PFT
is the selection index of the Italian Holstein breed; it combines milk
quality and functionality. The official ranking is based on PFT and
ranges from 0 to 99 dividing the population in percentiles. The ranking
is calculated separately for bulls and cows. The 99 Rank identifies the
best 1% of bulls and cows with calculated breeding values. Since 1998,
Rank 95 (best 5% of the population) is the official limit for a bull to
be used in A.I.. The table below shows the relative weight of each trait
included in PFT.
The formula for PFT is as follows:
PFT
=
12.50 x (0.32
x fat kg + 1.79 x protein kg + 0.087 x fat% x 100 +
+0.28 x protein% x 100+ 4.04 x type + 13.93 x ICM +
6.07 x IAP +
+9.21 x ((longevity-100)/5) + 11.51 x ((somatic cell
score-100)/5,70)) +
+10.59 x ((fertility-100)/5))
which
determines a ratio 49:51
between production and type.
PRODUCTION
WEIGHTS
FUNCTIONALITY
WEIGHTS
Milk
0
TYPE
4
Fat
8
ICM
13
Protein
36
Feet&Legs
(IAP)
6
Fat %
2
Somatic
cells
10
Protein %
3
Functional
longevity
8
Fertility
10
1.2.
ICM (Udder Composite Index)
The
goal of this index is to breed for a functional udder. Its formula is
based on percentages of weights relative to the linear scores of the
udder, defined according to their relation to the functional longevity
of the animals and is as follows:
ICM =
0.19 X fore
attachment
strength +
0.17 X rear
attachment
height +
0.21 X
ligament +
0.26 X udder
floor +
0.17 X teats
placement
1.3.
IAP (Feet & Legs Composite Index)
Used for the first time in May 2000,
this index combines three linear traits relative to feet and legs and to
their functionality (expressed by the subjective evaluation of the
classifier). The relating weights express (as a percentage) the relative
importance of each trait compared to the functionality of the breed, and
are the following:
IAP =
0.50 X feet & legs functionality +
0.50 X (0.48 X hoof depth +
0.37 X rear leg rear view +
-0.15 X rear leg set)
1.4.
TYPE
From
August 2009 index for TYPE is derived from 15 linear traits to ensure
the same definition across all bulls Italian and foreign and young and
older. The formula has been derived from genetic correlation among the
different traits and the genetic correlations with the actual definition
of Final Score officially used
by classifiers. The relative weight of each trait is as follows:
TYPE =
0.059 x stature + 0.066 x strength + 0.071 x body depth +
0.094 x angularity + 0.022 x rump angle +
0.035 x rump width – 0.006 x rear legs side view +
0.017 x rear legs rear view + 0.027 x foot angle +
0.136 x feet & legs functionality + 0.099 x front udder +
0.054 x rear udder height + 0.064 x udder support +
The Italian Breeders Association (AIA)
receives every month all the milk records collected by the personnel of
the Provincial Associations (APAs). Alternate recording data (AT) are
projected to 24 hours records complying ICAR standards. All available
records are used. Every lactation has a weighting factor expressing its
accuracy:
• AT records are worth 98% of monthly complete records (A records).
All the records collected between day 5 and day 305 of lactation are
used, up to third lactation. Besides ordinary data editing, records
abnormally deviating from each cow’s estimated lactation curve are
discarded.
2.2.
Environmental effects
A random regression test day model is adopted,
estimating every effect using a function that explains their variability
from day 5 to day 305 of lactation. Breeding values for milk, fat,
protein and somatic cells are estimated simultaneously, thus making use
of genetic correlations among traits that improve total accuracy of
estimates. Estimated fixed effects are age at calving, calving
season (spring or autumn), area of production (Northern,
Central or Southern Italy and “Parmesan cheese area”) and the
five-years period (“quinquennium”) in which production occurred
(from 1990).
