Gene Clustering Helps Rice Plants Fight Pathogens

Learning more about a plant's defense mechanisms – how it recognizes and fights the mutating pathogens – can help save crops like rice, the major food staple for about half the world's population, from pathogen attack.

Dean and an NC State colleague, Hua-Quin Pan, senior bioinformatics scientist, searched for and characterized resistance genes and downstream pathways likely involved in the resistance response.

Dean and Pan found 43 different resistance genes on chromosome 10, which contains a total of 3,471 genes, according to the Science paper.

"We found a variety of different types of resistance genes; some were novel and some were well known," Dean says. "The most interesting thing was that most were grouped in three major clusters that were quite similar."

Dean believes this clustering helps rice improve its specificity of resistance to pathogens. In other words, resistance genes form clusters and then recombine forces in order to repel specific harmful advances from pathogens.

Dean says finding out more about these resistance genes' functions will aid the rice plant's battle to defend itself.

"Identifying and characterizing these resistance genes – particularly these clusters – will give us a very good idea of how they change their specificities to different pathogens, specifically rice blast."

Rice blast, an important and powerful rice disease, is a major focus of Dean's lab. Dean and colleagues from the Whitehead Institute/MIT Center for Genome Research sequenced the rice blast genome last summer.

Dean calls the ever-evolving battle between rice and pathogens "a constant arms race."

"Pathogens mutate to bypass resistance mechanisms, while the host, rice, recombines various components in resistance genes so it can again recognize pathogens. These resistance genes are like generals in a battle who recognize what's going on with the enemy and then tell the troops downstream to fight the pathogen."

A consortium of eight different groups – the rice chromosome 10 sequencing consortium – representing various universities and institutes worked together to sequence and characterize chromosome 10. The Science paper chronicles a high degree of collinearity between rice and two other major cereal crops – sorghum and maize – providing further evidence that rice can be a model for cereal crop research.