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4 Genomics in plant disease management


Hello! I welcome to the fourth talk of this week, that is ‘Application of genomics in plant disease management’. What does genomics means? Genomics is the study of genomes of organisms. So why do we need to study genomes? Then, because if we just look into the biological development in this recently then we will see that a huge number of plant pathogens has been sequenced at the whole genome level. But what do we get out of these sequencing results? We can see that the pathogenic behavior and lifestyle of the pathogen can be known from the sequences, when population diversity of a pathogen in a geographical area that can also be known, from the sequences, and evolution of pathogen over a period of time that is another point that we can understand by studying the pathogen genomes, and relatedness of different fungal species that is also we come to know through studies of genome sequences.

Let us take an example where the genome sequence of the rice blast pathogen that is Magnaporthe grisea was studied and what do we got out of it? The genome sequence information has provided us the information that the pathogen contains approximately 11,000 genes and maybe of them eight thousand eight hundred genes were conserved hypothetical proteins and 2,233 are predicted proteins. So these sort of information we get out of genome sequences. Now what how they help us in understanding plant disease development and management? When it was studied that the on different surfaces when the same pathogen was allowed to germinate the conidia germinated by different processes and the genes that were responsible or that were activated or deactivated under both this condition at both time interval is given in this particular diagram and we can see that the same pathogen at 7:00 hour in different surface expression level of the genes were varied. That means in this way we can understand the pathogen behavior when it lands on a susceptible host and when it lands on an resistant host we can understand the mechanisms how the genes can be progressed in those particular conditions.

Then another example is Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. When this potato particular pathogen was sequenced we got information and the information was compared with two other Phytophthora species that is Phytophthora sojae and Phytophthora ramorum and we can see that in case of Phytophthora infestans it was approximately seventeen thousand seven hundred genes in comparison to Phytophthora sojae there are sixteen thousand nine hundred genes and Phytophthora ramorum contains approximately fourteen thousand four hundred genes. Now when we compare these genes with all these three species we could see that the genome of Phytophthora ramorum was the smallest one and the genome of Phytophthora sojae was of medium size, and the genome of Phytophthora infestans is of large size.

Now why this large size occurs? The expansion of Phytophthora infestans was resulted from proliferation of repetitive DNA that accounts for approximately 74% of the total genome. So this is an information that we can derive through whole genome sequencing. Then comparison with two other Phytophthora genomes showed that the turnover and extensive expansion of specific families of secretive disease effector proteins. This is very very important when we compare a Phytophthora infestans with Phytophthora sojae and Phytophthora ramorum we could see that there was an expansion of the effector producing genes in the Phytophthora infestans and that is probably why it has become a very difficult disease to control because it evolves very rapidly in comparison to other species of Phytophthora and its evolution is mostly based on diversity of effector molecules that are produced in this Phytophthora infestans. So that is why probably currently we don’t have a very good resistance source that is effective against different species or different races of Phytophthora.

Then another example where genome expansion and gene loss was studied in powdery mildew fungi which showed that in some of the powdery mildew fungus the genome size is very small whereas, in some the genome size is of medium size, but in some cases like Blumeria Golovinomyces and Erysiphe the genome size has expanded significantly. So this type of information that we can generate through studies of genome sequences of different organisms. Now expansion of these genomes just like Phytophthora if we just try to look into deeper then we will come to know what has caused the expansion of this genome? What are the genes that has been modified or repeated or what are the new genes that had been incorporated into these genomes to make this genome size so big? And it is probably that due to expansion of these genomes that facilitates the pathogen to infect new hosts or even to knock down the existing defense systems of the resistant plants so that, plants become more vulnerable to these particular organisms.

At the same time genome sequences of Blumeria and Botrytis again revealed us some interesting facts. Blumeria is an obligate fungal pathogen whereas Botrytis is a necrotrophic fungal pathogen but the genome of these two pathogens were all very very alike. They share a lot of genes that are very close to each other and they are conserved in this genome. So this is again a point to think about why this different lifestyle pathogens Biotrophs and Necrotrophs may share similar set of genes or their genome is so similar to each other. These are points that needs to be studied further to understand the biology of this pathogen so that we are able to understand their interaction with the host in a greater depth and we are able to devise or develop strategies to tackle these pathogens in long run. So this is a talk rather where we try to understand the application of genomics in understanding the pathogenic behavior. The genome expansion or modifications that has led to virulence or aggressiveness of the pathogen towards the host and these studies helped us to understand this by pathogens in a better way and we are able to develop strategies to tackle these problems in a better way.

Thank you.



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