Selection for the traits of economic importance

Faisal Ramzan
Compiled notes

Contents

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1 Progeny testing (By Prof. Sajjad Khan) 2
1.1 Step 1 Survey of the area for identification of potential farmers . . . . . . . . . . . 2
1.2 step 2 Training of Al technicians and recorders . . . . . . . . . . . . . . . . . . . . 2
1.3 Step 3 Registration of farmers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.4 Step 4 Identification and registration of cows/buffaloes . . . . . . . . . . . . . . . . 3
1.5 step 5 Milk recording . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.6 step 6 Breeding control of registered cows/buffaloes . . . . . . . . . . . . . . . . . . 3

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1.7 Step 7 Recording for other information . . . . . . . . .
1.8 Step 8 Processing of recorded information . . . . . . .
1.9 Step 9 Identification of elite cows/buffaloes . . . . . .
1.10 step 10 Feedback mechanism to the farmers . . . . . .
1.11 step 11 Selection and raising of bull calves . . . . . . .
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1.12 step 12 Selection of candidate bulls . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.13 Step 13 Semen collection and storage . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.14 Step 14 Artificial breeding In the registered herds . . . . . . . . . . . . . . . . . . . 5
1.15 step 15 Genetic evaluation of bulls . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
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1.16 step 17 Contractual matings of elites with elites . . . . . . . . . . . . . . . . . . . . 6

1.17 Step 18 Continuity of the progeny testing program . . . . . . . . . . . . . . . . . . 6
1.18 step 19 Practicability and authenticity . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.19 step 20 Beyond sustainability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
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1 Progeny testing (By Prof. Sajjad Khan)
Operating procedures for selection of dairy animals on the performance of their progeny (progeny
testing) are affected by many factors. However, there are certain minimums that can be delineated
to achieve adequate genetic gain from such an endeavor. Experience gained with the progeny
testing efforts in this country and elsewhere has helped in preparing such guidelines for initiating
such an effort for any dairy species in Pakistan. Progeny testing is a method of selecting bulls
for traits/qualities of economic importance such as milk production on the basis of lactation milk
yields of their daughters. The main objective of the program is to produce quality bulls and achieve
genetic progress for traits such as milk yield, beauty etc etc. Successes in artificial insemination
and embryo transfer technologies in dairy cattle and buffaloes necessitate that bulls with better
genetic potential may be disseminated widely. The judgment that a bull has better potential for
traits which are not expressed in the males, female relatives are evaluated. When a bull calf is

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born, information on its mother and other ancestors (e.g., grand mother) and even sisters (if they
had performance records) may be utilized for such a judgment. Such a decision making is called
pedigree or family selection. The problem with such a decision is that such an information is very
limited (e.g., few lactations in few herds) and therefore level of surety in declaring a calf good or
bad may not be very high. As such a male can have a very profound influence on the population
level of surety needs to be much higher to use it extensively. Information on the performance of
large number of daughters can help to really estimate whether a bull has good potential for traits

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like milk yield and such a selection is therefore called progeny testing. Nowadays, the availability
of computers have made it possible to utilize all available information on the relatives (pedigree,
progeny and other relatives) of a buil and therefore it is not just the progeny that contributes to
the evaluation of a bull. Still we may call it progeny testing instead of animal model evaluation or
some other kind of evaluation, for simplicity.
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Presumption: Before taking up the progeny testing program, traits of economic importance
for which the effort is to be carried out, need to be made clear i.e. breeding objectives needs to
be defined. For our situation, cattle and buffaloes are being progeny tested for milk yield while
traits like fat yield, type/beauty etc are assumed to be considered in years to come when such
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programs are permanent components of breed development efforts. In other words, focusing on
milk production may be okay in the beginning but other traits may follow. The procedures outlines
are therefore focused on progeny testing for milk production. Following steps will be needed

1.1 Step 1 Survey of the area for identification of potential farmers

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The area in which breed improvement effort is to be carried out through the progeny testing
program needs to be surveyed for the identification of potential farmers to be involved in progeny
testing. Bigger farmers (¿10 breeding females of the breed) that are willing to cooperate, are
intended to be included. Cooperation would mean that breeding of the farm will be controlled by
the project and identification/tagging of animals will be allowed along with performance recording
and sampling of milk for components if needed.
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1.2 step 2 Training of Al technicians and recorders

Milk recorders and artificial insemination technicians recruited for the project need to be trained
if already not trained. Even when trained technicians are available, formats of data recording and
emphasis on actual rather than fictitious recording need to be inculcated in the best possible way
as pedigree and performance recording are the key to the whole exercise. The milk recorder should
be a veterinary assistant so that he may be helpful to the farmer at least on the visit /record day.
As the efficient provision of Al service is expected, mediocre technicians are not needed. Only
those who can reach the calling farmer on the stipulated day and time and can satisfy the farmer
for the level of fertility of his/her herd are needed.

