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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (9): 2446-2461.doi: 10.3724/SP.J.1006.2023.24186

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Comparative transcriptome profiling of dormancy regulatory network in peanut

WANG Fei-Fei1(), ZHANG Sheng-Zhong1, HU Xiao-Hui1, CHU Ye2, CUI Feng-Gao1, ZHONG Wen3, ZHAO Li-Bo4, ZHANG Tian-Yu3, GUO Jin-Tao5, YU Hao-Liang6, MIAO Hua-Rong1,*(), CHEN Jing1,*()   

  1. 1Shandong Peanut Research Institute, Qingdao 266100, Shandong, China
    2Department of Horticulture, University of Georgia Tifton Campus, Tifton 31793, GA, United States
    3Shandong Seed Administration Station, Jinan 250100, Shandong, China
    4Qingdao Agricultural Technology Extension Center, Qingdao 266071, Shandong, China
    5Agricultural Service Center of Hezhuang, Xinzheng, Zhengzhou 451150, Henan, China
    6Yantai Fenglin Foodstuff Co., Ltd, Yantai 264108, Shandong, China
  • Received:2022-08-10 Accepted:2023-02-21 Online:2023-09-12 Published:2023-03-03
  • Supported by:
    Youth Fund Project of the National Natural Science Foundation of China(32001584);Youth Fund Project of the National Natural Science Foundation of China(32201876);General Project of Shandong Natural Science Foundation(ZR2022MC045);Shandong Province Agriculture Improved Seed Project(2020LZGC001);Innovation Project of Shandong Academy of Agriculture Sciences(CXGC2022A03);Innovation Project of Shandong Academy of Agriculture Sciences(CXGC2022A21);Qingdao People’s Livelihood Science and Technology Project(20-3-4-26-nsh);Major Science and Technology Program of Xinjiang Uygur Autonomous Region(2022A02008-3)

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Abstract:

Seed dormancy is an important and complex agronomic trait affecting yield and quality of peanut (Arachis hypogaea L.). Seed dormancy and germination was reported to be regulated by the balance between abscisic acid (ABA) and gibberellic acid (GA). In this study, transcriptomic sequencing was performed with Huayu 52 (HY52), a peanut cultivar with strong dormancy, and two EMS mutant lines from HY52 with a weak level of dormancy. Seeds from these three lines were imbibed for 0, 12, and 24 h before tissue harvesting and RNA seq analysis. GA content of M23 and M67 was significantly higher than HY52 at 12 h after imbibition, however, the ABA content and ABA/GA ratio were lower than HY52. A total of 31,374 differentially expressed genes (DEGs) including biosynthesis and signal transduction related genes of plant hormones such as ABA and GA were discovered. We identified 50 genes related to ABA, 8 genes related to GA, 49 genes related to ethylene, and 13 genes related to auxin. Expression profiles of ABA and GA related genes was consistent with the higher GA and lower ABA content in the mutants compared with HY52 after 12 h and 24 h imbibition. In addition, many DEGs involved in carbohydrate and lipid metabolism, amino acid metabolism, and glutathione metabolism pathway were also identified. There were 5 carbohydrate metabolism related genes (GPT) and 4 lipid metabolism related genes. In addition, differentially regulated circadian rhythm pathways were found to involve in the process of peanut seed dormancy release. These results suggested that the regulation of dormancy maintenance and release was more complicated than phytohormone balance.

Key words: peanut, dormancy maintenance, dormancy release, transcriptome, plant hormone, amino acid metabolism

Fig. 1

Dormancy difference and GA, ABA content of HY52, M23, and M67 after imbibition at 12 h and 24 h A: germination rate of dormant peanut variety HY52, weak dormant accessions M23 and M67, B-D: GA content, ABA content and ABA/GA of HY52, M23, and M67 after imbibition at 0, 12, and 24 h, respectively. GA: gibberellin; ABA: abscisic acid; HY52: Huayu 52. Asterisks indicate significant differences compared to HY52 by one-way ANOVA (* P<0.05, ** P<0.01, and *** P<0.001)."

Table 1

Summary of RNA-seq data collected from dormant variety Huayu 52 and weak dormant accessions M23 and M67"

