Genome-wide annotation and expression responses to biotic stresses of the WALL-ASSOCIATED KINASE - RECEPTOR-LIKE KINASE (WAK-RLK) gene family in Apple (Malus domestica)

The WALL ASSOCIATED-KINASE - RECETOR-LIKE KINASE (WAK-RLK) gene family has been reported to act as a sensor for disease. Apple (Malus domestica) can be affected by multiple biotic stresses, such as fungal diseases from Valsa mali (Vm), Alternariaalternata Apple Pathotype (AaAP), and Pythium ultimum (Pu). However, there has been no report of WAK-RLK genes involved in apple biotic stress response. In this paper, we performed a comprehensive study including genome-wide annotation, characterization and gene expression analysis of WAK-RLKs in apple (MdWAK-RLKs). We found 44 members based on structural domain identification. The number of amino acids, molecular weight, and theoretical pI of these identified members ranged from 302 to 998, 33.63 to 110.35 kD, and 5.1 to 9.26, respectively. Members of the family were anchored to 16 out of 17 chromosomes and were classified into six phylogenetic groups. We found two phylogenetic groups specific to the apple genome. Synteny analysis revealed that 11 gene pairs arose from segmental duplications and 7 gene clusters resulted from tandem duplications. Cis-elements in the promoter region of MdWAK-RLKs were found mainly in response to circadian rhythm, hormones, and multiple stresses. The large number of members that showed high expression in multiple tissues and differential expressed in response to stress revealed that the different functional roles of MdWAK-RLKs under physiological or pathological conditions. Several genes, such as MDP0000278283, MDP0000153539, MDP0000170906, and MDP0000251865, were significantly influenced by multiple diseases. This study provides new insights into the potential function of WAK-RLKs in Malus and in Rosaceae and its contribution to disease resistance.