ANIMAL BREEDING & GENETICS AS A TOOL FOR SUSTAINABLE DAIRY FARMING IN INDIA

 

ANIMAL BREEDING & GENETICS AS A TOOL FOR SUSTAINABLE DAIRY FARMING IN INDIA

The population explosion and a poor distribution of food are among the world‟s greatest problems today. Animals throughout the world supply human beings with milk, meat, egg, draft power, transportation, hides, fertiliser and many other useful products. Therefore, animal breeding is the beginning or the foundation to meet out the requirement. Hence, it behoves agriculturists and livestock breeders especially to give special attention to their programme of animal breeding. · Animal breeding is a fascinating discipline. It has long been recognised as one branch of arts and only recently it started to be recognised as a special branch of science. It is also one of the steps in the process of animal production, but it is the first step and fundamental to a sound animal husbandry. Application of improved methods of breeding, feeding, management and disease control during the last few decades has greatly increased the efficiency of production. · Animal breeding is the application of genetics and physiology of reproduction to animal improvement. The purpose of animal breeding is not only to genetically improve individual animals but to improve whole animal population i.e. to improve future generations of animals. To achieve this, the breeder is provided with two important tools: Selection and Breeding. These two tools are the decision making in livestock improvement. · Selection decides which animals are going to become parents to produce offspring for the future generation and breeding decides which males should be mated with which females. Therefore improvement in type, production, longevity, regularity of breeding etc. as well as the ability to transmit these desirable qualities to many progenies can be expected through application of proper selection and systems of breeding.

Cattle in India were primarily raised for milk and draught. The focus is currently on improving their milk production potential. This is in view of reduced requirement of draught animal power due to mechanisation and the need for more milk due to increasing demand. Cattle are generally maintained on agricultural by-products and crop residues with some grazing and little grain supplementation. The average holding size is one to three animals per household. The majority of the cattle are still managed under low inputs with only a few being raised under intensive management. Dairy cooperatives at village level for milk marketing have been established. In some areas these cooperatives are being used for delivering inputs and performance recording. Medium to large sized herds of cross-bred cattle have also arisen in the periphery of large towns and cities, mainly for supply of milk. Little or no information on the performance status of cattle breeds in their native environment is available. AI coverage is less than 20 percent and the AI services are available mostly at fixed places. Improvement in cattle production is also directed through feeding, generation of marketing facilities, advisory services and veterinary aid. To begin with the cattle breeding policy was to improve the milch and draught breeds through selection and the local cattle through up-grading. Herds of pedigreed cattle of various indigenous breeds were established for production of superior bulls for use in up-grading and improvement of indigenous breeds in their breeding tracts. The local cattle have poor growth rate (100-150 g per day), late sexual maturity (age at first calving, 60 months) and low milk production (less than 500 kg per lactation). The lactation milk yield in some of the breeds like Sahiwal, Red Sindhi, Tharparkar, Rathi and Gir is about 1 500 litres and in all other breeds is below 1 000 litres. Although some increase in milk production through up-grading of local cows with improved indigenous breeds was obtained, the impact of these programmes was limited because of reluctance from farmers to castrate scrub bulls and due to non-availability of sufficient number of good pedigreed bulls of improved indigenous breeds. Other limitations of the up-grading programme were, the low yield levels of the improver breed used, long generation interval in indigenous breeds and five to six generations needed to up-grade the level of improver breed. As local cows are the core of our action plan, indigenous breeds having lactation milk yield of more than 2 000 kg, need be to be used in up-grading programmes. Bulls with such potential are rarely available. Progeny testing programmes on organized farms for some important indigenous breeds were also initiated for testing bulls for milk production using 300 cows and ten bulls in a breeding cycle of 18 months. This system also failed to make any impact. Considering the need for rapid increase in milk production, cross-breeding of local cattle with exotic breeds in hilly regions and in urban areas around industrial township was started in 1961 as a matter of policy with the provision that bulk of the exotic inheritance should come from Jersey; Brown Swiss and Holstein may be tried on a limited scale. Subsequently, breeding of Holstein was allowed in areas which could support higher milk production. In hilly regions, use of Brown Swiss and Red Dane was recommended with exotic inheritance between 50 and 75 percent. Cross-breeding work on scientific lines was initiated between 1910 and 1930 in various institutes and military farms. Between 1960-1970, planned cross-breeding experiments were initiated to answer some questions about the choice of exotic breeds and the level of exotic inheritance to be introduced through cross-breeding. Simultaneously, cross-breeding work in field conditions was initiated under bilateral aided projects focussing on synthesis of high yielding cross-bred strains of cattle. Analysis of some of the well designed pure-breeding and cross-breeding programmes have been made to assess their impact including identifying their strengths and weaknesses and are used as input for re-designing the breeding programmes to make them more effective for bringing about faster genetic improvement in cattle productivity. Analysis of selection schemes for milk yield in the indigenous breeds revealed that genetic gains, in general, were negative or insignificant and had large standard errors. Genetic gain in milk production in a closed Hariana herd at a Government Livestock Farm at Hisar, which had been under selection for over 20 years, was estimated to be 10 kg or 1.5 percent of average first lactation milk yield per year. Although, the bulls used were selected from high yielding dams on the basis of pedigree and type, the progeny test information in retrospect indicated most of them had poor milk potential transmitting ability.

