Ph.D. student Abiskar Gyawali develops new method to spot genes that control plant traits

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University of Göttingen

Mizzou Biology Ph.D. student Abiskar Gyawali is part of an international team that developed a new approach that enables plant researchers to quickly and affordably identify genes that control plant traits. The method will enable scientists and breeders to develop more affordable, desirable, and sustainable plant varieties.  The research was published in BMC Plant Biology.

The new method is an extension of a tool known as GWA, or Genome Wide Association. GWA studies use genetic sequencing coupled with advanced statistics and computation to link differences in the genetic code with particular traits. When using GWA to study plants, researchers typically rely on inbred lines, plants that been bred to be genetically and physiologically identical. Inbred lines, however, can be costly and time consuming, sometimes taking up to six years before a study can even begin. The new technique is modeled after an approach to often used to study human traits, where DNA from thousands of individuals, who are certainly not identical, are compared.

The researchers wanted to see how whether this approach would work in plants. Since measurements of individual plants can be highly variable, the scientists developed a method that enabled them to combine the advantages of GWA with additional statistical analysis techniques. To test their approach, they investigated whether their combination of approaches could accurately detect genes involved in plant height, a trait that has been extensively studied in the scientific literature. They scientists planted four fields of an early variety of white corn, called Shoepeg, and measured the height of the plants. They identified three genes, from the potential 39,000 genes in the maize genome, that were controlling plant height. The effects of all three genes were supported by previous studies on other maize varieties. This showed that their method worked.

“Scientists usually have to measure huge numbers of genetically identical plants in order to have a powerful enough study for finding genes, but we used a diverse maize population and showed that our approach was powerful without relying on identical plants at all,” said Timothy Beissinger, head of the Division of Plant Breeding Methodology at the University of Goettingen, and corresponding author of the paper.

“This is great news for researchers interested in finding genes in crops where inbred lines are not available or are time-consuming to produce,” added Gyawali, who is lead author of the paper.

The study, titled “Single-plant GWAS coupled with bulk segregant analysis allows rapid identification and corroboration of plant-height candidate SNPs,” was published in BMC Plant Biology, DOI: 10.1186/s12870-019-2000-y

Additional authors include Vivek Shrestha, also a Ph.D. candidate in the Division of Biological Sciences at the University of Missouri, USA; Katherine Guill and Sherry Flint-Garcia with the USDA-ARS.