1.3 Step 3 Registration of farmers

The farmers may preferably be registered and a written agreement be signed. PersonaI relations
are always important in such a process. Social technicians make the job easier. Social/poiitical

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circumstances thus will need to be considered. Agreement should delineate the services provided
to the farmer and information to be collected from him. It should for example. specify that he
will not keep any bull and that about half of the females will be inseminated With young bulls
and other half with proven bulls. A thumb rule is that at least 1/3’0 of the cows/buffaloes will be
mated with semen from young bulls.

1.4 Step 4 Identification and registration of cows/buffaloes

Antmais of the specific breed for example Red Sindhi needs to be registered to allocate resources
appropriately and to precisely make breeding and other decisions. Freeze branding if feasible may
be a preferred identification method in adult animais while plastic ear tagging in calves and young
stock. A combination of the two may also be possible with a three digit animal number (as a
brand) and detailed identification number including farm number on the ear tag. Tags should be

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duplicated in both ears and only quality tags be used. Number of cows/buffaloes to be identified
will depend on the number of bulls to be tested. About 200 pregnancies per bull be intended and
assuming a calving interval of 1.5 years it would mean that 300 cows/buffaloes per bull need to
be identified. To test 100 bulls therefore 20000 to 30000 females are needed to be registered. All
the animals of the breed with the registered farmer need to be tagged and recorded. No minimum
milk production level is required. Such minimum levels are needed for identification of elites for
the production of bull calves, discussed later.

1.5 step 5 Milk recording

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Milk recording of all the registered cows/buffaloes is needed periodically. Approximately monthly
interval (for morning and evening) is an acceptable frequency. When cows/buffaloes are milked
in the presence of calf, milk consumed by the calf (e.g, one teat) may be appropriately accounted
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for the recorded production. Computational facilities along with a computer software to handle
data will be required where (duplicate) sheets will be monthly sent for data entry, editing and
generation of reports. Traits like fat yield may not be emphasized in the beginning but may be
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added as and when basic recording setup is established and laboratory facilities to test for fat
are available. Protein yield is normally not very important under our production set up but if
automatic milk testing equipments are used, protein may be included to estimate cheese yield for
export of semen for setups where this may be an important trait.

1.6 step 6 Breeding control of registered cows/buffaloes

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All the cows/buffaloes will be inseminated artificially with semen from young bulls and project’s
technical experts will make such a choice to ensure randomness in usage of young bulls to be tested.
Record of every insemination, bull used, pregnancy and birth will be kept on a specific recording
sheet.

1.7 Step 7 Recording for other information

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Other than milk and fertility records, health status also needs to be recorded for validation that
decline or increase (if any) in milk on a certain record day was due to certain ailment etc. and also
to monitor the herd health. Beauty may be an important trait but standard recording protocols
are neither available for humped cattle such as Sahiwal or Red Sindhi nor for buffaloes. In the
choice of the candidate bull calf, some attention should be paid to the udder of the dam of the
calf but color or horn structure or tail or other characters may not be emphasized. This is because
their transmission is complicated but more importantly, selection intensity may not be wasted on
non-commercial traits. If any specific attribute is preference of farmers, it may be emphasized
while selecting young bulls (i.e. male side of selection path).

1.8 Step 8 Processing of recorded information

The recorded data on farmers cows/buffaloes Will be edited monthly after they are received from
the field, Will be edited for consistency and for generation of reports for feed back to the farmers

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and for editing to check if it conforms to the already available information of the animal and the
farmer. Although such processing of information Will be done routinely, generation of reports for
feed back may be done quarterly (every three months) and genetic evaluations done biannually if
not at a more frequent interval. Lactation yields need to be predicted from monthly records and
decision for any cow/buffaio to be elite or not elite needs to be made and communicated to the
relevant field staff for planned breeding if needed. Choice of lactation length may be 10 months
to conform to international standard. Lactations ending normally may not be projected to any
standard lactation and lactations extending beyond 10 months may be truncated for milk yield at
the standard.

