conservation of genetic resources in india

8/4/2019 Conservation of Genetic Resources in India

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CONSERVATION OF GENETIC RESOURCES IN INDIA

Introduction

India has vast animal genetic resources with a wide variety of indigenous farm animals

including cattle. The cattle breeds have evolved over generations to adapt to the agro-climatic and

socio-economic needs of the people. Domestic animal diversity is defined as the spectrum of

genetic differences within each breed and across all breeds within each domestic animal species,

together with the species differences; all of which are available for the sustainable intensification

of food and agriculture production . The domestic animal diversity has evolved over millions of

years through the processes of natural selection forming and stabilizing each of the species used in

food and agriculture. Over the more recent millennia the interaction between environmental and

human selection has led to the development of genetically distinct breeds. Selection processes,

directed by both humans and the environment, together with the random sampling processescausing genetic populations to drift over generations, have accelerated the development of the

diversity within species leading to the creation of distinct genetic differences amongst breeds.

GENETIC DIVERSITY IN AnGR IN INDIA

India is the seventh largest country in the world and it is recognized as one of the 12-mega

biodiversity centres of the world. It is well marked off from the rest of Asia by mountains and the

sea, which gives the country a distinct geographical entity. Due to diverse agro-ecological regions

and topographic conditions, India has rich repository of both flora and fauna. India has vast

animal genetic resources with a wide variety of indigenous farm animals. It has 132 registered

Species As per World Watch List As per Indian literature

Cattle 70 30

Buffalo 20 10

Yak 5 Nil

Sheep 62 42

Goat 34 20

Horse 7 6

Donkey 3 Nil

Camel 9 (+1 Bactrian) 8

Pig 8 Nil

Rabbit 3 Nil

Fowl 19 15

Quail 2 Nil

Duck 6 Nil


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farm animal breeds viz. 30 cattle, 10 buffaloes, 42 sheep, 20 goats, 7 camel, 5 horses/ponies and

18 chickens, besides many other non-descript and mixed populations. Livestock husbandry is an

age-old important occupation for Indian farmers. The unique and rich animal biodiversity is

extensively referred to in Indian scriptures.

JUSTIFICATION FOR CONSERVATION OR REASON?

Different reasons for conservation of animal genetic resources include (Rao and Reddy, 1995):

1. Economic and biological reasons:

A. Genetic variation both within and between breeds is the raw material with which the animal

breeder works. Therefore, any loss of genetic variation will limit our capacity to respond to

changes in economic forces for the exploitation of animal production in future.

B. Breeds with specific qualities like disease resistance, heat tolerance, ability to survive andproduce under stress and low input conditions need to be preserved for future use.

C. Future requirements of type and quality of animal produce (milk, draught power) may change

and this requires conservation of animals with better performance in specific production traits.

D. Magnitude of heterosis depends upon the breeds crossed. For exploiting the heterosis in animal

production, it is necessary to maintain breeds which are complementary to each other and on

crossing result in maximum heterosis.

2. Scientific reasons:

i. Breeds with unique physiological or other traits are of great value as they provide missing links

in the genetic history of a livestock species by the study of blood groups or polymorphic traits. To

identify the DNA sequences causing the distinctive traits, preservation of breeds with unique traits

will be essential for long term research in molecular engineering.

ii To evaluate the magnitude of genetic change due to selection, maintenance of a sample as

control population is very much essential.

iii Investigations in different areas like physiology, biochemistry, genetics immunology, etc.

Require maintenance of diverse populations.

iv Variety of populations are an asset for research work in biological evolution, behavioural

studies, etc.

v Diverse populations form an excellent teaching material for students of animal science, ecology,

etc.

3. Historical and cultural reasons

Conservation of historically important, culturally interesting and visually unusual and attractive

population is very important for education, tourism etc. Further, conservation of breeds

a. Can be a valuable material of nature and culture,

b. Serve as research and teaching material in history and ethnography,


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c. Will be preservation of populations with diverse sizes, colours and other morphological

features, for aesthetic reasons, and

d. Need be done to take care of existence of different creations of the nature for posterity.

