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Development of a model webserver for breed identification using microsatellite DNA marker

Mir Asif Iquebal1, Sarika1, Sandeep Kumar Dhanda2, Vasu Arora1, Sat Pal Dixit3, Gajendra PS Raghava2, Anil Rai1 and Dinesh Kumar1*

Author Affiliations

1 Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India

2 Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India

3 National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001, India

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BMC Genetics 2013, 14:118  doi:10.1186/1471-2156-14-118

Published: 9 December 2013

Abstract

Background

Identification of true to breed type animal for conservation purpose is imperative. Breed dilution is one of the major problems in sustainability except cases of commercial crossbreeding under controlled condition. Breed descriptor has been developed to identify breed but such descriptors cover only “pure breed” or true to the breed type animals excluding undefined or admixture population. Moreover, in case of semen, ova, embryo and breed product, the breed cannot be identified due to lack of visible phenotypic descriptors. Advent of molecular markers like microsatellite and SNP have revolutionized breed identification from even small biological tissue or germplasm. Microsatellite DNA marker based breed assignments has been reported in various domestic animals. Such methods have limitations viz. non availability of allele data in public domain, thus each time all reference breed has to be genotyped which is neither logical nor economical. Even if such data is available but computational methods needs expertise of data analysis and interpretation.

Results

We found Bayesian Networks as best classifier with highest accuracy of 98.7% using 51850 reference allele data generated by 25 microsatellite loci on 22 goat breed population of India. The FST values in the study were seen to be low ranging from 0.051 to 0.297 and overall genetic differentiation of 13.8%, suggesting more number of loci needed for higher accuracy. We report here world’s first model webserver for breed identification using microsatellite DNA markers freely accessible at http://cabin.iasri.res.in/gomi/ webcite.

Conclusion

Higher number of loci is required due to less differentiable population and large number of breeds taken in this study. This server will reduce the cost with computational ease. This methodology can be a model for various other domestic animal species as a valuable tool for conservation and breed improvement programmes.

Keywords:
Bayesian network; Breed; Goat; Microsatellite; Prediction; Webserver