Genome-wide identification of SERK genes in apple and analyses of their role in stress responses and growth

Abstract

BackgroundSomatic embryogenesis receptor-like kinases (SERKs) are leucine-rich repeat receptor-like kinases associated with various signaling pathways. These kinases have a relationship with stress signals, and they are also believed to be important for regulating plant growth. However, information about this protein family in apple is limited.ResultsTwelve apple SERK genes distributed across eight chromosomes were identified. These genes clustered into three distinct groups in a phylogenetic analysis. All of the encoded proteins contained typical SERK domains. The chromosomal locations, gene/protein structures, synteny, promoter sequences, protein–protein interactions, and physicochemical characteristics of MdSERK genes were analyzed. Bioinformatics analyses demonstrated that gene duplications have likely contributed to the expansion and evolution of SERK genes in the apple genome. Six homologs of SERK genes were identified between apple and Arabidopsis. Quantitative real-time PCR analyses revealed that the MdSERK genes showed different expression patterns in various tissues. Eight MdSERK genes were responsive to stress signals, such as methyl jasmonate, salicylic acid, abscisic acid, and salt (NaCl). The application of exogenous brassinosteroid and auxin increased the growth and endogenous hormone contents of Malus hupehensis seedlings. The expression levels of seven MdSERK genes were significantly upregulated by brassinosteroid and auxin. In addition, several MdSERK genes showed higher expression levels in standard trees of ‘Nagafu 2’ (CF)/CF than in dwarf trees of CF/‘Malling 9’ (M.9), and in CF than in the spur-type bud mutation “Yanfu 6” (YF).ConclusionThis study represents the first comprehensive investigation of the apple SERK gene family. These data indicate that apple SERKs may function in adaptation to adverse environmental conditions and may also play roles in controlling apple tree growth.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5342-1) contains supplementary material, which is available to authorized users.

Function identification of MdTIR1 in apple root growth benefited from the predicted MdPPI network

“…To determine whether MdTIR1 regulates root growth via the auxin signaling pathway, we examined the expression levels of auxin‐responsive genes in MdTIR1 ‐overexpressing transgenic roots. The MdACO , MdLBD18 , MdEXP17 , and MdSERK1 genes were selected based on the results of previous studies (Zhu et al, 2011a; Lee and Kim, 2013; Zheng et al, 2018), and additional genes were selected on the basis of the homologous alignment of auxin‐responsive genes in Arabidopsis . The transcription of MdACO , MDP0000171672 , and MDP0000258781 was increased by 70‐, 45‐, and 28‐fold, respectively, in transgenic lines compared with that in the control (Figure 6H), suggesting that MdTIR1 might mediate root growth in an auxin‐dependent manner in apple.…”

Genome-Wide Analysis of Somatic Embryogenesis-Related Transcription Factors in Cultivated Strawberry (Fragaria × ananassa) and Evolutionary Relationships among Rosaceae Species

“…In the Rosaceae family, most studies related to SE have been focused on the establishment of culture conditions for somatic embryo development, based on other studies on Rubus, Rosa, Malus, Prunus, and Pyrus genus [64][65][66][67][68] and F. × ananassa [14][15][16]. However, the study of molecular bases in these agronomic species has not been addressed in depth [13,69,70].…”

Hydrogen sulfide and rhizobia synergistically regulate nitrogen (N) assimilation and remobilization during N deficiency‐induced senescence in soybean

“…In addition, the synergetic effects of H 2 S and rhizobia were highlighted more, suggesting that H 2 S could coordinate with rhizobia to regulate senescence in soybean caused by N deficiency by affecting the expression of NAC TFs in leaves and roots. Receptor‐like protein kinases are deemed to act as important cell surface receptors and are involved in a variety of biological processes, such as aging and stress responses (Zheng et al, ). Recent research revealed that the expression of RLKs was upregulated during leaf senescence in Arabidopsis (Li et al, ).…”