Comparative transcriptome profiling of low light tolerant and sensitive rice varieties induced by low light stress at active tillering stage

Abstract

Low light intensity is a great limitation for grain yield and quality in rice. However, yield is not significantly reduced in low light tolerant rice varieties. The work therefore planned for comparative transcriptome profiling under low light stress to decipher the genes involved and molecular mechanism of low light tolerance in rice. At active tillering stage, 50% low light exposure for 1 day, 3 days and 5 days were given to Swarnaprabha (low light tolerant) and IR8 (low light sensitive) rice varieties. Illumina (HiSeq) platform was used for transcriptome sequencing. A total of 6,652 and 12,042 genes were differentially expressed due to low light intensity in Swarnaprabha and IR8, respectively as compared to control. CAB, LRP, SBPase, MT15, TF PCL1 and Photosystem I & II complex related gene expressions were mostly increased in Swarnaprabha upon longer duration of low light exposure which was not found in IR8 as compared to control. Their expressions were validated by qRT-PCR. Overall study suggested that the maintenance of grain yield in the tolerant variety under low light might be results of accelerated expression of the genes which enable the plant to keep the photosynthetic processes moving at the same pace even under low light.

Comparative transcriptome analysis reveals the molecular regulation underlying the adaptive mechanism of cherry (Cerasus pseudocerasus Lindl.) to shelter covering

“…Lhcb (PSII) was reported to be transcriptionally amplified under low light intensity to enhance photon capture [30]. The differentially expressed transcripts of plant LHCs in response to low light stress might play collective roles in maintaining the normal metabolic activities under low light intensity; for example, the genes encoding Lchbs from the low-lighttolerant rice cultivar were up-regulated under low light intensity [15]; in the current study, all the DEGs associated with the members of LHCs, such as Lcha and Lchb, were up-regulated in cherry leaves under shelter covering. A total of 37 genes were involved in the regulation of light capture protein expression ( Fig.…”

“…play various roles in the response to abiotic stresses [41]. Under low light conditions, low-light-tolerant rice cultivars were shown to maintain their carbohydrate production level by holding an effective photosynthetic rate and oxygen resistance [15]. Similarly, the activities of antioxidant enzymes in sheltered leaves were higher, which could avoid membrane lipid peroxidation and help maintain photosynthetic efficiency (Fig.…”

“…To date, the adaptive regulatory mechanisms of plants under variable light and/ or temperature conditions have been analyzed using transcriptomic strategies in many crops; for example, differentially expressed genes (DEGs) in maize were mainly involved in most assimilation processes (photosynthesis and carbon fixation pathways), namely, photosynthetic light capture via the modification of chlorophyll (Chl) biosynthesis, suggesting the complex regulatory mechanisms and interactions between cold and light signaling processes [14]. Under low-light conditions, the expression of photosystem I and II complex and electron transportrelated genes increased in low-light-tolerant rice varieties; thus, the accelerated expression of photosynthesis-related genes under low light conditions contributed to the maintenance of rice yield [15]. In addition, under low light conditions, leaves need to maintain effectively antioxidant capacity to maintain their carbohydrate production level [16], which was enough to prove that adjustment or adaptation of leaves to low light conditions (hours or days) was achieved by integrating multiple signals, as shown by a study conducted on Arabidopsis thaliana [10].…”

Comparative transcriptome analysis reveals the molecular regulation underlying the adaptive mechanism of cherry (Cerasus pseudocerasus Lindl.) to shelter covering

“…play various roles in the response to abiotic stress [45]. Under low-light conditions, low-light-tolerant rice varieties were shown to maintain their carbohydrate production level by maintaining an effective photosynthetic rate and oxygen resistance [15]. Likewise, the activity of antioxidant enzymes in cherry leaves under sheltered conditions was higher, which could avoid membrane lipid peroxidation and help maintain photosynthetic efficiency (Figure 9).…”

“…For example, differentially expressed genes (DEGs) in maize were shown to be mainly involved in most assimilation processes (photosynthesis and carbon fixation pathways), namely, photosynthetic light capture via the modification of chlorophyl biosynthesis, suggesting the complex regulatory mechanisms and interactions between cold and light signaling processes [14]. Under low-light conditions, the expression of photosystem I and II complex and electron transport-related genes increased in low-light-tolerant rice varieties; thus, the accelerated expression of photosynthesis-related genes under low-light conditions contributed to the maintenance of rice yield [15]. The available evidence indicates that photosynthesis and the synthesis of photosynthetic pigments play major roles upon exposure to shaded conditions.…”