Average variabilities of milk, fat and protein within herds are
calculated every year, using all available test-day records; this
parameter measures variability of herd productions around total average
and helps in identifying higher and lower than average variability herds
before adjusting them to match the “correct” scale. The “correct” scale
is within-herd variability of primiparous cows born between 1999 and
2001 (the genetic base cows). This correction for heterogeneity of
variance allows differences among animals to be measured in a unique
scale for every herd. Animals are compared according to
herd-year-test day and parity. Cows are divided into first-
and multiple parity class; this last effect allows to account for every
management effect within herd and time.
2.3.
Random effects
The
animal effect, after which the Animal Model statistical method is
named, allows for the estimation of breeding values of all animals
within the population. In the random regression test day model the
hypothesis is that animals express a different genetic value each day of
lactation in response to environmental stimulation. Besides, all animals
with (cows) or without (bulls) production records are considered
simultaneously, together with all their relationships, allowing for the
deviation from contemporaries to be resolved into its dam and sire
components and taking into account, for instance, the fact that on the
best cows usually the best available bulls are used. A second random
effect is the permanent environmental effect: each cow can have
more than one lactation. Therefore it is necessary to estimate
occasional management effects that may have a negative (a mastitis which
severely damages one of the quarters), or a positive (a very positive
interaction with an healthy environment) influence on her lifetime
production. Also in this case, a 5 parameters function is estimated.
2.4.
How the breeding value is expressed
The
traits for which breeding values are calculated are milk, fat and
protein yields and somatic cell score (SCS).
2.4.1.
Production traits
Heritability varies according to
parity and day of lactation and usually is around 0.30, thus
establishing a 30:70 ratio between genetic and environmental
variability.
The three resulting breeding values, for first, second and third
lactation, are then combined in an index of total three-lactation
production:
EBV305tot=
0,333 x EBV3051 + 0,333 x EBV3052 + 0,333 x EBV3053
This index is expressed in kilograms as deviation from a
reference base, the genetic base, that sets the zero of breeding values.
The genetic base is a rolling base and it is updated in August every
year; its purpose is to express the breeding values relative to the
value of the cows in the herds at the present time. Current genetic base
reflects genetic value of the cows born between 1999 and 2001 and has
been updated in May 2007. Every year the triennium will be moved forward
one year (April 2008 it will be 2000-2002).
Percentages are computed with reference to the 305 days phenotypic
productions of cows of the genetic base. The base values are then used
in the following formula to calculate the breeding values for
percentages:
fat%
= 100 x (fat
base
+ fat) /
( milk
base
+ milk) – fat%
base
protein% = 100 x (protein
base +
protein) / (milk +
base)
– protein%
base
The
base values are published on the web page in the section related to
genetic proofs.
A bull is officially proven when he reaches a minimum reliability of 70%
and has at least 30 daughters with 120 DIM. The official breeding values
of foreign bulls are the Italian ones if reliability is at least 75% and
they have 30 daughters with 120 DIM; international results provided by
Interbull are used otherwise.
2.4.2. Somatic cell score
Heritability varies according to parity and day of lactation and usually
ranges from 0.17 in first lactation to 0.25 in third lactation. The
resulting three breeding values for first, second and third lactation
are combined in a total index for SCS, that express the mean somatic
cell score in the three lactations, using the following formula:
EBVtot=
0,333 x EBV1 + 0,333 x EBV2 + 0,333 x EBV3
This index is expressed on a scale with mean equal to 100 and standard
deviation equal to 5. Current genetic base represents the genetic value
of cows born between 1999 and 2001 as for the production traits. Also
for SCS indices, the Italian proof is the official one if reliability is
at least 75% with daughters in 20 or more herds; Interbull proofs are
used otherwise.
