Comprehensive Carcase Information Being Collected within Beef Information Nucleus
omprehensive abattoir chiller assessment and meat science information is being collected within the progeny test programs being conducted by several breed societies as part of the Beef Information Nucleus (BIN) and is providing valuable information relating to the genetic differences between sires for various carcase composition and eating quality attributes. Beef Information Nucleus progeny test programs are presently being conducted by Angus Australia, the Australian Brahman Breeders Association, the Charolais Society of Australia, Herefords Australia, the Australian Limousin Breeders Society and the Australia Wagyu Association with the assistance of funding from Meat & Livestock Australia (MLA) Donor Company, participating co-operator herds, bull suppliers and various industry partners. Within the BIN programs, elite sires in each breed are evaluated in a structured progeny test program in co-operator herds located across Australia. All progeny are comprehensively performance recorded across a range of commercially important traits, which in turn collects valuable information regarding the genetics of each sire. In the case of carcase attributes, progeny are measured for eye muscle area, fat depth and intramuscular fat via live animal ultrasound scanning and then traced through the abattoir where comprehensive chiller assessment measurements are collected. Abattoir measurements vary slightly between the different programs and abattoirs but include such traits as carcase weight, eye muscle area, fat depth, meat colour, fat colour, marble score (AUSMEAT and MSA), hump height, ossification, pH, butt shape and carcase value.
in Armidale for further analysis. Meat science laboratory measurements are collected for a range of eating quality attributes such as intramuscular fat, shear force (tenderness), cooking loss and meat colour.
Meat samples are also collected from each carcase and sent to the meat science laboratory at the University of New England
Abattoir carcase information is being collected on all progeny within the Charolais and Limousin programs, whereas
Comprehensive chiller assessment and meat science measurements are being collected on progeny within the Beef Information Nucleus.
â€œSBTS & TBTS provide A national extension network for genetic technologies for the Australian beef seedstock industryâ€? 1
Continued - Comprehensive Carcase Information Being Collected within Beef Information Nucleus
information is only collected on steer progeny within the Angus, Brahman and Hereford programs as female progeny are being retained for breeding.
The progeny test programs represent a significant commitment by each participating breed organisation in striving for continuous improvement in profitability through investment in performance recording and application of genetic technologies. This investment includes a significant commitment to research and development, particularly to generate the potential to achieve genetic improvement in difficult to measure traits such as carcase composition and eating quality.
2014 in this issue
Comprehensive Carcase Information Being Collected within Beef Information Nucleus
New Technical Areas Now Available on the SBTS and TBTS Websites
Enhancements to Angus GROUP BREEDPLAN
Genetic Improvement of Temperament 4 BullSELECT Workshops Prove Popular
Understanding the EBV Percentile Graph
“Getting Started with BREEDPLAN” Area Now Available 7 Using Male Reproduction Traits to Improve Female Reproduction in Tropical Cattle
Increasing Pedigree Accuracy with DNA Parent Verification
Docility EBVs Now Available for Hereford and Simmental Animals 12
In addition to providing valuable information on genetic differences between elite sires for carcase attributes through inclusion in routine BREEDPLAN genetic evaluations, the information being collected within the BIN programs will provide a valuable R&D resource for the possible future development of genomic breeding values. This information will contribute to the ongoing improvement of carcase composition and eating quality within the Australian beef herd, particularly within those breeds actively participating in BIN progeny test programs.
New Technical Areas Now Available on the SBTS and TBTS Websites
he SBTS and TBTS websites have recently been updated with the establishment of a specific “DNA Resources” area. The DNA Resources area has been compiled as a resource guide for producers considering the use and application of DNA technology within their seedstock enterprise. A specific “Breeding for Fertility” area has also been established on the TBTS website as a central resource for producers considering genetic selection for fertility traits and contains a range of useful technical documents. The new web pages will be routinely updated as new information comes to hand and can be accessed from Technical Documents links on the SBTS (http://sbts.une.edu.au) and TBTS (http://tbts.une.edu.au) homepages.
Recording Docility Scores for BREEDPLAN 13 Enhancements Made to Hereford GROUP BREEDPLAN
Follow SBTS & TBTS on Social Media
Staff Departures - Christian Duff and Andrew Byrne
Staff Movements - Gemma Wilkinson Now Based in Southern NSW 15 Accessing Support in Application of Genetic Technologies
Enhancements to Angus GROUP BREEDPLAN
number of significant enhancements were implemented into the BREEDPLAN software that is used to calculate EBVs for Angus animals within
the April 2014 Angus GROUP BREEDPLAN analysis. These enhancements are part of the routine maintenance of the BREEDPLAN software and have resulted in the calculation of improved BREEDPLAN EBVs for Angus animals. The enhancements include: Revisions to the main multi-trait analysis The main multi-trait model used in the Angus BREEDPLAN
Revised genetic parameters for the calving ease analysis
analysis has been revised to include several enhancements:
The genetic parameters used in the calving ease analysis have
> Revised adjustment factors - differences in performance
been re-estimated to ensure they remain appropriate for the
records are adjusted for non-genetic differences such as
records being analysed. The direct and maternal variances and
differences in the age of the animal, the age of the dam and
heritabilities for calving ease have increased, creating more
for carcase traits other than weight, differences in carcase
spread in the EBVs. More influence has also been given to both
weight. The adjustment factors that are used have been re-
birth weight and gestation length in the calculation of calving
estimated to ensure adjustments remain appropriate for
the performance information being analysed.
