services Club
8.45 am - 3.30 pm
Goulburn Soldiers Club
8.45 am - 3.30 pm
Comfort Inn Grammar View
For Further Information Contact Catriona Millen SBTS Technical OďŹ&#x192;cer Website: http://sbts.une.edu.au 5
Phone: (02) 6773 3357 Mobile: 0409 102 644 Email: email@example.com
2017 | SBTS REGIONAL FORUMS PROGRAM TIME
BREEDPLAN 101: Recording Performance Information In Your Herd
BREEDPLAN Contemporary Groups & Genetic Linkage
Making BREEDPLAN Work For You: Common Performance Recording Problems and How to Avoid Them
How Much Performance Data Do You Collect? Interpreting Your Completeness of Performance Report
Are You Making Progress? Interpreting Your Genetic Progress Report
Single Step BREEDPLAN: What Does Genomics Mean For You?
For Further Information Contact Catriona Millen SBTS Technical Oï¬&#x192;cer Website: http://sbts.une.edu.au 6
Phone: (02) 6773 3357 Mobile: 0409 102 644 Email: firstname.lastname@example.org
2017 REGIONAL FORUMS
REGISTRATION & FEES Registration Fees (All fees GST inclusive) Morning Tea & Lunch provided. Members of SBTS & TBTS Stakeholder Breed Societies:
SBTS: Blonde d'Aquitaine, Charolais, Devon, Hereford, Limousin, Murray Grey, Red Angus, Red Poll, Salers, Shorthron, Simental, Speckle Park. TBTS: Brahman, Brangus, Droughtmaster, Santa Gertrudis, Simbrah, Senepol. Members of Non SBTS or TBTS Stakeholder Breed Societies or Industry:
$ 70.00 TOTAL AMOUNT DUE
Cancellation Policy: Full refunds will be given if the SBTS office is notified at least 7 days before the date of each scheduled workshop. No refunds will be given for notification less than 7 days before the date of each scheduled workshop. You will be issued with confirmation of your workshop registration.
Registration Details WORKSHOP PARTICIPANT DETAILS Location of workshop: Title:
Preferred name for name tag: Postal Address: State: Phone:
Needs relating to diet or disability: ADDITIONAL INFORMATION Are you a member of a Breed Society/Association?
Yes / No (please circle one)
If Yes, please state the name(s) of the Breed Society/Association(s) and your Member Identifier(s) Breed Society /Association: Member Ident: If No, please list the breed(s) of cattle that you are running: Are you currently a member of BREEDPLAN?
Yes / No (please circle one)
PAYMENT: REGISTRATION FEES (ABOVE) Please tick one. A tax receipt will be posted to you upon receipt of payment. A cheque/money order is enclosed payable to Agricultural Business Research Institute I wish to pay by Credit Card. My card details are as follows: Visa
AMEX (a 2% processing fee will be charged for AMEX payments)
Card Number: _ _ _ _ / _ _ _ _ / _ _ _ _ / _ _ _ _
Expiry: _ _ / _ _ _ _ Amount AU$________
Name as it appears on card: ________________________________ Please return this form together with the total amount due to: SBTS, ABRI, University of New England, Armidale NSW 2351. 7
Scan Data for Heifers is Valuable
REEDPLAN currently produces a number of EBVs for carcase traits; these include Eye Muscle Area (EMA), Rib Fat Depth, Rump Fat Depth and Intramuscular Fat (IMF). The BREEDPLAN Carcase EBVs are calculated from two main sources of information â&#x20AC;&#x201C; from live animal ultrasound scanning records measured by BREEDPLAN accredited ultrasound scanners and from abattoir carcase data. Of these two sources, seedstock producers are most likely to collect live animal ultrasound scanning information. This article will outline the number of bulls and heifers which are being ultrasound scanned in seedstock herds across Australia, and the differences that are observed between the sexes. In addition, this article will discuss the benefits of collecting ultrasound scanning data on heifers for inclusion in BREEDPLAN. How Many More Bulls are Scanned than Heifers? The number of animals with ultrasound scanning records on file has continued to increase in recent years. Across all SBTS and TBTS Breed Societies, just 19.1% of the 2001 calving drop has an EMA scan record on file. In contrast, 28.0% of the 2013 calving drop currently has an EMA scan record on file.
However, whilst the percentage of animals with ultrasound scanning records on file has increased in recent years, the difference between the percentage of males and the percentage of females which have been scanned in each calving year has not changed. As Figure 1 shows, the percentage of females in each calving drop from 2001 to 2013 with an EMA scan record on file is consistently lower than the percentage of males with an EMA scan record on file.
Similar levels of improvement are seen when each sex is examined individually. As Figure 1 shows, 34.5% of male calves born in 2013 have an EMA scan record, up from 24.3% of male calves born in 2001. Of the females born in 2013, 24.8% have an EMA scan record, while just 14.6% of the female calves born in 2001 have an EMA scan record (Figure 1).
Figure 1. The percentage of male and female calves (registered across all SBTS and TBTS Breed Societies) in each calving year that have an EMA Scan recorded. 8
Indeed, in the 2001 calving year, 9.6% more males have an
Carcase EBVs. This is of particular importance for
ultrasound scan record than females (Figure 1). In the 2013
producers who are interested in IMF% as heifers will have
calving year, the gap has increased slightly, with 9.7% more
greater variation in IMF% than bulls.
males having been scanned than females (Figure 1). Similar
2. Heifers May Represent a Better Cross Section of Your Herd Than Bulls
trends have been observed when the ultrasound scanning records for Rib Fat, Rump Fat and IMF are examined.
Seedstock producers will find the percentage of female
It is possible that heifers may represent a better cross section of your calf drop than bulls. An example would be
versus male calves with ultrasound scan records on file for
where 50% of bulls had been culled or castrated prior to
their individual herds in their â&#x20AC;&#x2DC;Completeness of Performance
scanning whereas the entire heifer drop was available at the
Reportsâ&#x20AC;&#x2122;, which are available from Internet Solutions or on
time of scanning.
request from SBTS or TBTS.
