Comparative transcriptomic analysis of the super hybrid rice Chaoyouqianhao under salt stress

Abstract

Background Soil salinization is a threat to food security. China is rich in saline land resources for potential and current utilization. The cultivation and promotion of salt-tolerant rice varieties can greatly improve the utilization of this saline land. The super hybrid rice Chaoyouqianhao (CY1000) is one of the most salt-tolerant rice varieties and is widely used, but the molecular mechanism underlying its salt tolerance is not clear. Results In this study, the characteristics of CY1000 and its parents were evaluated in the field and laboratory. The results showed that aboveground parts of CY1000 were barely influenced by salt stress, while the roots were less affected than those of its parents. A comparative transcriptomic strategy was used to analyze the differences in the response to salt stress among the male and female parents of CY1000 at the seedling stage and the model indica rice 93–11. We found that the salt tolerance of CY1000 was mainly inherited from its male parent R900, and its female parent GX24S showed hardly any salt tolerance. To adapt to salt stress, CY1000 and R900 upregulated the expression of genes associated with soluble component synthesis and cell wall synthesis and other related genes and downregulated the expression of most genes related to growth material acquisition and consumption. In CY1000 and R900, the expression of genes encoding some novel key proteins in the ubiquitination pathway was significantly upregulated. After treatment with MG-132, the salt tolerance of CY1000 and R900 was significantly decreased and was almost the same as that of the wild type after salt stress treatment, indicating that ubiquitination played an important role in the salt tolerance mechanism of CY1000. At the same time, we found that some transcription factors were also involved in the salt stress response, with some transcription factors responding only in hybrid CY1000, suggesting that salt tolerance heterosis might be regulated by transcription factors in rice. Conclusion Our results revealed that the ubiquitination pathway is important for salt tolerance in rice, and several novel candidate genes were identified to reveal a novel salt tolerance regulation network. Additionally, our work will help clarify the mechanism of heterosis in rice. Further exploration of the molecular mechanism underlying the salt tolerance of CY1000 can provide a theoretical basis for breeding new salt-tolerant rice varieties.

Physicochemical Properties of the Rice Flour and Structural Features of the Isolated Starches from Saline-Tolerant Rice Grown at Different Levels of Soil Salinity

“…However, it is sensitive to salinity stress, with most cultivated varieties having a threshold of 3.0 dS/m 2 . , In China, there are 100 million hectares of saline-alkali land and nearly 2.333 million hectares of coastal beach area . Among them, 80% of saline-alkali land is desolate, and nearly 13.33 million hectares have ample rainwater resources that can potentially support rice cultivation. , Therefore, breeding rice for saline tolerance not only maximizes the utilization of coastal beaches and saline-alkali land but also ensures crop production to provide enough food for rice-consuming communities. Fortunately, the National Hybrid Rice Research Centre has cultivated a number of saline-tolerant indica rice varieties with adaptation to soil salinities of 0.3–0.6% (corresponding to 5.86–11.06 dS/m 2 ) and yields of over 4500 kg/ha .…”

“…Among them, 80% of saline-alkali land is desolate, and nearly 13.33 million hectares have ample rainwater resources that can potentially support rice cultivation. , Therefore, breeding rice for saline tolerance not only maximizes the utilization of coastal beaches and saline-alkali land but also ensures crop production to provide enough food for rice-consuming communities. Fortunately, the National Hybrid Rice Research Centre has cultivated a number of saline-tolerant indica rice varieties with adaptation to soil salinities of 0.3–0.6% (corresponding to 5.86–11.06 dS/m 2 ) and yields of over 4500 kg/ha . Environmental stresses normally affect the production and quality of rice, e.g., the salinity stress imposed at the seedling stage decreased the grain weight and fertility of rice at a relatively low salinity of 4 dS/m 2 .…”

“…Fortunately, the National Hybrid Rice Research Centre has cultivated a number of salinetolerant indica rice varieties with adaptation to soil salinities of 0.3−0.6% (corresponding to 5.86−11.06 dS/m 2 ) and yields of over 4500 kg/ha. 7 Environmental stresses normally affect the production and quality of rice, e.g., the salinity stress imposed at the seedling stage decreased the grain weight and fertility of rice at a relatively low salinity of 4 dS/m 2 . 8 Moreover, stressful environments can alter the biosynthesis of starch in cereal endosperm, and the composition and structure of starch are the major quality determinants influencing the physicochemical properties and edible qualities of rice.…”

A Combination of a Genome-Wide Association Study and a Transcriptome Analysis Reveals circRNAs as New Regulators Involved in the Response to Salt Stress in Maize

“…We identified three salt tolerance-related circRNAs, circ_000260 , circ_001362 , and circ_001730 , which originated from Zm00001eb013550 (6-phosphofructo-2-kinase), Zm00001eb198930 (non-coding gene), and Zm00001eb198990 (UBX domain protein), respectively. Intriguingly, the 6-phosphofructo-2-kinase protein and UBX domain protein in rice were significantly upregulated under salt stress [ 45 , 46 ].…”

Combined transcriptomic and metabolomic analyses elucidate key salt-responsive biomarkers to regulate salt tolerance in cotton

“…Wild barley responds to salt stress by activating ion transporters such as NHX (sodium exchanger), AKT (inward rectifying K +), HKT (high affinity potassium transporters) and CAX (vacuolar cation/proton exchanger) [ 23 ]. In recent years, there have been many studies using transcriptome and metabolome analysis techniques to analyze kiwifruit [ 24 ], Sugar beet [ 25 ], rice [ 26 ], and Sorghum bicolor [ 27 ]. Transcriptome technology can explore differentially expressed genes.…”