2.4.3. Persistency index and maturity rate
The
individual lactation curves that the random regression test-day model
provide for each cow, allow us to quantify the genetic component for
persistency of production; to express it with an indicator, we calculate
the percent ratio between 280 days and 60 days productions. The index is
on a scale with mean 100 and SD equal to 5. There are three indexes for
persistency, one for each lactation, and a combined indicator computed
using the following formula:
PERStot
= 0,50 x PERS1 + 0,25 x PERS2 + 0,25 x
PERS3
Maturity rate measures, on the other hand, the difference between the
sum of fat and protein kilograms in third and first lactation. The
results is then espressed on a scale with mean 100 and SD equal to 5. It
tells us which are the bulls whose daughters improve performances
through lactations (values above 100), compared to those whose daughters
perform the best in first lactation (values below 100).
Information of type evaluations carried out on all first-calf heifers
classified two or four times a year by the breed inspectors (over the
last ten years) is used for the calculation of the breeding values.
Unlike to what happens with the production proofs, in this case age
variation is not so strong and there is no repeated data. For each cow
only one evaluation is used.
3.2.
Environmental effects
Among the animals classified in a herd there are differences by age and
stages of lactation which undoubtedly influence their body condition and
appearance. The inspector measures what he/she sees, therefore the
statistical model must take into consideration this different condition
by using an interaction effect between age and stage of
lactation.
Cows are compared among them on an equal herd-year-
round of classification: this allows to simultaneously take into
account all managerial effects of each single herd and also the year and
the classifier who evaluated the animal.
3.3. Random
effects
Theonly
random effect taken into consideration is that of the animal. All
parental relationships existing among the population are taken into
consideration, and this allows to estimate the genetic value of all
animals, taking into account possible preferential or corrective mating.
3.4.
How the breeding value is expressed
The
breeding values of all linear type traits evaluated since 1984 and final
score are calculated. Table 1 illustrates the heritability data
utilized for the calculation. The breeding value for teat size has been
introduced in 1994 and in May 2000 a composite breeding value for rear
legs (rear view) and feet and legs functionality have been added.
A zero breeding value refers to the genetic level of animals born
between 2001 and 2003, i.e. the genetic base, for which the same rules
of the production traits apply.
All breeding values are standardized for the variability of the cows in
the genetic base. In this way, all traits can be measured on a same
scale (see figure), which goes from – 3 to + 3 both for cows and bulls.
In reality, bulls and cows do not vary in the same way, and therefore
bulls that have high breeding values, especially for production traits,
being all highly selected and well above the cows average, tend to vary
towards extremes which are higher than 3. On the Table you can see the
heritability values of all traits, the phenotypic average of the animals
in the genetic base, and the equivalent in points (linear scale) of one
standard deviation of that breeding value. The table values will vary
at every change of the base and will be updated on the web page were
genetic proofs are.
The breeding value is published when a bull has at least 10 daughters in
5 herds, in case of bulls with daughters in Italy. Conversion formulae
of breeding values to the Italian scale are used for bulls imported from
abroad with daughters still not classified.
For foreign bulls the official proof is the Italian one when reliability
is 75% and daughters are present in at least 20 herds; otherwise the
Interbull proof is used.
During milk testing, the technicians of the Provincial Association also
gather all available information on as many events as possible: births,
deaths, sales, breedings, calvings, etc. Data on calving include the
dairy farmer evaluation of the degree of difficulty, on a five
categories scale:
A =
easy calving
B =
help needed from one person only
C =
cesarean
D =
difficult calving
E =
embryotomy
Each category is evaluated on a
difficulty scale going from 0 to 100, where easy calving is 0 and
embryiotomy is 100. The sex of the new born calf is also used to further
differentiate the various degrees of difficulty. Data used for present
evaluation were collected starting from 1987. From August 2003 we
discard herd-year classes that:
had more than 92% records coded as A;
had more than 92% records coded as B;
had more than 50% records coded as C and over.
4.2.
Environmental effects
In the
model the interaction between year and month of calving, the
interaction between province and year and the interaction among
the age of the dam, the sex of the new born and the parity of
the cow are taken into account.
4.3.
Random effects
The
effects of herd-year, the sire and the maternal
grandsire are considered as random.
