Microsatellite Markers for genetic variability – study on India goat species | Think Science India

Microsatellite Markers for genetic variability – study on India goat species

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India has a great diversity in domestic livestock and poultry genetic resources. Economically important species of livestock and a large number of breeds / strains within each of these species exist. Among domesticated livestock species, there are over 30 breeds of cattle, 10 breeds of buffalo, 42 of sheep, 20 of goats, 8 of camel, 7 of horses and 18 of indigenous poultry.

Due to various reasons some livestock breeds are in immediate danger of loss and it is estimated that 1500 of the breeds of the world’s domestic animal species are now at high risk of extinction. Recognizing the importance of indigenous animal genetic resources, there is a need to conserve them for making their utilization in future.

The goats are important species of livestock for India as they contribute greatly to the agrarian economy, especially in areas where crop and dairy farming are not economical, and play an important role in the livelihood of a large proportion of small and marginal farmers and landless laborers.

Most of the breeds of goats are very well adapted to the harsh climate, long migration, and lack of vegetation and drinking water. There has been little effort to conserve and further improve the native breeds.

 

Need of Characterizing Goat Genetic Diversity: –

The plethora of unique indigenous goat germplasm has not been fully characterized and explored. At present very few genes controlling economically important traits of goat have been identified and even the mapping of the genes is a long way from fully understanding their structure and function. Since we cannot characterize the differences between the goat breeds in terms of economically ( growth, milk) important genes, therefore general genetic variability is the most suitable criteria for identifying the breeds for genetic uniqueness. Genetic Characterization is the first step in the conservation programme, as it will help in breed prioritization.

 

Global Strategy on Animal Genetic Diversity:-

Keeping in view the sharp decline in biodiversity and then urgency to characterize the indigenous germplasm of different countries, Food and Agricultural Organization (FAO, 1996) of the United Nations has proposed an integrated programme for the global management of genetic resources including cattle using microsatellite methodology for breeding characterization.

 

What are Microsatellites:- 

  • Microsatellites are markers that contain repetitive sequence composed of di-, tri-, or tetra- nucleotides.
  • Microsatellites are also known as simple sequence repeats(SSRs), Short tandem repeats(STRs) and sequence tagged Microsatellite repeats(STMRs)
  • The number of repeats may vary from one person to other, i.e. polymorphic and follow mendelian inheritance.
  • Microsatellites in different individual are not just the same or a different, they can differ by just a few repeats units.
  • The reasons of Microsatellite popularity as genetic marker are that their high mutation rate makes them highly polymorphic, and they are relatively dense in the genomes of many organisms.
  • Due to their high level of polymorphism, microsatellites are informative marker that can be used for many population genetic purposes, ranging from individual level to closely related species.
  • They can used to estimate effective population size (Allen et al.,1995), and to gain insight in to the degree of population substructure including both the amount of migration between subpopulations and genetic relationship among the various subpopulation

 

Occurance and distribution of Microsatellites:

A striking feature of the eukaryotes genome is that the coding sequences constitute only about 5 to 10 percent in the mammals, of the total genome. The apparently non- functional DNA is either the single copy DNA or the competitive DNA.The repetitive elements may be interspersed in the genome or may occur as tandem repeats. Tandem repeats consist of the same sequence repeated thousands or millions of times in tandem, thus forming discrete blocks of DNA. Interspersed repeats on the other hand consist of specific sequences dispersed around the genome but not forming tandem repeated blocks. In mammals, two major groups of the interspersed repetitive element can be recognized: the short interspersed elements (SINEs) and the long interspersed elements (LINEs). (Schmid and jelinek, 1982; Rogers 1983; Singer et al 1987). Both types of element are proposed to have originated by the reverse flow of information by retro position.

The tandem repeats are broadly refers to as the satellite type of DNA. The satellite type is further classified as satellite, telomeric, minisatellite, and microsatellite DNA. Satellite often has a repeats unit consisting of hundreds or even thousands of nucleotide.

