Accelerate Agrigenomics
Breakthroughs
Agrigenomics has undergone dramatic advancements, enabling higher-yielding crops and livestock, greater disease
resistance, and improved reproductive health. This progress translates to increased returns on investment and thedevelopment of long-term solutions for food production security.
Individual discovery efforts and the work of international research collaborations have facilitated significant
breakthroughs in cattle breeding. A pivotal innovation from Illumina was the BovineSNP50 BeadChip, which offers
greater accuracy in prediction of individual genetic merit in both dairy and beef cattle.

1970–1990

Observation
Sowing the seeds for genetic breakthroughs.
The Human Genome Research Initiative paves the way for mapping of livestock genomes.
Before 1990, beef and dairy cattle selection relies heavily on pedigree performance test information and progeny
testing. Trait-specific expected progeny differences (EPDs) in beef cattle and genetic predictions for dairy cattle
are in their infancy. Because limited DNA sequencing data are available for agriculture, the bovine genome isessentially unknown. Early genome research activity is primarily focused on the human genome. Technologies
for other species are being developed and applied. The use of restriction fragment length polymorphisms,
microsatellites, or STR markers is becoming more widespread and the concept for development of genetic
linkage maps for animals and plants slowly emerges.
Several key discoveries advance the field of bovine genomics during this time:
Soller M, et al.1–3 demonstrate the linkage of growth hormone restriction fragment length polymorphisms (RFLPs) with potential phenotypic
differences in traits for milk production in Israeli Holstein dairy cattle. This work introduces the concept of detecting linkage between markers andquantitative loci. This finding leads to the discovery of more DNA markers with the potential to transform genetic improvement in livestock throughmarker-assisted selection and breeding.

www.illumina.com/agrigenomics

The radiation hybrid (RH) panel developed by Womack JE, et al. (1986)4 fuels interest in cattle genomics and comparative gene mapping. The RH
panel is used to assign enzymes, DNA fragments, and gene sequences to syntenic groups, which are later assigned to chromosomes by Fries R,et al. (1986)5 using fluorescence in situ hybridization (FISH) cytogenetic tools. This work anchors the bovine physical and genetic linkage maps,
which continue to be developed and refined. Fries R, et al. and other collaborators later develop molecular cytogenetic techniques for hybridizing
large parts of the bovine genome in yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), and cosmids to specificbovine chromosomes.

1990–2000

Discovery
Exploring the potential of agrigenomics.
Development of physical and genetic linkage maps for cattle occurs, driving research interestand funding.
Interest in linkage associations with animal phenotypes continues to grow, leading to the discovery of markers
linked to economically relevant traits. Researchers around the world uncover significant markers for milk volume,
protein, and fat content in dairy cattle, catalyzing global interest, research, and funding. Scientists speculate about
unmasking additional genetic traits in cattle and how these differences might influence the agricultural industry.
Several key discoveries advance the field of bovine genomics during this time:
Fries R, et al. (1990)6 isolate and report the first ubiquitous microsatellites (di-, tri-, and tetranucleotide repeats) in the bovine genome. Many
additional microsatellites and RFLPs are discovered as a result of this finding.
Georges M, et al. isolate several dinucleotide repeats to assemble a linkage map for Holstein dairy cattle and apply genomic analysis tolivestock improvement.
The United States Department of Agriculture (USDA) Agricultural Research Service (ARS) and Meat Animal Research Center (MARC) publish
the first publicly available genetic linkage map for cattle7, which is followed by a genetic linkage map developed by researchers in Australia. The
original maps are updated and refined by the USDA and others during the 1990s. Research funding from the European Community (EC) is used todevelop and merge genetic linkage and physical maps. These maps facilitate identification of quantitative trait loci (QTL), the genes responsible forsimple and complex traits involved in meat and milk production in cattle.

2000–2010

Innovation
Cultivating the benefits of genomics.
Illumina introduces the revolutionary BovineSNP50 BeadChip, transforming the dairy andbeef industries.
For the first time, accurate and reliable estimates of genetic inheritance are possible. Theoretical evaluations
speculate that large numbers of markers evenly distributed across the bovine genome could be used to linkphenotype with genotype, predictably estimating the genetic merit of an individual animal. The collection ofphenotypic data over the previous decades accelerates the adoption of genomic selection. The BovineSNP50
BeadChip leads to a radical shift from phenotype- to genotype-based breeding.

