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United States Department of Agriculture

Agricultural Research Service

Research Project: DISSECTING COMPLEX TRAITS IN MAIZE AND BIOFUEL GRASSES BY APPLYING GENOMICS, BIOINFORMATICS, AND GENETIC RESOURCES

Location: Plant, Soil and Nutrition Research

Title: A large maize (Zea Mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome

Authors
item Ganal, Martin -
item Durstewitz, Gregor -
item Polley, Andrea -
item Berard, Aurelie -
item Buckler, Edward
item Charcosset, Alain -
item Clarke, Joseph -
item Graner, Eva-Maria -
item McMullen, Michael
item Falque, Matthieu -

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 5, 2011
Publication Date: December 8, 2011
Citation: Ganal, M.W., Durstewitz, G., Polley, A., Berard, A., Buckler IV, E.S., Charcosset, A., Clarke, J.D., Graner, E., Mcmullen, M.D., Falque, M. 2011. A large maize (Zea Mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS One. 6(12):e28334. DOI: 10.1371/journal.pone.0028334.

Interpretive Summary: Many applications of crop improvement are enhanced by development of high marker density genotyping platforms, identification of unique traceable loci on each of the chromosomes that define the genetic makeup of a crop plant. We report on the establishment and characterization of a 50,000 marker single nucleotide polymorphism (SNP) genotyping array for maize (corn). We demonstrated the utility of this genotyping array for characterizing genetic diversity across a broad range of maize germplasm and for the development of high density genetic maps for two reference populations of maize. These maps have an unprecedented level of genetic resolution. These maps also aid in correcting numerous mistakes in the current reference genome sequence in maize. This research is important for maize breeders and geneticists in enabling a new level of genetic resolution at low cost. This is important for advancing maize breeding in allowing routine genome selection strategies to be applied to maize.

Technical Abstract: SNP genotyping arrays have been useful for many applications that require a large number of molecular markers such as high-density genetic mapping, genome-wide association studies (GWAS), and genomic selection for accelerated breeding. We report the establishment of a large SNP array for maize and its use for diversity analysis and high density linkage mapping. The markers, taken from a set of more than 800,000 SNPs, were selected to be preferentially located in genes and to be evenly distributed across the genome. The array was tested with a set of maize germplasm including North American and European inbred lines, parent/F1 combinations, parents of important mapping populations and distantly related teosinte material. A total of 49,585 markers were of good quality for genotyping, with an average failure rate of 4% and rates up to 8% in specific germplasm or breeding material. To demonstrate this array's use in genetic mapping and for the independent validation of the B73 sequence assembly, two intermated maize recombinant inbred line populations -- IBM (B73xMo17) and LHRF (F2xF252) -- were genotyped to establish two high density linkage maps with 20,913 and 14,524 markers respectively. 172 mapped markers were absent in the current B73 assembly and their placement can be used for future improvements of the B73 reference sequence. Colinearity of the genetic and physical maps was mostly conserved with some exceptions that suggest errors in the B73 assembly. Five major regions containing non-colinearities were identified on chromosomes 2, 3, 6, 7 and 9, and are supported by both independent genetic maps. Four additional high-confidence non-colinear regions were found on the LHRF map only, suggesting structural rearrangements between its two parents and B73. Given the high quality of the array, it will be a valuable resource for maize genetics and many aspects of maize breeding.

Last Modified: 8/22/2014
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