Addition of new abattoir carcase data
> Revised genetic parameters - the calculation of EBVs
Implementation of the revised adjustment factors and genetic
requires information on the genetic variation expressed in
parameters for carcase traits now makes possible the inclusion
each trait, as well as the correlations between all traits. All
of a significant amount of abattoir carcase information that has
trait heritabilities and correlations have been re-estimated
been collected on Angus animals with heavier carcase weights.
to ensure that the genetic parameters remain appropriate
Update to base year
for the performance records being analysed.
The base year used within the Angus BREEDPLAN analysis has
> Revised definition of carcase traits - with the exception
been updated from 1995 to 2005. The change to the base year
of carcase weight, all carcase EBVs are now expressed as
will not have an effect on the EBVs of individual animals but
differences in a standard 400 kg steer carcase, while carcase
has been made to provide a more appropriate base population.
weight EBVs are now expressed as differences at 750 days
The base population acts like an â€œanchorâ€? point in the analysis.
of age. This increase in weight (from 300 kg) and age (from
A base adjustment has also been made to each of the selection
650 days) has little effect on the ranking of animals for the
indexes to bring the new average values in line with the old
carcase EBVs but was necessary in order to appropriately
average values for more recent animals (eg. 2012 born calves).
analyse the recent abattoir carcase information being submitted to BREEDPLAN, where the average weight and
Implications for selection index values
age of carcases has increased substantially.
Although no changes have been made to the production scenarios used in the calculation of the selection index values,
> Inclusion of net feed intake - the two trial net feed intake
the underlying genetic parameters within the BreedObject
EBVs currently reported for Angus animals, NFI-p (post-
software have been changed to reflect those now used in
weaning) and NFI-f (finishing) are now calculated as part
the main Angus BREEDPLAN analysis. This has resulted in
of the main multi-trait analysis. Previously, these EBVs
changes to the EBV weightings being used in the calculation of
were calculated as part of a separate analysis. This change
the selection index values.
means that NFI EBVs are now calculated and available for all animals in the main Angus BREEDPLAN analysis,
If you have any questions regarding the enhancements to
providing their EBVs meet minimum accuracy reporting
Angus BREEDPLAN, please contact Carel Teseling at Angus
Australia on (02) 6773 4602. 3
Genetic Improvement of Temperament
emperament (also known as docility) is described as the way that cattle behave when confined in yards or put in an unusual situation such as being separated
Talk to any savvy bull buyer and a trait up the top of their
from the mob. What we define as poor temperament is a
temperament themselves, and also to the ability of the bull to
survival trait in the wild – fear of anything unusual and the
sire progeny within their herd with acceptable temperament.
bull buying checklist will be good temperament or good docility. This relates to their bull purchase having acceptable
desire to escape. In domesticated cattle it can be exhibited as
Assessing Animal Temperament
flight, or at its extreme fight.
While it is common practice to observe animals and assess
Temperament is an important trait in beef herds with poor
their temperament when they are being handled, there are
temperament having considerable impact on the profitability
several methods of more formally measuring the temperament
of the beef enterprise. Among other things, poor temperament
in cattle will:
Collection of Docility Scores
Increase production costs.
Make cattle harder to muster and handle.
Docility scores, being the subjective assessment of animals’
Damage infrastructure e.g. yards and fences.
temperament, are recorded on animals at weaning or shortly
Increase risk of injury and stress to cattle.
afterwards. The advantage of scoring at weaning is that all
Increase risk of injury and stress to stock handlers.
calves should have had minimal handling and so will express
Increase weight loss during transit.
variation in temperament. Variation in handling between
Lower feedlot performance.
animals prior to scoring should also be minimised.
Increase risk of dark cutters in the chiller. It’s estimated
Docility scores are collected on animals using either a yard or
that dark cutting beef costs the Australian Beef Industry in
excess of $35 million annually. Lower eating quality (tougher beef ).
Yard Test - The calves are individually put into a small square yard and the handler attempts to hold the animal in
While different management techniques can be used to improve
one corner for about 30 seconds.
the overall temperament of a herd (e.g. yard weaning of calves),
n Crush Test - The calves are put up a race and held in a crush
temperament is a highly heritable trait which can be improved
or weigh scales for about 30 seconds but not head bailed.
in both the short and long term through genetic selection. There are also no known antagonistic genetic relationships with other
When using the crush or yard test, the behaviour of animals
traits of importance, enabling temperament to be improved
is observed and animals scored on a 1-5 scale, with 1 being
genetically without impacting negatively on other traits.
‘docile’ and 5 being ‘aggressive’.
Improvement of the genetics for temperament through genetic
More detailed information regarding the collection of docility
selection is of particular importance to seedstock producers.
scores is provided in the article on page 13.
In domesticated cattle poor temperament can be exhibited as fight or flight. 4
Measurement of Flight Time
indicate a longer time taken to exit the crush and hence better temperament. For example, a bull with an EBV of +0.40 would
Flight time measurements are recorded on animals using
be expected to on average produce progeny that took 0.25 of
specialised flight time equipment. Animals are held individually
a second longer to exit the crush than a bull with an EBV of
in the crush for a short period and then the head bail opened.
