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

Ruimei Li; Shuai Yuan; Yangjiao Zhou; Shijia Wang; Qin Zhou; Zhongping Ding; Yajie Wang; Yuan Yao; Jiao Liu; Jianchun Guo

doi:10.3390/ijms24010246

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

Int J Mol Sci. 2022 Dec 23;24(1):246. doi: 10.3390/ijms24010246.

Authors

Ruimei Li^{1

2

3}, Shuai Yuan^{1

2

3}, Yangjiao Zhou^{1

2

3}, Shijia Wang^{1

2

3}, Qin Zhou^{1

2

3}, Zhongping Ding^{1

2

3}, Yajie Wang^{1

2

3}, Yuan Yao^{1

2

3}, Jiao Liu^{1

2

3}, Jianchun Guo^{1

2

3}

Affiliations

¹ Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
² Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China.
³ College of Tropical Crops, Hainan University, Haikou 570228, China.

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.

Keywords: cassava; postharvest physiological deterioration; shelf life; storage; transcriptome analysis.

MeSH terms

Gene Expression Profiling
Gene Expression Regulation, Plant
Manihot* / metabolism
Plant Roots* / metabolism
Starch / metabolism
Transcriptome

Substances

Starch

Abstract

MeSH terms

Substances

Grants and funding