4.4.
How the breeding value is expressed
There are two resulting breeding values: one is the direct effect of the
bull (sire of the calf) and the second one is the maternal effect or the
calving ease of the daughters. Both are on a scale with mean 100 and SD
of 5 units. Bulls with values above 100 have an higher percentage of
easy calvings. Heritability is near 10%, which shows that for this trait
there is a strong predominance of the environmental effects in
determining what is really going to happen at calving. There is no
genetic base to refer to since there is no selection for this trait.
Twice a year, the persons in charge of the milk recording collect also
information on the milking speed of the cows. More specifically, they
ask the milkers to point out the cows which are below average for
milking speed. Repeated reports about the same cow will determine her
degree of slowness: the cow that is always identified as below average
in milking speed at each survey, will have a score of 1; the cow
surveyed three times and identified as “slow” one time only, will have a
score of 0.33, and so on. Her contemporaries are her herdmates of the
first survey or of the time when she was first identified as “slow”, if
there have been variations in time.
5.2.
Environmental effects
The
different lactation number of the surveyed cows is taken into
account; an adjustment is made also for the amount of milk
produced on the test day and for the herd-year-test day. By doing so it
is possible: a) to avoid mistaking high yields with slow milking; b) to
account for different management practices, in particular for the
management of the milking parlor and of the personnel in charge.
5.3.
Random effects
Another
relevant factor is the effect of the animal, therefore in the
evaluation of the genetic value of the bulls it is taken into account
the possible slowness of the dam of the surveyed cow.
5.4.
How the breeding value is expressed
Only
the sires breeding values are published and the heritability of the
trait is 6%, due to the limited accuracy of the data collected. The
value is expressed as a genetic value (IGT) on a scale with mean 100 and
SD of 5. The value 100 corresponds to the value average breeding value
of the genetic base (cows born between 1999 and 2001). The average
phenotypic value of cows in the base are published on the web site. The
phenotypic average is generally around 4%.
The general lactations record gives a
precious information: the productive career of all the Holsteins under
milk recording. It’s known for how many lactations an animal has
produced before disappearing from the farm, at what productive levels
his productions were located compared to the farm average, how often she
due etc.
It’s possible to notice, over time, the trend of the farms: some of them
are stable, some are at their closing point and other are enlarging
themselves. All these data, if properly analysed, tell us the dynamic of
the animals elimination from the farm. Next to those animals which have
already closed their career, there are those who have just started it.
6.2. Environmental
effects
The
production changes over time and so does the animal situation in the
farm. There are some stable factors which do not change such as the
first calving age of an animal, that, by the way, determines his
survival capacity over time. There are time dependent factors such as
the age effects on the lactations stage, the milk kg.
productive level within the year, divided into nine classes (four
under the average, average, four above the average), the fat
percentage productive level within the year (5 classes), the
protein percentage productive level within the year (5 classes), the
yearly changes in the herd size, and at the end the year-season
effect on which external factors have an influence, among those the
recoveries , the market dynamics (quota) or the pathologies that bring
to extraordinary elimination patterns of the animals.
6.3.
Random effects
The
bull, maternal grandsire and year-season effects are
considered. The applied model, based on the survival functions, derives
from medical studies and is called survival analysis; it is a
sire-maternal grandsire model.
6.4.
The combined index
The
accuracy of the survival index of the bulls, in particular for the young
animals, those who have all the daughters still in production, is
definitely low, a little bit higher than a pedigree index. Such an index
doesn’t tell us much on the real survival of his daughters. But we know
that from the type evaluation of the daughters is possible to get a
partial information on their longevity. From this originates the
composed index for the longevity : survival index, feet & legs and udder
index are combined together taking into consideration the genetic
correlation between the several characters in order to compute the final
combined longevity index. In particular the correlation between udder
and functional longevity is 0.48 and the one between legs functionality
and longevity is 0.14.
6.5.