1.9 Step 9 Identification of elite cows/buffaloes

Elite cows and buffaloes are routinely declared and there is no minimum level of milk production

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for such a declaration. Generally these are the best animals within a management group. Their
number will depend on the number of bulls to be tested every year. For example if 500 maie calves
are intended to be produced to get 200 candidate bulls, 800 births are expected which would require
at least 2000 elite cows/buffaloes and if they are top 20% of the recorded population, recorded
population will be ten thousand cows/buffaloes. For better selection intensity, recorded population
may be even higher. it may be made clear that under good management, elite may a cow/buffalo
producing more than 3500 liters a lactation while under ordinary management, elite may be a

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cow/buffalo producing more than 2000 liters a lactation (adjusted for age/parity, season of calving
and other differences). Farms will thus be categorized as good management farms (concentrate
feeding possible along with good health care) and mediocre management farms (concentrate feeding
rare and grazing mainly offered along with other management issues).
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1.10 step 10 Feedback mechanism to the farmers
Under small and medium sized farming system, farmers generally know how their individual ani-
mals perform or at least they can easily rank their animals from best to worse. The central idea of
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feedback is to inform them how their animals perform compared to the animals of other farmers in
the area and even across various production system. This helps them keep involved in the system
because selection and culling decisions can be more judicious. Monthly lactation summary reports
ranking farmers for average production of their cows/buffaloes and periodic rewarding of those who
excel should help farmers pay attention to recording and improving their management. Culling
decisions may also be helped by the project staff.
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1.11 step 11 Selection and raising of bull calves

The calves born to the elite cows/buffaloes need to be monitored carefully as they are the main
output of the program. Decision that they will be potentially purchased by the project after
weaning (at four months) be made in the first week based on the breed characters and physical
conditions of the calf. Farmers may be paid a calf allowance or may be facilitated with a calf
starter to help calf grow normally. They must be tagged in the first week and weighed as well.
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Then at weaning, final decision may be made and contract signed with the farmer for purchase at
the age of say one year if calf raising centre facility is wide enough, these may be taken to the calf
raising center (CRC) for raising with the other calves of that batch. It is however suggested that
they may be caryotyped for any chromosomal abnormality before taking to the CRC.

1.12 step 12 Selection of candidate bulls

The bull calves that mature to a breeding age (at the calf raising centers) and donate semen for
preservation and later use in the registered herds are called candidate bulls. Their selection is made
from among the calves bought to CRCs on the basis of breed characters, libido and semen quality.
Sometimes indices are used to rank them. It is however. suggested that selection of cntena such
as scrotal circumstance (SC) may no, overemphasized because contradictory reports are available
in the literature regarding tr. importance of SC for its relevance to puberty of daughters of the
bulls. Weil-fed young bulls should donate semen at 2 to 2.5 years of age. Age is slightly more in

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buffaloes than jn indigenous cattle. A performance sheet may be used to record performance of
buil calves and bulls.

1.13 Step 13 Semen collection and storage

The semen production units generally have adequate expertise to train bulls for semen collection
and then actual collection of semen, its evaluation and storage after freezing At least 4 to 5 thousand
doses any candidate bulls are generally required to be stored which means that a bull need to spend
about 3 years at the SPIJ. This time can be reduced tremendously by better management at the
SPIJ. After collection of desired doses of semen such bulls may be returned to the CRC as waiting
bull. Donating it to farmers for natural mating may also be possible especially for farms where Al
facilities are difficult to reach.

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1.14 Step 14 Artificial breeding In the registered herds
The registered herds need to be provided with Al facility as and when they need it. Preferred
method would be a central cailing facility where ail the Al technicians are hocked and nearest one
may reach the farm as and when such a request is received (like a taxi service). Periodic monitoring
of the system will also be needed to improve efficiency.

