Salt Stress Modulates the Landscape of Transcriptome and Alternative Splicing in Date Palm (Phoenix dactylifera L.)

Abstract

Date palm regards as a valuable genomic resource for exploring the tolerance genes due to its ability to survive under the sever condition. Although a large number of differentiated genes were identified in date palm responding to salt stress, the genome-wide study of alternative splicing (AS) landscape under salt stress conditions remains unknown. In the current study, we identified the stress-related genes through transcriptomic analysis to characterize their function under salt. A total of 17,169 genes were differentially expressed under salt stress conditions. Gene expression analysis confirmed that the salt overly sensitive (SOS) pathway genes, such as PdSOS2;1, PdSOS2;2, PdSOS4, PdSOS5, and PdCIPK11 were involved in the regulation of salt response in date palm, which is consistent with the physiological analysis that high salinity affected the Na+/K+ homeostasis and amino acid profile of date palm resulted in the inhibition of plant growth. Interestingly, the pathway of “spliceosome” was enriched in the category of upregulation, indicating their potential role of AS in date palm response to salt stress. Expectedly, many differentially alternative splicing (DAS) events were found under salt stress conditions, and some splicing factors, such as PdRS40, PdRSZ21, PdSR45a, and PdU2Af genes were abnormally spliced under salt, suggesting that AS-related proteins might participated in regulating the salt stress pathway. Moreover, the number of differentially DAS-specific genes was gradually decreased, while the number of differentially expressed gene (DEG)-specific genes was increased with prolonged salt stress treatment, suggesting that AS and gene expression could be distinctively regulated in response to salt stress. Therefore, our study highlighted the pivotal role of AS in the regulation of salt stress and provided novel insights for enhancing the resistance to salt in date palm.

Characterization of Salt-Tolerant Cultivars of Date Palm Based on Morphological and Biochemical Responses Under Salinity Stress

“…Results for relative dry weight % of different date palm cultivars in response to increasing salinity, dry weight % reduction was maximum for the plantlets of Halimi, Basrawali, Dhakki, Sanduri, Saghoi, Tarwali, Hamanwali, and Gajjar. Current findings on dry weight percentage are consistent with an earlier study by [23]. However, linear relationships between the decreases in dry weight of different tissues with an increase in salt concentration suggest that osmoregulation is effective for salt tolerance only to a limited range in the continuum of salt stress.…”

“…After measuring fresh weight, plant materials were placed in a drying oven (Memmert-110, Schawabach) for drying at 72ºC for a week. After one week of drying, the dried biomass percentage was weighted on a digital balance, and the average dry weight percentage of each replicate was recorded and described by [23]. After that, the roots were separated from the whole plant.…”

Understanding the physiological and molecular mechanism of salinity stress tolerance in plants

“…1 (Wei et al, 2021;Wu et al, 2018). Chlorophyll accumulation is significantly reduced under salinity stress in various plant species through downregulating the expression of glutamyl-tRNA reductase (HEMA1), Mg-chelatase (CHLH) and protochlorophyllide oxidoreductase (Xu et al, 2021b). Likewise, another study reported that salinity stress reduces chlorophyll biosynthesis through downregulation enzymes and chlorophyll biosynthesis genes such as HEM1, CHLH and POR (Wu et al, 2018).…”

“…Osmotic stress in the initial stage of salinity stress causes various physiological changes (Yang and Guo, 2018a;Zhao et al, 2021), such as interruption of membrane potentials, nutrient imbalance, impairment of the ability to detoxify ROS (Choudhury et al, 2017), unstable antioxidant enzyme activities, decreased photosynthetic capacity, and reduced size of stomatal apertures (Figure 1) (Wei et al, 2021). Increased accumulation of Na + and Cl − ions in tissues of plants (Al Hassan et al, 2016) causes severe ion imbalance and significant physiological disorders, and a large number of genes involved in the regulation of chlorophyll, photosynthesis, antioxidant enzymes, hormones, are upregulated in Phoenix dactylifera (Xu et al, 2021b).…”

DataSheet_1.xlsx

“…Previous studies have demonstrated that high salinity stress can promote the occurrence of alternative splicing of stress-responsive genes and affect the expression of the genes coding spliceosome components in Arabidopsis (Ding et al, 2014b;Feng et al, 2015;Gu et al, 2018), rice (Yu et al, 2021;Jian et al, 2022), wheat (Liu et al, 2018), Barley (Fu et al, 2019), Date Palm (Xu et al, 2021), grapevine (Jin et al, 2021), cotton (Zhu et al, 2018), Opisthopappus (Han et al, 2024), etc. However, the alternative splicing events in tomato root under salt stress remains to be resolved.…”