MOLECULAR GENETIC PROFILING FOR SELECTION OF DAIRY ANIMALS Archana Verma National Dairy Research Institute, KARNAL-132001

Introduction The advent of high-throughput DNA sequencing techniques, array technology and protein analysis has increased the efficiency of research in bovines with the ultimate objective of improving milk quantity or quality. For genetic purposes, polymorphisms in some key genes have been reported for their association with production traits. The sequencing of the bovine genome has dramatically increased the number of available gene polymorphisms. Some of these genes are specifically regulated by genetic and nutritional factors. Identification of superior animals is only one step in a breeding program. No animals have exactly the genes the breeder desire, but some have more nearly the ideal than others do. This makes it impossible to improve a herd or breed in all respects at once, simply by continually grading it up. This implies that optimum selection and mating strategies need to be developed to exploit the genetic variation between animals. Conventional selection programmes continue to deliver steady genetic improvement in all animal populations. New molecular methods offer the prospect of enhancing genetic gains, particularly for traits that are difficult or expensive to measure, or which have low heritability.

Genomic selection Genomics is the science of structure, function and interrelationships of both individual genes and entire genome. The field encompass wide spectrum of fundamental and practical tasks from molecular marker development to the sequencing and mapping of the complete genomes of different organisms. Following closely in the footsteps of the Human Genome Project, genome research in farm animals has progressed rapidly in recent years from routine trait genome maps to gene discovery. These advances are the result of several animal genome projects aimed finally to develop effective application of DNAbased tools to livestock health and production. Nowadays, DNA markers like single nucleotide polymorphisms (SNPs) or microsatellites (MS) linked to

specific traits can be already successfully used in breeding programs to select elite animals or eliminate an undesirable trait soon after the animals birth. It should be underlined, that in every practical application, the development of the informative and cost effective marker assisted selection (MAS) program requires detailed analysis of many genomic resources of the particular animal. Necessity to deal routinely with the abundant and growing complexity of the genome data sets created nowadays the novel branch of bioinformatics. Bioinformatics deals with methods and resources for storing, retrieving and analyzing of the genomic data including sequences, structures, functions, metabolic pathways, and the data on genetic polymorphisms. Both Genomics and bioinformatics encompass theoretical and practical tools for the propagation, generation, processing and understanding of the genomic data in different species in any applications. The goal of the genomics and bioinformatics is to improve the efficiency and wellbeing of farm animals and the quality of their useful products for the wide range of human needs by using genetic, genomic, and molecular tools. Rapid advances in the understanding of farm animal genomes was achieved due to genome sequencing projects of livestock, development of molecular marker and computer based tools. A large number of polymorphisms that have been characterised in many species, has globally boosted the search for genes involved in multifactorial economically important traits such as growth rate, milk production, disease resistance, reproductive efficiency, carcass quality etc. Taking into account statistically significant association between important traits and genomic DNA variations, fine density quantitative trait loci (QTL) maps were constructed for main farm animals. The development of molecular genetic technologies provides the opportunity to better understand the genetic basis of animal performance, especially for traits with complex genetic determination or low heritability. Dissecting these traits into their Mendelian components is an important driving force behind the ongoing efforts to map QTL in livestock. Information from phenotypes and marker genotypes can be utilized to pinpoint chromosomal areas that explain a substantial amount of genetic variation and this can be incorporated to improve the genetic evaluation of animals in several ways: 1) incorporating known genotypes; 2) marker-assisted genetic evaluation; 3) construction of a marker-based relationship matrix and 4) genomic model. Genome sequencing identifies huge numbers of the smallest genetic variations called SNPs. Most of these do not affect gene expression, but can be used as markers to track the inheritance of chromosome segments in animal population . Knowing even tens of thousands of SNPs brings closer to every genetic variant involved in causing variation in a particular trait. If you then have large numbers of animals (low thousands) with trait measurements, you can assign a value to

each SNP for its association with a particular trait. That allows equations to be developed to predict the animals genetic merit based on the SNP variants it has. This is the principle of Genomic Selection (GS, or genome-wide selection). Early results from the use of this technology in dairy cattle suggest that genomic selection is accurate, especially for low heritability traits. It seems to offer considerable potential, especially where the costs of obtaining good trait measurements are high such as progeny testing young dairy bulls for milk yield capacity, or identifying animals with greater resistance to endemic diseases. Balanced breeding goals Not all the consequences of selection are intended or desirable. Examples are the decline in fertility in dairy cows, or leg strength problems in fast-growing broiler chickens. These problems illustrate the competition for the allocation of resources within the animal. There is the risk that selection for one thing will withdraw resources from essential functions that may become apparent only when animals are environmentally stressed. It then begs the question - are there limits to selection? Or even, have the gains made by breeders been at the expense of something we would rather have kept? Clearly there must be limits to selection but there are no signs we are close to them for most traits. In addition, some improvement is from selection for more efficient biological systems, such as less wasteful ways of growing and maintaining tissue. It is possible that modern fast growing animals may have partitioned some resource away from immune function. These potential resource conflicts are however not simple black or white choices not all very high yield dairy cows have fertility problems. There are many animals that have the right combinations of DNA variants to do all things well and it is these animals breeders seek to choose as parents of the next generation. The potential to select for disease resistance or tolerance is a high research priority. For every farm animal disease studied to date there is genetic variation in disease incidence and severity. That may be a function of several factors such as the ability of the animals to avoid infection in the first place, to mount a rapid and effective immune response when infected, to avoid an inappropriate overreaction to infection that might be permanently damaging or fatal; or to restrict growth of the pathogen/parasite to a tolerable level. Considerable interest is there in exploiting this variation from breeders point of view. There may be a doubt that Selective breeding for resistance to one disease will increase susceptibility to another, but evidences are that it may not be the case alwaysThere are now a number of examples where selective improvements in