Two light beams are then used to objectively measure the time
Table 1- Breeds with Temperament Related EBVs (May 2014)
taken for the animal to travel approximately 2.0 metres at the exit of the crush (Figure 2). Similar to docility scores, flight
Angus Brahman Hereford Limousin Simmental Santa Gertrudis
time measurements are normally recorded early in an animal’s life, usually at or around weaning.
Trial Docility EBV Trial Flight Time EBV Trial Docility EBV Docility EBV Trial Docility EBV Flight Time EBV
* The “Trial” status on the Docility or Flight Time EBV indicates that the EBV should be considered preliminary and may change as further data is submitted by breeders. This advises that breeders are also encouraged to provide feedback on the EBV to the breed society or BREEDPLAN
Calculation of EBVs for temperament has several major advantages over simply selecting animals based on their docility score or flight time measurement.
Specialised equipment is required to record flight time measurements
all production traits of economic importance, the
observed temperament of an animal is a combination
While both methods have proven to be useful measures of an
of the genetics inherited from the sire and dam, and the
animal’s temperament, it is currently common practice for the
environment and management under which the animal has
tropical beef breeds to measure temperament through collection
been run. While it should not be overlooked, selection of
of flight time measurements due to its genetic relationship
animals simply based on their own observed temperament
with beef tenderness in tropical breeds. Conversely, British and
may have limited value in identifying animals with the most
European breeds more commonly record docility scores due to
superior genetics for temperament due to the influence of
there being no requirement for specialised equipment when
the environment and/or management factors.
using the subjective scoring system while still providing a high
heritability for the trait.
EBVs for temperament related traits (as with other traits) focus on the genetic differences between animals for temperament by accounting for any environment and
Calculation of Estimated Breeding Values (EBVs) for Temperament
management influences. n
Additional to the collection of docility score or flight time
EBVs for temperament take into consideration not only the temperament of the individual animal, but also the
information, several breeds now produce BREEDPLAN EBVs
temperament of all the animal’s relatives. In this manner,
for temperament related traits based on this information.
the EBVs provide a better indication of an animal’s genetics for temperament than an assessment of the animal’s
Docility EBVs are expressed as differences in the percentage
of progeny that will be scored with acceptable temperament
(ie. either “docile” or “restless”). Higher, more positive, Docility
allow for genetic differences in temperament to
be identified between animals who themselves may
EBVs are more favourable. For example, a bull with an EBV
have acceptable temperament. Animals who may have
of +20 would be expected to on average produce 15% more
acceptable temperament but are likely to produce a high
progeny with acceptable temperament than a bull with an EBV
percentage of progeny with poor temperament can be
removed from the breeding herd, or conversely, if two
Flight Time EBVs are expressed as differences in the number
animals of similar genetic merit for other traits are being
of seconds taken for an animal to travel approximately 2.0
considered for use within a breeding program, the animal
metres after leaving the crush. Higher (ie. longer or slower)
that is likely to produce a higher percentage of progeny
Flight Time EBVs are more favourable. That is, higher EBVs
with superior temperament can be selected. 5
Continued from pg 5 - Genetic Improvement of Temperament
Improving Genetics for Temperament
a herd both short term and long term through daughters if
Beef producers aiming to improve the genetics of their herd for
temperament can achieve this using several different selection
The most effective information for selecting animals with
superior genetics for temperament is the Estimated Breeding Value (EBV) for Docility or Flight Time. If EBVs are not
Culling for Poor Temperament - It is common practice for beef breeding enterprises to cull animals from the breeding
available then selection using the raw docility scores or flight
herd that show unacceptable temperament. Any or all of the
time records should be considered. This is with the knowledge
methods of assessing temperament listed in this article can
that they will have limited scope to drive genetic progress for
assist with this.
temperament in comparison to selection with an EBV.
Selection for Improved Temperament - Selecting animals
Who do I contact for further information?
that have superior genetics for temperament is paramount to
For further advice on the genetic improvement of temperament
genetically improving this trait in a beef breeding enterprise.
including recording docility scores or flight time information
Like other production traits, it is also important to select animals for breeding this year that are genetically superior
for the calculation of Docility EBVs or Flight Time EBVs
to those used last year. This is particularly important when
contact staff at Southern Beef Technology Services (SBTS) or
selecting sires due to the overall influence of their genetics in
Tropical Beef Technology Services (TBTS).
BullSELECT Workshops Prove Popular
he BullSELECT workshop package has proven popular since its launch in early 2014 with 11 workshops already delivered across Australia and New Zealand.
The BullSELECT workshop package educates beef breeders about how to use the available tools to select the best bull for their enterprise. Workshop sessions include a mix of interactive discussions and presentations covering topics such as understanding the value of genetics, interpreting BREEDPLAN EBVs and using online searches including a smartphone or tablet app to source the right genetics.