Consider the scenario where producers are only scanning sale bulls. These sale bulls are the pick of the males born
Why Scan Heifers?
in that calving year with a significant proportion having
There are several reasons to consider collecting scan data on
been steered or culled. This level of selection may have
unintentionally biased the sample of bulls that are being
1. Heifers Mature Earlier Than Bulls
scanned as only the top bulls, including those with the
better Carcase EBVs, are being kept entire. If this is
Under similar nutrition heifers carry more fat than bulls at
occurring, then the average scan data collected on these
the same age. Animals that are fatter at the time of scanning
sale bulls will be higher than the average scan data would
will exhibit greater variation in rib and rump fat depth and
be for the whole male cohort. This will affect Carcase EBVs
marbling than animals which are lean (average of less than
as any sale bull that performs under the sale bull average
3mm rib fat). The reason you should not scan cattle when
will look inferior to his group, whereas he may in actual fact
they are too lean is that they have little variation for rib and
be above average for the whole male cohort.
rump fat and IMF% Scanning heifers will generally provide a greater variation in all of the scan traits, and this variation
is particularly useful for the calculation of BREEDPLAN
In the above situation, scanning a larger cohort of heifers (including half-sisters of the sale bulls) may help to counter
this. If a large proportion of the heifers have been retained they are unlikely to have been culled for Carcase EBVs (instead they are likely to have been culled for fertility reasons). Therefore the heifers may represent a better cross section of the rib and rump fat depths and marbling in your herd than your sale bulls alone. Why Arenâ&#x20AC;&#x2122;t Producers Scanning Heifers? Given the importance of including ultrasound scanning information on heifers in BREEDPLAN analyses, why are many seedstock producers not scanning their heifers? There are couple of reasons that may be contributing to the decision of seedstock producers to not scan heifers. 1. Expense
Ultrasound scanning is charged on a per head basis. It is not uncommon for seedstock producers to pay around $15 per head for ultrasound scanning, plus travel although discounts are usually available for larger numbers scanned. Given the expense associated with ultrasound scanning, it may not be feasible for producers to scan all young animals in the herd. In this situation, SBTS and TBTS recommend that scanning heifers is given preference to scanning bulls.
For those producers who are based a long distance from BREEDPLAN accredited ultrasound scanners, consider
Only scan animals when they are between 300 and 800 days of age
BREEDPLAN can analyse the scanning performance from animals that are between 300 to 800 days of age
approaching other seedstock producers in your area to
when measured. The majority of animals are scanned as
discuss the possibility of scanning animals from multiple
rising two year olds (e.g. at 600 days of age).
herds in the one week. This may help to reduce the travel costs for each individual stud.
Aim to scan your animals when they are in the best
2. Pregnant Heifers
condition possible. As a rough guide, animals should have
Many producers are joining heifers so that they calve
an average minimum rump fat depth of 5mm and an average
down at around 2 years of age. Therefore, many heifers will
minimum rib fat depth of 3mm. The IMF results are further
be pregnant when they are old enough to be ultrasound
optimised if the majority of animals have between 2% and
scanned. Pregnant heifers can be ultrasound scanned
8% IMF at the time of scanning.
for carcase traits. If heifers are more than 3 to 4 months pregnant ensure they are of a similar stage of pregnancy (maximum range of 10 weeks). Considerations for Collecting Ultrasound Scan Records
Only submit one set of ultrasound scanning records per animal to BREEDPLAN
BREEDPLAN will only analyse one EMA, one rib fat, one rump fat & one IMF ultrasound scanning measurement on each animal.
For producers who wish to collect ultrasound scanning records on young animals in their herds, it is important to observe the following when collecting scan information: n
Use a BREEDPLAN accredited scanner
BREEDPLAN can only analyse scanning data that has been
Ensure animals are in sufficient condition to scan
Wagyu breeders please note:
Ultrasound scanning for IMF has little value in Wagyu seedstock animals to inform the estimation of genetic potential or marbling when the progeny is killed after 400 or more days on feed.
measured by a BREEDPLAN accredited scanner. A list of the BREEDPLAN accredited scanners for Australia and
For further information on collecting ultrasound scan data,
New Zealand is available on the BREEDPLAN website here:
or to discuss scanning your heifers, please contact staff at
Southern Beef Technology Services (SBTS) or Tropical Beef
Technology Services (TBTS). 10
Do Estimated Breeding Values(EBVs) Really Work?
(which may change as these young sires have their own
o EBVs really work? That is the question that the new SBTS & TBTS Technical Note ‘Do Estimated Breeding Values Really Work’ sets out to answer. Using several
progeny) can be minimised. The new ‘Do Estimated Breeding Values Really Work’
case studies from both Tropical and Temperate Australian
Technical Note is now available on both the SBTS (http://sbts.
breeds, this Technical Note examines the effectiveness with
une.edu.au/) and TBTS (http://tbts.une.edu.au/) websites,
which EBVs can predict the progeny performance for a team of
in the Technical Note section under Technical Documents.
sires, and for individual animals.
A number of other Technical Notes, which cover a range of
This Technical Note also outlines ways in which the risks
topics relating to the application of genetic technologies within
associated with using young sires with low accuracy EBVs
a breeding program, are also available on the websites.
SBTS &TBTS Technical Notes on Genomic Technology Available
isitors to the SBTS (http://sbts.une.edu.au/) and TBTS (http://tbts.une.edu.au/) websites in recent weeks may have noticed some updates to both the Technical Notes
2. Single Gene Traits This section includes Technical Notes which discuss traits controlled by single genes, such as many of the genetic conditions found in beef cattle.
and the DNA Resources pages (these pages can be found by following the Technical Documents link from the home page).
The first of the new SBTS & TBTS Technical Notes on
This section includes Technical Notes which discuss genomic technology and the application of genomics to cattle breeders.
genomics, ‘An Introduction to Genomics’, is now available from both the SBTS and TBTS websites. In addition, a number of other Technical Notes on genomic technology and the
For further information on the SBTS & TBTS Technical Notes, or to further discuss genomic technologies and its application, please contact staff at SBTS or TBTS.
