Transcriptomic and metabolomic reveals silicon enhances adaptation of rice under dry cultivation by improving flavonoid biosynthesis, osmoregulation, and photosynthesis

Abstract

Dry cultivation is a new rice crop mode used to alleviate water shortage and develop water-saving agriculture. There is obvious genetic difference compared with drought-tolerant rice. Silicon (Si) plays an important role in plant adaptation to adverse environmental conditions and can significantly improve the drought tolerance and yield of rice. However, the regulatory mechanism via which Si provides plant tolerance or adaptation under dry cultivation is not well understood. The present study investigated the changes in plant growth, photosynthetic gas exchange, and oxidative stress of the rice cultivar “Suijing 18” under dry cultivation. Si improved photosynthetic performance and antioxidant enzyme activity and subsequently reduced lipid peroxidation of rice seedlings, promoted LAI and promoted leaf growth under dry cultivation. Further, transcriptomics combined with quasi-targeted metabolomics detected 1416 and 520 differentially expressed genes (DEGs), 38 and 41 differentially accumulated metabolites (DAMs) in the rice leaves and roots, respectively. Among them, 13 DEGs were involved in flavonoid biosynthesis, promoting the accumulation of flavonoids, anthocyanins, and flavonols in the roots and leaves of rice under dry cultivation. Meanwhile, 14 DEGs were involved in photosynthesis, promoting photosystem I and photosystem II responses, increasing the abundance of metabolites in leaves. On the other hand, 24 DAMs were identified involved in osmoregulatory processes, significantly increasing amino acids and carbohydrates and their derivatives in roots. These results provide new insight into the role of Si in alleviating to adverse environmental, Si enhanced the accumulation of flavonoids and osmoregulatory metabolites, thereby alleviating drought effect on the roots. On the other hand, improving dehydration resistance of leaves, guaranteeing normal photosynthesis and downward transport of organic matter. In conclusion, Si promoted the coordinated action between the above-ground and below-ground plant parts, improved the root/shoot ratio (R/S) of rice and increased the sugar content and enhancing rice adaptability under dry cultivation conditions. The establishment of the system for increasing the yield of rice under dry cultivation provides theoretical and technical support thereby promoting the rapid development of rice in Northeast China, and ensuring national food security.

Identification of cell-type-specific response to silicon treatment in soybean leaves through single nucleus RNA-sequencing

“…However, there is a lack of a comprehensive molecular understanding of Si uptake and translocation in dicot species, including soybean. Also, previous studies in other plants primarily relied on bulk transcriptomics, a methodology inherently unable to discern cellular heterogeneity and prone to overlooking cell-specific gene expression (Fauteux et al, 2006; Chain et al, 2009; Ma et al, 2016; Zhu et al, 2019; Jiang et al, 2022).…”

Comprehensive analysis of silicon impact on defense and metabolic responses in rice exposed to herbivory stress

“…Earlier studies proposed that Si amendment alters basal gene expression in rice, which may be subsequently changing metabolic profiles, possibly as means of priming prior to and/or during stress responses ( Brunings et al., 2009 ; Van Bockhaven et al., 2015 ; Frew et al., 2018 ; Jiang et al., 2022 ). In plant-pathogen interactions, application of Si to rice plants mediated differential expression of genes involved in nitrogen metabolism and transport, glycolysis and cell wall biosynthesis and degradation, while the amino acid metabolism-related genes were down-regulated ( Van Bockhaven et al., 2015 ).…”

Silicon nutrition improves the quality and yield of rice under dry cultivation

“…To ensure the integrity of root sampling, root samples were collected from potted plants for analysis. The root volume was measured according to the drainage method and the number of roots was recorded 7 . After digital scanning with the special scanner for root morphology (Epson Perfection V800 photo; EPSON, Tokyo, Japan), the number of root tips was analyzed, repeating the measurement three times for each treatment, and the average value was calculated.…”

“…It mainly depends on natural precipitation throughout the reproductive period, with appropriate recharge only during critical periods of water demand or drought, and no water layer during the whole growth period. 6,7 Drought tends to reduce grain yield and quality, and making rice more resilient to drought and increasing yield and quality is a challenging scientific problem. 8 Some scholars have proposed a 'blue' revolution in rice, through the innovative cultivation of water-saving and drought-resistant rice, aiming to achieve a dry planting and dry management model of rice production.…”

“…Dry cultivation of rice does not require seedlings or transplants and is sown directly under dry land preparation conditions. It mainly depends on natural precipitation throughout the reproductive period, with appropriate recharge only during critical periods of water demand or drought, and no water layer during the whole growth period 6,7 . Drought tends to reduce grain yield and quality, and making rice more resilient to drought and increasing yield and quality is a challenging scientific problem 8 …”