Participants discussing bull selection at the Wirruna Poll Hereford BullSELECT workshop at Holbrook, NSW during February 2014
Any individual seedstock breeder, groups of seedstock breeders, private consultants or State departments of Agriculture interested in hosting a BullSELECT workshop can contact staff at SBTS or TBTS to register their expression of interest. Further information, including a workshop program, is available from either the SBTS (http://sbts.une.edu.au) or TBTS website (http://tbts.une.edu.au).
Participants complete a bull selection exercise at the Yancowinna Angus BullSELECT workshop at Cape Paterson, Victoria in March 2014
Understanding the EBV Percentile Graph
percentile bands are listed across the horizontal access, with the 50th percentile being the median (or middle) value.
he EBV Percentile graph provides a pictorial representation of the percentile band in which an animal’s EBVs are ranked for each particular trait.
Percentile bands enable you to assess exactly how the current estimate of the animal’s breeding value for each trait ranks compared to the genetics of other animals that have been evaluated within the same genetic evaluation, usually being animals of the same breed. An animal’s percentile band rank for a particular trait provides the percentage of two year old animals within the genetic evaluation whose EBV is higher than or equal to the animal’s EBV. For example, a percentile band rank of ‘top 20%’ for 400 Day Weight would indicate that 20% of two year old animals within the genetic evaluation have a 400 Day Weight EBV that is equal to or higher than the individual animal. Or put another way, 80% of two year old animals within the genetic evaluation have a 400 Day Weight EBV that is lower than the individual animal’s EBV.
In the example EBV Percentile graph above, the animal’s EBVs would be ranked in approximately the top 25th percentile for 400 and 600 Day Weight and in the top 95th (or bottom 5th) percentile for Milk. The EBV Percentile graph for animals can be accessed from within the EBV Enquiry facility on Internet Solutions. To access the graph, click on the bar graph icon in the top left hand corner of the animal’s EBV table, as shown below.
The EBV Percentile graph displays a separate bar for each individual trait, with the trait listed on the vertical axis. The direction of the trait, or trait descriptor, is also provided as a reference to which direction EBVs have been ranked in the percentile bands. Generally the more favourable direction for the trait is placed on the right hand side of the graph. The
“Getting Started with BREEDPLAN”
Area Now Available
he BREEDPLAN website now features a “Getting Started with BREEDPLAN” area, created specifically for herds that are either new to BREEDPLAN or potential BREEDPLAN members. This features the newly compiled “BREEDPLAN : A Guide to Getting Started” booklet, a comprehensive guide for herds enrolling with BREEDPLAN, as well as BREEDPLAN enrolment forms, BREEDPLAN fee schedules and a range of technical resources. To access the “Getting Started with BREEDPLAN” webpage, visit the BREEDPLAN website (http://breedplan.une.edu.au) and click on the link displayed on the homepage.
Using Male Reproduction Traits to Improve Female Reproduction in Tropical Cattle
major research project within the Cooperative Research Centre for Beef Genetic Technologies (Beef CRC) studied ways to define the genetic control of traditional and novel measures of reproductive performance in Tropical cattle in Northern Australia. One of the major project aims was to estimate the genetic association of young bulls’ reproductive traits with female reproduction and to identify the male genetic indicator traits that can be used to increase the rate of improvement in female reproduction in Northern Australia.
The male progeny were bred and run till weaning on research stations at “Brian Pastures” Gayndah, “Toorak” Julia Creek, “Brigalow Theodore”, “Swan’s Lagoon” Ayr and “Belmont” Rockhampton. After weaning the male progeny were transported and run at 2 locations being “Brigalow” (progeny from “Brian Pastures”, “Toorak”, “Brigalow” and “Swans Lagoon”) and “Belmont” (progeny from “Belmont”). A small number of male calves from Belmont were sent to Brigalow to maintain linkage. The bulls were recorded pre-weaning (4 months), at weaning (6 months), and then every 3 months through to 2 years of age for a range of reproductive traits. The measurements that were recorded are outlined in Tables 1 and 2 (see next page)
Project Design A total of 4063 male progeny were generated by natural mating between the years 2004-2010 from cows involved in the Beef CRC Lifetime Fertility Project. These were comprised of 1629 Brahmans and 2124 Tropical Composites. A total of 136 sires were used to generate the progeny, comprised of 60 Brahmans and 76 Tropical Composites. Of these, 40 sires, 13 Brahmans and 27 Tropical Composites, were used in multiple years and locations to generate genetic linkage.
Reproductive trait measurements included scrotal circumference, bull breeding soundness evaluation (BBSE), sperm morphology assessment at 12, 18 and 24 months of age and analysis of blood hormones levels for Luteinising hormone (influences testosterone production and onset of puberty), Inhibin (influences the regulation of sperm production), and Insulin-like growth factor-1 (IGF-1). In addition, male progeny were measured for a comprehensive range of other production traits such as live weight, flight time, fatness, eye muscle area (EMA) and hip height.