STATUS OF SPECIES -FEMALE POPULATION (Tomar et al)

MECHANISM OF CONSERVING CATTLE GENETIC RESOURCES

Once genetic resources have been identified and characterized, two basic conservation activities

can be followed,

1. IN SITU CONSERVATION2. EX-SITU CONSERVATION

IN SITU CONSERVATION

1.haploid forms a.frozen semen

b. frozen eggs/oocyte

2.diploid forms a. frozen embyo

b. live animal

In situ conservation requires establishment of live animal breeding farms and their maintenance.

The generation and loss of alleles is a dynamic process that should be maintained at close

equilibrium through sound management. In situ conservation strategies emphasize wise use of

indigenous cattle genetic resources by establishing and implementing breeding goals and

strategies for animal sustainable production systems. Information for animal recording and

breeding is well established in developed countries through breeding associations which zealously

protect the interest of breeds including rare ones. Infrastructure appropriate to systems in

s,.no Status Number

1 Normal >10,000

2 Insecure 10,000-5,000

3 Vulnerable 1,000-5,000

4 Endangered 100-1,000

5 Critical < 100


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developing countries remains scarce. In India, such efforts are limited to only six breeds of cattle,

in a herd registration program organized by the Central Animal Husbandry Department. Similar

programs are required for the rest of the breeds and species as well. In any such program, the

success depends upon the participation of the farmer for which he needs support and incentive.

Therefore, it is difficult to organize the farmers for conserving the breeds which are no more

economical to him. In the case of breeds which are no more economically viable, therefore, the

only alternative is to bring them under government farms. In situ conservation is very costly if the

entire population has to be retained for which at least 26 females and 10 males in cattle have to be

maintained that would keep the inbreeding coefficient at 0.2 per cent per year. Therefore, this

approach would have to be limited to those breeds which are highly endangered. Modalities for

simplified animal recording, genetic development and dissemination are needed for each species

for a range of national livestock structures in developing countries.MAJOR ADVANTAGES OF IN-SITU CONSERVATION:

1. Live animals can be evaluated and improved over the years.

2. Genetic defects can be detected and eliminated.

3. Live animals are always available for immediate use.

4. They are a gene bank for future use.

5. They are a constant reminder that the needs of posterity must be considered.

6. The herd may have some economic advantages (heat tolerance, disease resistance) which can

be exploited and so render the enterprise economically viable.

7. The produce from live animals partly compensates the expenditure, if not entirely.

8. From aesthetic point of view, the live animals are, visible, a pleasure to look at, the people are

delighted to see variety of animals and have some cultural value.

THE MAJOR LIMITATION OF LIVE ANIMAL CONSERVATION

While fixing the number for preservation of a breed,

1. The cost of maintenance,2. Availability of animals and rate of inbreeding should be taken into consideration.3. With small population size, the effective population size decreases and the genetic

structure of the population is affected due to inbreeding and random drift.

4. Many models are now available which reduce inbreeding to a minimum, but random driftover long periods may lead to a population very different in genetic composition from the

initial one.

5. Gene X environment interactions is another disadvantage.6. In situ conservation involves

A large infrastructure of land, Buildings,


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Feed and fodder resources, Water supply, Labour, Technical and supervisory man-power, etc.

It should be made to maintain a rate of inbreeding of less that 0.5% per generation for

long term programmes while slightly higher rate could be tolerated for short term programmes. A

flock/herd of 150 breeding females with 20 breeding males, the males being unrelated as far as

possible, for preservation purposes. A maximum inbreeding level of 1` % per generation as

tolerable and a herd size of 200 breeding animals in necessary to breed and selected successfully

for a quantitative trait.

EX-SITU CONSERVATION

Ex-situ conservation includes cryogenic preservation. It is the storage of genetic resources, whichthe farmers are currently not interested in using. Ex situ conservation is based on the use of live

animals populations wherever practicable, supported by cryopreservation where technology exists

or can be developed, combining within-country gene banks with global repositories. Interested

governments, norgovernmental organizations, research institutions and private enterprises should

be encouraged to maintain in vivo samples of breeds at risk, with national inventories being

established and kept up to date so that the genetic resources are readily available for use and

study. Because of random drift and possible gene by environment interactions, ex situ methods are

generally preferred over in situ. Ex situ conservation is comparatively more convenient,

economical and easy with the application of modern reproductive technologies.

