Vet. World, 2012, Vol.5(7):433-436 REVIEW Genomic selection- Revolutionary breeding practice in Domestic animals

With more and more Single Nucleotide Polymorphisms (SNPs) being identified throughout the genome, some of those SNPs will be found to be located within candidate genes, allowing the researchers to use the candidate gene approach on a genomewide scale. SNPs have some drawbacks but when compared to other markers they are more efficient and SNP consortium is growing to meet the requirements of genome-wide scans. Genomic selection should be able to at least double the rate of genetic gain in the dairy industry but the incorporation of genomic information into the breeding programs must be carefully considered. One needs to have around 2000 genotypes means a large reference population (population with both phenotype and genotype recorded) to achieve meaningful increases in accuracy. The available information, selection objectives, production circumstances and benefit/cost analysis must be evaluated in order to decide whether or not the population is suitable for GS implementation, and which would be the most convenient way, if any, for its implementation. Animal breeders will need to lead the way on the integration of genomic and phenotypic data into a new era of genome-enabled animal improvement and management.


Introduction
determine a person's susceptibility to disease or any adverse reaction to drug.Since the completion of the In the past century DNA has moved from being a human genome project, there has been a huge effort in mysterious molecule only of interest to a handful of establishing maps of genetic markers, especially of the specialists to being the heart of a technology that is most abundant source of DNA variation, the single transforming many aspects of the way we all live.The nucleotide polymorphism (SNP).A subsequent major study of human genetics has recently undergone a quest is to identify the variation in the human genome dramatic transition with the completion of both the causally involved in the genetic etiology of complex sequencing of the human genome and the mapping of diseases and drug response.Studies to explore which human haplotypes.In February 2001, two largely genes are involved in a trait include essentially two independent draft versions of the human genome were major approaches.published.Both studies estimated that there are 30,000 to 40,000 genes in the human genome, roughly one-Candidate Gene approach third the numbers of previous estimates.After human In the hypothesis based approaches the involvement (2001) and Mice, Whole Genome Sequence of the of candidate genes and pathways is being investigated chicken (2004), Dog (2005), Bovine (2006), Horse by testing for genetic association.A candidate gene is a (2007) and Pig (2009) are entirely available in the gene, located in a chromosome region suspected of public domain.However, we still have to make being involved in the expression of a trait such as a guesses at the actual number of genes and the work disease, whose protein product suggests that it could assigned to them because not all of the genome be the gene in question.A candidate gene can also be sequence is properly annotated.Humans differ in identified by linkage analysis to a region of the genetic makeup by only 0.1%, but that small part of the genome.In this approach, genotyping is targeted to genome contains the key differences that can functional and positional candidate genes [1].not the case for STRs, which have high mutation rates Functional candidates are genes that have been shown (often around 1/1000 to 1/250 per generation).or are suspected to have a functional role in the Genome-scans with microsatellites will result ~350 phenotype of interest, for example, lipid lowering by a markers with one marker every 5-10cM (1cM ~ 1000 drug.Allelic variants of such genes may be causal for bases) whereas with SNPs 3000 -10000 markers can the observed natural trait variation.In this case, DNA be obtained with one SNP in every 5Kb.polymorphisms located within the candidate gene or Genome-Wide Approaches can complement the physically close to it will be associated with trait candidate gene approach by providing relatively variation.To select the most promising candidates unbiased survey of the genome to identify previously from a large number of functional candidate genes, unrecognized candidate genes.Genome wide scan is a gene sequences are tested for linkage to QTL very extensive and elaborate study method for (quantitative trait loci) for the trait of interest by determining the effects of various allelic variants molecular mapping, thereby identifying positional occurring throughout the genome and the drug candidates [2].The candidate gene approach mostly response in a disease condition [5].This method depends on and takes advantage of the knowledge involves identification of all the allelic variants in the available in the literature and databases on physiology, entire human genome and the creation of a SNP map.biochemistry and molecular genetics of a trait of The first major GWA (genome wide association) study interest.Association studies with candidate genes in humans was published in Nature in February 2007 have been widely used for the study of complex by Sladek and his coworkers [6] in a study searching diseases.However, this approach has been criticized for type II diabetes variants.The work was mainly because of non-replication of results and limits on its carried out in the Genome Quebec centre at McGill ability to include all possible causative genes and University although it included collaboration with polymorphisms.
