Genome‐wide characterization and function analysis uncovered roles of wheat LIMs in responding to adverse stresses and TaLIM8‐4D function as a susceptible gene

Abstract

The Lin‐11, Isl‐1, and Mec‐3 domains (LIM) transcription factors play essential roles in regulating plant biological processes. Despite that, there is a lack of a full understanding of LIMs in wheat (Triticum aestivum L.). In this study, 28 wheat LIM s (TaLIMs) were identified and designated as TaLIM1‐1A to TaLIM12‐7D. The cis‐regulatory element analysis showed that TaLIMs were rich in elements related to biological and abiotic stresses. Expression profiling analysis showed that certain members of TaLIMs were responsive to biotic and abiotic stresses, such as TaLIM1‐1A, TaLIM3‐2B, TaLIM8‐4D, and TaLIM10‐5D, were significantly induced by heat, drought, sodium chloride (NaCl), abscisic acid (ABA) and Fusarium graminearum stresses. Furthermore, the biological function of TaLIM8‐4D was analyzed and results showed that it was subcellular localization in the nucleus and could induce weak cell death in Nicotiana benthamiana leaves. Additionally, overexpression of TaLIM8‐4D could upregulate plant pathogenesis‐related (PR) genes, promoting the infection of hemibiotrophic pathogen, implying that TaLIM8‐4D could function as susceptible gene in the nucleus by upregulating PR genes and inducing cell death to promote the colonization of hemibiotrophic agent F. graminearum. Overall, the systematic identification, characterization, expression profiling, evolutionary, and function analyses provided the ability to understand TaLIMs and laid a foundation for the further function study of LIM family members in wheat.

Phylogenomic analysis of phenylalanine ammonia-lyase (PAL) multigene family and their differential expression analysis in wheat (Triticum aestivum L.) suggested their roles during different stress responses

“…In order to better understand the origin of TaPAL genes, The PAL family genes in T. urartu, T. dicoccoides, and A. Tauschii were identified by the Blastp analysis. The cutoff values (e-value < 10 -10 , identity > 80%) were used to ensure the reliability of homologous (Li et al, 2022) . The original definition of an ortholog was two genes from two different species that were derived from a single gene of the last common ancestor of that species.…”

“…Original data sets, including different development stages and tissues from variable treatments, were downloaded from the NCBI Short Read Archive (SRA) database and mapped to the wheat reference genome using Hisat2 (Li et al, 2022). The SRA numbers of those data were listed in Supplementary file 1.…”

Multiple roles of TaCPP family genes during growth and stress treatment

“…In each TaCPP promoter region, more than 20 cis ‐acting components were predicted (Figure 4b). Seed‐specific regulation element (RY‐element), cell cycle regulation element (MSA‐like), differentiation of the palisade mesophyll cells element (HD‐Zip1), endosperm expression element (GCN4 motif), MYB binding site involved in flavonoid biosynthetic genes regulation (MBSI), zein metabolism regulation element (O2‐site), circadian control element (circadian), and meristem expression element (CAT‐box) were linked to growth and development (Liu et al., 2010). The number of cis ‐elements for growth and development was the largest in TaCPP genes promoter region (Figure 4c).…”

“…Wheat was placed in a light incubator at 42 °C for high‐temperature stress (Zhang et al., 2015). Wheat was watered with water containing 20% (v/v) PEG6000 as a drought simulation (Gao, 2016; Li et al., 2022). After being treated for 12, 24, 48, and 72 h, the plants were sampled, and the wheat pollens were collected for the tissue expression analyses.…”

Mining the Roles of Cucumber DUF966 Genes in Fruit Development and Stress Response

“…The relative quantity was calculated with the 2 –ΔΔCt method. Primers were designed with Primer Premier 5.0 software ( Table S6 ) [ 49 ].…”