Results Young bulls and heifer puberty The research showed that the genetic correlation between male semen quality traits, mass activity, motility and percent normal sperm (PNS), and scrotal circumference were generally moderately correlated and consistent in the direction of their relationship with heifer puberty traits in both Brahmans and Tropical Composites. The genetic correlation between male hormone traits and heifer age of puberty were low with the exception of IGF-1 in Brahmans Young bulls and female reproduction at mating 1 and mating 2 Genetic correlations between male reproductive traits and female reproduction at mating 1 were generally low to moderate for both Brahmans and Tropical Composites
Male reproductive traits are useful indicators of female reproduction in Tropical cattle.
showed consistent correlations with mating 2 female traits
Table 1- Reproductive Trait Measurements Collected at Each Different Age
when measured on male progeny at 18 and 24 months of age. Scrotal circumference was moderately correlated with mating
Age Weight Scrotal Blood BBSE (Mths) Sample 0 3 4 3 3 6 3 3 3 9 3 3 12 3 3 3 3 15 3 3 18 3 3 3 3 21 3 3 24 3 3 3 3
2 female traits when measured at 18 months of age in Brahman but had a low correlation with no consistent trend in Tropical Composites. Young bulls and lifetime female reproduction Genetic correlations between male semen quality traits, mass activity and motility, were highly correlated with lifetime female reproduction when measured at 18 months of age. Scrotal circumference showed no consistent relationship with lifetime female reproduction.
Table 2 - Measurements Collected Within Bull Breeding Soundness Evaluation (BBSE)
Genetic correlations between male reproductive traits and
Physical Reproductive Semen Sperm Scores Check Evaluation Assessment
lifetime female reproduction were generally low for male hormone traits.
Leg Scrotal Mass Morphology Structure Circumference Activity Feet Testis Tone Motility
Percent Normal Sperm
Percent Abnormal Sperm
The results also showed that bulls with a larger protruding prepuce were genetically related to female with lower reproduction performance.
Body Penis Condition
The results illustrate that substantial opportunity exists to improve female fertility in tropical beef cattle breeds by recording and selecting on early-in-life bull reproduction traits.
Table 3 - Genetic Correlation Between Key Bull & Female Reproduction Traits Bull Traits Female Traits Age of Puberty Brahman IGF-1 (6) -0.56 (0.11) Scrotal (18) -0.27 (0.10) Circumference Mass Activity (18) -0.51 (0.17) Motility% (18) -0.49 (0.20) Percent -0.48 (0.21) Normal Sperm (18)
Scrotal circumference at younger ages is a modest genetic
Post Partum Lifetime Female Anoestrus Reproduction
predictor of heifer age of puberty but not on lifetime female
-0.21(0.15) -0.27 (0.13)
0.20 (0.19) 0.12 (0.17)
Semen quality such as motility, mass activity and percent
-0.27 (0.18) -0.37 (0.22) -0.52 (0.31)
0.54 (0.26) 0.51 (0.28) -0.01 (0.31)
were highly correlated with female reproduction, particularly
Tropical Composites IGF-1 (6) -0.43 (0.11) -0.10 (0.18) Scrotal -0.17 (0.11) 0.13 (0.16) Circumference (18) Mass activity (18) -0.24 (0.20) -0.68 (0.36) Motility% (18) -0.38 (0.18) -0.73 (0.35) Percent -0.24 (0.17) -0.30 (0.25) Normal Sperm (18)
reproduction. normal sperm, sheath traits and some male hormone levels, with the post partum anoestrus traits in first lactation females. These traits are consequently useful as indirect selection criteria for improving female reproduction in Tropical cattle.
-0.02 (0.17) 0.14 (0.16)
Opportunities exist to improve lifetime weaning rates by using
0.21 (0.25) 0.29 (0.24) 0.41 (0.22)
from which they were derived. Preferably, these bulls should
bulls that have some information on the fertility of the dams have an EBV for Days to Calving (DTC) and at the minimum, a history of their female relativesâ€™ previous calving outcomes. Replacement bulls should be measured and selected based on
* Age at measure included in brackets
favourable Scrotal Circumference EBVs and favourable results
followed a similar pattern observed to their relationship with
in BBSE for semen traits such as motility, mass activity and
heifer age at puberty.
percent normal sperm. It would also be advantageous to select
Genetic correlations between male reproductive and female
bulls with good temperament and good sheath score.
traits at mating 2 were low for the male hormone traits, while
Further information is available from Paul Williams at TBTS
semen quality traits in both Brahmans and Tropical Composites
in Rockhampton on (07) 4927 6066 or email@example.com. 9
Increasing Pedigree Accuracy with DNA Parent Verification
ccurately recording pedigree information is one of the most fundamental jobs of a beef seedstock producer. Amongst other things, accurate pedigree information is fundamental for the maintenance of an accurate herd book by registered breed societies, it plays a crucial role in enabling the calculation of Estimated Breeding Values (EBVs) from genetic evaluation programs such as BREEDPLAN, and allows seedstock producers to meet their duty of care to provide the most accurate information as possible on their sale animals (e.g. bulls, semen or embryos).
Artificial breeding technologies can add another source of error. If the backup bull is put in soon after the AI program, there will not be a clear break in calving between the AI calves and calves sired by the backup bull.
Four calves were incorrectly assigned to the back up bull whereas they were actually sired by the AI sire.
Human error occurred during the data entry for another three calves.
Two calves born on the same day had clearly swapped mothers at birth.
