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United States Department of Agriculture

Agricultural Research Service

Title: Development of Single Nucleotide Polymorphism (SNP) Markers for Use in Commercial Maize (Zea Mays L.) Germplasm)

item Jones, Elizabeth
item Chu, Wen-chy
item Ayele, Mulu
item Ho, Julie
item Bruggeman, Ed
item Yourstone, Ken
item Rafalski, Antoi
item Smith, Oscar
item Mcmullen, Michael
item Bezawada, Chethana
item Warren, Jana
item Babayew, Jean
item Basu, Sutirtha
item Smith, Stephen

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/1/2009
Publication Date: 8/20/2009
Citation: Jones, E., Chu, W., Ayele, M., Ho, J., Bruggeman, E., Yourstone, K., Rafalski, A., Smith, O.S., McMullen, M.D., Bezawada, C., Warren, J., Babayew, J., Basu, S., Smith, S. 2009. Development of Single Nucleotide Polymorphism (SNP) Markers for Use in Commercial Maize (Zea Mays L.) Germplasm. Molecular Breeding. 24:165-176.

Interpretive Summary: Single nucleotide polymorphism (also called SNP) genetic markers are the most cost effective genetic markers currently available. To characterize relationships among corn germplasm and aid corn breeding efforts, a reliable core set of SNP markers would be of great benefit, particularly if the set was publically available for use by all groups to enable comparison of genetic studies conducted in different laboratories. In this collaborative effort a panel of 786 SNP markers were developed and tested against a range of corn germplasm. Effectiveness and information on genetic map position and polymorphism rate in differing sets of germplasm is provided. This study is important because it provides corn geneticists and corn plant breeders with a uniform, highly cost-effective set of genetic markers.

Technical Abstract: The development of single nucleotide polymorphism (SNP) markers in maize offer the opportunity to utilize DNA markers in many new areas of population genetics, gene discovery, plant breeding, and germplasm identification. However, the steps from sequencing and SNP discovery to SNP marker design and validation are lengthy and expensive. Access to a set of validated SNP markers is a significant advantage to maize researchers who wish to apply SNPs in scientific inquiry. Here we present information for 640 SNPs that were discovered in 60 public genotypes used in maize breeding in North America and Europe. We also describe the development of a 768 marker multiplex assay for use on the Illumina® BeadArrayâ„¢ platform. While SNPs were found on average every 43 bases in 1,088 maize gene sequences, SNPs that were amenable to marker design were found on average every 308 bases. In addition, 20% of markers that passed design subsequently failed validation on the Illumina platform. Validated SNP markers were mapped on the IBM2 intermated B73 x Mo17 high resolution genetic map using either the IBM2 segregating population, or segregation in multiple parent-progeny triplets of Pioneer-proprietary inbreds. A high degree of colinearity was found with the genetic Nested Association Maps (NAM) maps. For each SNP presented we give information on map location, polymorphism rates in different heterotic groups and performance on the Illumina® platform.

Last Modified: 05/21/2017
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