Advantages

1. If the preservation is to maintain populations without genetic change, it can be best done by

cryogenic storage as it is difficult to breed many generations of animals without any change in the

genetic structure.

2. The resources requirement for in situ preservation is quite large as compared to cryogenic

methods.

Limitations

1. Ex situ preservation using frozen semen delays the restoration of a breed as it can be restored in

the future only by upgrading. But this could be overcome through preservation of embryos.

2. Another important factor is the danger faced by a breed restored from cryogenic preservation

from important changes in the environment like germs, climate, etc., that have taken place over

the years.

3. Variability in cryogenic storage of germplasm, accessibility to their physical location,

ownership, behaviour of animal, response of germplasm to freezing and thawing techniques, and

poor conception rate


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EX SITU/CRYOGENIC PRESERVATION INCLUDES

1. Preservation of frozen semen

2. Preservation of oocytes

3. Preservation of embryos

4. Preservation of ovaries

5. Use of embryonic stem cells or blastomeres

6. Production of chimeras

7. Production of embryos in vitro

8. Embryo splitting

9. Transgenesis

10. DNA libraries

1. Semen preservation:Semen cryopreservation and artificial insemination are important tools of animal

improvement with vast scope of genetic improvement, conserving indigenous cattle resources

because of their simplicity and relatively cheaper costs. Semen storage and distribution activities

are being carried out in a few well-known indigenous milch cattle. Still, many breeds like

Amrithmahal, Dangi, Gaolao, and Punganur lack such facilities. Spermatozoa may also be

collected from the epidydimis

2. Oocyte preservation:

This method provides an opportunity for conserving females in the same way as sperm is

conserved. The oocyte can be recovered by surgery, laparotomy or slaughtering of donor animals.

The frozen thawed oocyte can be used for IVF successfully (Schellander et al, 1988). The

immature and mature oocyte from slaughtered animals could be useful in near future for

cryopreservation of genetic material of endangered breeds.

3. Embryo preservation:

The main advantage of cryopreservation of embryo over that of sperm or oocyte is that

it contains the complete genome. The embryo transfer technique coupled with micro

manipulation, embryo sexing and splitting are more useful and economical to carry out ex situ

conservation of animal genetic resources. This technique is very useful in conservation of genetic

resources by rapid multiplication of superior or rare germplasm. MOET can be used in

resurrecting the endangered cattle breeds like Sahiwal, Punganur and Vechur.

4. Preserving of ovaries:

The preservation of slices of ovaries in liquid nitrogen is a new technology

which may be of great use in conservation of animal genetic resources. The ovary slices might be

transferable into suitable recipients to obtain oocytes which can be fertilized.


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5. Embryonic stem cell and nuclei:

Preservation of embryonic stem cells could represent an important method

of genome conservation and would be helpful in propagating animals from a single embryo of

elite or rare animals belonging to endangered breed/species. Embryonic stem cells represent

progressively growing cultures of embryonic cells which retain their pluripotential characteristics.

They are derived by culturing blastocysts in vitro in such a way that the cells from the inner cell

mass proliferate but do not differentiate. Embryonic stem cell lines can be isolated and then

multiplied by continued culture. The importance of embryonic stem cell lines is that, if they are

incorporated with normally developing embryos, they will participate in the formation of the inner

cell mass and produce chimaeric animals, including germ line chimaeras which are fertile. A more

direct route of regenerating animals from embryonic stem cells might be to use the nuclei from

these for nuclear transplantation into enucleated oocyte and embryonic multiplication.6. Chimaeras:

Chimaeras mean the animals having body cell population with different karyotypes

which have been formed from two or more zygotes with different karyotypes. Chimeric embryos

have been frequently made by the aggregation of cells from two individual embryos or by

injecting cells from one embryo into the blastocyst cavity of another embryo. So long as cells

from both embryos are represented in the inner cell mass, the composite embryo will develop into

a chimaeric animal. A more important aspect of chimaerism in genetic conservation is the

potential use for inter-species embryo transfer. Using this technology sheep have been born to

goat foster mother and vice versa. This would be especially important if it was a species rather

than a breed of animal that was on the verge of extinction.