application of genomic technology to beef cattle producers are currently being developed. These Technical Notes are expected to be available on the SBTS and TBTS websites in coming months. The publication of new Technical Notes, including those which relate to genomic technologies, will continue to be announced via the SBTS and TBTS social media platforms. Beef cattle producers interested in reading these documents are advised to check the sites regularly for any updates. For simplicity and to allow for easier navigation, the DNA Resources Technical Notes have recently been categorised into three sub-categories. These are: 1. General This section includes Technical Notes which provide a general introduction to DNA technologies. 11
2016 Wagyu Genetics & Genomics Field Day & Workshop
n 14 and 15 November 2016, 160 Wagyu breeders and a range of other industry representatives gathered at Jondaryan and Toowoomba. During
the two days they were updated on the importance of Net Feed Intake, collection and use of performance information, advances in the genetic improvement and current and future use of genomic technology in the Wagyu breed. Kerwee Feedlot Visit The Australian Wagyu Associationâ&#x20AC;&#x2122;s CEO Graham Truscott welcomed attendees on arrival at Kerwee feedlot and encouraged all to ask lots of questions to ensure everyone gets as much as possible out of the couple of days. Kerwee Feedlot general manager Steve Martin supplied some background about the feedlot and its history before dividing attendees into three groups. The groups then rotated through the feedlot to hear more about the day-to-day management of the cattle, rations fed and the role of the newly installed GrowSafe feed bins in identifying sires that produce the most feed efficient progeny by testing their feed intake. Kerwee feedlot is currently building additional pens and when the expansion is completed, will have almost double its existing capacity. This expansion is largely in response to the domestic and international demand for quality, highly marbled Stockyard Beef.
price premiums for Wagyu cattle have triggered a momentous
Importance of NFI and genetic improvement
growth phase for the breed, both through existing breeders expanding their herds and newcomers being attracted to
The afternoon session was held at the historic Jondaryan
the industry. He is concerned that, in response to the high
Woolshed. Daren Hamblin the breeder of the first 180 steers
prices, some producers will keep animals as breeding stock
which, at that stage, just finished their feed intake testing,
which should have been culled and slaughtered. With larger
explained the value of feed intake information to his breeding
numbers of Wagyu feeder animals set to become available
operation. He stated that, prior to being involved in the feed
in coming years, producers will be well advised to develop
efficiency testing of his steers, he knew which bulls produced
supply relationships rather than to simply sell to the highest
progeny with heavy and highly marbled carcases.However; the
bidder. Steve felt that those producers who developed supply
feed intake testing now allows him to complete the financial
relationships and used feedback information to improve the
picture by identifying those bulls that consume the least feed
genetics of their stock to meet customer requirements would
to achieve the best financial outcome when all three these factors (weight, marbling and feed intake) are combined. Based
be best positioned to benefit as Wagyu numbers grew.
on the feed intake over the test period, the projected average
The Australian Wagyu Association (AWA) Technical Services
difference in feed cost between the progeny of the most and
Manager Carel Teseling explained that the installation of the
least efficient sires was $500 per calf or almost 30% higher for
GrowSafe feed bins at Kerwee is a very significant development
the inefficient sires.
for the Australian beef industry. It is a first for Australia where
Steve Martin emphasised the importance of Wagyu breeders
a feed efficiency testing service is offered by a commercial
improving the genetics of their cattle. The exceptionally high
feedlot. The AWA will work in close collaboration with Kerwee 12
feedlot to capture the entry and exit weights, days on feed, feed
The 15th of November was dedicated to educating members
efficiency and carcase data of Wagyu animals. This data will
and discuss the exciting opportunities genomics will unlock
then be included in the AWA genetic analysis to improve the
and what this means for the Wagyu industry. MLA’s Sam Gill
ability to accurately estimate the genetic merit of breeding
emphasised that Single Nucleotide Polymorphism (SNPs)
animals for these traits.
genotyping is now the industry standard for genomic research
Graham Truscott and Practical Systems CEO, Mark Morton,
and industry application. SNPs make it possible to do parent
explained the benefits of using a herd management system and
verification, parentage discovery, determine the genetic merit
how to use it to register animals and capture performance data.
of animals (seedstock and commercial), inform about genetic
The major advantages of a herd management system are that
conditions and can be used to determine the genetic condition
it makes the registration and performance recording straight
status of an animal. The many benefits offered by Single
forward. However; it also serves as a business planning exercise
Nucleotide Polymorphisms (SNPs) highlighted the need to
to understand what drives profitability and additionally helps
change the technology used for parent verification from the
with inventory management.
currently used Microsatellites (MiPs) to SNPs.
The rest of the afternoon was dedicated to better understanding
Demi Lollback of the MLA presented the industry benefits
how BREEDPLAN information can be used to improve a herd,
Livestock Data Link will deliver. This MLA initiative is another
how carcase data from different feeding regimes can be utilized
very exciting development that will have significant advantage
in the same analysis, how to record fertility information and the
to the Wagyu industry. The AWA is working closely with the
importance of the F11 genetic condition in the Wagyu breed.
MLA to facilitate the flow of commercial whole of supply chain
The last session of the day was the 2016 Annual General
data into the AWA genetic analysis.
Meeting which reported on the exciting progress made by the
The workshop was concluded by a question and answer
AWA’s many programs and the Wagyu brand during 2015/16.
session moderated by AWA President, Peter Gilmour
It also shed some light on the sensational forecasts for future
featuring the AWA board addressing important issues about
years where the rate growth is expected to increase. Long-
Wagyu breeding, feeding and marketing. This session very
standing member Greg Gibbons (“Gibbo”) was honoured for his outstanding contribution to the AWA by appointing him an
competently answered practical questions on how to manage
Honorary Life Member of the Association.
and run successful Wagyu operations.
Australian Wagyu Association Crossbred Wagyu Test (CWT)
he Australian Wagyu Association has developed a genomic test to determine the level of Japanese Black (Black Wagyu) in non-pedigreed crossbred animals.
animals. Testing may be particularly valuable before feedlot entry, offering a new cost-effective means for producers,
This ground-breaking development, known as the Crossbred
cattle buyers, and processors to determine the Black
Wagyu Test (CWT,) will help the supply chain determine
Wagyu content in commercial crossbred cattle mobs. The
feeding regimes and the propensity of cattle to produce a
results could, for instance, facilitate categorising crossbreds
genuine Wagyu eating experience. AWA’s Carel Teseling
into the progeny of the Black Wagyu bull or a mickey bull.
explains the purposes of the test, how it works and delves into
This knowledge would significantly influence the choice of
the prefectural nuances of the breed in Japan.
optimum feeding regimes, processing, and marketing.
