Bringing genotype and phenotype together
The Sequenom MassARRAY© System, a new mass spectrometer machine for genotyping at Iowa State, will speed up genomic plant mapping and lead to more efficient plant breeding.
But more importantly, pointed out Kendall Lamkey, director of the Raymond F. Baker Center for Plant Breeding, it will start to close the gap that lies between genomics research and the application of that research to crop improvement.
"At the crux of the matter is this: for plant breeders to survive in the academic world, they're going to have to get into the application of genomics to crop improvement," said Lamkey, Pioneer Chair in Maize Breeding and chair of the agronomy department. "The flip side is that lots of claims have been made about what great things genomics does, but very little has been put into application."
The Sequenom, funded by the agronomy department and the Plant Sciences Institute and housed in the Center for Plant Genomics, gives scientists who base their research on phenotypes (physical traits) access to high-throughput genotyping (genetic make-up information).
The instrument allows users to identify single nucleotide polymorphisms (SNPs) over a large percentage of a genome quickly—10,000 SNP genotypes can be determined per hour. An SNP is a variation in the DNA sequences of single nucleotides A, C, G, T. The variations, where for instance an A may be in place of a T, differ between varieties. Once mapped out, these SNPs can narrow down regions of the genome that hold traits of interest, or find genes that control the traits.
Patrick Schnable, director of the Center for Plant Genomics and professor of agronomy and genetics, development and cell biology, and his team recently used the Sequenom to validate 900 SNPs from sequenced inbred lines of maize. These validated SNPs will be used to understand the gene activity behind hybrid vigor. Once that's understood, he said, hybrids that hold desired traits can be bred more rapidly. The SNPs will also be made available to other maize geneticists and breeders.
The Sequenom is not specific to plants, Lamkey pointed out. It could also be used by animal breeders and genomicists in the animal science department.