scientists of Imperial College, London and other research institutions.The group tested 3,92,935

Genomic Selection
single-nucleotide polymorphisms and identified Alternatively, recently explorative approaches several associations.Ironically, the developments in are applied which include genome-wide scans that molecular genetics over the last 20 years or so have first localize the gene(s) and subsequently identify the acted as catalysts to bring human and animal complex causal genetic variation at that locus.In this approach, and quantitative trait genetics closer together.The populations of individuals related by descent are development of molecular markers, first RFLPs, then genotyped with DNA-based markers covering the microsatellites and now SNPs, have increasingly whole genome, ideally positioned at regular intervals made the dissection of complex and quantitative traits on the physical map.The genome-wide approach feasible, into the effects of individual genes and essentially requires a sequenced genome and a large networks of genes in both animals and humans.In number of markers and is therefore expensive and human population studies and subsequently in the statistically complex [3].Out of the different kinds of major livestock species, attention has been switched to molecular markers, i.e. restriction fragment length association-based studies harnessing the linkage polymorphisms (RFLPs), random amplified polydisequilibrium across the population that can be found morphic DNA (RAPDs), amplified fragment length with dense marker panels (upto 1 million SNPs in polymorphisms (AFLPs), microsatellites and single humans compared to around 60 thousand currently nucleotide polymorphisms (SNPs), for the near future, used in cattle and pigs).SNPs are singled out as promising markers.SNPs

Application of Genomic selection in Animal
(pronounced 'snips') are single base-pair variations in breeding DNA.It is the most common source of genetic Animal breeding, one can say, is at the crossroads.variation in the human genome, accounting for about A range of new tools and technologies is becoming 90% of sequence differences [4].
available and this may change the methods used and Now the question arises, why are SNPs used, as the organization of breeding systems.In the last few opposed to the more polymorphic microsatellite loci?years, it has been witnessed that animal breeding and The reason is subtle, namely mutation rates.SNPs genetics evolves and expands from substantiation of have very low mutation rates and are closely spaced, basic population genetics to development of quantitative and hence any decay in association between a SNP and genetics leading to today's relatively sophisticated linked QTL is entirely due to recombination.Such is genetic prediction systems.Genomic selection, a variant The application of GS in dairy cattle has been of marker assisted selection (MAS) has become one of reported in many countries, including USA, Canada, the main areas of interest throughout the world.It is Australia, Norway, NewZealand, Netherland, well known that most economically important traits Denmark, Germany and Ireland.The traits currently for livestock are quantitative traits and in traditional being evaluated using genomic information include all breeding, breeders improve these traits by recording the target traits that are included in the traditional phenotypes and pedigrees.But, for traits with low breeding programs.A reasonable explanation is that heritability, sex-limited traits, longevity traits, and the bovine DGAT1 gene located on chromosome 14 traits that are difficult or expensive to measure (such as explains a considerable proportion of the genetic carcass traits); traditional selection methods have been variance for fat percentage.This would result in an of little use or are inefficient.With the advance of obvious deviation from the infinitesimal model for molecular genetics in the past 20 years, genetic this trait which might favor BayesB.Different types of markers have been used in animal breeding programs.chips based on the use of SNPs are also available for These new technologies can change both the rates and livestocks and can be used to achieve different systems of genetic change, by increasing accuracy, objectives.The bovine 50 K SNP chip has become the intensity or timeliness of selection.Unlike traditional standard tool for breeding industries in dairy cattle, MAS which uses only the few markers that are thought and a higher density chip 800 K SNP is also available to have large effects on the underlying trait of interest to screen for more genes and for a deeper implemento predict breeding values, Genomic selection (GS) tation of genomic selection.A smaller and less simultaneously uses high density (HD) markers expensive 3 K SNP chip is also available now to screen (particularly SNPs) covering the whole genome to large