AgBiotechNet^® Proceedings 004 Paper 5

© CAB International 2004
Conference Proceedings

Whole-genome Association Studies to Determine the Molecular Genetic Value of Cattle

Sue DeNise*

Director of Research and Development, MMI Genomics, Davis CA, USA

Abstract

MMI Genomics has rights to 1x coverage of whole-genome shotgun sequence for livestock species. The bovine fragments from sequencing were assembled and over 600,000 putative single nucleotide polymorphisms (SNP) markers were identified. From this putative set of markers, a sample was selected to create a dense, informative map by in silico selection of SNPs in fragments syntenic to the human genome with an average spacing of 500,000 bp. Over 20,000 markers have been evaluated in vitro for assay design and allele frequency in cattle to identify 6,000 markers. This SNP map will be used in whole-genome association studies using commercial populations to discover the regions that contribute additive and non-additive genetic variation to traits of economic importance. The expected outcome of this research is the development and commercialization of SNP-based diagnostic tools that predict the molecular genetic value of individual animal for specific traits. In conjunction with our beef cattle research partner, Cargill Inc., the resulting diagnostic assays will be internationally commercialized in cattle.

Keywords: genomics: cattle: genetic improvement: molecular genetics: single nucleotide polymorphisms: animal breeding

1. Introduction

It is fitting that on the 50th anniversary of three publications describing the molecular structure of the genetic template (Watson and Crick [1]; Wilkins et al. [2]; and Franklin and Gosling [3]), we meet to discuss the goals of the next 50 years of beef cattle genetics and breeding. Building upon the discoveries and subsequent research unraveling the genetic code and techniques for analyzing molecular structures, two recent publications have provided a working draft of the human genome [4-5]. These strategies have provided a framework for developing research programs that can help unravel the underlying basis of the inheritance of genetic traits in livestock.

To date, livestock improvement has relied on quantitative analysis linking phenotypes to genotype through individual performance and pedigree analysis. Animals with the best predicted genetic merit for the traits of interest are selected as parents. Further dissection of complex traits into individual genetically inherited components by molecular biology methods has not been possible until recently because the tools and analysis platforms were not capable of identifying genes with small effects and interactions among genes.

The explosive growth of genomics research has driven the life sciences industries to develop information and analysis platforms that allow livestock improvement programs to consider different pathways to genetic analysis. The number of within family genomic locations reported for cattle (for examples see [6-10]) have provided the proof of concept data for developing marker assisted selection programs. Carlborg et al. [11] reported that molecular data can elucidate epistatic interactions that could be used to design mating strategies for breeding programs.

Tailoring or identifying animals that match specific environments, market conditions, and labor needs will allow increased efficiencies in meat, milk and egg production. Estimation of genetic value directly from genotypes instead of phenotypes will allow the development of specific selection and management strategies to optimize environments for specific genotypes of animals allowing for reduced costs of production and product branding. These discoveries create the foundation for the future development of therapeutics that enhance consumer acceptance, improve animal health and reduce costs of production (i.e. enhanced lean muscle growth or milk production).

2. Discussion

In February 2001, two competing research programs published working drafts of the human genome [4-5]. The two efforts were different, Celera Genomics relied on whole-genome shotgun sequencing of individual libraries created from five individuals [4]. The public effort relied on sequencing of the minimum tiling path of BAC clones [5]. Both assembled the DNA: Celera relied on enormous computer power to assemble all fragments sequenced by using overlapping fragments and sized selected libraries to determine the distance between fragment reads. The IHGSC assembled contigs within BAC clones then joined the BAC clones to create a single consensus sequence. Celera's strategy had an advantage that as sequences were aligned, single base pair changes were identified that uncovered naturally occurring genetic variation called single nucleotide polymorphisms (SNPs). Over 2 million putative SNPs were identified during Celera's sequencing of the human genome.

Following the completion of the whole genome human sequence, Celera Genomics evaluated how the research assets could be applied to create value in other species. Although individual markers and genes could be licensed from academic and government research organizations, the conclusion was reached that to have a product that would have sustainable commercial value, it would need to account for a substantial portion of the genetic variation. Celera adopted the same strategy uncovered from the human sequencing effort to discover SNP markers dispersed throughout the genome in livestock species. Approximately three billion bases of the cattle genome were sequenced from four libraries. Each library consisted of fragments of DNA from one male animal representing Angus, Limousin, Simmental and Brahman breeds. These fragments were aligned using algorithms developed at Celera and overlapping fragments identified putative SNP markers. Over 600,000 putative SNP markers were identified and 177,000 of the fragments containing SNPs were syntenic to the human genome. Thus, a humanized bovine physical map was created with signposts of SNP markers. When binning the human genome into 500,000 bp lengths, 99% of the bins had at least 1 putative bovine SNP marker. The bovine sequence and SNP markers were licensed by MMI Genomics in March, 2002.