To make dairying profitable, Productivity (milk production per animal) needs to be increased. Productivity of dairy animals can be increased by:

• Better feeding and management of the existing animals. However, by this, milk production cannot be increased beyond the animal’s genetic potential
• Improving Genetic potential for milk production in future generation of animals by using animals with high genetic potential for milk production as parents

Selecting parents with high genetic potential is a highly complex and scientific process and requires collaborative efforts with farmers, breeding services providers, semen production centers and research institutes.

For a successful genetic improvement programme it is essential to

• Identify and performance record of large number of animals of the selected breed in an area.
• Identify best performing animals (Bulls and Cows/ buffaloes) for producing next generation of bulls and heifers – called “Selection”
• Maximise use of these ”Selected” animals in breeding programme to produce all the replacement heifers – called “Multiplication”

Identification and Performance Recording

It is important to measure and record the relevant traits/ characters along with the pedigree details of large number of animals in an area. From this pool of recorded animals, best animals can be identified and selected.

Efforts are made to measure and record all traits, which affect milk production, milk quality and reproduction of animals such as milk volume, important milk components, body conformation, growth rates, age at first calving, fertility etc.

For maintaining complete records of individual animals in computerised data base for further analysis, it is necessary that each animal is identified with a 12-digit ear tag digit number which is unique to each animal in the country i.e., no other animal in the country will have the same number. Every service (AI, Treatment, Vaccination etc.) received by the animal needs to be recorded against this tag number. Official milk recorders visit farmer’s house at the time of milking on designated days and measure amount of milk produced by the identified animal. The milk recorder also takes a sample of the milk for testing of Fat per cent, Protein per cent, SNF per cent etc.

Data from across the country is collected through INAPH. This data is used for analysis of animal information. All these information is collected in INAPH and used for recording the individual animal wise information. INAPH also generates useful information for use of Managers of the services, AI Technicians and even farmers to help them take informed decisions.

Selection

The challenge is to accurately identify animals with higher genetic capacity to produce more and not just physical appearance. Selecting animals for traits which are expressed by them is easy – such as selecting cows/ buffaloes for milk production.

However, it is difficult to select animals for traits which they themselves do not express. For example selecting bulls for their milk production potential. For such traits, animals are selected based on the performance of their relatives which express that trait (Mother, Sisters or Daughters). Selection based on the performance of large number of daughters of the bull will be much more accurate than just based on mother’s, sisters’ or grand parents’ performance. Records of grand-parents, mother’s and sisters’ would additionally add to the accuracy of selection based on daughters’ record.

Multiplication

Multiplying Best Bull

Genetic contribution of a bull to next generation can be maximized through use of Artificial Insemination (AI). A good bull, if used in natural service can produce on an average around 450 – 500 calves in its life time (5 years) whereas, if we produce frozen semen doses from the bull and use in AI, it can produce approximately 45 – 50 thousand calves in its lifetime.

Multiplying best animals

For producing future bulls, we should only use the best few bulls of the selected lot on best performing cows/ buffaloes from the recorded population. However, care should be taken to avoid breeding of close relatives to avoid deleterious effects of inbreeding. The genetic merit of the bulls thus produced will improve over generations. The use of elite cows/ buffaloes can be intensified further through use of embryo transfer, which help to produce more number of calves from top cows/ buffaloes in a shorter period.