populations [9].predict the breeding values of each genotyped India is blessed with huge livestock population.individual [7].A breeding value predicted in this way Apart from varied climatic conditions, it has a vast is termed the genomic estimated breeding value genetic diversity which exists as a result of 3.5-4.5 (GEBV).In GS, it is assumed that each gene or QTL billion years of evolution.Domesticated cattle are the (quantitative trait locus) affecting the trait of interest is descendants of groups of races of Bos primigenius, in linkage disequilibrium (LD) with at least one of the known as 'urus' or 'auroch' and thought to be markers.Theoretically, all genetic variance can be domesticated around 6000 B.C. India, the goldmine tracked by markers if the marker density is high and vast reservoir of germplasm of indigenous cattle enough.Hence, GS has shown to overcome the accounts for 15% of world's cattle population.It has drawback of traditional MAS and predict breeding approximately 19.9 crores of cattle, comprising of values more accurately.Such experiments had used 16.6 crores indigenous cattle and 3.3 crores crossbred reference populations of between 650 and 4,500 cattle.It is also the largest producer of milk in the progeny-tested Holstein-Friesian bulls, genotyped for world.This enormous milk yield can be attributed to approximately 50,000 genome-wide markers.both indigenous and crossbred cattle population of the Reliabilities of GEBV for young bulls lacking progeny country.In fact, in this country indigenous cattle are testing results, in the reference population were found able to perform better under harsh climatic conditions, to be between 20 and 67%.
are resistant to diseases and able to convert coarse and To calculate GEBV, a prediction equation based dry fodder into valuable animal products.on the SNP is first derived.A variety of methods has However, about 75-80% of total indigenous animals been suggested for the calculation of GEBV, ranging are nondescript and hence remain undocumented.This from BLUP, Bayesian methods such as BayesB [8], is in sharp contrast to developed countries where each and machine learning techniques.These methods animal is known for its pedigree.Livestock developdiffer in their assumptions about the underlying ment in India is mostly characterized by policy genetic model: BLUP assumes the infinitesimal model, inadequacies, lack of political will and vision, adoption i.e. large numbers of genes each with small effects are of programmes without any long-term impact and scattered along the chromosomes; the machine learning wasteful government expenditure on subsidies.The technique assumes that there are a limited number of almost total absence of effective genetic improvement genes, and thus also a limited number of SNPs, and dissemination programmes is a fundamental worthwhile to be fitted; and BayesB is in between, i.e. constraint to the development of the livestock sector in it assumes few genes with large effects and many India.genes with small effect.
Keeping all these factors in consideration recently one Indo-Denmark Workshop on Genomic efficient and SNP consortium is growing to meet the Selection in Cattle and Buffaloes was held at National requirements of genome-wide scans.Genomic Agricultural Science Centre Complex, New Delhi, selection should be able to at least double the rate of th th genetic gain in the dairy industry [10] but the incorpo-India from 11 to 12 April 2011.The purpose of the ration of genomic information into the breeding workshop was to exchange knowledge and enhance programs must be carefully considered.One needs to cooperation between India and Denmark, focusing on have around 2000 genotypes means a large reference the potential and feasibility of genomic selection population (population with both phenotype and applied to animal breeding. genotype recorded) to achieve meaningful increases in Recommendations of the meeting: accuracy.The available information, selection -Traditional selection tools need to be combined objectives, production circumstances and benefit/cost with biotechno-logical tools to have higher rates analysis must be evaluated in order to decide whether of genetic improvement.Phenotypic and SNP or not the population is suitable for GS implemendata have to be combined for selection of animals tation, and which would be the most convenient way, if using multivariate analysis for genomic selection.
any, for its implementation.Animal breeders will need -Quality data is a key for the success of genomic to lead the way on the integration of genomic and selection.More numbers of sire families need to phenotypic data into a new era of genome-enabled be developed besides improvement in the accuracy animal improvement and management. of performance of recording systems.
-Highly-skilled manpower in the area of bio-References informatics, database development and mana-