Transcriptomic profiling suggests candidate molecular responses to waterlogging in cassava

Abstract

Owing to climate change impacts, waterlogging is a serious abiotic stress that affects crops, resulting in stunted growth and loss of productivity. Cassava (Manihot esculenta Grantz) is usually grown in areas that experience high amounts of rainfall; however, little research has been done on the waterlogging tolerance mechanism of this species. Therefore, we investigated the physiological responses of cassava plants to waterlogging stress and analyzed global gene transcription responses in the leaves and roots of waterlogged cassava plants. The results showed that waterlogging stress significantly decreased the leaf chlorophyll content, caused premature senescence, and increased the activities of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) in the leaves and roots. In total, 2538 differentially expressed genes (DEGs) were detected in the leaves and 13364 in the roots, with 1523 genes shared between the two tissues. Comparative analysis revealed that the DEGs were related mainly to photosynthesis, amino metabolism, RNA transport and degradation. We also summarized the functions of the pathways that respond to waterlogging and are involved in photosynthesis, glycolysis and galactose metabolism. Additionally, many transcription factors (TFs), such as MYBs, AP2/ERFs, WRKYs and NACs, were identified, suggesting that they potentially function in the waterlogging response in cassava. The expression of 12 randomly selected genes evaluated via both quantitative real-time PCR (qRT-PCR) and RNA sequencing (RNA-seq) was highly correlated (R2 = 0.9077), validating the reliability of the RNA-seq results. The potential waterlogging stress-related transcripts identified in this study are representatives of candidate genes and molecular resources for further understanding the molecular mechanisms underlying the waterlogging response in cassava.

Physiological and sucrose metabolic responses to waterlogging stress in balloon flower (Platycodon grandiflorus (Jacq.) A. DC)

“…2 c). Similar physiological responses have been seen in peanut, wheat, avocado, and cassava (Wu et al 2015 ; Cao et al 2022 ; Lin et al 2022 ; Zeng et al 2022 ).…”

Genome-Wide Identification and Expression Analysis of the SHI-Related Sequence Family in Cassava

“…Real-time PCR was performed on a 7500 Real Time PCR System (Thermo Fisher Scientific) with a total reaction volume of 20 μL, containing 2 μL cDNA template, 1 μL forward primer, 1 μL reverse primer, 10 μL qPCR Master Mix, and 6 μL sterilized ddH 2 O. The real-time PCR amplification protocol was set at 95 °C for 30 s for 40 cycles, 95 °C for 5 s, 55 °C for 30 s, 72 °C for 30 s, and 72 °C for 10 min [ 48 ]. Relative fold expression changes of the eight MeSRS genes were normalized to the EF1α gene and calculated using the 2 −ΔΔCt method described by Schmittgen and Livak [ 49 ].…”

Genome-wide identification and expression of TIFY family in cassava (Manihot esculenta Crantz)

“…A 7500 Real-Time PCR System with a total reaction volume of 20 μL was used for real-time PCR, which included 2 μL cDNA template, 1 μL forward primer, 1 μL reverse primer, 10 μL qPCR Master Mix, and 6 μL sterilized ddH 2 O. The real-time PCR amplification protocol was set at 95°C for 30 seconds (s) for 40 cycles, 95°C for 5 s, 55°C for 30 s, 72°C for 30 s, and 72°C for 10 minutes ( Cao et al., 2022 ). The ΔΔCT technique described by Schmittgen and Livak (2008) was used to analyze the relative expression levels of JAZ , PPD , and ZML genes, and relative changes in gene expression were computed using elongation factor 1 alpha ( EF1α ) as a reference gene.…”