1. Breeds
2. Bull Production
3. Latest Sire Proofs

Breeding Policy

It is desirable that every state has a defined breeding policy based on geographical and climatic conditions of the state and distribution of different breeds in the state. Breeding policy is a guideline to indicate what breed and breed combination or exotic blood level would be most suitable in the given agro climatic condition of the state. It should be followed to get the optimum output from your animals and to conserve the native breed available in the state.

Bull Production

As parents pass on half their genes to their progenies, better performing animals selected as parents, produce offspring that have better than average genetic values than the previous generation. How much genetic progress is achieved depends on genetic variation, intensity and accuracy of selection and generation interval.

Three basic methods are used to select parents: Progeny Testing (PT), Pedigree Selection (PS), and Sib Selection. Of these, Progeny Testing is considered to be the best tool to achieve higher genetic progress in any population. However, an effective Progeny Testing programme needs an extensive infrastructure for its implementation.

Progeny Testing

Progeny Testing refers to evaluation of bulls on the basis of their daughter’s performance. This long term and complex programme is considered to be scientifically best approach in achieving genetic improvement in a particular breed.

Progeny testing is a practical and the best option for achieving genetic improvement in the breed spread over many villages in its breeding tract and these villages have facilities for AI services.

A typical breeding design for a PT Programme that can be implemented in smallholder production situations are as under:

• A set of young bulls produced using the elite dams and sires are put under test.
• Adequate number of semen doses per test bull are distributed in selected herds/villages to get 80 to 100 complete first lactation records of daughters per bull. Availability of the daughters with complete lactation records in as many herds/villages as possible helps in estimating breeding values of bulls with a very high reliability.
• The top 1-10 per cent of progeny tested bulls and the very best 1 to 10 per cent of recorded cows are used for producing the next generation of young bulls. The young bulls are again put to test and the cycle is repeated. The top 10 to 15 per cent of the progeny tested bulls are used for producing replacement heifers.

One variant of the PT programme, known as young Sire Programme, is where young bulls are produced using top progeny tested sires and top recorded dams. Here, unlike the progeny testing programme, replacement heifers are produced using bulls selected based on pedigree information. It should be noted here that although the young sires used on the sire-to-dam path i.e. bulls used to produce heifers at the farmers herds are not progeny tested, young bulls are on an average better than the generation from which the proven bulls are selected, as the young sires are produced using the top progeny tested semen and the top recorded dams. Young bulls therefore could be as good as progeny tested bulls of previous generations. When one uses young bulls on sire-to-dam path, the generation interval becomes less than one third of that when only progeny tested bulls are used. This often outweighs the loss in accuracy. The genetic gain thus achieved in many practical schemes of young sire programme is as good as if not better than what is achieved under the classical progeny testing programme.

Progeny Testing through Young Sire Programme

Pedigree Selection

When bulls are evaluated and selected only on the basis of performance of their parents and grand parents, the process is referred to as Pedigree Selection (PS).

In a situation where a large numbers of animals of a particular breed spread over many villages in the breeding tract and where there is a limited or no infrastructure is available for implementation of progeny testing programme, Pedigree Selection appears to be the suitable alternative to bring genetic improvement in those particular breeds.

A usual strategy adopted under Pedigree Selection programme is to divide available villages having animals of the breed into two categories: one as multiplier villages about 20-40 having better quality animals and the remaining as other villages having animals of the breed. The females are performance recorded and the best genetics is used in multiplier villages to produce bulls, best among them are used in the multiplier villages and others are used in the base population. Thus, Pedigree Selection programme not only helps in disseminating best genetic material from multiplier villages/herds to other villages/herds, but it also helps in popularising AI in the project villages.

The infrastructure created under Pedigree selection programme may act as a stepping stone to implement Progeny Testing programme for those valuable Indigenous breeds in future.

Pedigree Selection

Sib Selection (Open Nucleus Breeding System (ONBS))

ONBS using Multiple Ovulation and Embryo Transfer (MOET) is to set an elite herd (or a few elite herds) of males and females and carry out intensive selection and testing within herd/s selecting males and females at an early age using family information and not on their progenies as in the case of the Progeny Testing Programme or just on their parents as in the case of pedigree selection.