7. Production of embryos in vitro:

This technology involves salvaging mature oocyte from ovaries of slaughtered

animals and developing methods for their maturation, fertilization and in vitro culture for normal

embryonic development. For conservation of rare breeds, such a method could provide an

opportunity to salvage a few oocytes from the ovaries of rare and superior animals even after their

normal reproductive life and to produce some blastocysts for conservation by deep freezing.

8. Embryo splitting:

Embryo splitting is more advantageous in the circumstances where only few

embryos of particular genotype or breed or species are available. This technique of manipulating

embryos could be helpful in producing more number of animals from a few stored embryos of

rare and endangered animals.


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9. Transgenesis:

Recent developments in molecular biology have enabled introduction of specific

genes into the animal genome. A small amount of DNA is injected into the nucleus of an egg soon

after fertilization. In some instances the DNA becomes integrated into the chromosomes and an

embryo and foetus develops in which all the nuclei contain copies of the inserted gene. As any

sequence can be spliced with any other (Anderson, 1986), transportation of genes across breeds

and species is possible by recombinant DNA techniques. Successful microinjection of genes in

mice embryo and their expression .the creation of transgenic forms a possibility, and for the future

a viable technique for improving animal production, and for conservation and capitalize on of

important genes across breeds and species.(Gordon et al)

10. DNA libraries:

Theoretically, an animal can be produced from its complete DNA complement.However, at present technical developments are limited to the identification and manipulation of

only a few genes. But the direction in which technical advancements are taking place gives an

indication that in future breeds/species can be reconstructed from their DNA complements. This

gives the hope that if complete DNA complement is stored either in lyophilised form or as

cryopreserved cells, reconstruction can be taken up when techniques are standardised. Advances

in biotechnology are emerging in a big way and could be of great utility in near future for animal

improvement and animal genetic resource conservation programmes.

THE MAIN CAUSES OF THE REDUCTION IN NUMBERS OF INDIGENOUS

LIVESTOCK ARE

1. The intensive efforts being made to introduce superior germplasm to overcome the lowproduction of the local genotypes, without any consideration to the local ecological and

socio-economic situation (demand for increased milk production and introduction of

exotic milk breeds of cattle like Jersey, Holstein).

2. No serious organized effort in maintaining the purity of the breeds - inter-mating amongbreeds located in each others vicinity resulting in dilution of breed characteristics and

Changes in cropping pattern and increased mechanization of agriculture with neglect of

indigenous draught breeds of cattle.

3. The global awareness for conservation of domestic animal diversity was touched up on atthe International Conference held in Rome in 1936, which resulted in several

recommendations being made in this regard. Based on these recommendations, the

Government of India had initiated herd registration schemes for several established breeds

of cattle, viz., Gir, Hariana, Kankrej, Ongole and Tharparkar.


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4. Standards of performance were laid down for registration of animals both in registered andfarmers herds, and also including milk recording of animals. However, this scheme was

not entirely successful. Efforts were made from time to time by the Government of

India/Indian Council of Agricultural Research to define the breed characteristics of

important breeds of livestock and a bulletin containing breed characteristics of important

breeds of cattle and a buffalo was published by ICAR in 1979.compiled information on

important indigenous breeds of livestock (Acharya et al)

THE OBJECTIVES OF NBAGR WITH REGARD TO CONSERVATION ARE AS

FOLLOWS:

1. To develop inter-institutional co-operative programs for the genetic evaluation and

conservation of animal genetic resources.

2. To develop infrastructural facilities and train manpower for the execution of the project.3. To estimate demographical distribution of breeds in their respective tracts by undertaking

proper surveys.

4. To obtain need-based information for breed description and characterisation of various

special/animal types by evolving suitable formats and questionnaires to collect data through

scientific surveys.

5. To obtain data on certain qualitative and quantitative morphological characteristics which are

related to production and reproduction.

6. To identify superior germplasm and rare variants for the specific breeds.

7. To devise suitable strategies for the purpose of in-situ conservation and propagation.

8. To develop an inventory breeds/animal typos which are declining or are at the verge of

extinction.