To assist the beef industry in identifying the approximate
The Australian Wagyu Association has developed a genomic
level of Black Wagyu content from a non-pedigree
test to determine the level of Japanese Black (Black Wagyu)
crossbred animal’s DNA sample. n
content in a DNA sample from a crossbred animal. The
Assist in selecting a new class of breeding animals to
test measures Black Wagyu content in terms of the animal’s
purchase or to register with the AWA. Animals with tested
relationship to the mainstream Black Wagyu sub-population
Black Wagyu content can be registered into the Wagyu
available in Australia. While some Australian fullblood animals
Content Register and used for breeding purposes. n
chain verification of non-pedigree, crossbred
will return lower CWT values, this needs to be recognised as
The AWA board is reviewing the Bylaws to determine the
an indication of their importance as “outliers” within the local
appropriate level at which animals with tested Black Wagyu
gene pool, and the valuable contribution they can make to
content can enter the Herdbook as a Purebred animal.
maintaining genetic diversity and providing future selection
Figure 1. Principle component analysis illustrating the genomic distance between breeds. 14
flexibility. Further development work will endeavour to
Approximately 7,000 genotypes from 10 other beef breeds
measure better and define these outlier populations, which
largely provided from the Beef Co-operative Research
have already been identified as descendants of specific, original
Centres (Beef CRC’s) I, II and III co-funded by the beef
Japanese Black prefectural herds.
industry and the MLA Donor Company. n
HOW THE TEST WORKS
The 11 breeds currently having genotypes in the reference dataset are Angus, Brahman, Charolais, Droughtmaster,
Essentially the CWT measures the genomic “distance”
Hereford, Limousin, Murray Grey, Santa Gertrudis,
between the genotype of a particular animal being tested and
Simmental, Shorthorn and Wagyu.
the “clouds” or reference sets of genotypes available for other
This reference dataset of the various breeds in their genomic
breeds and delivers the estimated breed content level of each
“clouds” is graphically represented in Figure 1 below, showing
breed within that animal.
the distance between each breed “cloud”.
The CWT software has been developed by the Animal Genetics & Breeding Unit (AGBU) at the University of New
The Wagyu reference dataset
England. It uses a reference dataset for each breed type whose
The term Wagyu is a general term for about five breeds of cattle
genotypes are currently available. At least 100 individual animal
bred in Japan. The Japanese word is ‘our’ (wa) and ‘cattle’ (gyu).
genotypes, representing the genetic variation in the breed, are
The CWT measures only content from the dominant Japanese
required to form an accurate representation of a particular
Black breed. There are three major Japanese Black bloodlines
breed, so only the major breeds have sufficient genotypes to
well represented in the Australian sub-population:
enable them to be included at this stage. Each animal in the
Kumanami and Tajima from the Hyogo Prefecture
Nucleotide Polymorphism) density to enable accurate breed
Itozakura & Fujiyoshi from the Shimane Prefecture
determination, with the Low-Density GeneSeek Genomic
Kedaka and Eikou from the Tottori Prefecture
reference set requires a genotype of sufficient SNP (Single
Profiler (GGPLD) of some 34,000 SNPS currently the minimum
Two major red (Japanese Brown) sub-populations (Akaushi)
(previous GGPLD SNP levels were 10K, then 20K and these
are also represented in Australia, but are not covered by the
have also been used). The breed genotypes have been provided
CWT. These are:
by a range of industry contributors including AWA through
its Wagyu Collaborative Genetics Research Project, Meat &
Livestock Australia through the various Beef Cooperative Research Centre projects and other breed associations.
Modern Wagyu cattle breeds are the result of crossing of
The CWT uses a two-step process to calculate the breed
the native cattle in Japan with imported breeds. Systematic
crossing began in 1868 during the Meiji restoration. Brown
Swiss, Devon, Shorthorn, Simmental, Angus, Ayrshire and
Firstly, the software calculates the unique allele frequencies for each breed in the reference dataset. An allele is one
Korean cattle were imported during this period.
of a pair of genes that appear at a particular location on a
The infusions of these British, European and Asian breeds
particular chromosome and control the same characteristic,
ceased about 1910. However, it can be expected that some
such as blood type or coat colour. n
evidence of these breeds still exists in some prefectural
Secondly, it calculates the correlations between the allele
Fullblood Wagyu cattle herds in Japan. The red population
frequencies of the test animal’s genotype and those of the
was strongly influenced by Korean and European breeds,
other breeds, and this represents the breed percentages.
Breeds in the reference dataset
The Australian herd is descended from a foundation Black
The reference dataset currently has more than 10,000 genotypes
Wagyu population exported to the USA and Australia from Japan between 1976 and 2001. This comprised some 300
representing 11 of the most prominent Australian beef breeds
and consists of: n Approximately
1,600 Wagyu and Crossbred Wagyu
THE CROSSBRED WAGYU TEST RESULTS
genotypes ranging from Fullblood Wagyu 100% (almost
exclusively Japanese Black) to Crossbred Wagyu F1 50% provided by AWA derived from its Wagyu Collaborative
An animal is regarded as a Fullblood Wagyu whose forebears
Genetics Research Project co-funded through the MLA
originate from Japan. Registered Fullbloods require DNA
parent verification to both the sire and dam to ensure complete 15
pedigree accuracy. Over 300 registered Black Fullblood Wagyus
genomic content may show less than the expected genetic
were represented in the reference dataset with their test results
norm. Providing the sire is registered with known performance
shown in figure 2 below.
through its Estimated Breeding Values (EBVs), this will not pose a problem and indeed may be a distinct advantage if the
The results highlight the genetic diversity available in the registered black Australian Fullblood population. The
sire has higher growth and other attributes.
Fullblood animals with lower CWT results are highly valuable
HOW THE CWT MAY BE USED
to the future of the Black Wagyu population in Australia as they provide the only current opportunities available to retain
Wagyu Content Register
genetic diversity and deliver enhanced selection options for
There are many animals with Wagyu content in member
traits such as superior conformation, growth and maternal
herds where pedigree cannot be proven through DNA parent
capability, with retained marbling.
verification and so cannot be registered as Fullbloods or
Purebreds. However, they are of considerable value to the
Initially, it was expected that the Black Wagyu content in
Wagyu Content Register and their performance data input for
Wagyu gene pool. These animals can now be registered in the
crossbred Wagyu animals would follow the traditional genetic
analysis through Wagyu BREEDPLAN. The Crossbred Wagyu
norm of: n
F1 or first Wagyu cross delivering 50% Wagyu
F2 or second cross Wagyu delivering 75% Wagyu
F3 or third cross Wagyu delivering 87% Wagyu
F4 or Purebred Wagyu delivering 93% Wagyu
Test can provide the Black Wagyu breed percentage required by the Content Register Bylaws: 2.5. CONTENT REGISTER 2.5.1. The Content Register makes provision for the registration of Wagyu influenced animals not eligible for registration in the fullblood or purebred registers.