Limousin Progeny Test Program was following best practice guidelines, it is probably indicative of the lower level of pedigree errors occurring across the registered cattle industry and highlights the benefit of DNA parentage verification.
just how accurate is the pedigree information in the average seedstock herd? Many situations can compromise the accuracy of pedigree information, including: In a naturally joined single sire joining mob there is always a possibility of another bull (known or unknown) mixing with the mob at some stage.
The wrong straw of semen was used or the sire recorded incorrectly for three calves during the AI program.
In total, 12 of the 227 calves (5.3%) were given incorrect sires when the pedigree information was collected. Considering the
Even with a concerted effort to record accurate pedigrees,
How does DNA Parentage Verification Work? There are currently two types of DNA tests for parentage verification available in Australia; microsatellite testing, which has been used for a number of years and is still a highly accurate test, and Single Nucleotide Polymorphism (SNP) testing, a new
multiple sire joining programs, individual sire identification is impossible without the assistance of sire verification through DNA testing.
â€œMothering upâ€? cows and calves may be compromised by mismothering, particularly in first calf heifers.
error when recording the mating details either from natural or artificial breeding programs.
DNA parentage verification offers seedstock herds with a tool for accurately determining animal parentage and reducing pedigree errors that may otherwise occur.
DNA Parentage Verification in Practice An interesting case study into how easily errors can occur in pedigree recording, even in a herd following best practice guidelines, was demonstrated in the Beef Information Nucleus Progeny Test Program conducted by the Australian Limousin Breeders Society. To ensure accuracy of sire information, the sires for all calves from the first joining in 2011 were checked by DNA profiling and verification. The parentage verification highlighted a number of pedigree recording errors including:
DNA testing for parent verification excludes potential parents based their DNA profile. In this simple representation based on microsatellite testing, Sire 2 is excluded as the calf â€™s parent while sire 1 qualifies as the parent.
technology which has more recently become available as an option for parentage verification. In general, parentage verification is based upon the detection of genetically inherited markers present in a calf â€™s DNA. Calves receive one chromosome from each of their parents, and so genetic markers are passed down from parent to offspring. Both microsatellite and SNP parentage verification are based on exclusion, proving that the animal is not the offspring of a sire or dam rather than proving it is. For example if a marker is present in a calf but not in the nominated parents, then the calf is excluded as an offspring of that mating. As a result no test is 100% accurate at positively identifying an animalâ€™s parentage. However 99.9% of incorrect matings will be detected by DNA parentage analysis.
Collecting a DNA Sample for DNA parent verification, pull 20-30 thick hairs from the brush of the animalâ€™s tail including the hair roots.
Unfortunately, microsatellite profiles cannot be imputed or converted to a SNP profile equivalent (or vice versa), therefore animals that require parent verification via DNA, need to have
A microsatellite marker is a repeat of a particular base pair sequence over and over, for example CACACACA, with current tests utilising a panel of multiple microsatellites. For example, the current microsatellite test offered by the Animal Genetics Lab (AGL) at the University of Queensland generally utilises a microsatellite marker panel of up to 21 markers, including the 12 internationally standardised markers recommended by the International Society for Animal Genetics (ISAG). A further 11 markers are available where necessary to resolve difficult parentage cases (maximum of 32 markers.). Microsatellite DNA markers have been used for nearly twenty years and remain an accurate method of parentage verification. Parentage verification tests using microsatellites are currently available in Australia through two laboratories being the AGL at the University of Queensland and Zoetis Genetics.
the same DNA test as their parent(s). For example if the calf has a SNP profile, the sire also needs a SNP profile. If the sire only has a microsatellite profile, it needs to be re-genotyped to have a SNP profile available. Hence transitioning to SNP parentage verification can come at an additional cost to the seedstock breeder and as a result some Breed Societies have chosen to continue using microsatellite markers in the short term.
Breed Society Regulations In addition to the benefit of using DNA parentage verification to improve pedigree accuracy, most breed societies have registration requirements and regulations around DNA profiling and parent verification. These will include minimum DNA parentage verification requirements and which type of profile they accept (e.g. microsatellite or SNP) both now and in the future. It will also include the process to follow to submit the sample (e.g. facilitated by the breed society or direct to the laboratory). If you are not aware of the regulations for your breed, you are encouraged to contact your breed society directly for this information.
SNP Markers Single Nucleotide Polymorphisms (SNPs) are markers which identify a difference in a single nucleotide base pair. As an example, the SNP parentage verification test offered by the AGL uses a panel of ~150 SNPs, including the 100 internationally standardised ISAG SNPs. Many breed societies have or have indicated that they will be transitioning from the use of microsatellite markers to SNP markers for parentage verification in the future. The major benefit of SNP based parentage verification over microsatellites is that it is more compatible with use of DNA technology for other purposes. For example, if breeders choose to genotype their animals with a larger SNP panel for utilisation in future genetic evaluation for their breed (e.g. GeneSeek Genomic Profiler panel available through UQ AGL, including 20,000 SNP markers), the 150 SNP profile for parentage would automatically be collected, removing the need for duplicate DNA tests to be conducted.