The technical programme of the project is as follows:

1. Demographical and geographical distribution

2. Enumeration of breeds in terms of age, sex in a population.

3. Qualitative and quantitative characterisation of breeds in relation to specific phenotypes traits

like type, production potential and reproductive status etc.

4. Qualitative and quantitative descriptions of unique animals, elite producers, and rare or unusual

characteristics in certain specimens

5. Collection of blood samples from 100 males and 100 females of each breed/type for genetic

evaluation work pertaining to blood typing and biochemical polymorphism, immunogenetics,

cytogenetics, gene marker studies, restriction fragment length polymorphism of DNA and other

recently developed molecular genetic techniques.


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Immediate strategies would involve the Survey, Conservation of Livestock Genetic

Resources, Research on Conservation and Training in Conservation and Management.

Serious efforts should be made to organizing conservation and evaluation strategies.

Since the major emphasis in any system of conservation is the lack of information in gene

resources, it is absolutely important that evaluation and conservation should go hand in hand and

can be achieved by the following:

1. All universities, educational institutions, religious trusts and organizations associated or having

interested in historical preservation should be aided by the Government and encourage to maintain

small groups of animals in their natural habitat or intended management systems. These groups

should be under a uniform recording system, in a computer readable format with the evaluation

and documentation being done at the NBAGR.

2. All the developmental programs being taken up by the state governments should have amandatory prerequisite that breeds being used for crossbreeding or grading up should be

maintained in nuclear herds in their natural habitat and subjected to continuos evaluation as

described above.

A SIMPLE DIAGRAM OF THE INTERACTIONS AMONG THE POSSIBLE STAKEHOLDERS IN A COMMUNITY-BASED

BREEDING PROGRAMME


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Steps taken in India

In India the need for conservation of animal genetic resources has now "become clear, and the

lack of necessary documentation and evaluation has been recognized. A National Bureau of

Animal Genetics Resources and one for fish have been sanctioned, which will have the following

functions:

1. To undertake systematic cataloguing of animal germ-plasm and to establish a data bankand information service on animal genetic resources.

2. Identification, evaluation, cataloguing and conservation of herds or flocks identified asvaluable for purposes of conservation consisting of important indigenous breeds of

livestock and poultry in the country.

3. To undertake survey for the evaluation of merits or attributes of breeds discovered recentlyor threatened with extinction.

4. Formulation of criteria and parameters to enable identification of animals and flocks ofsuperior genetic merit or worthiness for conservation. To take steps for the preservation of

germplasm both as live animals or by setting up frozen semen and embryo banks.

5. Documentation of pertinent information in regard to identity of herds and flocks on acomputer readable format.

6. Processing of information collected under surveys carried out for the identification ofvaluable animal resources material.

7. Dissemination of information in a cogent manner to enable individuals and agencies to useinformation in regard to the available animal genetic resources,

8. Maintenance of national/international liaison with institutions concerned with similarwork.

9. Rendering financial assistance to universities, IGAR institutes and government and privatebodies, where maintenance of such valuable germ-plasm is considered desirable.

10.Monitoring of the entire improvement programme and maintenance of rare breeds/herds/flocks in the country.

11.Monitoring of new introduction of animal germ-plasm and new synthetics.12.To stimulate programmes for improvement in the various breeds and to give adequate

financial and technical support to these.


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STEPS IN MOLECULAR CHARACTERISATION

BEFORE YOU START

Ideally, molecular characterization should be undertaken as part of a comprehensive national

programme for management of AnGR, the development of which is outlined in FAO Guidelines

for Preparation of National Strategies and Action Plans for Animal Genetic Resources. For

maximum efficiency, molecular characterization of AnGR should be done in concert with

phenotypic characterization, which is addressed in FAO Guidelines for Phenotypic

Characterization of Animal Genetic Resources.

KNOW YOUR BREEDS

Collect and critically evaluate the available information on the breeds you want to investigate:

scientific literature, breed handbooks, FAO Global Data Bank or other data banks, non-scientific

literature and even anecdotal information. It is most relevant to identify the traditional rearing areaand any evidence for genetic subdivision: different ecotypes, phenotypes, agroclimatic zones or

isolated subpopulations.