样品名称
Sample name		 原始读长
Raw reads		 有效读长
Clean reads		 有效碱基
Clean bases (Gb)		 有效读长的比例
Valid ratio (reads) (%)		 基因组上的比对率
Mapped ratio (%)		 ≥Q30 (%) GC含量
GC content (%)
HY52_0_1 47,336,764 46,882,472 7.03 99.04 92.15 94.54 46.00
HY52_0_2 40,239,562 39,850,56 5.98 99.03 92.52 96.56 45.50
HY52_0_3 42,126,764 41,757,916 6.26 99.12 92.29 94.37 47.00
M23_0_1 53,524,396 47,595,296 7.14 88.92 84.53 90.44 48.50
M23_0_2 54,811,458 53,791,824 8.07 98.14 91.70 96.29 48.00
M23_0_3 58,964,636 58,493,438 8.77 99.20 92.87 96.57 45.50
M67_0_1 44,573,54 44,010,372 6.60 98.74 92.02 95.24 47.00
M67_0_2 43,794,954 43,380,290 6.51 99.05 91.63 92.85 45.50
M67_0_3 43,654,578 43,168,590 6.48 98.89 92.05 93.96 46.00
HY52_12_1 43,666,144 43,006,610 6.45 98.49 92.15 95.24 49.00
HY52_12_2 40,974,886 40,618,232 6.09 99.13 92.86 93.45 46.00
HY52_12_3 48,252,204 47,774,688 7.17 99.01 92.33 94.51 45.50
M23_12_1 44,263,360 43,728,20 6.56 98.79 92.87 94.23 47.00
M23_12_2 44,207,630 43,791,190 6.57 99.06 92.59 94.40 46.00
M23_12_3 57,707,210 57,167,752 8.58 99.07 93.87 96.48 46.50
M67_12_1 47,514,726 46,870,288 7.03 98.64 92.41 95.52 47.00
M67_12_2 47,016,098 46,486,226 6.97 98.87 92.85 94.35 45.00
M67_12_3 41,492,948 41,145,894 6.17 99.16 92.88 93.62 45.00
HY52_24_1 51,701,800 50,178,368 7.53 97.05 93.48 96.37 47.50
HY52_24_2 39,391,916 39,016,270 5.85 99.05 92.14 93.33 46.50
HY52_24_3 48,847,594 48,142,426 7.22 98.56 93.28 96.44 47.00
M23_24_1 42,599,196 41,768,316 6.27 98.05 92.71 94.42 46.00
M23_24_2 63,130,436 62,578,018 9.39 99.12 93.84 95.84 45.00
M23_24_3 60,429,598 59,883,810 8.98 99.10 94.47 96.12 46.50
M67_24_1 44,066,802 43,632,302 6.54 99.01 94.07 95.96 47.50
M67_24_2 41,088,448 40,772,706 6.12 99.23 94.22 96.06 45.50
M67_24_3 42,584,300 42,214,250 6.33 99.13 93.06 92.79 45.00

Table 2

Functional annotation of full-length transcriptome in Huayu 52"

数据库
Database		 总基因簇
Total_unigene		 KOG数据库
KOG database		 KEGG数据库
KEGG database		 NR数据库
NR database		 SwissProt数据库
SwissProt
database		 GO数据库
GO database		 注释基因总数
Overall_
annotated
Gene_Number 47,697 25,840 19,192 43,623 33,161 19,468 43,930
Annotation_Ratio — 54.18% 40.24% 91.46% 69.52% 40.82% 92.10%

Fig. 2

Comparison and Venn diagram of differentially expressed genes in nine treatments HY52: Huayu 52; DEGs: differentially expressed genes."

Fig. 3

Enriched profiles of differentially expressed genes (DEGs) during peanut seed imbibition period Profiles of HY52 (A) and M67 (C) were clustered into two groups, namely Up (upregulated) and Bi (biphasic expression pattern), however, M23 (B) were clustered into three groups, namely Up (upregulated), Down (downregulated), and Bi (biphasic expression pattern). Profile numbers are indicated in the top left-hand corner, and the corresponding P-values for each profile are shown in the bottom left-hand corner. The number of DEGs with each profile is shown in the brackets. HY52: Huayu 52."

Fig. 4

GO enrichment of the DEGs during peanut dormancy maintenance period HY52: Huayu 52."

Fig. 5

KEGG enrichment of DEGs during peanut dormancy maintenance period HY52: Huayu 52."

Fig. 6

GO enrichment of the DEGs during peanut dormancy release period"

Fig. 7

KEGG enrichment analysis of DEGs during peanut dormancy release period"

Fig. 8

DEGs involved in plant hormone biosynthesis, metabolism and signal transduction in dormant variety HY52, and weak dormant accession M67 in the process of imbibition A: the diagram of biosynthesis, metabolism, and signal transduction in ABA, GA, ethylene, and auxin; B: the heatmaps of the relative expression patterns of DEGs related to plant hormones. HY52: Huayu 52."

Fig. 9

DEGs involved in synthesis and metabolism of carbohydrate and lipid in dormant variety HY52 and weak dormant accession M67 in the process of imbibition A: the relative expression patterns of DEGs related to lipid metabolism displayed by heatmap; B: the relative expression patterns of DEGs related to carbohydrate synthesis and metabolism displayed by heat map. HY52: Huayu 52; DEGs: differentially expressed genes."

Fig. 10

Heatmap showed the expression patterns of DEGs in the top 20 GO terms related to plant hormone and stress generated from HY52_12 vs M67_12 (A) and HY52_24 vs M67_24 (B), respectively HY52: Huayu 52."

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