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.H., McNally, K.L., Rey, J., Tung, C., Reynolds, A., Scheffler, B.E., Eizenga, G.C., McClung, A.M., Hyunjung, K., Ismail, A.M., De Ocampo, M., Mojica, C., Reveche, M., Dilla, C.J., Mauleon, R., Leung, H., Bustamante, C.D., McCouch, S.R. 2011. High-throughput SNP genotyping for breeding applications in rice using the BeadXpress platform. Molecular Breeding. 29:875–886.

Interpretive Summary: Technology to utilize a new type of molecular marker called a single nucleotide polymorphism (or SNP) needs to be adapted in order to be used to genotype cultivated rice. Currently SNP markers are routinely used in mammalian genetics, including human genetics, and routine use of these markers for genotyping rice plants would cut the time needed to obtain genotypic data by about 30%. Rice breeders and geneticists use genotypic data for many different reasons including determining which varietial group a rice cultivar belongs to, following the incorporation of selected traits into new rice varieties under development, identifying the chromosomal location of traits of interest, and selecting rice varieties to make crosses with. This pilot study demonstrated the use of seven different sets of SNP markers for the aforementioned purposes. Based on current results, three sets of SNP markers were modified and improved. In the future, we expect numerous additional sets of SNP markers to be designed following the procedures described in this pilot study. The selection of the particular set of SNP markers will be based on the purpose of genotyping and set of rice plants being genotyped.

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.