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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (7): 1785-1798.doi: 10.3724/SP.J.1006.2023.24137


Integrated analysis of transcriptome and metabolome reveals the metabolic response pathways of sweetpotato under shade stress

WANG Yan-Nan1(), CHEN Jin-Jin1, BIAN Qian-Qian1, HU Lin-Lin2, ZHANG Li3, YIN Yu-Meng1, QIAO Shou-Chen1, CAO Guo-Zheng1, KANG Zhi-He1, ZHAO Guo-Rui1, YANG Guo-Hong1, YANG Yu-Feng1,*()   

  1. 1Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China
    2School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
    3Institute of Agricultural Economics and Information, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China
  • Received:2022-06-08 Accepted:2022-11-25 Online:2023-07-12 Published:2022-12-28
  • Contact: *E-mail: yyfyyf5@163.com E-mail:alman001@qq.com;yyfyyf5@163.com
  • Supported by:
    The Natural Science Foundation of Henan Province(212300410170);The Science and Technology Research Program of Henan Province(212102110251);The Henan Joint Research Program for Improved Agricultural Varieties(2022010401-2);The Special Fund for Henan Agriculture Research System(HARS-22-04-G1);The China Agriculture Research System of MOF and MARA(甘薯);The China Agriculture Research System of MOF and MARA(CARS-10-C14)


Sweetpotato is a heliophile crop. However, it is usually shaded in the lower position in the interplanting cultivation mode. During the middle and late field growing period, it often faces rainy weather with little illumination, which affects the dry matter accumulation in tuberous roots. Thus, analyzing the metabolic response pathways of sweetpotato under shade stress will provide the theoretical basis for the varieties’ genetic improvement of shade tolerance. In this study, the sweetpotato variety Zhenghong 23 was exposed to shade stress with 50% light transmittance for 15 days. Results showed that chlorophyll b and the total chlorophyll contents of Zhenghong 23 under shade stress were significantly increased compared with those under natural light. The maximum photochemical efficiency (Fv/Fm), the potential activity (Fv/Fo), and the comprehensive index of photosynthetic performance (PIABS) of the chlorophyll photosystem PSII decreased significantly under shade stress. The net photosynthetic rate and water use efficiency decreased significantly, while SOD and POD enzyme activities increased significantly. In addition, shade stress increased significantly the vine length and specific leaf area of Zhenghong 23, but reduced significantly the fresh weight of roots. Transcriptome and metabolome analysis of leaf tissues under shade stress and natural light conditions showed that the DEGs and DMs were mainly enriched in phenylpropanoid biosynthesis, sugar metabolism, sphinolipid metabolism, and arginine biosynthesis pathways. Most of the up-regulated DEGs enriched in the phenylpropanoid biosynthesis pathway were POD enzyme family genes, indicating that the shade stress triggered the ROS scavenging system in sweetpotato. Meanwhile, shade stress reduced sugar metabolism level of sweetpotato, decreased the soluble sugar content of leaves, inhibited both the synthesis and degradation of starch, and blocked the expansion of tuberous roots. In addition, the sphinolipid and arginine metabolism pathways may better adapt sweetptoato plants to shade stress through improving the stability of biomembranes and increase the synthetic substrates of polyamine anti-stress factors. These results provide new theoretical basis for understanding the metabolic response pathways of sweetpotato under shade stress.

Key words: sweetpotato, shade stress, transciptome, metabolome, the response pathways

Fig. 1

Comparison of plant morphology of Zhenghong 23 under natural light and shade stress"

Table 1

Effects of shade stress on plant morphological indexes and leaf enzymatic activity of Zhenghong 23"

Vine length
Stem internode number
Specific leaf area
(cm2 g-1)
Root fresh weight (g)
SOD activity
(U g-1 FW)
POD activity
(U g-1 FW)
光照Light 43.5 (6.9) 13.3 (0.5) 211.9 (28.3) 17.9 (9.9) 339.7 (80.2) 1096.1 (230.0)
遮阴Shade 65.7 (9.3)** 14.8 (2.1) 457.6 (39.2)*** 1.2 (0.5)* 547.2 (72.8)** 2366.9 (398.0)**

Table 2

Effects of shade stress on chlorophyll content (mg g-1 FW) and fluorescence characteristics of Zhenghong 23"