However, the genomic variation identified in the genotyped registered Black Fullblood animals was reflected in their
2.5.2. It shall be a requirement for the registration of a Content
crossbred progeny resulting in a range for any given crossbred
Register calf that its sire has a DNA profile recorded
grade as shown in figure 3 below.
with AWA at a minimum level to be specified by AWA. 2.5.3. Prior to registration a hair sample of the animal will be
Note: It is expected that F3 animals with higher than 92% were
provided to AWA.
out of cows that already had some Black Wagyu influence. Therefore, crossbred progeny of a high scoring Black Fullblood
2.5.4. Parent verification of calves will not be required.
sire can be expected to have content close to the expected
2.5.5. Random parent verification of calves will be conducted
genetic norm, while progeny from sires with other prefectural
at a frequency determined by the board at no cost to the
Figure 2. Frequency distribution of registered black Fullblood animals 16
animal owners. Animals found to have an incorrect sire
cost-effective means for producers, cattle buyers, and
will be deregistered if the correct sire is not identified by
processors to determine the Black Wagyu content in
the owner at the ownerâ&#x20AC;&#x2122;s cost.
commercial crossbred cattle mobs.
2.5.6. If no Wagyu content is claimed for a base animal, the
The results could, for instance, facilitate categorising crossbreds
breed (or breed combination) of the base animal shall be
into the progeny of the Black Wagyu bull or a mickey bull.
This knowledge would significantly influence the choice of optimum feeding regimes, processing, and marketing.
2.5.7. If Wagyu content is claimed for a base animal, a breed content test will be required for the animal. Animals
HOW TO ORDER THE CWT
registered in the content register shall be assigned a
Producers who wish to do a Crossbred Wagyu Test on animals
percentage breed content calculated from the percentage
should contact AWA staff or download a DNA test request form
Wagyu of the sire and dam or results from the Crossbred
from the AWA website. The form contains the instructions for
the collection of the sample and testing as follows:
Registration of animals with Wagyu content is expected to significantly increase the animalâ&#x20AC;&#x2122;s sale and therefore capital
1. Take a DNA hair or ear notch (using the Allflex Tissue
value as buyers can have greater confidence in the claimed
Sampling Unit) sample from the test animal
2. Send the DNA sample to the University of Queensland Animal Genetics Laboratory (UQAGL)
Testing Animals with the CWT
3. Email the order form requesting a Crossbred Wagyu Test
An animal can be tested to determine its Black Wagyu content
using the Crossbred Wagyu Test. This may be of value in: n
Assisting in selecting breeding animals to purchase or to
4. UQAGL will make the GGPLD genotype available to AWA.
register with the AWA. Animals with tested Black Wagyu
5. AWA will use the GGPLD genotype to conduct the
content can be registered in the Wagyu Content Register
Crossbred Wagyu Test analysis and return the result to
and used for breeding purposes.
Upgrading an animal into the Herdbook. The AWA board
The CWT will cost $79.00 (inc. GST) per animal.
is reviewing the Bylaws to determine the appropriate level
at which animals with tested Wagyu content can enter the
Herdbook as a Purebred animal.
For further information contact Carel Teseling, Technical
Supply chain verification of animals.
Services Manager on phone 02 6773 4222, mobile 0439 368
Testing may be
particularly valuable before feedlot entry, offering a new
283 or email email@example.com.
Figure 3. Frequency distribution of F3 Wagyu cross animals 17
Brahman BIN Projects Update
he Australian Brahman Progeny Test Project is a large scale sire progeny testing project for Brahman cattle and is coming to an end. The Progeny Test Project has been
Performance data has been collected on 844 steers and 949
conducted by the Australian Brahman Breeders’ Association
assessments were also conducted on these animals. Steers
heifers for the Brahman BREEDPLAN traits for weight, carcase scanning and flight time. Structural soundness
with funding assistance from the Meat & Livestock Australia
and heifers were scanned for rib fat, rump fat and eye muscle
Donor Company under the Beef Information Nucleus (BIN)
area (EMA). The female progeny have been retained in the
program. A total of 75 Brahman sires were joined either by AI
project for their first two calves with joining information to
or natural mating to a commercial cow base over three years
be submitted to BREEDPLAN for use in the calculation of
in three co-operator herds; Banana Station, Banana, Baradoo
Days to Calving EBVs. Heifers from the first two cohorts have
Station, Bauhinia and CSIRO Belmont, Rockhampton. All
had the opportunity to have two calves and joining data has
calves bred at Banana Station and Baradoo were by AI, while
been submitted to BREEDPLAN. The third and last cohort is
both AI and “back-up” bulls were used at CSIRO Belmont.
currently being mated for the second joining. All females were
The female progeny from Belmont were transferred to Banana
joined for 12 weeks in each of the matings during the project
Station and run with the Banana Station heifers, while the
on both Banana and Baradoo.
Baradoo heifers remained at Baradoo to produce progeny
Full MSA chiller assessments have also been conducted on
which are managed commercially as one cohort and measured
the carcases of all the 844 steers from the three cohorts. Meat
for a range of economically important traits. All steer progeny
samples from all of these carcases have been analysed by the
were transferred at weaning to Banana Station, where they were
UNE meat science laboratory for tenderness, cooking loss,
run together and finished on grass to Jap Ox weight. The high
meat colour and intramuscular fat percentage (IMF%).
quality performance data provides head-on-head comparison
between the young and proven sires progeny which is analysed
tables below allow a look at some of the results from the data
in the Brahman BREEDPLAN analysis.
collected on the steers for carcase traits.
Figure 3. Frequency distribution of F3 Wagyu cross animals
Table 1: Summary of Brahman BIN Slaughter Data
P8 Fat (mm)
Rib Fat (mm)
962 (903 to 1045)
316 (253 to 383)
12 (2 to 30)
7 (1 to 20)
73 (44 to 107)
The slaughter data results are presented in Table 1 and
of 18.8 kg (Table 2) as young bulls. As the expected average
summarise the average for age, carcase weight, fats and EMA
progeny difference is equal to half of the difference in EBVs
over the six slaughter groups. Steers in groups one and two
between the two sire groups (e.g. expected average progeny
were slaughtered in 2014, groups three and four in 2015 and
difference = 19.2/2), the expected average progeny difference
groups five and six in 2016. The steers were turned off at a
between these two groups is 9.6 kg. Analysis of progeny carcase
younger age in the last two years while maintaining very similar
weight for the top five sires (carcases averaging 334 kg) and
fat cover and carcase weight across the six groups. There was
bottom five sires (carcases averaging 294 kg) shows that there
large variation in all of the carcase traits, with carcase weight at
was an observed average difference of 40 kg in carcase weight
slaughter varying by 130 kg, P8 fat varying by 28 mm and Eye
between the progeny of these two groups of sires (Table 2). In
Muscle Area varying by 63 cm2.
this case the difference in the EBVs of the top five and bottom
The top five sires had an average Carcase Weight EBV of 38.0 kg
five sires significantly underestimated the differences in the
and the bottom five sires had an average Carcase Weight EBV
carcase weights of the progeny.
