Nematode resistance

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Plants' genetic resistance to their pathogens is as natural as animal and human immunity. Depending on the time, frequency and intensity of exposure to a particular pathogen, plants can evolve and develop resistance or immunity in their genetics. Sometimes, in the search of good agronomic traits and domestication, we seem to have selected for crops that are not as fit as their wild ancestors. Since nematodes and other pests reproduce significantly faster and more in numbers compared to plant hosts, human intervention in combining disease resistant varieties with agronomically preferred varieties has been crucial for our food security. For example, it might take several centuries for a plant to evolve resistance on its own. But plant breeding has helped us combine the genetics of cultivars or varieties of soybeans we love, with fitness to resist nematodes and that is how we have nematode resistant seeds within a matter of 2-3 decades. Other gene editing technologies and gene manipulative technologies can help us get there faster, in less than a decade even. However, whether it is breeding or gene editing, it is pertinent to identify the special resistance genes well. Once we know what these genes are, there are several other questions to ask. Where are these genes? How do these genes work? Do they cost the plant some of their yield? (everything costs something) can these genes provide resistance against multiple types of pathogens?

Every living species has its own genetic code made of DNA. These pieces of DNA contain information required to make and direct every organ and function in the organism, these are called the genes. A collection of all the necessary DNA for an organism is called a genome. The genome may be organised into several fragments called chromosomes. Imagine the different genes to be the different coloured threads necessary to make a colourful quilt. All the different colour threads come in their own bundles. The genome is like the colourful quilt while the chromosomes are like the different coloured thread bundles. Every genome has set number of colours/ chromosomes. The human genome has 23 sets of chromosomes. Likewise, every soybean has 20 different chromosomes (Gm1 to Gm20 as pictured below). Why is this important? When we want to find the exact location of the genes or genetic codes that are responsible for a trait in the organism, it is easier to look for it when we know where it is. Knowing the organisation of a genome is like knowing where things are in your closet or pantry, in that case. Resistance genes are specific genes within the plant's genome whose presence helps the plants resist a particular disease. In this case, we are interested in Soybean genes that provide resistance against the soybean cyst nematode. In the past decade, scientists have been able to identify the exact genes and their locations within the soybean's genome. In my current research, I am trying to tease out the actual mechanism by which these genes confer resistance to soybeans against SCN.

Image: McClean et al. 2010 and Deepak Haarith (right)

There are 3 different genes seated next to each other in the soybean genome, on it's 18th chromosome. The location or locus at which these genes are positioned is called rhg1 (for resistance to Heterodera glycines 1). However, there are many variants of this locus scattered within the different soybean varieties and their ancestral relatives across the globe. The two main variants (haplotypes) are recognised and are bred into the commercial varieties available today in North America: rhg1-a (from Peking source) and rhg1-b (from PI88788 source). We have also recently discovered that while rhg1-b is necessary and sufficient to confer resistance to SCN, the rhg1-a type resistance also relies on another genetic locus called Rhg4 being available in the cultivar. Also, over 95% of the nematode resistance in the fields comes from PI88788 or they use the rhg1-b type resistance. Naturally, we have used this type of resistance long enough for the nematodes to evolve and overcome it. This makes it all the more important to understand how this resistance works, so we can effectively engage in finding options to manage nematodes that have overcome it.

For a more whimsical presentation of my current research, please watch this Soybean-SCN Musical that I wrote and directed.

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