Light treatment
Chlorophyll a
Chlorophyll b
Chlorophyll a/b
Total chlorophyll
光照Light 1.08 (0.11) 0.45 (0.12) 2.44 (0.34) 1.53 (0.23) 0.749 (0.022) 2.838 (0.210) 0.570 (0.055)
遮阴Shade 1.21 (0.04) 0.73 (0.05)** 1.66 (0.15)** 1.94 (0.05)* 0.670 (0.033)** 2.107 (0.364)* 0.398 (0.046)**

Table 3

Effects of shade stress on photosynthetic parameters of Zhenghong 23"

Net photosynthetic rate
(μmol m-2 s-1)
(mmol m-2 s-1)
Intercellular CO2 concentration
(μmol mol-1)
(mmol m-2 s-1)
Vapor pressure deficit
Water use
光照Light 9.13 (0.87) 2.29 (0.53) 241.8 (28.2) 103.5 (8.9) 2.07 (0.18) 4.07 (0.54)
遮阴Shade 2.45 (0.54)*** 1.93 (0.46) 341.0 (13.7)** 97.3 (10.1) 2.18 (0.23) 1.02 (0.37)***

Fig. 2

Heatmap of the Pearson correlation between RNA-seq samples (a) and principal component analysis plots of samples in metabolome (b) S: shade treatment; L: light treatment."

Table 4

RNA-seq quality of samples"

Sample name
Clean reads and
percentage (%)
Number and proportion of reads
on the genome (%)
Unique mapped reads
and percentage (%)
Q30 ratio
S1 46,514,384 45,395,970 (97.60) 32,813,096 (72.28%) 31,148,789 (68.62%) 92.72
S2 45,595,318 44,524,818 (97.65) 32,073,379 (72.03%) 30,310,383 (68.08%) 93.15
S3 48,243,946 46,619,848 (96.63) 33,903,203 (72.72%) 32,580,570 (69.89%) 93.16
S4 45,242,868 43,886,694 (97.00) 31,090,577 (70.84%) 29,766,110 (67.82%) 92.72
L1 51,826,126 50,453,206 (97.35) 36,601,089 (72.54%) 35,349,491 (70.06%) 92.79
L2 52,046,026 50,516,688 (97.06) 35,620,398 (70.51%) 34,152,030 (67.61%) 93.27
L3 43,082,564 42,246,862 (98.06) 29,421,358 (69.64%) 28,373,138 (67.16%) 92.76
L4 45,214,902 43,699,856 (96.65) 30,949,611 (70.82%) 29,612,170 (67.76%) 93.30

Fig. 3

Number of total genes (a) and DEGs (b) identified under shade stress and natural light conditions S: shade treatment; L: light treatment."

Fig. 4

Top 30 function terms significantly enriched by GO (a) and the top 20 pathways significantly enriched by KEGG (b) BP: biological process; CC: cellular component; MF: molecular function. Numbers of DEGs enriched are marked above the bars. The higher the ordinate value is, the more significant the enrichment is."

Fig. 5

Correlation chart of the Top20 DMs (a) and the bubble chart of the KEGG enrichment of DMs (b) (a): the red shape indicates the positive correlation and blue indicates the negative correlation. The dot with no color means the correlation is not significant at P > 0.05. (b): the color and size of the bubble represent the enrichment reliability and the number of DMs enriched, respectively. The bigger the-log10 (P-value) is, the more reliable the enrichment is. S: shade treatment; L: light treatment."

Fig. 6

Correlation heatmap of the Top50 DMs (top) and Top100 DEGs (left) (a) and the bubble chart of the KEGG pathways jointly enriched from DEGs and DMs (b) (a): the red indicates the positive correlation and blue indicates the negative correlation. The flatter the ellipse, the higher the absolute value of the correlation. (*) means significant difference at P < 0.05. (b): triangles are DEGs and dots are DMs. The bigger the-log10(P-value) is, the more reliable the enrichment is. S: shade treatment; L: light treatment."

Fig. 7

Content heatmap of DMs enriched in the phenylpropanoid biosynthesis pathway (a) and correlation heatmap of the DMs and DEGs enriched in this pathway (b)"

Fig. 8

Content heatmap of DMs enriched in the sugar metabolism related pathways (a) and correlation heatmap of the DMs and DEGs enriched in these pathways (b)"

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