Wall-Associated Kinase (WAK) and WAK-like Kinase Gene Family in Sugar Beet: Genome-Wide Characterization and In Silico Expression Analysis in Response to Beet Cyst Nematode (Heterodera schachtii Schmidt) Infection

The wall-associated kinase (WAK) and WAK-associated kinase-like (WAKL) genes belong to the major receptor-like kinase (RLK) gene family in plants. They are well-known as important candidates for directly transmitting extracellular signals to the cytoplasm by connecting the extracellular matrix with intracellular compartments. As a result, they participate in developmental processes as well as stress responses. Although genome-wide investigations of the WAK/WAKL gene family have been carried out in a number of plant species, little is known about the WAK/WAKL genes in sugar beet, Beta vulgaris subsp. vulgaris L. (BvWAK/WAKLs). In this study, we performed a computational large-scale characterization of the members of this gene family in sugar beet. Fifty five (55) sugar beet WAK/WAKL proteins exhibited a wide range of physicochemical properties. A total of 10 conserved motifs were identified from all BvWAK/WAKL proteins, of which 3 motifs could be used as specific motif markers for distinguishing BvWAKs from BvWAKLs. Gene structure analysis showed that most BvWAK/WAKL genes contained 3 or 4 exons with no obvious phylogenetic organization. Among BvWAK/WAKL genes, 50 were assigned to their chromosomal locations and shown to have expanded primarily through tandem duplication. Comparative phylogeny revealed that sugar beet WAK/WAKL genes were divided into six clades, and orthologous gene pairs were identified between sugar beet and its wild-related species, the sea beet (Beta vulgaris subsp. maritima L.), while B. maritima lineage-specific genes provided clues for the introduction of wild genes in sugar beet cultivars. The gene expression data analysis revealed that the BvWAK/WAKL genes of susceptible and resistant cultivars were differentially expressed in response to beet cyst nematode (BCN) infection, and that 13 BvWAK/WAKL genes were up-regulated only in the resistant cultivar, suggesting that they are potentially involved in the resistance of sugar beet against this nematode. For the first time in sugar beet, our study presents an extensive computation-based knowledge platform on WAK/WAKL gene family and provides candidate genes for deeper molecular investigation of their potential role in sugar cyst nematode resistance.