How to Get your Cattle Tested The genotyping laboratories offering this service in Australia (e.g. Zoetis Genetics and AGL) generally use tail hair samples (hair roots attached) as a source of DNA, however they can use other samples such as blood, semen or tissue if required. Most breed societies have regulations for DNA profiling which may include the preferred use of one or both of these laboratories. They will also have a process in place for collection and submission of the DNA sample for profiling and parent Continued on pg 12 11
Continued from pg 11 - Increasing Pedigree Accuracy with DNA Parent Verification
verification. This may include supplying the DNA sample collection kits and facilitating the submission of the kits to the laboratory. Or the breed society may prefer that you work with your preferred laboratory directly.
4. Mail the forms plus the DNA sample to your breed society or the genotyping laboratory. This depends on your breed society’s arrangement with the genotyping laboratory 5. The results to be returned by email or mail. The results may also be supplied direct to you breed society. The turnaround time will depend on the laboratory and level of activity at the time of submission. As a general guide, turnaround time is 4 to 6 weeks.
General Guidelines for submitting DNA for parentage verification: 1. Contact your Breed Society or the DNA lab for a DNA sample collection kit
2. Pull 20-30 thick hairs from the brush of the animal’s tail including the hair roots.
UQ AGL - “DNA Parentage Testing - Fact Sheet”. Link - http://www. uq.edu.au/vetschool/content/animal-genetics-laboratory/dnaparentage-testing.pdf
3. Complete the required submissions forms
Docility EBVs Now Available for Hereford and Simmental Animals
erefords Australia and the Australian Simmental Breeders Association recently became the latest breeds to publish EBVs for temperament with the release of Trial Docility EBVs for Hereford and Simmental animals in February and March 2014 respectively. Trial Docility EBVs are now calculated as part of the routine monthly TransTasman Hereford and Simmental BREEDPLAN analysis for animals that have either been scored for docility, or have progeny scored for docility, and are being made available in a similar fashion to other EBVs. Trial Docility EBVs can be viewed in BREEDPLAN herd reports, on the Hereford and Simmental online animal search facility (i.e. Internet Solutions) or through herd recording programs (e.g. HerdMaster) by importing the latest GROUPEBV file.
Recording Docility Scores for BREEDPLAN
REEDPLAN now produces Docility EBVs for animals within the Angus, Hereford, Limousin and Simmental breeds, based on the collection of docility scores. Seedstock producers within these breeds who place importance on improved temperament within their breeding objective should consequently consider the submission of docility score information to BREEDPLAN.
Table 1- Docility Scoring Codes and Descriptions Description
Mild disposition, gentle and easily handled, stands and moves slowly during handling, undisturbed, settled, somewhat dull, does not pull on headgate when in crush, exits crush calmly.
2 Restless Quiet but slightly restless, may be stubborn during handling, may try to back out of crush, pulls back on headgate, some flicking of tail, exits crush promptly.
Docility scores, being the subjective assessment of animals’ temperament, can be recorded on animals when the animals are between 60 and 400 days of age. Animals are usually scored at weaning or shortly afterwards, which in practise is often coordinated with the collection of 200 day weight information. The advantage of scoring at weaning is that all calves will
3 Nervous Manageable but nervous and impatient, a moderate amount of struggling, movement and tail flicking, repeated pushing and pulling on headgate, exits crush briskly.
have had minimal handling and so will express variation in temperament, while variation between animals in handling prior to scoring will also be minimised. Either a yard test can be used where calves are individually put into a small square yard and the handler attempts to hold the animal in one corner for about 30 seconds, or a crush test where calves are put up a race and held in a crush or weigh scales for about 30 seconds but not head bailed. When using the crush or yard test, the behaviour of animals is observed and animals scored on a 1-5 scale, with 1 being ‘docile’ and 5 being ‘aggressive’. A detailed description of the different scores is included in Table 1.
Jumpy and out of control, quivers and struggles violently, may bellow and froth at mouth, continuous tail flicking, defecates and urinates during handling, frantically runs fenceline and may jump when penned individually, exhibits long flight distance and exits crush wildly.
May be similar to score 4 but with added aggressive behaviour, fearful, extreme agitation, continuous movement which may include jumping and bellowing while in crush, exits crush frantically and may exhibit attack behaviour when handled alone.
can accept half scores if animals exhibit behaviour which is intermediate to the above scores.
should be assigned a different “temperament management group” if they have had a different level of handling prior to scoring.
When docility score information is being collected, it is important to consider: n
There needs to be some variation in the scores for them to be useful. That is, scoring all animals in a group with a docility score of  will not identify any genetic differences in docility.
The method of scoring used (ie. crush or yard) should be specified when submitting the docility scores to BREEDPLAN.
When recording docility scores, it is important that both a consistent scoring method is used and the same person scores all animals that are being assessed in the herd on that particular day.
Docility scores should be submitted directly to the BREEDPLAN office at ABRI, with updated Docility EBVs becoming available at each routine monthly GROUP BREEDPLAN analysis. While Docility EBVs are currently only published for Angus, Hereford, Limousin and Simmental animals, several other breeds have also indicated a desire to publish Docility EBVs once sufficient docility score information has been collected. Seedstock producers from other breeds are consequently encouraged to consider the collection of docility score information.