Table 2: Top five sires and bottom five sires for Carcase Weight with more than 10 progeny
ELROSE YOU BET
BUNGOONA CORBEN MANSO
SHA ANN WISE N UP
LORIMAR PARK EXODUS
LANCEFIELD BURTON MANSO
PBF AUSTIN MANSO
CBV TOM RABIDO
RAGLAN MR JOSHUA
FBC D MONDO MANSO
Table 3: Top five sires and bottom five sires for Shear Force with more than 10 progeny
LANCEFIELD S BUCHANAN
CBV 10-8194 TOM RABIDO
FAIRY SPRINGS RED LEADER
SAMARI PLAINS LUKE
Shear Force, a measure of tenderness, is measured using the Warner-Bratzler shear force test. The unit of measurement is kilograms of force needed to shear a 1 cubic centimetre muscle sample. The top five sires had an average Shear Force EBV of -0.2 kg and the bottom five sires had an average Shear Force EBV of +0.3 kg (Table 3). The average shear force measurement for the progeny of the top five sires was 4.0 kg while the progeny of the bottom five sires averaged 5.6 kg (Table 3). In this case the expected average progeny difference was 0.25 kg in shear force, while the observed progeny difference was actually 1.6 kg of shear force. This is just a snapshot of some of the carcase trait results from the Brahman Progeny Test Project. The reason that the young bull EBVs for carcase weight and shear force underestimated the measured differences in their progeny is most likely because they were based on very little actual carcase data for relatives and were therefore very low accuracy. Even with the lack of actual data behind the young bull EBVs they were able to predict the high and low performing progeny for these traits. For more information on the Brahman Progeny Test Project please contact Paul Williams from Tropical Beef Technology Services (TBTS) on 0427 018 982 or via email firstname.lastname@example.org. 20
Understanding Why & How to Measure Scrotal Size
he most important factor influencing the profitability of beef operation in Australia is the number of calves weaned in comparison to the number of cows mated during the breeding season. The bull influences the overall herd fertility more than any of the other animal. As half of the genetics of the calves come from the sires, selecting the right bulls can be the most successful way of genetically improving fertility within the whole herd. Conversely, selecting bulls with low fertility can cause substantial losses by reducing the number of calves born.
Soundness Evaluation (VBBSE), which is used to assess whether bulls have normal reproductive function prior to making selection and management decisions. Scrotal circumference is:
One easy measure that can help identify bulls with better fertility is to measure and record scrotal size (circumference) with BREEDPLAN. This article will outline the benefits of measuring scrotal size and discuss how to ensure scrotal size it is being measured correctly.
A good indicator of daily sperm production especially in young bulls, which is fairly constant per gram of testis.
A highly repeatable measure (with appropriate technique) and highly heritable (30-45%).
Correlated with sperm motility and morphology. However, these are independently assessed as part of a routine VBBSE.
Genetically correlated with earlier age at puberty in female relatives.
Genetically correlated with earlier return to cyclicity after calving in female relatives within tropically adapted cattle, and especially Bos indicus cattle.
Why Measure Scrotal Circumference? Measuring scrotal circumference can indicate the likelihood that a bull has reached puberty, and whether testicular development is within the normal range. Scrotal circumference assessment is an important part of a Veterinary Bull Breeding
The following standards are recommended by the Australian Cattle Veterinarians (ACV) when measuring scrotal size. These standards were published in 2013 as part of the VBBSE documentation. A logical sequence of events in scrotal size (circumference) measurement is to: 1. Ensure the bull is safely restrained for assessment. 2. Observe. 3. Systematically palpate the scrotum and scrotal contents. 4. Measure scrotal size. Measurement of scrotal size first requires that the bull is restrained such that he is unable to harm either himself or the operator, and that the scrotum is readily accessible. It is highly advisable that: n
All materials used for bull restraint are adequate to hold the bull.
All restraining facility latches are securely closed.
are restrained with a backing bar or chain at approximately the level of the scrotal attachment.
Figure 1. Correct method for measurement of scrotal size. 21
The bull is unable to move significantly forward from this bar, and side to side movement is significantly restricted.
There is at least 300 mm of space behind the backing bar or chain and a further 700 mm standing room from which to safely approach the animal. A 700-800 mm high barrier in front of the standing area to work over increases safety.
Systematic visual inspection before palpation may reveal abnormalities that can be further investigated by direct palpation. If the scrotum, testes, epididymides and blood supply are considered normal, then scrotal size should be measured. In place of a measurement, a comment outlining the reason why scrotal size was not recorded should be made; examples include left testicular hypoplasia, scrotal lesions, bilateral cryptorchid, right testicular degeneration, swollen testes, castrated, hernia. Key elements of measurement of scrotal size to ensure high repeatability within and between operators are illustrated in Figures 1 and 2. If all of these cannot be met, a valid measurement cannot be taken or reported. The technique is: Figure 2. Correct application of a Barth tape.
1. Both testicles are manipulated by downward massage so that they are completely within and against the lowest point
A Barth tape (Figure 2) is the preferred instrument for
in the scrotum, lying side by side, and with no evidence of
measuring scrotal size. The correct tension is achieved by
wrinkling of the scrotum.
placing the thumb against the piston and then firmly drawing the tape in contact with the entire circumference. The
2. The testes are then held firmly in the scrotum with one hand
reading is taken at the edge of the measurement block when
(usually the right had if the person taking the measurement
approximately 2 mm of green piston is showing; appearance
is right handed). The other (usually left) hand is moved from
of red indicates excessive tension. Repeat the measurement at
the side and above to encircle the scrotal neck gathering up any loose scrotum and finally holding both testes firmly
least once to ensure accuracy to the nearest 0.5 cm.
into the lower scrotum (Figure 1). The thumb of the hand
Other measurement devices, especially one composed of
holding the neck of the scrotum should NOT cause any
material prone to stretching, should not be used, as these can
pressure on the middle of the scrotum.
lead to inaccurate measurements of scrotal size.
