Single nematode sequencing of the soybean cyst nematode highlights different strategies to breakdown resistance

The soybean cyst nematode [Heterodera glycines - SCN] is the most damaging pest of soybean worldwide causing in excess of 1.3 $U.S. billion in yield loss annually. Management of SCN typically relies on the use of resistant soybean varieties to hinder nematode development and reduce losses. In North America, two main resistant germplasm are commonly used in breading programs: PI 88788 and Peking. While still effective, widespread use, combined with prolonged exposure to both of these resistance sources, has lead to a progressive shift towards highly virulent SCN populations. It is hypothesized that effector proteins may play a key role in resistance breakdown, yet little is known about the genes or the biological mechanisms responsible for this shift in virulence. In this study, we make use of an adapted single-nematode transcriptomic sequencing approach to highlight genes responsible in the breakdown of resistance between different nematode virulence phenotypes. We show that nematodes virulent against Peking-type resistance are characterized by a highly altered transcriptome with differential expression in many putative effector proteins. In contrast, the transcriptome of PI 88788-virulent nematodes is more similar to that of the avirulent nematodes with the exception of a few differentially expressed effector proteins.