The density of this putative map has the potential to allow whole-genome association studies directly in commercial animals without an underlying pedigree structure. This is a very different approach from the within family QTL studies typically found in research populations. Association studies provide the opportunity to measure the entire genotype and measure interactions among alleles, to evaluate and estimate the effects of dominance, epistasis and pleiotropy as was not possible before. The result of the association study will be the development of diagnostic tools for economically important traits that account for enough of the genetic variation to create value for customers in the beef production and processing chain.

An important outcome in the development of the humanized bovine physical map has been the development of a high-resolution comparative map that can be used for gene discovery. Genomic regions identified from the whole-genome association studies will be used for targeted research aimed at identifying causative mutations for traits of commercial value.

3. Commercialization and Applications

Until the final results of the research are completed, it is difficult to define the exact nature of the products that will ultimately be commercialized. Our vision is that we will identify both additive and non-additive genetic factors that allow assignment of a molecular genetic value to individual animals. If the molecular genetic value is assigned at the feedlot, the feeder could make management and marketing decisions based on the genetic potential of an animal to reach certain grid quality and yield targets to optimize profits on individual cattle. If the molecular genetic value is assigned in the breeding herd, it becomes a molecular breeding value for selection decisions and its additive component could be combined with choices of mates based on the non-additive component to enhance genetic progress in the breeding herd.

Livestock improvement has progressed almost entirely through selection on additive genetic components predicted from genetic evaluation. Maintaining constant improvement in the elite genetic group and producing multiplier breeding animals that are uniform for all the traits under selection is difficult. Improved performance due to non-additive genetic effects is based on average heterotic effects. It is rare that animal breeders get the opportunity to capitalize on specific combining ability because of the long generation interval and the cost of producing test crosses. A molecular dissection of the additive and non-additive components would allow breeders to optimize specific crosses, which has not been feasible under classical breeding programs.

One of the primary challenges in marketing breeding stock from commercial breeding companies is lack of differentiation of the product. Every commercial company has the same set of tools and access to the same type of animals making it difficult to create product differentiation; and, even if unique breeding animals are identified, it is nearly impossible to prevent other companies from transferring the improved genetic resources to their own populations. Sustainable profits in animal breeding companies are marginal due to fierce competition, uncertainty of genetically exceptional animals and inability to protect high-value genetics. Under this system it is difficult for companies, breed associations or individual breeders to justify investment in technology that may have a dramatic effect on the genetic merit of their animals.

A molecular genetic value that focuses on traits of importance for specific product specifications will allow for product differentiation and certification. This approach is a natural progression from genetic evaluation based solely on phenotypes through recent attempts to incorporate family-linked markers into genetic evaluation. We believe that the next generation of genetic evaluation will include direct markers for specific traits combined with phenotypic measures. In addition, these research programs will drive the discovery and commercialization of novel products we do not even envision today. Therapeutic products, environmental manipulation of genotypes, epigenic factors, and other outcomes may result from the discovery strategies.

4. Planning the Research Objectives of the Future

There are a number of potential outcomes and pitfalls as planning for the future directions in animal breeding research progresses. Genetic improvement of crops was primarily achieved in public institutions until the 1960s when it moved predominantly into the commercial sector (see [12] for examples). It might be argued that the role of public institutions had passed as the technology moved from a very risk prone research and development phase into a more 'mature' applied phase and, therefore, adoption of the technology by the private sector. However, commercial companies target new 'improved' products to large, intensively managed cropping systems because of the balance between time and costs associated with research and development and return on investment. As this shift occurred, funding for public plant breeding programs has disappeared. As a result, some regions of the world, with very specific selection requirements, do not have research programs directed toward their specific needs.

Along with the shift in research emphasis, training of students in the applied breeding area has diminished. Educated researchers are essential for the future to develop new technologies and to transfer new developments in animal breeding from both the private and public research perspectives to the livestock industries. Future directions in animal breeding research must include the goal of training qualified scientists to meet the challenges of tomorrow. Broadly trained professionals will be an important component in forging genetic improvement programs of the future.

5. The Opportunities

The prospects for developing commercial products as a result of genomics research in livestock look very promising. The technology and research has progressed to move discovery from the lab to the feedlot and the ranch. There are a number of companies that are incorporating genomics across the spectrum of products, providing the improved animal product or the tools for early determination of an animal's genetic potential for economically important traits. The next generation of products will provide tools to select and manage animals in ways that were never possible before.

References

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*Author for correspondence: sue.denise@mmigenomics.com