Since the merit of males is judged on the basis of performance of their sisters and half-sisters – referred to as sibling test – and not on the performance of their progenies, the generation interval is considerably reduced. Although, the accuracy of selection under sibling test is lower than that achieved in the progeny test, the benefits of reducing the generation interval outweighs the loss of accuracy. The genetic response under a well-run ONBS could be as high as that is achieved under the conventional progeny-testing programme. As selection and testing is done within a herd or in a few herds, the greater degree of control on the determinants of genetic change i.e. intensity of selection, generation interval and accuracy of selection is possible.

Genomics

Selection of animals based on pedigree information alone is less reliable. Waiting for daughter performance for selection of bull is very costly and takes 8-10 years in Indian condition. Genomic Selection refers to selecting animals using information from pedigree as well as information on dense DNA markers (i.e. Single Nucleotide Polymorphism-SNP) spread across genome. This can be done at the early age of an animal and will give more accurate estimated breeding value compared to pedigree based selection.

In recent time, Genomic selection approach has emerged as a promising tool in the field of animal breeding as it enables selection of animals at younger age thus facilitates achieving faster genetic progress.

With large number of animals milk recorded in various Progeny Testing and Pedigree Selection projects, NDDB initiated its efforts to implement Genomic selection for the Cattle and Buffaloes in India during 2014 with the objective to establish suitable methodologies for selection of animals on the basis of more reliable Genomic Breeding Values (GBV) under small holder dairy system of the country.

A DNA repository from milk recorded animals of various Cattle and Buffalo breeds has been established to create huge reference population to facilitate implementation of genomic selection.

In 2015, a medium density customized chip named as “INDUSCHIP” was developed by NDDB for genotyping the indicine breeds of cattle and their crosses with technical guidance from Center for Quantitative Genetics and Genomics, Aarhus University, Denmark. Currently INDUSCHIP2 is in use with around 53K SNPs informative for various Indian cattle breeds and their crosses.

The Genomic breeding values of HF crossbred and Gir cattle using INDUSCHIP was estimated and published in 2018 and 2019, respectively. For the first time in the country, the selection of young bulls on the basis of genomic breeding value has been initiated. These genomically selected bulls for HFCB, JCB, Gir and Murrah breeds are now supplied to semen stations for faster genetic progress in various cattle and buffalo breeds.

In 2019, NDDB developed First near complete haplotype phased genome assembly of River buffaloes using tri binning approach.

Subsequently, in 2020, a medium density (59K) custom genotyping chip named as BUFFCHIP was designed with technical assistance from USDA and initiated genotyping in Buffaloes.

Using INDUSCHIP and BUFFCHIP genotypes, it is possible to know breed composition of bull calves, heifers, cows and bulls of various breeds. Also genomic breeding values of young bull calves and heifers can be estimated and their production potential can be known for early selection.

NDDB has made this facility available to farmers, semen stations and various institutions for assessment of breed composition of their individual animals and estimation of genomic breeding value (GBV) on cost basis.

Selecting Breeding Stock on their Breeding Values for achieving higher Genetic progress in Cattle and Buffaloes

Breeders focus on selecting parents to increase the average productivity of future generations. Phenotypic records of economically important traits on which parents are selected are usually quantitative in nature and are influenced by both genetics and environmental factors. However, parents pass on only their genes to their progenies and not environmental influences. For selecting parents, therefore, the important job for breeders is to disassociate environmental influences from phenotypic records and estimate what animals can transmit to their progenies. The genetic worth of animals in terms of what they can transmit to their progenies is expressed in terms of breeding values (BV) or probable transmitting ability (PTA). BV is simply twice of PTA.

The question then is how to estimate BV or PTA of animals. As all economically important traits are influenced by both environment and genetics, first phenotypic records of the animals available for selection are corrected for environmental factors and the resultant values are then used for estimating breeding values making use of relationship among individuals. Though breeding value can be estimated for an individual animal, it can only be estimated for a group of animals. In this paper first, the statistical procedure used for estimating breeding values of bulls put under test and all females recorded in progeny testing programs implemented under the National Dairy Plan is described in simple terms. In the second part, all common questions raised by persons involved in selection of bulls for semen production on the procedure used in estimation of breeding values and the advantages of using BVs for selection of parents over phenotypic values are answered in simple language.