How the breeding value is expressed
Just the index of those bulls which have at least a reliability of 50%
or higher is published. The heritability of this trait is around 10%.
The longevity index is expressed like a genetic value (IGT) on a scale
with mean 100 and SD of 5 just like for the other functional traits,
minimum and maximum value are between 80 and approximately 120.
6.6.What does it really mean
The functional longevity concept is
not easy to explain: is not the rough longevity the one which is
possible to observe in the farm, because this one is correlated to the
productive level of the animals. The concept itself of longevity is
related to fertility, to health of the animal, etc…
Besides this, between functional longevity and real longevity, and by
this we mean the number of lactations that the animal is able to carry
on during his career, there is a precise relation.
In order to try to quantify the real difference between animals, carrier
of very positive longevity genes, and those carrier of genes with very
negative effects on the longevity of their daughters, we computed a
simple statistic of the data for the bulls having more than 200
daughters and born between 1980 and 1988.
The
differences we found are listed in the below table:
Genetic level
Average number of
daughters’ lactation
Average number of eliminated
daughters’ lactation
Lower than 90
2.30
2.10
Around 100
2.58
2.30
Higher than 110
3.20
2.90
The
expected difference is of one lactation. Another very similar result,
has been calculated in Canada, where the genetic standard deviation is
approximately 1/4 of lactation and therefore the difference between the
best and the worst bulls is around one lactation.
The data base for inseminations and
calving are the information used for genetic evaluation for fertility.
On this data base several checks guarantee that only good quality
records will be used for genetic evaluation (about 20% of the total
records are discarded). The majority of records discarded are
questionable first insemination data. Together with this data bases also
linear trait and lactation data base are used.
For a complex trait as fertility in fact, direct and indirect traits are
used all together. The direct traits considered are: days to first
insemination. Non return rate at 56 days and calving interval. Indirect
traits are: angularity and ME 305 first parity lactation. All the traits
are measured on first parity cows in order to evaluate daughter
fertility of all bulls.
The five traits are considered simultaneously in order to exploit at
best the genetic correlation that do exist across these traits and
maximize the estimation precision.
7.2. Environmental
effects
Every trait is affected
by different and specific environmental factors. Thus every traits has
its own statistical model. Factor accounted for for days to first
inseminations and calving interval are:
a) herd-year-season
of calving,
b) calving month,
c) age at calving
by year of calving;
for non return rate
at 56 days factors are:
a) herd-year-season
of insemination,
b) month of
insemination,
c) age at calving
within year of calving by year of insemination;
environmental
factors considered for angularity are the same used for genetic
evaluation for type traits:
a) age at calving
by stage of lactation,
b) herd-year-round
of classification.
Last
but not least environmental factor considered for 305ME milk is
simply the herd-year-season of calving effect.
7.3.
Random effects
The
animal effect is evaluated thus considering bull and cows at the
same time, accounting for genetic level of mating and using all
available pedigree information. It is a multiple trait animal model.
7.4.
The
combined index
At
the end of the computation step five genetic proofs are available. The
objective of selection is to improve fertility in general terms. In
order to achieve this in an easy to understand and simple way the chosen
objective traits is conception rate at first service. This trait is
genetically correlated to each of the five evaluated traits and the
final proofs combines all of them to maximize the improvement on
conception rate giving to each of the relative importance shown in the
Table below.
Trait
Genetic correlation
with conception rate
Relative importance in
the combined proof
Days to first insemination
-0.18
16
NRR56
+0.42
17
Calving Interval
-0.62
51
Angularity
-0.15
7
305ME milk
-0.17
9
7.5.
How the breeding value is expressed
Just the index of those bulls which have at least a reliability of 50%
or higher is published. The heritability of the traits varies from 2 to
26%. The fertility index is expressed like a genetic value (IGT) on a
scale with mean 100 and SD of 5 just like for the other functional
traits, minimum and maximum value are between 80 and approximately 120.
Bulls with higher fertility have values greater than 100.