Litt and Luty(1989) introduced the term microsatellite to characterize the simple sequence repeats amplified by PCR as a new kind of polymorphic marker. These are tandemly repeated motifs of 1-5 nucleotides that are densely and evenly distributed through out the genome and often exhibit substantial variation in the number of repeats. They occur at a frequency of one SSR per 10kb DNA and numbering to a total of 50,000- 100,000 in the mammalian genome and follow Mendelian co-dominance Inheritance. The most common Microsatellites in mammals are

 

AAAAAAAAAAAAAAAAAAAAAA………… (A)n

CACACACACACACACACACACACACACACACA……………(CA) n

AAATAAATAAATAAATAAATAAATAAATAAATAAATAAAT…………(AAAT)n

AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG…………..(AG)n

 

Application of Microsatellite in caprines

  • Genetic Characterization.
  • Linkage analysis and gene mapping
  • Individual identification of parentage testing

 

Study : Genetic Variabilty in Goats

Genetic variability in a small local goat population from the south of Italy were evaluated and compared with some international breeds. DNA polymorphism at microsatellite marker BMS2508 in four goat breed were studied by Ouyang xuxiang et al(2005) in order to obtain molecular markers for multiple embryos on goat.

Goat Data

Genetic structure and phylogeny status of Chaidamu goat population were studied by Zhang Xifeng et al (2005) using simple random Samplings. Genetic structure was analyzed by five aspects and phylogeny status was also investigated. The results indicated that

  1. The average phenotypic heterozygosity degree of coat colour and morphological character were 0.3419 and 0.5207respectively.
  2. Polymorphous blood albumin existed in six loci and the average loci heterozygosity was 0.2584
  3. Polymorphism existed in marker gene by DNA- RAPD

All these indicated that Chaidamu goat is a domestic Goat with less intensively selected breeds.

Dinesh Kumar et al (2005) studied the genetic variation and management of Marwari goat. Genetic variation at 25 microsatellite loci, population structure and genetic bottleneck hypothesis were examined in Marwari goat in arid region of Rajasthan(India). The average polymorphism between the studied loci and the expected gene diversity in the population were 1.295 and 0.623±0.041 respectively.The population was observed to be significantly differentiated into groups and showed a fairly high level of inbreeding and global heterozygote deficit.

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Pic: Kalahari red goat

A genetic profile of the Kalahari red goat from South Africa was studied by Kotze.A et al (2004). The erosion of Kalahari Goat with red boer goat is a major concern among breeders. Eighteen Microsatellite markers were applied to investigate the genetic diversity of the breed and to set up a molecular inventory.

Genetic variation of the three commercial and three indigenous goat populations in South Africa was studied by Visser C et al (2004) by using ten microsatellite marker.

Jandurova O M et al (2004) analyzed microsatellite variation in two breeds of goat, White short haired(WSH) and Brown short haired (BSH). Three markers originated from cattle, three from goat, and three from sheep within these seven loci- Allele frequency, Heterozygosity (H) Polymorphism information Content (PIC) and Genetic distance (D) were calculated. Both breed exhibited relatively high level of heterozygosity.

Genetic diversity of sub Saharan African goat was assessed using 19 Microsatellite marker studied by Chenyambuga SW et al in 2004 breeds were sampled from eastern Africa (Massai, kigezil, Mubende) and western Africa ( Dwarf, Maure) and European breeds (Grizons , Stripped) and a middle breed were also included. It was concluded that the relationship of sub- Saharan African goat breeds were accordingly to their geographical location implying that the goat of eastern Africa, west and south Africa are generally distinct within each sub region, goat population could be differentiated according to morphological characteristics.

These are some example of researches done on finding goat genetic diversity. In the next episode we will see the research done on finding genetic diversity in Attapady goat by using 25 Microsatellite markers and its comparison with Mahasana Goat.

Author : Savita Bubna,Asst Editor TSI

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