3. The scrotal tape is then looped around the testes and
Understanding the Relationship Between Weight and Scrotal Size
placed at the level judged to have the largest circumference. The tape is then drawn firmly in contact with the entire circumference to cause moderate indentation of the
The Bull Power Project, which ran from 1992 through to 2003,
allowed the relationship between live weight and scrotal size to
Figure 3. Liveweight effects on average scrotal circumference (mm) of common breeds of Australian beef bulls. 22
be examined. This project involved approximately 1000 bulls,
it is recommended that the minimum acceptable scrotal
which were comprised of 2- to 4-year-old Santa Gertrudis, 5/8
circumference is the bottom 5% value at any weight.
Brahman, Brahman and Belmont Red bulls. The bulls were
It should be noted that the minimum recommended is “bare
subjected to physical and reproductive examinations prior to
minimum”. For example, bulls close to the minimum threshold
mating. Many of these bulls were followed through multiple
are more likely to suffer from some of the problems associated
sire joining’s and mating outcomes established.
with small scrotal circumference than bulls well above the
Some of the finding included: n
threshold. Bull breeders may consider setting a higher scrotal circumference minimum for sale bulls than what is indicated
Live weight appears to be a superior reference point in
by normal range.
comparison to age as a measure for assessing acceptable scrotal circumference in young bulls. Age can also be used,
What considerations should be made when recording scrotal circumference information for BREEDPLAN?
but the variation at any age is higher because of nutrition effects on weight per day of age. n Across
BREEDPLAN can analyse scrotal circumference information
the 13 breeds included in the study, scrotal
from bulls that are between 300 - 700 days of age when measured.
circumference x weight relationships have the same pattern
Subsequently, it is essential that scrotal circumference
in most breeds. The range across breeds of average scrotal
information is recorded when bulls are within this age range.
circumference at any weight between 250-750 kg is 5-7 cm
It is recommended that you measure scrotal circumference
as shown in Figure 3. Temperate breeds tend to have larger
when the bulls are reaching puberty, which will vary according
scrotal circumference at the same weight than tropically-
to seasonal conditions and the maturity pattern of your cattle.
adapted breeds; some of this is related to the lower width
In the majority of cases, scrotal circumference should be
to length ration of Bos indicus testes.
recorded when bulls are being weighed at 400 days.
There is no clear point at which a scrotal circumference indicates an increased risk to fertility. Thus, scrotal circumference needs
While more than one scrotal circumference measurement
to be interpreted along with other elements of the physical
can be recorded for an individual animal, BREEDPLAN is
examination, and with crush side semen and morphology
only analysing the first measurement for each bull at this
results if available. Bulls with a scrotal circumference that is not
stage. Subsequently, it is only necessary to record one scrotal
within “normal limits” should be viewed with suspicion unless
circumference measurement on each bull.
it can be shown by other means that this does not pose a risk.
For further information on collecting scrotal circumference
Details of normal scrotal circumference in the Australian bull
measurements on your bulls, contact Southern Beef Technology
population are provided in Figure 4. As a general principle,
Services (SBTS) or Tropical Beef Technology Services (TBTS).
Figure 4. Liveweight effects on minimum recommendation (fifth Percentile) for scrotal circumference (mm) of common breeds. 23
2016 SBTS & TBTS Webinars Presentations Now Available
he 2016 SBTS & TBTS Webinar Series consisted of six webinars, which were run on Monday nights in September, October and November. Each webinar
but a number of non BREEDPLAN members also attended the
went for approximately one hour, with the webinars being
length. For each webinar, attendees were asked whether they
webinars. At the end of each webinar, attendees were asked to answer a short survey of between two to four questions in
presented by SBTS, TBTS and BREEDPLAN staff.
had found the webinar useful. Averaged across all six webinars, 12% of attendees strongly agreed and a further 74% of attendees
The topics presented in the 2016 SBTS & TBTS Webinar series
agreed that they had found the webinar useful. Attendees were
also asked a number of ‘As a result of this webinar, do you
1. Choosing Bulls to Suit Your Program
have a great understanding of…’ questions. On average, 85% of
2. Getting It Right: Contemporary Groups & Genetic Linkage
attendees agreed that they had a greater understanding of the
3. Making BREEDPLAN Work For You: Performance
topics presented in the webinars as a result of their attendance
Recording Problems to Avoid
at the webinars.
4. Fertility Matters: Recording Fertility Information with
Recordings of all six webinars from the 2016 SBTS & TBTS
Webinar Series are now available to view online. To view the
5. Collecting Abattoir Carcase Information for BREEDPLAN
webinars, go to the webinars page on the SBTS website (http://
6. Where to With Genomics?
sbts.une.edu.au/Webinars/webinars.html). From here, click on
A total of 152 individuals attended the webinars, of which 99
the title of the webinar on interest; this will open the webinar in
were unique attendees (i.e. there were a number of individuals
YouTube. Alternatively, webinars can be accessed directly from
who attended multiple webinars).
the SBTS & TBTS YouTube channel (https://www.youtube.
The webinar attendees represented seedstock and commercial
cattle producers who breed and/or run a range of beef cattle
A copy of the slides is available on request. For those who are
breeds, and also industry representatives (e.g. extension
unable to access the webinars via the SBTS & TBTS YouTube
personnel and breed society personnel).
Channel (e.g. due to poor internet connectivity), a CD of the recorded webinars is available on request. To request a copy
While the majority of attendees resided in Australia, several overseas attendees (including those from New Zealand and
of the slides, or to request a CD, please contact Catriona
South Africa,) also attended the webinars. Furthermore, the
Millen, SBTS Technical Officer, on (02) 6773 3357 or via email
majority of the cattle producers were BREEDPLAN members,
Monthly GROUP BREEDPLAN Analyses for Australian Salers
n 2016, the Australian Salers Association upgraded the software used to manage their pedigree and performance database to ABRI’s new generation of breed registry software known as ILR2. The new software includes several new features such as the running of monthly GROUP BREEDPLAN analyses and production of enhanced GROUP BREEDPLAN herd reports. This will significantly enhance the BREEDPLAN service that is provided to members of Salers GROUP BREEDPLAN. 24
Victorian BullSELECT Workshops
n early September, SBTS staff presented two BullSELECT Workshops in Victoria. These workshops were organised by the More Beef from Pastures and the Victorian Department of Economic Development, Jobs, Transport and Resources (DEDJTR), and were held at Black Star Angus in Mudgegonga and Anvil Angus in Acheron. Both workshops were attended by a mix of seedstock beef producers and commercial beef producers. Attendees at the BullSELECT workshops learnt about BREEDPLAN EBVs and Selection Indexes through a mix of presentations and interactive discussions at the cattle yards. One highlight of the BullSELECT workshop is the mock Helmsman auction, where participants can put into practice what they had learnt throughout the day to select a bull or team of bulls to suit a particular scenario. Those interested in hosting a BullSELECT workshop should contact staff at SBTS or TBTS to register their interest. Further information, including a BullSELECT program, is available from the SBTS (http://www.sbts.une.edu.au) or TBTS (http:// www.tbts.une.edu.au) websites.
