Genome mapping technique speeds process of finding specific genes

March 24, 2010

WEST LAFAYETTE, Ind. - A Purdue University scientist was part of a global team that has demonstrated a specialized mapping technique that could speed work in genomic fields by quickly finding genetic associations that shape an organism's observable characteristics.

Using plants from 93 different Arabidopsis thaliana populations, a team led by the Gregor Mendel Institute of Plant Biology in Austria was able to find genetic associations among multiple phenotypes, or traits, suggesting that the same genes or closely related genes controlled those traits. David E. Salt, a Purdue professor of plant biology and co-author of a Nature paper on the study released Wednesday (March 24), said the ability to find these types of genetic links could speed scientists' ability to find and isolate genes and understand their function.

"This may show that multiple phenotypes are being controlled by a specific region of the genome," Salt said. "It helps us understand the mechanisms."

A traditional search for a gene responsible for a particular characteristic requires using plants that have been phenotyped, or identified by characteristics. They are then crossed with others, and the offspring are phenotyped.

Scientists then check for similarities in offsprings' genes with the desired trait. The process can be painstaking and time consuming because many thousands of individuals may need to be checked, Salt said.

Genome-wide association mapping compares the sequence of DNA in genomes of many individual plants or animals to find similarities that narrow the scope of the search for a particular gene.

"We can look for a region in the genome that is in common among the individuals," Salt said. "For plant biologists, it's a much more efficient way of getting to genes. And for animal biologists, where making test crosses is more difficult, this is critical."

In this study, specific differences in DNA, called single nucleotide polymorphisms, or SNPs, were compared at 250,000 sites across the genomes of many individuals. The genomes were matched up against specific traits for each individual in order to find SNPs that are associated with the trait of interest. If scientists were looking for plants that produce high seed yields, for example, they would compare the genomes of plants that have a range of seed yields. The places where the genomes match in individuals with high seed yields are possible locations of sought-after genes.

Genome-wide association mapping is a faster process because fewer plants - usually in the hundreds - need to be grown and phenotyped. Finding genetic associations among multiple phenotypes could reveal more information about how those characteristics might be connected.

Of the 107 phenotypes used in the research, Salt was responsible for phenotyping the plants for 18 characteristics, which focused on nutrient and micronutrient content. He said the next step in the research would be to test those associations to determine the genes responsible for particular plant characteristics.

The National Institutes of Health funded the research. 

Writer: Brian Wallheimer, 765-496-2050, bwallhei@purdue.edu

Source: David Salt, 765-496-2112, dsalt@purdue.edu

Ag Communications: (765) 494-8415;
Steve Leer, sleer@purdue.edu
Agriculture News Page

 

ABSTRACT

Genome-wide Association Study of 107 Phenotypes
in a Common Set of
Arabidopsis Thaliana Inbred Lines

Susanna Atwell, Yu S. Huang, Bjarni J. Vilhj´almsson, Glenda Willems, Matthew Horton, Yan Li, Dazhe Meng, Alexander Platt, Aaron M. Tarone, Tina T. Hu, Rong Jiang, N. Wayan Muliyati, Xu Zhang, Muhammad Ali Amer, Ivan Baxter, Benjamin Brachi, Joanne Chory, Caroline Dean, Marilyne Debieu, Juliette de Meaux, Joseph R. Ecker, Nathalie Faure, Joel M. Kniskern, Jonathan D. G. Jones, Todd Michael, Adnane Nemri, Fabrice Roux, David E. Salt, Chunlao Tang, Marco Todesco, M. Brian Traw, Detlef Weigel, Paul Marjoram, Justin O. Borevitz, Joy Bergelson, Magnus Nordborg

Although pioneered by human geneticists as a potential solution to the challenging problem of finding the genetic basis of common human diseases, advances in genotyping and sequencing technology have made genome-wide association (GWA) studies an obvious general approach for studying the genetics of natural variation and traits of agricultural importance. They are particularly useful when inbred lines are available because once these lines have been genotyped, they can be phenotyped multiple times, making it possible (as well as extremely cost effective) to study many different traits in many different environments while replicating the phenotypic measurements to reduce environmental noise. Here we demonstrate the power of this approach by carrying out a GWA study of 107 phenotypes in Arabidopsis thaliana, a widely distributed, predominantly selfing model plant known to harbor considerable genetic variation for many adaptively important traits. Our results are dramatically different from those of human GWA studies in that we identify many common alleles with major effect, but they are also, in many cases, harder to interpret because confounding by complex genetics and population structure make it difficult to distinguish true from false associations. However, a priori candidates are significantly overrepresented among these associations as well, making many of them excellent candidates for follow-up experiments by the Arabidopsis community. Our study clearly demonstrates the feasibility of GWA studies in A. thaliana and suggests that the approach will be appropriate for many other organisms.