resistance to one disease have coincided with improvements in resistance to others. So, disease traits are one area where Genomic Selection may provide a solution it may be feasible to record performance in commercial environments and do the association with DNA variants in the presence of the important diseases for that farm and then use the DNA prediction methods to choose within healthy nucleus herds and flocks the animals which will perform best in the presence of the disease. Profiling Genetic Potential The objective of breeders is to exploit the variability among animals by selecting those with a superior genetic potential for the trait of interest. Many traits suitable for improvement using quantitative genetic methods are easy or inexpensive to measure on a great number of animals, but many of the important traits are not. Several of the milk quality traits are difficult to improve, so researchers are currently looking for genes that influence genetic potential for these traits to select animals. This is a promising approach because genotyping is now increasingly easy and less expensive to perform. One important benefit of high-throughput techniques of genomics will indeed be the identification and the practical use of polymorphisms within DNA sequences of those genes. The discovery of DNAmicrosatellites that are highly polymorphic has stimulated research on detection and mapping of QTL in animal species. Many studies have been undertaken on the use of DNA-microsatellites (genetic markers) in the selection of animals in breeding programmes, a process known as marker assisted selection. The use of those DNA-microsatellites to introgress genes from a donor to a recipient animal, process known as marker assisted introgression (MAI), is under increasing consideration for the purpose of livestock improvement. Single nucleotide polymorphisms (SNP) are another the most frequent form of DNA variation in mammals. They are abundant, normally biallelic and easy to detect by automatic techniques. So far, polymorphisms in some genes have been reported for their association DGAT1, TG , caseins, lactoglobulins, lactalbumins, GH, leptin etc. Other efforts are devoted to the identification of SNP in a large set of candidate genes. Many of these associations have been confirmed in independent studies, although some have failed to be confirmed. The failure to confirm an association usually occurs in samples where there are fewer than 1000 animals in the study. A number of high throughput SNP genotyping platforms have recently become commercially available for the bovine. This genotyping platform will allow the analysis of many samples in parallel on a single microarray with over a number of SNPs per sample. Research groups all over the world are currently applying these

genotyping tools to populations of cattle extensively phenotyped for beef and dairy production and health traits.(Womack, 2006). Gene sequencing and SNP discovery in our domestic animal species will soon give us information about linkage disequilibrium over large genomic regions and the identification of haplotype blocks in various populations and breeds of livestock. Rapid progress in discovering patterns of genetic variation that can predict animal performance can be expected from these international efforts. The increased knowledge of functional candidate genes, which will be discovered from functional genomics approaches (array data, proteomic studies) is expected to further contribute to the progress of this field. Knowledge of the genes underling the expression of a trait will allow researchers to search for novel combinations of alleles to make further improvements in desired traits, as the most beneficial alleles and allele combinations may not occur in the production populations. Breeding schemes could then be designed to test novel combinations of alleles at different loci. Some of these novel allele combinations may result in the improvement of particular traits beyond that which would be possible by selecting phenotypically superior animals within a population. It is therefore important to maintain a diverse range of genetic backgrounds to provide sources of variation.

Conclusion Molecular genetic tools are now delivering new insights into the genome of livestock and other species. The development of genetic markers allows us to better understand and control relationships between breeds and animals within breeds. The development of complete genetic maps based on molecular markers has allowed some of the loci affecting qualitative (major gene) and quantitative traits (QTLs) to be mapped. In some cases, genes controlling variation have been located and causative mutations identified. This information allows the application of marker assisted selection to complement the more established tools of animal breeding. In this way, it is becoming possible to better manipulate traits such as milk quality, reproductive performance and disease resistance, which have been difficult to tackle in the past. In future many more loci will be mapped, biology of the traits of economic importance will be better investigated, the corresponding genes and their functions, genes underling the expression of a particular trait are expected to be identified and studied to provide animal breeders with effective tools of enhancing animal performance. In addition, it may be possible to address the difficult-to-measure traits through genomic selection. Modern molecular genetic

and biotechnology tools will greatly increase our understanding of, and ability to manipulate the biology of farmed animals and the biology of disease. Given the considerable change that has already been achieved, and the new tools we have and can envisage having, it might be pause for thought to ask what might our farm animals be like by the middle of the 21st Century?

Further Reading Ahmed S. and Khosa AN (2010) An introduction to DNA Technologies and their role in livestock production: A Review. The Journal of Animal & Plant Sciences 20(4): 305-314. Fadiel A., Anidi I., Eichenbaum KD (2005) Farm animal genomics and informatics: an update. Nucleic Acids Res 33: 6308 6318. Hocquette, J.-F., Lehnert,S., Barendse, W., Cassar-Malek, I. and Picard, B. (2007) Recent advances in cattle functional genomics and their application to beef quality .Animal Science. 1: 159173. Meade Kieran (2006) Molecular genetics the future for animal breeding. Irish Veterinary Journal .59: 634-638. NCBI: http://www.ncbi.nlm.nih.gov/ Spedding, Alan (2009) Current farming and rural issues for rural professionals. http://www.emda.org.uk Thara N, Takasuga A, Mizoshita K, Takeda H, Sugimoto M, Mizoguchi Y, Hirano T, Itoh T, Watanabe T, Reed KM, Snelling WM, Kappes SM, Beattie CW, Bennett GL, Sugimoto Y (2004) A Comprehensive Genetic Map of the Cattle Genome Based on 3802 Microsatellites. Genome Res 14: 1987 1998. Williams JL (2006) The use of marker-assisted selection in animal breeding and biotechnology. Rev Sci tech Off int Epiz. 24: 379 391. Womack JE (2006) Advances in livestock genomics: Opening the barn door. Genome Res 15: 1699 1705.