ARS | Publication request: High-throughput SNP genotyping for breeding applications in rice using the BeadXpress platform

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 22, 2011
Publication Date: November 20, 2011
Citation: Thomson, M.J., Zhao, K., Wright, M., Mcnally, K.L., Rey, J., Tung, C., Reynolds, A., Scheffler, B.E., Eizenga, G.C., Mcclung, A.M., Kim, H., Ismail, A.M., Ocampo, M., Mojica, C., Reveche, M., Dilla, C.J., Mauleon, R., Leung, H., Bustamante, C., Mccouch, S.R. 2011. High-throughput SNP genotyping for breeding applications in rice using the BeadXpress platform . Molecular Breeding. 29:875-886.

Interpretive Summary: Single nucleotide polymorphism (SNP) DNA markers are extremely useful DNA markers and when used in a multiplex format they can greatly increase the efficiency of genetic mapping or breeding. In addition, multiplexed SNP markers can be very cost efficient. Rice breeding has a specific problem in that in many breeding programs the level of genetic diversity is fairly low and this in turn limits the usefulness of many DNA marker technologies. SNPs are more frequent in the genome than other DNA markers and this in turn makes SNPs a very desirable technology to utilize for a crop like rice. In this study, an international effort utilized various resources to identify SNPs relative to many of the world’s rice breeding efforts. Once identified, multiplex SNP assays were developed as GoldenGate VeraCode oligo pool assay (OPA) sets for the Illumina BeadXpress Reader. OPAs were developed for different types of rice species and rice breeding programs, with one targeting U.S.A. mid-south rice efforts.

Technical Abstract: Multiplexed single nucleotide polymorphism (SNP) markers have the potential to increase the speed and cost-effectiveness of genotyping, provided that an optimal SNP density is used for each application. To test the efficiency of multiplexed SNP genotyping for diversity, mapping and breeding applications in rice, we designed seven GoldenGate VeraCode oligo pool assay (OPA) sets for the Illumina BeadXpress Reader. Validated markers from existing 1,536 Illumina SNPs and 44K Affymetrix SNP chips developed at Cornell University were used to select subsets of informative SNPs for different germplasm groups with even distribution across the genome. A 96-plex OPA was developed for quality control purposes and for assigning a sample into one of the five Oryza sativa population subgroups. Six 384-plex OPAs were designed for genetic diversity analysis, DNA fingerprinting, and to have evenly-spaced polymorphic markers for QTL mapping and background selection for crosses between different germplasm pools in rice: Indica/Indica, Indica/Japonica, Japonica/Japonica, Indica/O. rufipogon, and Japonica/O. rufipogon. After testing on a diverse set of rice varieties, two of the SNP sets were re-designed by replacing poor performing SNPs. Pilot studies were successfully performed for diversity analysis, QTL mapping, marker-assisted backcrossing and in developing specialized genetic stocks, demonstrating that 384-plex SNP genotyping on the BeadXpress platform is a robust and efficient method for marker genotyping in rice.