title: Locus minimization in breed prediction using artificial neural network approach.
abstract: Molecular markers, viz. microsatellites and single nucleotide polymorphisms, have revolutionized breed identification through the use of small samples of biological tissue or germplasm, such as blood, carcass samples, embryos, ova and semen, that show no evident phenotype. Classical tools of molecular data analysis for breed identification have limitations, such as the unavailability of referral breed data, causing increased cost of collection each time, compromised computational accuracy and complexity of the methodology used. We report here the successful use of an artificial neural network (ANN) in background to decrease the cost of genotyping by locus minimization. The webserver is freely accessible (http://nabg.iasri.res.in/bisgoat) to the research community. We demonstrate that the machine learning (ANN) approach for breed identification is capable of multifold advantages such as locus minimization, leading to a drastic reduction in cost, and web availability of reference breed data, alleviating the need for repeated genotyping each time one investigates the identity of an unknown breed. To develop this model web implementation based on ANN, we used 51,850 samples of allelic data of microsatellite-marker-based DNA fingerprinting on 25 loci covering 22 registered goat breeds of India for training. Minimizing loci to up to nine loci through the use of a multilayer perceptron model, we achieved 96.63% training accuracy. This server can be an indispensable tool for identification of existing breeds and new synthetic commercial breeds, leading to protection of intellectual property in case of sovereignty and bio-piracy disputes. This server can be widely used as a model for cost reduction by locus minimization for various other flora and fauna in terms of variety, breed and/or line identification, especially in conservation and improvement programs.
authors.affiliation: Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India.
authors.forename: M A
authors.initials: MA
authors.lastname: Iquebal
authors.forename: M S
authors.initials: MS
authors.lastname: Ansari
authors.lastname: Sarika
authors.forename: S P
authors.initials: SP
authors.lastname: Dixit
authors.forename: N K
authors.initials: NK
authors.lastname: Verma
authors.forename: R A K
authors.initials: RA
authors.lastname: Aggarwal
authors.forename: S
authors.initials: S
authors.lastname: Jayakumar
authors.forename: A
authors.initials: A
authors.lastname: Rai
authors.forename: D
authors.initials: D
authors.lastname: Kumar
mesh_terms: D000465:Algorithms; D000483:Alleles; D000818:Animals; D001947:Breeding; D016172:DNA Fingerprinting; D056426:Genetic Loci; D060005:Genotyping Techniques / Q000379:methods*; D006041:Goats / Q000145:classification / Q000235:genetics*; D007194:India; D020407:Internet; D018895:Microsatellite Repeats; D008957:Models, Genetic; D016571:Neural Networks, Computer; D020641:Polymorphism, Single Nucleotide
keywords: DNA markers; breed assignment; goat breed; webserver