INVOLVE LOCAL EXPERTS

Most of the expertise on local breeds rests with the farmers and breeding societies, who should be

informed on the objectives of the study. Coordination with national breeding societies and

livestock research institutions is desirable, as they are expert on the breeds, are familiar with local

circumstances and may serve as liaison with the owners. Inform also FAO National Coordinators

for Animal Genetic Resources, because, as noted earlier, characterization studies should ideally be

undertaken as part of an over National Strategy and Action Plan for AnGR.

DEFINE THE OBJECTIVES

Ranging from an inventory of the pattern of diversity to a reconstruction of the history of breeds

or formulation of specific guidelines for genetic management, objectives are most relevant for the

sampling, choice of markers and data analysis.

ACT LOCALLY, THINK GLOBALLY

The data collected will invariably become more interesting if analyzed and evaluated in an

international context. Combining results with other datasets requires the use of the same

molecular markers, the use of common reference samples and, preferably, having one or more

breeds in common.

DEFINE THE SCOPE

Depending on the breeds and the objectives of the study, the following considerations maybe relevant.

Breeds most likely to be distinct from other breeds are those with a long history of geneticisolation, raised in a unique environment or having unique phenotypes.


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Priority should be given to local breeds, but common or economically importantinternational transboundary breeds should be included as a reference.

For regional transboundary breeds it will be useful to include populations across theborders or to collaborate with institutes who have studied those populations.

For breeds that are of hybrid origin by introgression, upgrading or by the planned creationof a synthetic breed, it is essential to have data from parental breeds.

For breeds having a recent history of intense selection and/or inbreeding, sampling ofanimals of previous generations, which may be available by cryopreservation of semen

samples or from museum specimens, may be appropriate.

For mammalian species, sampling of at least 10 males allows studies on Y chromosomevariation, whereas samples of poultry species preferably should contain at least 10 female

birds for eventually studying W-chromosomalCOLLECT SAMPLES

For this most crucial step, the following considerations are relevant:

Almost all cells or tissues may be used for DNA analysis: blood, semen, hide, bone, tissue(e.g. ear tissue), plucked hair (only the root cells contain nuclei, but cut hairs can be used

for mtDNA analysis) and feathers,

High quality DNA is most easily obtained from samples of peripheral blood, organs orother tissues. Most convenient are blood samples, to be collected in an anti-coagulant

(EDTA or Na-citrate).

Collect enough material for present and future studies. For PCR-based applications, 10 mlof blood is adequate, but for high-density SNP typing and genomic sequencing, it is

advisable to sample 50 ml or more. Note that poultry species have enucleated erythrocytes

and, therefore, much less blood (~1 ml) is required.

Transport of blood samples can be at ambient temperatures, but in tropical regions samplesshould be processed within 36 hours.

For longer storage, samples can be placed in a room temperature preservative such asQueen's buffer (0.01. M Tris/HCL , 0.01 M NaCl, 0.01 M EDTA and 1 %

nlaurosylsarcosine, pH 8.0).

Tissue samples of 1 cm squared should be minced to 1 mm squared pieces and placed inQueens buffer or 70% ethanol. Air-drying of ethanol-treated samples allows long term

storage and the easy transport of samples. Alternatively, pieces of tissue may be directly

dehydrated by placing in vials on crystals of silica gel.

Hair samples should be desiccated as soon as possible and stored dry.


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FTA cards can be used for collection of genetic material with DNA to be amplified byPCR, but special protocols are required to obtain double-stranded DNA and the stranded

DNA obtained with standard isolation protocols is not suitable for all other applications.

Samples that are to be used for cloning, Southern blotting or genomic sequencingprotocols require double-stranded DNA of high molecular weight.

From each animal, duplicate samples should be taken and kept separate during subsequenttransport and storage.

Labelling of samples should be unambiguous and permanent. The labelling proceduresshould be developed and supervised by the responsible scientist of the project.

Bank it: store all samples and document all relevant information unambiguously in such a

way that they can be retrieved and understood, even by persons not involved in the sampling.