New Protocols for Feed Efficiency Measurement & Data Submission
n the past the measurements of feed efficiency for cattle have been largely carried out at research stations such as the Trangie Research station or the University of New England’s
edu.au/). This Tip Sheet provides detailed information on the
Tullimba research feedlot. On farm feed intake measurements
conduct the feed intake measurements and submit the results.
needed to be submitted to the Trangie Research Centre to
Why Collect Feed Intake Information?
procedures for measuring feed intake including a schedule for the weighing of animals and a detailed description of how to
check for quality before submission to breed society databases.
Feed efficiency is recognised as one of the most economically
The availability of the more modern “GrowSafe” feed intake
important production traits, both in grazing enterprises
measuring equipment where all of the intake data is collected
and feedlot operations. Research has shown that significant
and analysed by the Growsafe company has meant there has
variation exists in feed intake and feed efficiency between
been a change in the protocol for collection and submission of
animals, and that a proportion of this variation is due to genetic
feed intake measurements for BREEDPLAN analysis.
The new protocol is outlined in the ‘Collecting Feed Intake
Obtaining feed intake measurements for the generation of
Information for BREEDPLAN for Post Weaning and Finishing
NFI EBVs calculated within BREEDPLAN provides a valuable
Tests’ Tip Sheet which is now available from the Technical
source of information when attempting to identify animals
section of the BREEDPLAN website ((http://breedplan.une.
with superior genetics for feed efficiency to use in a beef
Feed Intake Collection on Steers using the GrowSafe system at Tullimba Feedot, Kingstown, NSW.
breeding program. Feed intake and weight data is analysed in BREEDPLAN to produce two Net Feed Intake EBVs being:
Bulls, steers or heifers can be tested. Sexes should not be mixed in the same pen.
Net Feed Intake- Feedlot Finishing EBV (NFI-F EBV): This EBV is an estimate of genetic differences between animals in feed intake at a standard weight and rate of weight gain when animals are in a feedlot finishing phase.
Net Feed Intake - Post Weaning EBV (NFI-P EBV): This EBV is an estimate of genetic differences between animals in feed intake at a standard weight and rate of weight gain when animals are also in a feedlot but in a younger growing stage, immediately after weaning.
Animals should be tested in contemporary groups (i.e. animals of the same sex which are born within an individual herd in a 60 day period) to ensure that comparisons are made between animals which have been run under identical conditions, both before and during the feed intake test.
The animals must be recorded with the breed society/ BREEDPLAN prior to the start of the test and it is strongly recommended that they have at least a 200 Day weight recorded which includes management group information
Animals that are in small or single animal contemporary groups prior to the test (e.g. Twins, sick animals) should not be included.
For effective sire comparisons it is recommended to have a minimum of five progeny per sire with at least two sires represented.
The largest practical number of animals in a contemporary group representing the progeny of more than one sire is recommended as it will provide more comparative information per animal.
If it is necessary to split a large contemporary group for the feed intake test (e.g. due to pen size) then it is important that each sires progeny are equally represented in each subgroup. For example, if a contemporary group of 120 steers’ needs to be split into 3 sub-groups due to the pen size of 40 head then 1/3 of the progeny of each sire should be randomly selected for each sub-group.
In both cases, NFI EBVs are expressed as kilograms (kg) of feed intake per day. Lower, or more negative, NFI EBVs are more favourable. For example, a bull with a NFI-F EBV of –0.6 kg/ day would be expected to produce progeny that consume less feed per day than the progeny from a bull that has a NFI-F EBV of +0.8 kg/day (when the progeny are of similar weight, are growing at a similar rate, and are in a feedlot finishing phase). Whilst there is a positive relationship between the two EBVs, some animals will rank differently for feed efficiency in the two different scenarios. How Much Effort is Involved? Breeders who are considering collecting feed intake information for BREEDPLAN need to be aware that it can be challenging, expensive, time consuming and must be collected in a standardised way. However if effective feed intake information can be collected and analysed through BREEDPLAN, the economic benefits from a selection perspective can be considerable.
Further information can be found in the ‘Collecting Feed Intake Information for BREEDPLAN for Post Weaning and Finishing Tests’ Tip Sheet which is available on the BREEDPLAN website (http://breedplan.une.edu.au/).
Where and How can I Collect Feed Intake on my animals? Feed Intake collection can be conducted either ‘on-farm’, or at a ‘central-test’ facility (e.g. Tullimba Feedlot, Kingstown, NSW). Commercial feeding systems that automatically record feed intake of individually electronically identified animals are recommended. Currently most feed intake data is collected using the GrowSafe system (See http://www.growsafe.com/ our-systems/feed-intake/) however there are other systems such as the Calan Broadbent Feeding System that can effectively capture feed intake data. The recommendations and requirements that follow apply to all testing locations and systems. Feed Intake Collection on Steers using the GrowSafe system at Tullimba Feedot, Kingstown, NSW. What Animals Should Be Tested for Feed Intake? n
Animals must be between 210 and 700 days of age at commencement of the test. 27
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:
email@example.com T (02) 6773 2472 M 0412 811 123
Blonde dâ&#x20AC;&#x2122;Aquitaine Charolais Devon Hereford Murray Grey
Red Angus Red Poll Salers Shorthorn Speckle Park
firstname.lastname@example.org T (02) 6773 3357 M 0409 102 644
Brahman Brangus Droughtmaster
Santa Gertrudis Senepol Simbrah
email@example.com T (07) 4927 6066 M 0427 018 982
firstname.lastname@example.org 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: email@example.com Web: http://tbts.une.edu.au
Southern Beef Technology Services Telephone: (02) 6773 3555 Email: firstname.lastname@example.org Web: http://sbts.une.edu.au 28