Candidate Genes and Pathways in Rice Co-Responding to Drought and Salt Identified by gcHap Network

Abstract

Drought and salinity stresses are significant abiotic factors that limit rice yield. Exploring the co-response mechanism to drought and salt stress will be conducive to future rice breeding. A total of 1748 drought and salt co-responsive genes were screened, most of which are enriched in plant hormone signal transduction, protein processing in the endoplasmic reticulum, and the MAPK signaling pathways. We performed gene-coding sequence haplotype (gcHap) network analysis on nine important genes out of the total amount, which showed significant differences between the Xian/indica and Geng/japonica population. These genes were combined with related pathways, resulting in an interesting mechanistic draft called the 'gcHap-network pathway'. Meanwhile, we collected a lot of drought and salt breeding varieties, especially the introgression lines (ILs) with HHZ as the parent, which contained the above-mentioned nine genes. This might imply that these ILs have the potential to improve the tolerance to drought and salt. In this paper, we focus on the relationship of drought and salt co-response gene gcHaps and their related pathways using a novel angle. The haplotype network will be helpful to explore the desired haplotypes that can be implemented in haplotype-based breeding programs.

Keywords: QTL/genes; drought tolerance; gcHap-network; pathway; rice; salt tolerance.

Figure 1

Diagram of reaction mechanisms involving drought and salt in rice. The left box of the larger picture is the regular mechanism of underground and aboveground parts under drought stress. Root composition can affect the water absorption and it is crucial to improve plant drought resistance. Leaf morphology and stomatal conductance of aboveground plants play a decisive role in water retention. The right box is the response mechanism under salt stress. The rejection of Na⁺ in roots can reduce the accumulation of Na⁺ in tissues. The response mechanisms of ion transport, reactive oxygen species and Ca²⁺ content in aboveground parts can effectively alleviate the effects of salt stress. The rightmost box shows the co-response mechanism under drought and salt stress. Some secondary messengers, such as Ca²⁺, and ROS can alleviate the damage of osmotic stress to plants and improve the drought and salt tolerance through ABA-dependent and ABA-independent pathways. The main components in the core ABA signaling transduction pathway include ABA receptor PYLs, SnRK2s, ABA co-receptor branch type A 2C protein phosphatase (PP2Cs) and SnRK2.

Figure 2

Frequencies of the ‘‘favorable’’ gcHaps of nine drought and salt co-response genes affecting fifteen yield traits (DTH, PH, TGW, FLL, FLW, PN, PL, CN, CL, GW, GLWR, LRI, SH and LL) in Xian/indica (XI) and Geng/japonica (GJ) modern varieties and different rice populations.

Figure 3

Dissection of gcHap-network pathway of important drought and salt co-response genes. These gene-related pathways and elite haplotypes for drought and salt co-response genes are indicated in the blue box. Firstly, OsAUX1, OsPYL5, and OsbZIPs (3 genes) were enriched in osa04075 that mainly included the auxin (AUX), ABA, and salicylic acid (SA) related pathways. The two rice auxin receptor genes OsTIR1 and OsAFB2 were targeted by OsmiR393, and the MYB transcription factor MYB77 interacted with both IAA19 and ARFs. H₂O₂ has been found to be involved in the morphogenesis of ARF. ABA occupies an important position in plant growth and plant development, and the components of the ABA signaling pathway mainly include OsPYLs, OsPP2C, OsSAPKs, and some transcription factors (TFs). Secondly, RNA secondary structure was influenced via the osa03040 or another pathway, which changed the activity and expression of HSF associated genes. Moreover, OsHSPs are associated with primary metabolism and signal transduction. Thirdly, the interaction of the Ca²⁺ and ROS signaling pathways has an important role in the regulatory network of plant immunity. Component changes in the MAPK cascade pathway were influenced by the activation of the ROS pathway. The PYL-PP2C-SnRK2 core ABA-signaling module activates a MAPK cascade, which may regulate many ABA effector proteins through phosphorylation. The MAPK cascade could also be activated by the PYL-PP2C-SnRK2 core ABA signaling module, which regulates ABA-related proteins through phosphorylation.