ESTIMATION OF BREEDING VALUES

Animal’s milk record is influenced by environmental factors such as herd, village, year of calving, season of calving, age of animal, etc. (collectively referred as environment) and animal’s genetics. This can be expressed mathematically as:

Milk = Herd + Year of calving + Season of Calving + Age of animal + Animal’s Genetics + Error

For estimating the genetic worth of an animal, milk production records are first corrected for various environmental factors. After correction with such factors relationship among all animals are used for calculating their breeding values. The correction of records for the environmental factors and estimation of genetic worth based on differences among records of related and not related animals is done simultaneously using the following modified formula:

Milk = Herd + Year of calving + Season of Calving + Age of animal + Animal’s ID*(matrix of relationship of animal with all other animals) + Error

A solution of this equation is obtained by a statistical procedure. One of the best and most popular methods used is BLUP (Best Linear Unbiased Prediction) which does correction for environmental factors and estimation of breeding values simultaneously. For estimating breeding values of bulls and recorded females under progeny testing programs, we use Random Regression Test Day BLUP procedure, wherein instead of lactation yield test day records are used.

Every estimated breeding value is provided with its reliability. Reliability provides the confidence that one can place on the estimate of breeding value. Larger the number of pedigree and progeny records of an individual used for estimating its breeding value higher will be the reliability of its estimate of breeding value.  One can go to NDDB’s web site (NDDB.org) and see the latest estimates of breeding values along with the reliability of bulls having more than 30 daughter records under progeny testing programs.

If an animal’s relationship is not known we can correct the record for all other environmental effects by the following formula:

Milk = Herd + Year of calving + Season of Calving + Age of animal + Error

And the difference of animal’s corrected yield then is multiplied by heritability (a factor that determines what proportion of difference is controlled by genetics) to arrive at a breeding value of an animal.

BV= (Corrected yield of animal-Average of all animals)*heritability

We can correct for as many factors affecting milk production as possible provided we have records for all those factors along with milk production records.

 

Answering frequently asked questions

1. What factors are considered for calculating breeding values? 

In most projects, we consider owner, village, year of calving, season of calving, and lactation number as factors influencing animal’s record. In case there are not sufficient observations in any one sub-class, we combine sub-classes to create a sub-class with a larger number of observations. For example, if many villages have 2 or 3 records each, we then combine nearby villages into a Tehsil factor. If most of the owners have only one animal recorded, we consider a village as a herd instead of an owner. And pedigree information i.e a matrix defining relationships among animals is added in all breeding value estimation runs. Besides, now we also add genotype information wherever feasible.

Theoretically, as many factors as we can record accurately can be used for breeding value estimation provided the factor has a biological justification of its influence on the trait under consideration and there are at least 5-10 observations in each sub-class of that factor.

Apart from the factors that we currently use for estimating breeding values many other factors such as owner of animal, farm condition, animal house type, feeding practices (low protein, high protein, medium protein diet, etc.), temperature-humidity on the farm on the day of record, body size of animal, breed percentage of animal, etc. can be considered provided we can measure accurately these factors and there are sufficient observations in each sub-class of the factor.

1. What are the consequences of not correcting for environmental factors?

Let me explain this with an example. Take two cows one which calved during summer in the month of May during which the farm had a water crisis and produced 4000 lit milk in lactation, and the other cow calved during winter in the month of December during which the farm had plenty of food and water and produced 4400 Kg milk. We if do not correct for the season of calving, in this case, we would consider the second cow superior then the first. However, if we have records of many cows on the farm both calved in summer as well as in winter, it would be possible to estimate the effect of season on milk production. Let us assume the effect of season calculated for this farm is 900 kg. i.e cows calved in winter produce 900 kg. more milk than those calved in summer. The season corrected milk production of the first cow will be 4900 (4000+900) and that of the second cow will be 3500 kg. This means the first cow has better genetic worth than the second cow. In this case we would have selected a wrong cow if we had not corrected for season effects.