Comprehensive docility score information has now been collected on Limousin animals 13
Enhancements Made to Hereford GROUP BREEDPLAN
number of significant enhancements were applied to the BREEDPLAN software that is used to calculate EBVs for Hereford animals within the February 2013 TransTasman Hereford GROUP BREEDPLAN analysis. These enhancements have resulted in the calculation of improved BREEDPLAN EBVs for Hereford animals and are part of the normal evolution of the BREEDPLAN software. The enhancements include:
Upgrade to BREEDPLAN Version 6.2 This latest version of BREEDPLAN software has several enhancements over the software previously used within the TransTasman Hereford BREEDPLAN analysis including a revised method for calculating accuracy values for Days to Calving EBVs, a revised method for handling different groups of “base” animals, and the ability to “blend” genomic prediction information (ie. DNA information) into the analysis when genomic predictions relevant to Australian and New Zealand Hereford animals become available.
Introduction of a Trial Docility EBV Following the collection of docility scores on over 7,000 Hereford animals, a “trial” Docility EBV has been published for animals within the TransTasman BREEDPLAN evaluation. Further information is included on page 12.
by producers conducting straight bred Hereford programs and targeting high quality, highly marbled markets)
Revised Selection Indexes The parameters used to calculate the Supermarket, Grass Fed Steer, Grain Fed Steer and EU selection indexes for Australian Hereford animals has been updated following a review of the previous indexes by members of the Herefords Australia Technical Committee. The most notable changes include: n the
economic and production parameters within all selection indexes have been updated
modification has been made to the Grass Fed Steer index to make it suitable for use by producers using Hereford bulls over a Bos indicus based cow herd (in addition to use by producers conducting straight bred Hereford programs and targeting the production of heavy steers off grass)
modification has been made to the EU index to reflect both grass and grain fed finishing production systems
increased emphasis has been placed on improved eating quality and tenderness in all selection indexes to favour animals that are suited to producing progeny that meet MSA requirements
Further information regarding the Supermarket, Grass Fed Steer, Grain Fed Steer and EU selection indexes that are now calculated for Australian Hereford animals is available from the BREEDPLAN website.
modification has been made to the Grain Fed Steer index to make it suitable for use by producers conducting black baldy crossbreeding programs where Hereford bulls are being used over an Angus based cow herd (in addition to use
If you have any questions regarding the enhancements to Hereford BREEDPLAN, please contact staff at Southern Beef Technology Services on (02) 6773 3555 or via email office@ sbts.une.edu.au.
Follow SBTS & TBTS on Social Media
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. Information is routinely posted on Twitter and Facebook such as articles, webinars and event details, while the YouTube channel contains video presentations such as webinars from past webinar series and short “Understanding BREEDPLAN EBVs” video clips.
SBTS & TBTS
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relevant icon, or go directly to the SBTS & TBTS Facebook account at http://facebook.com/SBTSTBTS, Twitter account at http://twitter.com/SBTSTBTS or YouTube Channel at
simply go to the SBTS or TBTS website and click on the
Staff Departures - Christian Duff and Andrew Byrne
he SBTS & TBTS teams bidded farewell to Christian Duff and Andrew Byrne during June 2014 with both resigning from their current positions to pursue other career opportunities within the beef seedstock industry. Christian and Andrew will be replaced by Alex McDonald as the Technical Officer allocated to provide technical support services to Charolais, Hereford, Red Angus, Shorthorn, Simmental and Wagyu seedstock producers regarding the application of genetic technologies.
employed as the General Manager of the Australian Limousin Breeders Society since 1992 but stepped down from this position on 30 June.
Alex has been closely associated with the SBTS team since the inception of the SBTS project in 2005 during which time he has performed an important role as a senior consultant. Alex has had a long career within the beef industry having been
The SBTS & TBTS teams would like to thank both Christian and Andrew for their contribution over the past 12 and 9 years respectively and wish them both the very best with their future endeavours.
Staff Movements - Gemma Wilkinson Now Based in Southern NSW
echnical officer within the SBTS project, Gemma Wilkinson, has recently relocated from the ABRI office in Armidale and is now based in Young, NSW.
Gemma has retained all her existing responsibilities within the SBTS & TBTS projects, including the provision of technical support to members of the Murray Grey, South Devon, Gelbvieh, Devon, Red Poll, Blonde d’ Aquitaine and Salers breeds. Gemma can be contacted by phone on 0459 823 067 or email firstname.lastname@example.org.
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:
Charolais Red Angus Shorthorn Simmental Wagyu
email@example.com (02) 6773 2472
firstname.lastname@example.org (02) 6773 2472
Belmont Red Brahman Brangus Charbray
Droughtmaster Santa Gertrudis Senepol Simbrah
Blonde dâ€™Aquitaine Red Poll Devon Salers Gelbvieh South Devon Murray Grey
Alex Limousin McDonald
email@example.com (07) 4927 6066
firstname.lastname@example.org (02) 6773 3265
email@example.com (02) 6773 2472
Peter firstname.lastname@example.org Angus Parnell (02) 6772 3011
If you would like any further information on SBTS and TBTS please contact:
Southern Beef Technology Services Telephone: (02) 6773 3555 Email: email@example.com Web: http://sbts.une.edu.au
Tropical Beef Technology Services Telephone: (07) 4927 6066 Email: firstname.lastname@example.org Web: http://tbts.une.edu.au
The Winter 2014 edition of the SBTS & TBTS Update publication