Application Of “Omics” Technologies In Animal Nutrition

Sequencing of the bovine genome offers new opportunities to understand the biology of dairy cattle and provides the framework to identify the genetic basis for the improvements and animal differences in productive efficiency. The new areas of biomics era includes genomics (covering DNA), transcriptomics (RNA), proteomics (protein), metabolomics (metabolites) and systems biology (integrating all of these), with bioinformatics. Omics technologies help to design better dietary regimensmatching to genotype of the animal. Gene expression profiling using microarray technology is rapidly becoming an important tool for nutritional studies and for evaluating nutritional strategies. 

Nutrigenomics  applies genomic technologies to study how nutrients affect expression of genes. The study of how genes and gene products interact with dietary chemicals to alter phenotype and, conversely, how genes and their products metabolize nutrients is called Nutritional genomics or Nutrigenomics (Kaput  et al., 2005). Nutrigenetics focuses on how the genetic composition (i.e., genetic variation) of an animal influences their response to a given diet. Nutrigenomics studies will aid in formulating nutritionally appropriate diets that may be optimized for animals based on their genomic underpinnings. Individual gene markers may have variable response in individual animals receiving similar diets, hierarchical cluster analysis and pattern recognition methods are becoming tools for comparing nutritional responses with different diets. There are two areas where the developments in genomics are already affecting our understanding related to nutrition, feed efficiency and the biology of milk production. 

The use of residual feed intake as a selection tool identify cows with superior genetics for feed efficiency. Koch et al. (1963) first proposed the use of RFI as an attempt to partition feed intake into growth and maintenance components. Residual feed intake is defined as the difference between the actual feed intake of an animal and its expected feed requirements for maintenance and growth (Basarab et al., 2003). A significant improvement in profitability could be achieved through a reduction of production costs via implementation of selection strategies to improve feed efficiency with superior genetics , independent of growth rate. Genetic variation in maintenance energy requirements of cattle is moderately to highly heritable and, therefore, an opportunity to select for more efficient cattle may exist (Carstens et al., 1989). Genetic selection based on RFI can result in progeny that eat less without compromising growth performance (Richardson et al. 1998). 

Nutrigenomics describes how the amount and/or type of feed an animal receives, relative to its genetic and physiological requirements, affects its molecular phenotype, thus changing production, energy balance, reproduction, and health. The uncoupling of the somatotropic axis and the level and duration of this uncoupling can be influenced by diet.  Factors that influence energy balance, such as nutrition and milking frequency, have different effects on the metabolism of the mammary gland, liver, and adipose tissue. For example, although once-daily milking and greater feeding levels improve energy balance, once-daily milking lowers milk production through reduced secretary cell activity and number, whereas, greater feeding levels increase milk production through the provision of more nutrients. These effects are independent and at least partially additive; if both strategies are used, the outcome is a combination of the two. Experimental results indicate that the molecular changes underpinning these effects can persist beyond the period of treatment. Less frequent milking results in an earlier recoupling of the somatotropic axis post-partum and adipose accretion, physiological changes that are also influenced by energy balance, but are dependent on feed type as well as availability. A greater understanding of the effects of nutrition on the molecular phenotype is required to optimize cow management for productivity and welfare. 

Nutrition affects metabolism homeostasis and metabolic pathways of different cell (Kardia 2000). Nutrients can directly act on gene expression as well as regulate gene expression by metabolites or hormones. Nutrient intake also entrains the daily rhythm of metabolism through regulation of a transcriptionally regulated biological clock. Although the exact nutrient is not clear, nutritional entrainment of the mammary gland clock has been demonstrated. In studies of steers under nutritional restriction due to intake of poor quality feeds, expression of specific genes associated with protein turnover, cytoskeletal remodeling, and metabolic homeostasis was clearly influenced by diet. These studies provide application of nutrigenomics to resolve the molecular markers important in nutrition research (Byrne et al., 2005). Understanding the mechanisms of bioactive nutrients has allowed development of targeted nutritional strategies and has great future potential as an experimental approach. 

Milk fat depression is caused by specific intermediates of ruminal biohydrogenation of polyunsaturated fatty acids and is a clear example of nutritional regulation of metabolism. Advances in lipid analysis and chemistry allowed identification of the bioactive conjugated linoleic acid isomers, but nutrigenomic approaches were key to identification of mechanism. Thus, under certain dietary conditions rumen biohydrogenation is altered so that unique FA intermediates are produced and some of these are potent inhibitors of milk fat synthesis. To date three conjugated linoleic acid (CLA) isomers have been identify as bioactive FAs that inhibit milk fat synthesis – trans-10, cis-12 CLA, cis-10, trans-12 CLA and trans-9, cis-11 CLA. This inhibition involves a coordinated down regulation of gene expression for key enzymes in the synthesis of milk fat. This has been best studied for trans-10, cis-12 CLA and the cellular mechanism involves the SREBP1 transcription factor family. The genes for key enzymes in FA synthesis have a base sequence in their DNA code that is referred to as a SRE element. The SRE element binds the active fragment of SREBP1 thereby reducing gene expression (Bauman et al., 2011). Improving our understanding of the role that specific nutrients play in the regulation of gene expression and metabolism represents a developing area that should offer exciting new opportunities to improve productive efficiency of dairy cows.

Healthy adult and senior animals given the same foods can be studied to identify the gene expression and biochemical differences characteristic of the aging process. Foods for senior animals can then be rationally designed and evaluated for their ability to modify gene expression profiles in animals to more closely reflect those found in healthy adult animals, which has the potential to improve health and quality of life. In some of the more classical studies, expression studies have allowed for an improved understanding of the physiological basis on the beneficial global effects of caloric restriction on aging (Lee et al., 2002) and the effects of minerals such as selenium on intestinal function (Rao et al., 2001). In poultry, gene expression studies have lead to a better understanding of disease resistance (Liu et al., 2003), and of growth and tissue differentiation. These tools have also been used to differentiate effects of specific nutrient forms. 

In the next decade these “omics” technologies  will  redefine the criteria for evaluating nutrient requirements and can focus on the ability of dietary components to meet physiological needs rather than on specific requirements for key nutrients. Nutrigeonmics will be a path breaking tool through identification of pathways and candidate genes responsible for dietary induced diseases and ultimately reduction in production losses due to these diseases in animals. The discoveries of gene markers related to economically important traits like milk, meat, wool production etc whose expression can be improved by dietary regimens is a need of today’s nutrigenomic research which will help for sustainable livestock production. It will provide methods and specific markers for rapidly evaluating the nutritional status of individual and groups of animals. It will help us define the hidden effects of specific nutrients and nutrient interactions. Nutrigenomics also aims to demonstrate the effect of bioactive food compounds on health, which should lead to the development of functional foods that will develop and maintain health according to the needs of the individual. 

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