1. Is estimation of BV of calves possible only with the records of their dams and no pedigree records?

Yes, it is possible. For this, we would require a sizable number of dams recorded in the same area. We can calculate the effect of factors such as tehsil, season, year of calving, and so on based on a substantial number of records of cows/buffaloes and correct for the phenotypic records for environmental effects. The corrected record is then multiplied by heritability for estimating a breeding value as shown earlier. In a situation where we do not have pedigree records, but have a reasonably large number of animals recorded in an area (like in the PS projects), we can calculate BV of animals based on environmental corrections. Reliability of such a breeding value, of course, will be very small as very little information on the animal available for breeding value estimation.

1. Can we use both dam yield and BV for selecting a bull calf for semen production? 

The formula for calculating breeding value considers dam’s yield. Once we have calculated BV, the dam’s yield should not be looked into. BV would be sufficient and can be used as a sole criterion for selection of bull calves.

1. Why the estimation of BVs from the PT projects is more accurate than those in the PS projects? Are BVs from the PT and PS projects the same?

In the PS projects, we do not record pedigree. So we can only correct dams’ records for environmental factors and not for different bulls used. Besides, in the PT projects, each sire has a large number of daughter records measured in varied environments making correction for environmental factors and pedigree much better. All these make the estimate of reliability of breeding values under the PT projects much larger than what is possible under the PS projects. However, breeding values estimated under the PS projects will be much more accurate compared to those estimated just based on raw dam’s yield.

1. Can we select bulls for the entire country based on breeding values calculated in one area?

If we have breeding values estimated based on daughters produced in different environments with reasonable reliability like ones estimated in the PT projects, the breeding values estimated in one project area could be used for the entire country. However, this is applicable for comparing bull/bull calves produced within a system. An animal (bull calf) that is not at all related to these animals is not comparable. Nevertheless, if we want to make a decision on selecting a calf between the one with only dam’s yield and the other with BV, selecting the bull calf with BV poses less risk.

1. Does the genetic base of a breed influence the estimation of breeding values and ranking of bulls?

The genetic base for a particular breed will definitely influence the estimation of breeding value and ranking of bulls. However, the genetic base for a breed in different states in India is not very different. The main differences in productivity are due to differences in feeding, management, and environment practices rather than the genetic base. For example, we cannot say Murrah in Haryana, Western UP and Punjab are very different genetically though one finds average productivity of Murrah buffaloes in Haryana higher than those in Punjab. The differences in productivity are more due to differences in feeding and management practices in Haryana than Punjab rather than due to differences in the genetic bases. A lot of animal movements happen between states in India making a genetic base of a particular breed no different in two states. For example, Gujarat farmers have been procuring a very large number of CB cows form Punjab making the genetic base of crossbreds in Gujarat and Punjab more or less the same. But still, we know the productivity of Gujarat CBs is lower than those in Punjab perhaps due to differences in environmental factors between the two states. In practical terms, it means that a bull having high breeding value in Gujarat is used in Punjab, its daughters will definitely perform better than the daughters of an average bull in Punjab.

1. Can we predict the performance of a daughter produced from a particular cow and particular bull?

If one wants to predict the performance of a daughter of a particular bull mated to a particular cow, it will be guesswork only.  Breeding Values are comparison of individuals on the basis of averages. That means on average daughters of a high BV bull are expected to perform better than daughters of other bulls. But still there will be variability both due to gene segregation and due to environmental differences. That is why we get the same EBV for full-sibs but different genomic BVs.

1. How many observations are required for estimating breeding values? 

The basic idea behind estimating breeding value is to remove the influence of non-genetic factors and then estimate breeding values based on the relationship among animals. For correction of non-genetic factors, we need repeated records in that environment. Statistically, we should have a minimum of five observations per level of factor. If we consider a season as one factor, then for each season we should have a minimum of five observations. If we can satisfy this condition, we can correct records for environmental influence and estimate breeding values.

If we have more observations, our corrections will be more accurate, and consequently, estimated breeding values will be more reliable. As there are many factors that influence milk production we need a large data set to estimate the effects of all factors and estimate breeding values with reasonable level of reliability. Thus, larger the dataset higher will be the reliability of BV estimates. One can, of course, estimate BVs with smaller data set but then reliability of breeding values will be smaller. There are theories giving method to estimate breeding values on smaller farm data, or data with no pedigree information or dataset with a few environmental factors.

