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.

Plant-specific TIFY [TIF(F/Y)XG] proteins serve important roles in the regulation of plant stress responses. This family encodes four subfamilies of proteins, JAZ (JASMONATE ZIM-domain), PPD (PEAPOD), ZML (Zinc-finger Inflorescence-like), and TIFY. In this work, a total of 16 JAZ, 3 PPD, 7 ZML, and 2 TIFY genes were found in cassava (Manihot esculenta Crantz) at the genome-wide level. The phylogenetics, exon-intron structure, motif organization, and conserved domains of these genes were analyzed to characterize the members of the JAZ, PPD, and ZML subfamilies. Chromosome location and synteny analyses revealed that 26 JAZ, PPD, and ZML genes were irregularly distributed across 14 of the 18 chromosomes, and 18 gene pairs were implicated in large-scale interchromosomal segmental duplication events. In addition, JAZ, PPD, and ZML gene synteny comparisons between cassava and three other plant species (Arabidopsis, Populus trichocarpa, and rice) uncovered vital information about their likely evolution. The prediction of protein interaction network and cis-acting elements reveal the function of JAZ, PPD, and ZML genes. Subsequently, expression patterns of JAZ, PPD, and ZML genes were validated by qRT-PCR as being expressed in response to osmotic, salt, and cadmium stress. Moreover, almost all JAZ subfamily genes were responsive to jasmonic acid (JA) treatment. In particular, MeJAZ1, MeJAZ13, and MeJAZ14, were highly up-regulated by three treatments, and these genes may deserve further study. This comprehensive study lays the groundwork for future research into TIFY family genes in cassava and may be valuable for genetic improvement of cassava and other related species.

The SHORT INTERNODES (SHI)-related sequences (SRS) are plant-specific transcription factors that have been quantitatively characterized during plant growth, regeneration, and stress responses. However, the genome-wide discovery of SRS family genes and their involvement in abiotic stress-related activities in cassava have not been documented. A genome-wide search strategy was used to identify eight family members of the SRS gene family in cassava (Manihot esculenta Crantz). Based on their evolutionary linkages, all MeSRS genes featured homologous RING-like zinc finger and IXGH domains. Genetic architecture and conserved motif analysis validated the categorization of MeSRS genes into four groups. Eight pairs of segmental duplications were detected, resulting in an increase in the number of MeSRS genes. Orthologous studies of SRS genes among cassava and three different plant species (Arabidopsis thaliana, Oryza sativa, and Populus trichocarpa) provided important insights into the probable history of the MeSRS gene family. The functionality of MeSRS genes was elucidated through the prediction of protein–protein interaction networks and cis-acting domains. RNA-seq data demonstrated tissue/organ expression selectivity and preference of the MeSRS genes. Furthermore, qRT-PCR investigation of MeSRS gene expression after exposure to salicylic acid (SA) and methyl jasmonate (MeJA) hormone treatments, as well as salt (NaCl) and osmotic (polyethylene glycol, PEG) stresses, showed their stress-responsive patterns. This genome-wide characterization and identification of the evolutionary relationships and expression profiles of the cassava MeSRS family genes will be helpful for further research into this gene family and its function in stress response. It may also assist future agricultural efforts to increase the stress tolerance of cassava.

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