Also collect dataEssential is recording of the following information for each sample:

1. Sample (and duplicate) number2. Date3. Location and GPS coordinates,4. Name of collector5. Breed6. Sex of animal7. Type of sample8. Any relevant phenotype9. Basic pedigree information10.Size of herd11.Digital photograph with measuring stick,

Any interesting morphological features .Notes about any recent change in geographic location of

the animal should be compiled once for each breed, to the extent that is possible based on the

information available. This form addresses breed origins, farming practices, basic production

information, and features of the breed such as productivity, disease resistance or adaptation to

local conditions should also be recorded.

LABORATORY PROTOCOL

Extracting DNA

Several reliable protocols for DNA extraction are available. Older protocols are based on

Proteinase K/SDS lysis of cells, organic extraction and alcohol precipitation. Salt precipitation

avoids the organic solvents, but the long-term stability of the DNA samples is problematic. Now,

convenient commercial kits based in the specific binding of DNA to resins are available for

several kinds of tissues and generally perform well. It is recommended to test out before


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application to field samples any DNA extraction procedures that have not been used routinely.

Consider the amount of DNA required by the different protocols.

Genotyping.

Protocols for genotyping are generally available and straightforward, but the followingfactors should be taken into account:

Analyze in each experiment at least one reference sample in order to cross-validatesuccessive genotyping experiments and include this in all experiments.

For microsatellites, use the FAO recommended panel and include international referencesamples in order to link your data with other datasets.

Include blank extraction and amplification samples in order to check contamination of thereagents.

Outsourcing the genotyping to dedicated custom service laboratories may very well ensurehigh quality and cost-effective results without requiring investment in new equipment and

expertise. Outsourcing does not, however, lift the requirement of analyzing reference

samples and critically checking the quality of the data.

In collaborative projects with microsatellites, it is preferred that one laboratory performsall typings for a given marker in order to exclude laboratory-dependent scoring. If this is

not feasible, it is most essential to share samples of reference animals in order to be able to

standardize allele sizes.

Multiplexing the PCR can reduce the costs, but results should be checked carefully toensure it does not increase the percentage of missing genotypes. This applies especially to

samples with low DNA concentration. As a compromise, PCR reactions can be carried out

separately and be combined on the gel (multiloading).

Data analysis

Check the data

Remove uncertain scores and delete markers and animals with an excess of missing data.Also check for outliers. Be aware that erroneous genotypes may distort the results of the

analysis. The following checks should be carried out in order to minimize the error rate ,

Matching duplicate samples, indicating errors during sampling or processing of samples Examining unusual alleles, this may result from clerical mistakes or incorrect

interpretation of electrophoretic patterns.

Check for an excess of apparent homozygosity in samples with low DNA concentrationbecause of allele dropout.

Standardize allele-calling with other laboratories, particularly for microsatellites. Compare allele frequencies with data from breeds that are likely to share the most frequent

alleles in order to detect inconsistent allele sizing.


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Check for absence of laboratory-dependent clustering of breeds, which may result fromsystematic differences in allele calling. One cause of laboratory-dependence may be the

lab-dependent differentiation of microsatellite alleles that only differ by one bp in length.

Linkage disequilibrium (LD). Markers in LD in all populations are probably geneticallylinked.

Hardy-Weinberg (HW) equilibrium. Markers that in most breeds are not in HW may havenull alleles or be linked to loci under selection, hence breaking the assumption of

neutrality.

Always keep the original version of the data in which no corrections have been carried out,so data can be recovered if deleted in error.

Within-breed analysis. Expected heterozygosity or allelic richness within breeds indicates the

influence of drift on breed diversity, where decreased heterozygosity is associated with increaseddrift. Differences between expected and observed heterozygosity as well as departure from Hardy-

Weinberg equilibrium indicate non-random mating or the existence of population substructures.

The presence of inbreeding can be tested by F statistics, in particular by testing if the FIS

parameter is significantly larger than zero. Genetic subdivision may be explored further by model-

based clustering

Analysis of breed relationships. Breed formation has led to a partitioning of the total diversity in

a within-breed and an among-breed component. These components and others, e.g. the component

due to the geographic location of breeds, can be quantified by AMOVA analysis and reflect

history and breeding practices. Typically, 50 to 90% of the total diversity corresponds to the

within-breed component, depending upon the group of breeds sampled and the sources of

variability considered.

What are the data trying to tell us? Place the results in a historic perspective.