1. Is the sample size different for different projects?

Yes. Different projects have different follow-up levels, different rearing practices, different geography, etc.  Hence, different projects have different daughter numbers or animal recorded numbers.

1. Is the accuracy of factors and breeding values is different for different projects? 

There are two factors affecting breeding value’s reliability. The first is the accuracy of data recording (both production records and pedigree records- parentage), and the second is the volume of data. It is true that as a project grows older, the parentage errors decreases and the volume of data increases, and we get better reliabilities.

1. Is it true that BVs for some projects are more reliable than others?

As discussed above, projects differ in their reliability. Along with BV, we should always consider its reliability. If I want to choose a bull with 250 BV and 90% reliability versus a bull with 300 BV and 30% reliability, I would prefer the bull with 250 BV.

However, if I want to choose a bull with 1000 BV with 30% reliability and bull with 100 BV with 90% reliability, I may take a risk of selecting 1000 BV bull. Here the word “risk” is significant. With less reliability, one is not confident whether this 1000 is really 1000 or with more information it will come down or go up.

With higher reliability, we have more confidence on the estimates of breeding values and less risk. For AI bulls, risk should be as minimum as possible. With increasing information, reliabilities increase as shown in Figure 2.

 

1. If reliability is low, would it be better to simply consider the dam’s lactation yield?

As explained earlier, the raw dam’s lactation yield has low reliability than breeding value calculated based on accurate record and environmental corrections. This is even more desirable if we wish to compare bulls from different sources like from a few organized farms, from farm and field together, etc.

1. How the breeding Values are expressed?

Breeding values are expressed in terms of superiority over their population mean. If an animal is having 100 BV for a trait, it means that this animal has superior genetic potential of producing 100 kg. above the current population mean.

1. What is PTA and how it is expressed?

PTA is half of BV. PTA estimates what is passed on to the progeny from its sire or dam which is half of what the sire or dam transmits to their progenies. The offspring gets 50% of the genetic superiority of its sire and dam.

1. If breeding values are expressed as deviations from a population mean (in which the testing has happened) and the bulls are to be used in a different population with a different population mean, will we get  the same level of genetic improvement in the other population? For example, say a BV for milk yield of a bull in the population where it is tested is +300 and the mean is 5000 Kg. If we have a population with an average of 6000 kg., is it advisable to use the above bull in the population?

If the two populations represent the same/closed breed with no much genetic distance, the BV estimates in one population are valid irrespective of current productivity levels of these two populations. When there are no genetic differences between the two populations, the phenotypic differences in production levels are attributed to environmental differences. This is similar to examining performance of Murrah in Haryana, Western UP, and Punjab. Another example is Jersey crossbred performance in Tamil Nadu and Andhra Pradesh. In such conditions, the differences in BV may amplify meaning if difference between two bulls breeding value is 100 in low producing population, the difference will be around 125 in high producing population.

In our country, we can use BVs that have been estimated in one area to another area with reasonable confidence. To bring in more confidence/accuracy, under the PT projects, we have started projects for the same breed in multiple locations and have been sharing bulls across projects so that we can have joint breeding value estimation and the estimated breeding values could be used across the entire country.

However, if the genetic base of the two populations is different, the ranking will change considerably. Also if environment is drastically different, the ranking will change considerably. This is the case with HF in US and its performance in India. Here also bulls with very high BV will not have negative or very low BV in other population but ranking among bull will change considerably due to different genes may get activated differently in different environments.

1. Should we distribute bulls ranked 1 to 20 or say 1 to 50 based on breeding values irrespective of their breeding values? Can we also define MSP for breeding value?

Ideally, we should produce twice or thrice the numbers of bulls required through nominated mating and then select the best one third or one-half of bulls for semen production. The nominated mating also should be based on BV and not on raw-production records. If we mate best dams (by BV) with best bulls (by BV), the progenies are bound to have better BVs. The bull calves with very small but positive BV will be average bulls. They will give small genetic gain. But consider the bulls selected from their raw-dam yields which may have negative BV. Such bulls may lead to negative genetic progress. Initially, we may say bulls with positive breeding values should be used. Later as we progress we may set certain percentage of top bulls that may be used for semen production, but it should be dynamic. It may not be advisable to fix a percentage limit, as what you select depends on the actual demand of bulls for semen production. In fact, we must think about a differential price system based on breeding values and demand as our systems of bull evaluation and production matures.

