Comparative Transcriptome Profiling of Cassava Tuberous Roots in Response to Postharvest Physiological Deterioration

Abstract

Cassava is one of the most versatile tuberous-root crops on Earth. However, the postharvest storage properties of cassava tuberous root mean that it is perishable through a process known as postharvest physiological deterioration (PPD), which seriously affects its starch quality. Therefore, a comprehensive understanding of the transcriptional regulatory activity of cassava against the PPD response is necessary in order to extract key molecular mechanisms related to PPD tolerance. In this study, we found that RYG1 tuberous roots showed delayed PPD compared to those of SC8. In addition, RYG1 roots maintained a more stable cell wall structure after storage than those of SC8. The transcriptome changes in tuberous roots were analyzed for both RYG1 and SC8 after 21 days of storage (SR and SS) compared to fresh (FR and FS) by the RNA-Seq method. The total number of differentially expressed genes (DEGs) in the various comparisons of these four samples ranged from 68 to 3847. Of these, a total of 2008 co-DEGs in SR vs. SS were shared by either SR vs. FR or SS vs. FS. GO and KEGG enrichment analysis revealed that upregulated co-DEGs in SR vs. SS were mainly enriched in photosynthesis, protein processing, hormone and cutin, suberine and wax biosynthesis. By contrast, the downregulated co-DEGs were mainly related to cell wall organization, starch and sucrose metabolism, galactose metabolism, phenylpropanoid biosynthesis, diterpenoid biosynthesis, cysteine and methionine metabolism and flavonoid biosynthesis. The protein–protein interaction (PPI) networks of the co-DEGs showed a complex interaction of genes in different pathways, and 16 hub genes were characterized to have a degree in excess of 15, among which eight genes were associated with photosynthesis. These results provide new information for the study of cassava resistance to PPD and lay a foundation for the further molecular breeding of storage-tolerant cassava varieties.

Integrated Characterization of Cassava (Manihot esculenta) Pectin Methylesterase (MePME) Genes to Filter Candidate Gene Responses to Multiple Abiotic Stresses

“…As an important food and renewable bioenergy raw material that is widely cultivated in tropical and subtropical regions of the world, cassava has many advantages and disadvantages. It is very suitable for arid and barren soil, but it is very sensitive to low temperatures, and its storage roots very readily deteriorate after harvest [41,63]. In this study, we filtered out five MePMEs (MePME1, MePME2, MePME27, MePME65 and MePME82), which were shared by different stress treatments, namely, PPD, chilling, 50 µmol/L ABA and 7% PEG stresses.…”

“…Therefore, we analyzed the expression of MePMEs in cassava transcriptome data in response to PPD. A total of 31 MePME genes with values of transcription per kilobase per million mapping readings (FPKM) in each sample were found in the transcriptomic data of two cassava varieties (PPD-sensitive cassava SC8 and PPD-tolerant cassava RYG1) after 0-and 21-day storage (SC8 severely deteriorated, while RYG1 maintained good quality) [41]. A total of ten MePME genes were found to participate in the response to PPD in the transcriptome data of SC124 cassava during PPD at time points of 0 h (control), 6 h (no symptoms of PPD), 12 h (local symptoms of PPD) and 48 h (global PPD symptoms) after deterioration [50].…”

“…The cassava storage roots are full of starch, which can be used not only for food, but also for ethanol production and medicine [38][39][40]. Cassava has several advantages as a crop staple such as its high tolerance to heat, drought and poor soil, but it also has some disadvantages such as a susceptibility to mosaic virus infection, the tendency to easily suffer postharvest deterioration as well as an intolerance to salt and low temperatures [41,42]. In recent years, the function of several genes in cassava have been analyzed [43][44][45][46].…”

Integrated Analysis of Morphological, Physiological, Anatomical and Molecular Responses of Cassava Seedlings to Different Light Qualities

“…Cassava ( Manihot esculenta Crantz) is ranked the sixth most important crop in the world and is planted globally in tropical and subtropical areas. Cassava tuberous root contains large reserves of starch, which comprises approximately 85% of the dry weight [ 1 , 2 ]. As such, cassava is a stable crop that feeds almost one-tenth of the global population.…”

“…In addition, cassava grown in the field is likely to be attacked by viruses, bacteria and pests, as well as damaged by cold and salt stress. Moreover, the postharvest quality of cassava decreases rapidly [ 2 , 6 , 7 , 8 , 9 ]. To overcome these limitations, gene manipulation strategies are increasingly being taken in order to generate new varieties.…”