Although it is well established that flavonoid synthesis is induced in diverse plant species during nematode parasitism, little is known about the regulation of genes controlling flavonol biosynthesis during the plant–nematode interaction. In this study, expression of the <i>Arabidopsis thaliana</i> flavonol-specific transcription factor, <i>AtMYB12</i>, the flavonol synthase genes, <i>AtFLS1</i>, <i>2</i>, <i>3</i>, <i>4</i>, and <i>5</i>, and the gene encoding the central flavonoid enzyme, chalcone synthase (<i>AtCHS</i>), were examined in plant roots during infection by <i>Heterodera schachtii</i> (sugar beet cyst) and <i>Meloidogyne incognita</i> (root-knot) nematodes. These experiments showed that <i>AtMYB12</i> was transiently upregulated at 9 dpi in syncytia associated with sugar beet cyst nematode infection and that an <i>Atmyb12</i>-deficient line was less susceptible to the parasite. This suggests that, rather than contributing to plant defense, this gene is essential for productive infection. However, the <i>AtCHS</i> and <i>AtFLS1</i> genes, which are controlled by AtMYB12, did not exhibit a similar transient increase, but rather were expressly downregulated in syncytia relative to adjacent uninfected root tissue. Genetic analyses further indicated that <i>AtFLS1</i> contributes to plant defense against Cyst nematode infection, while other <i>AtFLS</i> gene family members do not, consistent with prior reports that these other genes encode little or no enzyme activity. Together, these findings indicate a role of <i>AtMyb12</i> in promoting the early stages of Cyst nematode infection, while flavonols produced through the action of AtFLS1 are essential for plant defense. On the other hand, a transient induction of <i>AtMYB12</i> was not observed in galls produced during root-knot nematode infection, but this gene was instead substantially downregulated, starting at the 9 dpi sampling point, as were <i>AtCHS</i> and <i>AtFLS1.</i> In addition, both the <i>AtMYB12</i>- and <i>AtFLS1</i>-deficient lines were more susceptible to infection by this parasite. There was again little evidence for contributions from the other <i>AtFLS</i> gene family members, although an <i>AtFLS5</i>-deficient line appeared to be somewhat more susceptible to infection. Taken together, this study shows that sugar-beet cyst and root-knot nematodes modulate differently the genes involved in flavonol biosynthesis in order to successfully infect host roots and that AtFLS1 may be involved in the plant basal defense response against nematode infection.
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