1. What is the relation between traditional breeding value and genomic breeding value?

Genomic breeding values build on traditional breeding values. For estimating genomic breeding values in any population, we need performance records of a large number of animals along with recording of various factors. If pedigree information is available, genomic breeding values will be more accurate. Genomic breeding values will have better reliability than traditional breeding values.

For example, in traditional analysis, two full-sib bulls with no daughter information will have the same breeding value as its sire and dam are the same. However genetic information of these full-sib bulls will differ and hence their genomic breeding values will be different. Thus we can further differentiate which full-sib is better than the other.

1. If we have 3 bulls produced through OPU-IVF and ET, what would be their BVs? 

If three bulls are produced through OPU-IVF/ET with the same donor cow and sire, they will have the same breeding values in the traditional way of estimating breeding values. However, their genomic breeding values will differ as they will have different genes. Only monozygotic twins will have the same Genomic Breeding Values.

1. Once a breeding value is established for the bull, do we need to continue the breeding value estimation for the same bull?

With an increasing amount of information, bulls BV will change and its reliability will increase. However, once the reliability crosses 90%, there will be no considerable change in BV of a bull. This means we need to continue looking at BV for a bull till it crosses 90% reliability. Afterward, the bull will be there in the system as we have to use all relationship and information available, but the BV will not change much.

1. Which scientific method will provide the best bulls for breeding – Genomic breeding values or traditional Breeding Values or any other?

If we can use only bulls with BV calculated based on 100 daughter records for semen production (proven bulls), this is the best scientific method. This is what the classical PT program in developed countries have done before the genomic selection was introduced.

However, in our conditions, when we get 100 daughter records, the bull will not be available for breeding/semen production. This means the above-mentioned best method is not practicable in our situation.

The compromise we did was to store 3000 doses and use these doses for nominated mating when we have BVs from a large number of daughter records. Here, we are using male calf born from nominated mating sired by top proven bulls for semen production. The young bull will have BV for its sire and dam. This will give relatively lower reliability. An improvement over selecting bull calf, produced using semen of proven bull, is its selection having its Genomic Breeding Value (this is genomic selection). This is superior to nominated mating bull calf, but not as good as of using proven bulls for semen production.

1. Is there any standard operating protocol for breeding values results which can be considered by the semen stations for selection/ rejection of particular bulls?

We should look at differences in breeding values among bulls. If differences are not too high (say 50-100 for 305-day milk yield), we should choose bull with high reliability. If differences are very high (say more than 250-300 for 305-day milk yield), one may think about taking a bit of risk and select bull with high BV even though its reliability is low.

1. Is it possible to establish breeding values based on sisters’ milk yield?

Yes, BV can be estimated from sisters’ milk yield. However, the reliability will be lower than those estimated based on several daughters’ performance.

1. Why are daughters of the bulls given more weightage for estimating breeding values?

Any estimate that is based on a repeated sample will have higher reliability. Daughters receive half of the bull’s gene pool. This means in daughters we have the multiple samples of bull’s gene pool. Estimation of BV of bulls made based on their daughter records always has high reliability than any other relationship.

1. What is the possibility of errors in estimating breeding values?

Reliability gives an estimate of possible error in the estimation of breeding values. Lower the reliability, higher will be the error.

1. How to know that data provided from the field is having errors and cannot be considered for breeding value estimation?

There are a few statistical ways to find out extremely wrong data. However, there is no way to know wrong data that fall within the biological range and follow established pattern. After completion of BV estimation analysis, when we look at results, we can sense the accuracy of records but we cannot pin-point which record is wrong. If parameters like heritability are very different from established norms, we may suspect high errors in recording.

1. Can we estimate the breeding value of bulls with say 10 daughter records per bull? 

Yes, we can estimate breeding value from small number of daughter records, but their reliability will be lower than one that is estimated with a very large number of daughter records.

COMPILED BY DR B. RAGHVAN, DAIRY CONSULTANT

SOURCE-NDDB