Transcriptomic analysis of tuberous root in two sweet potato varieties reveals the important genes and regulatory pathways in tuberous root development

Cai, Zhaoqin; Cai, Zhipeng; Huang, Jingli; Wang, Aiqin; Ntambiyukuri, Aaron; Chen, Bimei; Zheng, Ganghui; Li, Huifeng; Huang, Yongmei; Zhan, Jiasui; Xiao, Dong; He, Long-Fei

doi:10.1186/s12864-022-08670-x

Cited by 22 publications

(15 citation statements)

References 72 publications

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“…sweet potatoes [23], and cassava [24,25]. Subsequently, the weight gain ratio of the tuberous root slowly increased.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Profiling Reveals the Genes Involved in Tuberous Root Expansion in Pueraria (Pueraria thomsonii Benth.)

Xiao

Zhang³

et al. 2023

Preprint

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Pueraria is a dry root commonly used in Traditional Chinese Medicine or as food and fodder, and tuberous root expansion is an important agronomic characteristic that influences its yield. However, current research has identified no specific genes regulating tuberous root expansion in Pueraria. Therefore, we aimed to explore the expansion mechanism of Pueraria at six developmental stages (P1–P6), by profiling the tuberous roots of an annual local variety “Gange No.1” harvested at 105, 135, 165, 195, 225, and 255 days after transplanting. Observations of the tuberous root phenotype and cell microstructural morphology revealed that the P3 stage was a critical boundary point in the expansion process, which was preceded by diameter thickening and yield gain rapidly of the tuberous roots, and followed by longitudinal elongation at both ends. A total of 17,441 differentially expressed genes (DEGs) were identified by comparing the P1 stage (unexpanded)against the P2–P6 stages (expanded) using transcriptome sequencing; 386 differential genes were shared across the six developmental stages. KEGG pathway enrichment analysis showed that the DEGs shared by P1 and P2–P6 stages were mainly involved in processes related to the “cell wall and cell cycle”, “plant hormone signal transduction”, and “sucrose and starch metabolism”. This finding is consistent with the physiological data collected on changes in sugar and hormone contents for Pueraria. The combination of KEGG and trend analyses revealed six essential candidate genes involved in tuberous root expansion; of them, CDC48, ARF, and EXP genes were significantly upregulated during tuberous root expansion while the INV, EXT, and XTH genes were significantly downregulated. These findings provide insights into the complex mechanisms of tuberous root expansion in Pueraria and candidate target genes, which can aid in increasing Pueraria yield.

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“…sweet potatoes [23], and cassava [24,25]. Subsequently, the weight gain ratio of the tuberous root slowly increased.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Profiling Reveals the Genes Involved in Tuberous Root Expansion in Pueraria (Pueraria thomsonii Benth.)

Xiao

Zhang³

et al. 2023

Preprint

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“…The upregulation of starch biosynthesis and downregulation of lignin biosynthesis in potential storage roots are the main events during the storage root formation period [ 8 , 15 , 22 ], probably because the activity of carbon flow towards carbohydrate metabolism is stronger than the delivery into phenylpropanoid biosynthesis during the storage root formation period [ 14 , 30 ]. Previous findings have shown that low sucrose and high hexose content in the root system could facilitate storage root formation [ 14 , 31 ].…”

Section: Discussionmentioning

confidence: 99%

“…Ibkn1, Ibkn2, and Ibkn3 are members of the class I knotted 1-like (KNOX-box) gene family, and they are expressed in primary cambium cells [ 8 , 15 ]. They regulate cell proliferation and differentiation in potential storage roots [ 22 , 23 ], and their expression in storage roots was two-fold higher than that in fiber roots [ 8 , 15 ].…”

Section: Introductionmentioning

confidence: 99%

Influence of Planting Density on Sweet Potato Storage Root Formation by Regulating Carbohydrate and Lignin Metabolism

Liang

Chen

Chang

et al. 2023

Plants

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An appropriate planting density could realize the maximum yield potential of crops, but the mechanism of sweet potato storage root formation in response to planting density is still rarely investigated. Four planting densities, namely D15, D20, D25, and D30, were set for 2-year and two-site field experiments to investigate the carbohydrate and lignin metabolism in potential storage roots and its relationship with the storage root number, yield, and commercial characteristics at the harvest period. The results showed that an appropriate planting density (D20 treatment) stimulated cambium cell differentiation, which increased carbohydrate accumulation and inhibited lignin biosynthesis in potential storage roots. At canopy closure, the D20 treatment produced more storage roots, particularly developing ones. It increased the yield by 10.18–19.73% compared with the control D25 treatment and improved the commercial features by decreasing the storage root length/diameter ratio and increasing the storage root weight uniformity. This study provides a theoretical basis for the high-value production of sweet potato.

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“…Through transcriptome analysis, researchers discovered that the expression of potato genes varies greatly among different varieties [32], which directly affects individual differ-ences in potato growth. Among cultivars, there are significant variations in the expression profiles of genes that affect tuber development [33]. The variation in gene expression is more prominent in potatoes with high heterozygosity and tetraploid inbreeding inhibition [34].…”

Section: Rna-seq Screened 85 Cadmium Tolerance Genes In Potatomentioning

confidence: 99%

The Expression of the StNRAMP2 Gene Determined the Accumulation of Cadmium in Different Tissues of Potato

Zhang

Tian

et al. 2023

IJMS

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Cadmium (Cd) is a toxic metal that threatens human health when enriched in crops. NRAMPs are a family of natural macrophage proteins reported to play a key role in Cd transport in plants. In order to explore the gene regulation mechanism of potato under Cd stress and the role of NRAMPs family in it, this study analyzed the gene expression differences of two different Cd accumulation levels in potato after 7 days of 50 mg/kg Cd stress and screened out the key genes that may play a major role in the differential accumulation of Cd in different varieties. Additionally, StNRAMP2 was selected for verification. Further verification showed that the StNRAMP2 gene plays an important role in the accumulation of Cd in potato. Interestingly, silencing StNRAMP2 increased Cd accumulation in tubers but significantly decreased Cd accumulation in other sites, suggesting a critical role of StNRAMP2 in Cd uptake and transport in potatoes. To further confirm this conclusion, we performed heterologous expression experiments in which overexpression of StNRAMP2 gene in tomato resulted in a threefold increase in Cd content, which further confirmed the important role of StNRAMP2 in the process of Cd accumulation compared with wild-type plants. In addition, we found that the addition of Cd to the soil increased the activity of the plant antioxidant enzyme system, and silencing StNRAMP2 partially reversed this effect. This suggests that the StNRAMP2 gene plays an important role in plant stress tolerance, and future studies could further explore the role of this gene in other environmental stresses. In conclusion, the results of this study improve the understanding of the mechanism of Cd accumulation in potato and provide experimental basis for remediation of Cd pollution.

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Transcriptomic analysis of tuberous root in two sweet potato varieties reveals the important genes and regulatory pathways in tuberous root development

Cited by 22 publications

References 72 publications

Transcriptome Profiling Reveals the Genes Involved in Tuberous Root Expansion in Pueraria (Pueraria thomsonii Benth.)

Transcriptome Profiling Reveals the Genes Involved in Tuberous Root Expansion in Pueraria (Pueraria thomsonii Benth.)

Influence of Planting Density on Sweet Potato Storage Root Formation by Regulating Carbohydrate and Lignin Metabolism

The Expression of the StNRAMP2 Gene Determined the Accumulation of Cadmium in Different Tissues of Potato

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