Several key discoveries advance the field of bovine genomics during this time:
Meuwissen, et al. (2001)8 introduce the concept of using genomic selection in agriculture.
Research geneticist Curt Van Tassell develops an algorithm for selecting evenly spaced SNPs that reflect allele frequencies in cattle breeds.
Many of these SNPs inform the content of the first BovineSNP50 BeadChip. The reduced representation sequencing method for SNP discovery
proposed by Van Tassell is used to generate approximately 62,000 high-quality SNPs that are found on the BovineSNP50 BeadChip9 andsubsequent Illumina arrays.
The bovine genome sequence is annotated and analyzed10–12, providing new insights into cattle biology.
Illumina scientists Marylinn Munson and Cindy Taylor Lawley lead an organized effort to consolidate SNP genotyping data from around the world,
forming the BovineSNP50 Consortium. The SNP content gathered from this consortium is used to develop the BovineSNP50 BeadChip9—thefirst SNP genotyping assay for cattle—in collaboration with the USDA, the University of Missouri, and the University of Alberta. The BovineSNP50
BeadChip is adopted globally by many organizations, including the National Institute for Agricultural Research (INRA), the Centre for IntegrativeGenetics (CIGENE), the Commonwealth of Scientific and Industrial Research Organization (CSIRO), and others to build an even broader
consortium. Researchers, breed associations, and industry leaders begin using the BovineSNP50 BeadChip to combine genotype information withphenotypes, enabling accurate prediction of genetic merit in Holstein, Jersey, and Angus cattle breeds.

2010–2013

Widespread Adoption
Genotype-based breeding is born.
Illumina introduces the BovineLD and BovineHD BeadChips.
Following the introduction of the BovineSNP50 BeadChip, genotyping from sire selection to birth is widely adopted
by cattle breeders. Cattle selection intervals and breeding cycles are compressed by leveraging both genomic
and reproductive technologies. The BovineSNP50 and subsequent BovineHD and BovineLD BeadChips become
industry-leading arrays for cattle screening.
Several key discoveries advance the field of bovine genomics during this time:
In collaboration with several agricultural organizations, Illumina develops the BovineHD BeadChip, a high-density array for genomic selection incattle. This collaboration involves many prominent agricultural research organizations, including USDA ARS, Pfizer Animal Genetics, the Universityof Missouri, the National Association of Livestock and Artificial Insemination Cooperatives (UNCEIA), and INRA.
Illumina develops the BovineLD BeadChip13—a low-density array for cost-effective genomic selection in beef and dairy cattle—in collaboration withthe Department of Primary Industries Victoria, INRA, UNCEIA, and USDA ARS. Illumina BeadChips for bovine genotyping are widely adopted formany cattle breeds and species with large amounts of phenotypic data, statistical predictions of genetic merit, and training populations of animals
available. Physical traits in cattle can be evaluated by direct association, as correlated traits, or as haplotypes of many SNPs that accountfor variation.

Breeding future successthrough agrigenomics.
Early research and discovery efforts in agriculture lay a strong foundation for modern agrigenomics methods. The
BovineSNP50, BovineHD, and subsequent BovineLD+ BeadChips from Illumina revolutionized marker-assisted breeding
and selection techniques in agriculture. Today, cattle breeders and farmers are equipped with the accurate genetic
information they need to produce commercially viable crops and animals. Through collaboration with the agriculturalcommunity, Illumina is committed to developing new solutions for embryonic selection, epigenetics, metagenomics,
disease resistance, and more. At Illumina, the innovation in Agrigenomics continues.

To learn more about Illumina technology for genomic selection and how consortia canreduce costs for agricultural researchers, visit www.illumina.com/agrigenomics
References
1. Soller M, Brody T, Genizi A (1976) On the power of experimental designs for the detection of linkage between marker loci andquantitative loci in crosses between inbred lines. Theor Appl Genet 47: 35–9.
2. Soller M, Genizi A (1978) The efficiency of experimental designs for the detection of linkage between a marker locus and a locus
affecting a quantitative trait in segregating populations. Biometrics 34: 47–55.
3. Soller M, Beckmann JS (1983) Genetic polymorphism in varietal identification and genetic improvement. Theor Appl Genet 67:25–33.
4. Womack JE, Moll YD (1986) Gene map of the cow: conservation of linkage with mouse and man. J Hered 77: 2–7.
5. Fries R, Hediger R, Stranzinger G (1986) Tentative chromosomal localization of the bovine major histocompatibility complex by in situ
hybridization. Anim Genet 17: 287–94.
6. Fries R, Eggen A, Stranzinger G (1990) The bovine genome contains polymorphic microsatellites. Genomics 8: 403–6.
7. Bishop MD, Kappes SM, Keele JW, Stone RT, Sunden SL, et al. (1994) A genetic linkage map for cattle. Genetics 136: 619–39.
8. Meuwissen TH, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics
157: 1819–29.
9. Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, et al. (2009) Development and characterization of a high density SNP
genotyping assay for cattle. PLoS One 4: e5350.
10. Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, et al. (2009) A whole-genome assembly of the domestic cow, Bos taurus.
Genome Biol 10: R42.
11. Bovine Genome Sequencing and Analysis Consortium, Elsik CG, Tellam RL, Worley KC, Gibbs RA, et al. (2009) The genome
sequence of taurine cattle: a window to ruminant biology and evolution. Science 324: 522–8.
12. Bovine HapMap Consortium, Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, et al. (2009) Genome-wide survey of SNP variation
uncovers the genetic structure of cattle breeds. Science 324: 528–32.
13. Boichard D, Chung H, Dassonneville R, David X, Eggen A, et al. (2012) Design of a bovine low-density SNP array optimized forimputation. PLoS One 7: e34130.

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Pub No. 1370-2014-008 Current as of 23 July 2014