1.15 step 15 Genetic evaluation of bulls

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The bulls to be ultimately used in Al are tested at many stages but final selection is through
genetic evaluation for the milk yield (and other traits). Just in the first cycle, procedures are
different because information on the prospective bulls and dams is limited but when recording
of the cows/buffaloes is completed for the first time, only elite cows/buffaloes are selected to
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become the parents of next crop of bulls. Such a selection must not oniy be based on the apparent
attributes (phenotype), performance records must be used for selecting calves with good pedigree
performance. Highest miik yield in any lactation of the dam (as in vogue) should not be the criteria.
it would be much better that a most probable producing ability indexes (average of the standard
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lactations deviated from contemporaries and multiplied by a factor accounting for repeatability of
the trait) be calculated which utilize all available lactations instead of just lactation with highest
milk yield. A pedigree index (average estimated breeding value of dam and the bull) may even
be a better tool for making such a decision. The calves are selected for breed characteristics and
growth and those with any physical or genetic abnormality are culled just at weaning. Then their
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selection process continues at the CRC and even at the SPIJ. Semen quality must meet a minimum
standard. When information on daughters (just first lactation record for example) is received,
genetic evaluation be done using all available information. The model to estimate breeding values
be an animal model that can account for ail available information and relationships among the
individuals. Definition of contemporaries is crucial in these estimations and for this management
groups must be herds or clusters with similar level of inputs. In the beginning year of calving
may not be very important to be included in the models but models should account for year
and season of calving differences. Age of the cows/buffaloes would be another factor that would
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need to be taken care of. Parity may be an alternate to this. Precorrection of lactation length
adjustment is not needed if lactations ended normally and that needs to be recorded in the lactation
recording sheet. Yields should however be truncated at 305 days to conform it to international
standard. For Sahiwai/Red Sindhi yield upto 280 days may also be okay but a uniform standard
needs to be adopted. A computer software to be utilized for genetic evaluation is also important.
The computing facilities and expertize available should determine its usage. However, Estimated
Breeding Values (EBV) and reliabilities needs to be published along with number of daughters and
number of herds in which daughters are distributed. Generally Predicted Transmitting Abilities
(half of the EBV) are preferred as they are actual contribution of bulls to the next generation.
Average lactation milk yield Of daughters and number of records are also needed. Minimum
criteria for any bull to qualify for getting PTAs published may be reliability which may be 50Step
16 Disposal of semen from below average bulls Bulls having negative (below average breeding
values for the trait (lactation milk yield) or some form of index need to be disposed off even when
reliabilities on the estimated breeding values are not very high. The bulls if alive may also be

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disposed off accordingly. These are difficult decisions but must be carned out because if such an
effort is not undertaken, the whole purpose of progeny testing is lost. Reputation of the program
increases the demand of such bulls or semen from such bulls and programs fail at this stage of
decision making if worst are not disposed off. Disposal of semen may however, be delayed if storage
facilities are adequate till the reliabilities of estimated breeding values become adequate (e.g 70%)
i.e.. second crop daughters have performance records. A general thumb rule is to select one out
of every eight (or more) bulls. But for the recording set ups. four out of eight bulls may be a
minimum standard.

1.16 step 17 Contractual matings of elites with elites

The top most bulls (say top 5%) need to mated with top cows/buffaloes to get more than 200
pregnancies for each bull to get bull calves again. The choice of the elites will be from step 14

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where genetic evaluation of cows/buffaloes and the bulls is done simultaneously. This will complete
the first cycle.

1.17 Step 18 Continuity of the progeny testing program

Continuity of the program will depend on the resources and commitment of all involved. System
should be developed in such as way that if a person or two leave, the system does not collapse.

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So more than one persons be trained at every level. Program should have capacity to adjust to
new technologies and innovations in the field of biotechnology and computational breeding. It may
start from simple and feasible data collection protocols and should lead towards an ideal situation
of automation with the passage of time. If information generated can not be used, it should not be
collected from the very beginning. Good workers must be rewarded and success must be projected
to encourage all those who want to excel.
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1.18 step 19 Practicability and authenticity
Starting any progeny testing program is difficult and marinating is even more difficult. The exit
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strategy i.e. from project to a permanent entity may be sorted out in the beginning. Govemment
sponsored programs are few in the world and most efforts are by breed associations. So while
progeny testing program may be started with the help of Government resources, farmers may be
taken on board from the beginning. Also, recording less may be acceptable but recording false is
not. Simplicity helps at least in the beginning and socio- economic factors may be very important
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to any tailor-made effort.

1.19 step 20 Beyond sustainability

Sustainability of the progeny testing program is extremely important and requires dedication under
a developing country scenario. The other options such as open nuclei may however, be an alternate
options and this can be built into such an effort if developments in sciences such as molecular
genetics can practically replace the need for field recording at a wider scale.
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