Keep in mind that genetic events migration, introgression, admixture, crossbreeding, population

bottlenecks, and selection have happened at different times, which may complicate the pattern of

diversity. Consider alternative explanations and do not interpret according to preconceived ideas.

Conservation priorities., the usefulness of the currently available algorithms is still a matter of

debate . The use of genetic marker information in prioritization of breeds for conservation has

been discussed in the FAO Guidelines for In Vivo Conservation of Animal Genetic Resources.

PUBLISH RESULT

Publish your findings in a scientific journal. Open-access journals are recommendedbecause of their wide diffusion and free accessibility.

Properly acknowledge contributors of samples and/or data. After publication, deposit your data in a public database and/or comply with requests to

make datasets available.


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If appropriate, formulate recommendations for genetic management and conservation anddisseminate these to breeding organizations and government agencies such as the National

Advisory Committee on AnGR, assuming that one exists, as well as the FAO National

Coordinator for AnGR. Below are a number of examples that show how molecular

observations are relevant for genetic management:

CONCLUSIONS AND RECOMMENDATIONS

1. Zebu breeds are endowed with highly desirable characters like adaptability to harsh conditions

and resistance to diseases. A more reliable and objective assessment of performance of indigenous

breeds with special emphasis on diseases resistance and adaptability to harsh environments is

essential,

2. In view of the rapidly increasing costs of conventional energy inputs, it is highly desirable to

generate adequate information on draft ability of indigenous cattle and buffaloes which is very

insufficient at present.

3. Precise and reliable estimates of different genetic components of variability of important

economic traits of indigenous breeds of livestock should be obtained. This would be needed for

evolving appropriate breeding plans for their improvement.

4. An atlas of performance of indigenous breeds and the appropriate breeding plans based on the

information thus collected be drawn up. Such information would allow the best utilization of

genetic resources in cattle and buffaloes and other specie

5. Properly designed selection experiments should be carried out for important indigenous breeds

which are not involved in genetic improvement experiments through crossbreeding.

6. Since sizeable populations of different crossbreds are available around a number of milk shed

areas, such populations should be utilized for performance recording and progeny testing of

crossbred sires, in order to take full advantage of crossbreeding, progeny tested half bred bulls

should be used for the development of new breeds/strains adapted to the given environment.

7. The present evaluation of different breeds and breed crosses is being done only under intensive

management system. Such evaluation should be done under intensive, medium and low input (as

close to the existing practices in the farmers fields as possible) so that the most efficient genotypes

for each of these management levels could be identified.


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8. A number of native breeds, strains or varieties are, or may be, in danger of genetic dilution

through indiscriminate crossbreeding with exotic breeds. Such native breeds should be identified,

so that they can be evaluated before this process leads to their essential loss.

9. Some native breeds are in danger of losing genes for high production because high-performing

animals are withdrawn from breeding populations for use in units of high production and/or

subsequent slaughter (e.g. city milk production in India or slaughter animals closen because of

large size). Such breeds should be identified and breeding units kept intact.

REFERENCES

1. Acharya, R.M., 1982, FAO Animal Health and Production Paper No. 30.2. Acharya, R.M. and Bhat, P.N., 1984, Livestock and poultry genetic resources in India,

IVRI, Research Bulletin No. 1, Indian Veterinary Research Institute, Izatnagar, India.

3. Anderson, G.B., 1986, Identification of sex in mammalian embryos. In GeneticEngineering of Animals;

4. Gordon, J.W., Scangos, G.A., Plotkin, D.J., Barbosa, J.A. and Ruddle, F.H., 1980, Genetictransformation. of mouse embryos by macroinjection of purified DNA. Proc. Nati. Acad.

Sci., USA, 77: 7380 - 7384.

5. Rao, M.K. and Reddy, A.O., 1995, Livestock Genetic Resources in southern region:conservation for posterity. Symposium on Breeding strategies for optimum animal

production conducted by Dakshin Animal Breeders Society on 24 -25 February at

Bangalore.

6. Tomar s.s. 2009.Conservation of animal genetics resources .chapter in :Text book ofanimal breeding ,kalyani publishers page no. 61-62.

conservation of genetic resources in india

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