Axiom Analysis Tools Enable Cutting-Edge Agrigenomics Research

Agrigenomics continues to drive sustainable productivity. Bringing modern genetics and genomic tools to bear on problems of agriculture has already led to improvements, from selective poultry breeding to the evolution of new varieties of more nutritionally complete rice to combat blindness in developing countries. The Applied Biosystems Axiom Genotyping Solution for agrigenomics provides breeders and researchers with powerful genotyping tools to identify, validate and screen complex genetic traits in plants and animals to fulfill research and breeding objectives.

Ali Pirani, Manager of Bioinformatics at Thermo Fisher Scientific, notes that the Axiom Genotyping Solution offers a large catalog of arrays available for use with multiple, diverse plant and animal species, featuring thousands of established markers optimized for each species’ ploidy level, copy number variants, degree of homozygosity and other genetic quirks. The Axiom Genotyping Solution also offers advanced customization to assist with creating arrays for other species of interest, including those with complex ploidy levels. Pirani explains: “For most researchers, any organism that you are studying, we probably already have an array that you can purchase from us to interrogate your species. We also provide a great deal of flexibility. If we don’t have an organism of your interest, or if you believe that your population is a bit diverse, we can design an array that caters to exactly your population and is able to interrogate your high-value markers with high effectiveness.”

Researchers using Axiom arrays have successfully investigated genes related to insect-bite hypersensitivity in horses¹ and Marek’s disease in poultry.² The Axiom array has also contributed to our understanding of the genetics of indigenous Chinese Dongxiang spotted pigs,³ harness-racing success in horses,⁴ and exploration behavior in great tits.⁵ At a finer scale, researchers using Axiom arrays have identified breed-specific genes associated with clutch size in white leghorn and Rhode Island red laying hens, informing future selective breeding efforts as well as understanding of established breeds.⁶ In plant science, researchers show that the Axiom array validated 74% of haplotype-based SNP markers, “considerably higher than previous methods used for peanut,” proving its worth in a complex genetics situation.⁷

The Axiom Genotyping Solution product line also features the Axiom Microbiome Array, designed for detailed surveys of complex microbiota mixtures with markers from archaea, bacteria, protozoans, viruses and fungi. This array addresses research questions within and outside agrigenomics, assisting with efforts to understand microbial communities in the service of agriculture, human health and more. According to Pirani, “The microbiome array will work across any sort of research you’re doing on the microbiome. We have researchers who are looking at the flora in the human gut; we have researchers who are looking at methane production in [cattle]; we have other researchers who are looking at the microbiome in soil and how it impacts plant growth. So I think the possibilities are endless.”

Detailed and accurate data are not useful without the tools to understand and interpret them. Software tools are also available to automate as much data analysis as possible, and flexible enough that researchers have the option to alter settings and parameters to fit their needs. Axiom Analysis Suite software also contains procedures for recognizing and addressing markers that are not functioning as intended, allopolyploid species with variable levels of effective heterozygosity between regions of their genome, the variation induced by meiosis in polyploid species, the high levels of homozygosity that characterize inbred populations, and more. Software is also available to export its findings in standardized formats, allowing Axiom output to be used with pre-existing tools as well. As Ali Pirani puts it, Axiom “provides essentially a one-click analysis to data, and it also gives you power to do really deep-level analysis if that’s something you’re interested in.”

For more about the power of the Axiom Genotyping Solution and its associated software tools, watch Ali Pirani’s presentation here.

To see how the Axiom Genotyping Solution can improve your breeding program, receive a free consultation with a genotyping specialist here.

References

1. Schurink, A., et al. (2018) “Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity,” BMC Genetics, 19(1) (p. 49).
2. Xu, L., et al. (2018) “Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marek’s disease,” Journal of Animal Science and Biotechnology, 13(9) (p. 65).
3. Wang, C., et al. (2018) “Genome-wide association studies for two exterior traits in Chinese Dongxiang spotted pigs,” Animal Science Journal, 89(6) (pp. 868–875).
4. Velie, B. D., et al. (2018). “A genome-wide association study for harness racing success in the Norwegian-Swedish coldblooded trotter reveals genes for learning and energy metabolism,” BMC Genetics, 19(1) (p. 80).
5. Kim, J. M., et al. (2018) “A high-density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour,” Molecular Ecology Resources, 18(4) (pp. 877–891).
6. Wolc, A., et al. (2018). “Investigating the genetic determination of clutch traits in laying hens,” Poultry Science [epub ahead of print].
7. Clevinger J.P., et al. (2018) “Haplotype-Based Genotyping in Polyploids,” Frontiers in Plant Science, 9(1) (564).

For Research Use Only. Not for use in diagnostic procedures.