7.6.
What does it really mean?
In
spite of the low heritability value, especially for direct traits, the
genetic variability among animals is very high. In the top %5 bull
population group for PFT there are individuals that have an 85 proof and
other that do reach 110. Every standard deviation (that correspond to a
value of 5 on the proof scale) above 100 correspond to: +2.67%
conception rate, -8 days calving interval, -2 days to first insemination
and +0.68% on NRR56.
The
differences we found among bulls in the population are listed in the
table below:
Input data for International genetic evaluation are the Official
Breeding Values computed in each Country participating to the service.
The service of international evaluation is run by International Bull
Evaluation Service (INTERBULL) in Sweden. All Countries, including
Italy, are sending their official proofs to this centre at a given date
determined by a calendar of pubblication approved each year. All
breeding values for bulls with at least 10 daughters in 10 herds are
sent to INTERBULL. For test day model data the proof sent to Interbull
is the proofs for first, second and third lactation weighted according
to number of test days. In August 2007 the traits for which an
international evaluation was provided were: milk, fat, protein, standard
conformation traits, calving ease direct and maternal, somatic cells and
fertility.
8.2. MACE MODEL
Each trait is evaluated by Interbull with
a Multiple Across Country Evaluation (MACE in brief): in practice the
protein proof in each Country contributing to the evaluation is
considered as a separate trait. In this way is possible to compare bull
rankings across countries. The difference across countries is measured
through genetic correlation among the various Countries. The factors
accounted for in the model are the Country average and the
genetic groups for the maternal grand dam and for the material grand
sire in case they are born before 1986. Table 1 shows the genetic
correlations between Italy and some of the participating Countries for
all the traits for which the international evaluation is provided.
Country
Type traits
Protein
Type
Somatic cells
Longevity
Fertility
Calving ease
USA
0.92
0.90
0.91
0.75
0.58
0.68
CAN
0.90
0.88
0.90
0.81
-
0.63
FRA
0.88
0.86
0.92
0.64
0.55
0.78
DFS1
0.87
0.73
0.91
0.55
0.84
0.65
NLD
0.86
0.84
0.89
0.73
0.82
0.59
DEU
0.85
0.89
0.93
0.74
-
-
AUS/NZL
0.75
0.66
0.78
0.35
0.60
0.52
8.3. How it works: an example
When a bull has a proof only in one Country the model
transfers, using the available information about genetic correlation and
difference in scale in another Country, the daughter deviation i.e. the
bull proof once we subtract from it the parent average. The final proof
of the bull in the other Country is then computed adding to the rescaled
deviation the parent average in the new Country. When a bull has
daughters in more than one country the deviations are weighted by the
number of daughters and then summed together before re-adding the
pedigree in the Country of interest. As an example the figure illustrate
the case of a bull having an official proofs in only one Country. In you
are interested in knowing more the link international proofs, in the
section genetic evaluation of ANAFI web site, will bring you to an excel
file where you can test how a bull proofs changes when some of the
parameters in the system do vary.
8.4. What is
published
INTERBULL computations give back to each Country the
breeding value of all the bulls evaluated in the World (around 70000) on
the Country scale. Each Country has approved rules of publications of
those proofs. These rules are subject to changes and the rules up to
date are always published on the WEB site in the area related to
breeding values. In August 2007 in Italy rules of pubblications were as
follows:
PRODUCTION – INTERBULL proof is official
only for foreign bulls if their Italian proof does not have a least 30
daughters with 120 DIM and 75% reliability.
CONFORMATION – INTERBULL proof is official for all the foreign bulls.
LONGEVITY – INTERBULL proof is official only for foreign bulls that do
not have at least 50 % reliability on their Italian proof.
FERTILITY– INTERBULL proof is official only for foreign bulls that do
not have at least 50 % reliability on their Italian proof.
CALVING EASE – INTERBULL proof is official only for foreign bulls that
do not have at least 50 % reliability on their Italian proof.
