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Acta Agronomica Sinica ›› 2024, Vol. 50 ›› Issue (6): 1503-1513.doi: 10.3724/SP.J.1006.2024.34172

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

Transcriptomic analysis of differences in the starch content of different potatoes

ZHAO Na1,2(), LIU Yu-Xi1,2, ZHANG Chao-Shu1,2,*(), SHI Ying1,2,*()   

  1. 1College of Agronomy, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
    2Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Harbin 150030, Heilongjiang, China
  • Received:2023-10-20 Accepted:2024-01-31 Online:2024-06-12 Published:2024-02-21
  • Contact: * E-mail: shiying01@163.com;E-mail: zhangchaoshu@126.com
  • Supported by:
    “Open Bidding for Selecting the Best Candidates” Scientific and Technological Research Project of Heilongjiang Province(2022ZXJ06B02);Natural Science Foundation of Heilongjiang Province(LH2021C027)

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Abstract:

Starch is one of the most important quality characteristics of potatoes, which is widely used in the food, medical, petrochemical and other industries. The demand for starchy potato varieties in the market is increasing year by year. To explore the characteristics and key genes of starch accumulation and regulation of potato tuber, in this study, transcriptome profiling of creeping stems (a), pre-tuber expansion (b), mid-tuber expansion (c), late tuber expansion (d), and mature stage (e) of high and low starch potato cultivars DXY and DS1 were conducted by RNA sequencing analysis, and a total of 9494 differentially expressed genes (DEGs) were identified at five stages. Binding function annotation revealed that the differential genes were mainly enriched in molecular functions such as binding and catalytic activity. Metabolic pathway analysis revealed that the differential genes were mainly enriched in carbohydrate-related metabolic pathways, and 137 DEGs were associated with starch and sucrose metabolism. Nine key genes regulating starch synthesis were examined, and the relative expression level of the sucrose synthase gene PGSC0003DMG400013547 was higher during growth period of DXY than that at any stage. The relative expression level of the fructokinase gene PGSC0003DMG400026916 was significantly higher in DXY than in DS1 during the a and b periods. The relative expression level of amylase gene PGSC0003DMG400009891, PGSC0003DMG400001549, and glucan endo-1,3-β-glucosidase gene PGSC0003DMG400024642, PGSC0003DMG400003181 in DS1 was significantly higher than that in DXY with starch-rich cultivars during the c and e periods. The described gene might be a key regulatory gene for starch synthesis and accumulation. This study provides a clue for the investigation of the regulatory mechanism of tuber starch metabolism in different potato cultivars.

Key words: potato, developmental period, accumulation of starch synthesis, transcriptome sequencing

Table 1

Primer sequences"

基因编号Gene ID 正向引物Forward primer (5'-3') 反向引物Reverse primer (5'-3')
PGSC0003DMG400026916 TGATCAAGGTCAGCGATGTG GTCTTCACGTGGAATCCTCC
PGSC0003DMG400016481 ACAGTTCTGCGTTTCAGAGC AGCAGCATGGTAAAGCTCCAA
PGSC0003DMG400013547 ACAAGGGGTGCTTTCGTTCA GTAGCCTTGTCGCCCTGATT
PGSC0003DMG400003181 CGCTGAGAGGAATTTCGGGT TTTGGTTGCCCTTTGTTGCC
PGSC0003DMG400024642 TACAAACGGACCTTGCTTTA AGTAGCAGGATAAACACAGC
PGSC0003DMG400009891 GATCATATTGCAGGCATTCG CAAGCAGTTGTGAAACCAG
EF1a GATGTTGTGCCAAAGGATGT AACTTGGTCAATGCGAGA

Fig. 1

Different developmental stages of potato tuber of DS1 and DXY Da-De represent the samples of DS1 were taken at 25 days, 40 days, 61 days, 82 days, and 103 days after planting the seedlings, respectively; Xa-Xe represent the samples of DXY were taken at 25 days, 40 days, 61 days, 82 days, and 103 days after planting the seedlings, respectively."

Fig. 2

Changes in starch content and starch content ratio of DS1 vs DXY over different periods A: starch content histogram; B: starch content ratio line chart. Da-De represent the samples of DS1 were taken at 25 days, 40 days, 61 days, 82 days and 103 days after planting the seedlings, respectively; Xa-Xe represent the samples of DXY were taken at 25 days, 40 days, 61 days, 82 days and 103 days after planting the seedlings, respectively. Asterisks indicate significant differences compared to DS1 by one-way ANOVA (** P < 0.01, *** P < 0.001), ns indicates no significance (P > 0.05)."

Table 2

Statistics of sequencing data quality"

样品名称
Sample name		 有效数据
Clean reads		 基因组比对
Mapped reads		 基因组比对率
Mapped reads (%)		 GC含量
GC content (%)		 ≥Q20 (%) ≥Q30 (%)
Da-1 41,710,042 35,971,385 86.24 42.61 97.77 93.98
Da-2 43,243,492 37,736,387 87.26 42.56 97.67 93.48
Da-3 38,555,946 34,064,046 88.35 42.86 97.96 94.21
Db-1 40,147,012 34,518,026 85.98 42.47 97.95 94.06
Db-2 41,452,450 35,287,769 85.13 43.29 97.64 93.87
Db-3 41,485,436 35,915,281 86.57 42.84 98.07 94.60
Dc-1 38,488,084 30,296,884 78.72 41.65 97.88 93.99
Dc-2 38,988,180 30,707,745 78.76 41.46 97.99 94.24
Dc-3 40,364,158 34,737,460 86.06 42.59 98.10 94.55
Dd-1 39,833,928 31,152,181 78.21 41.68 97.96 94.32
Dd-2 41,331,412 32,215,855 77.95 41.58 97.97 94.34
Dd-3 41,865,794 33,566,589 80.18 41.71 97.85 93.99
De-1 41,161,928 35,155,400 85.41 44.47 97.31 93.57
De-2 38,363,322 29,762,706 77.58 42.16 97.46 93.60
De-3 42,150,428 32,190,017 76.37 42.13 97.71 93.98
Xa-1 40,619,164 35,357,453 87.05 42.54 98.28 94.87
Xa-2 40,601,792 35,382,889 87.15 42.68 97.95 94.07
Xa-3 41,200,382 35,910,567 87.16 42.65 97.67 93.37
Xb-1 44,599,490 38,997,447 87.44 42.85 98.26 94.79
Xb-2 41,602,324 35,537,658 85.42 42.59 98.12 94.52
Xb-3 42,202,702 35,250,119 83.53 43.60 97.99 94.49
Xc-1 40,274,444 31,599,634 78.46 42.08 98.18 94.72
Xc-2 39,511,076 32,460,237 82.15 42.20 97.88 94.03
Xc-3 40,493,952 31,485,795 77.75 41.53 98.09 94.57
Xd-1 40,558,872 32,781,195 80.82 41.94 98.16 94.59
Xd-2 40,557,808 32,991,680 81.34 41.88 98.31 94.91
Xd-3 40,031,264 30,777,525 76.88 41.10 98.02 94.18
Xe-1 40,503,764 33,015,497 81.51 42.09 98.24 94.84
Xe-2 41,759,668 34,419,851 82.42 42.56 98.13 94.62
Xe-3 39,888,416 31,042,204 77.82 41.33 98.10 94.51

Fig. 3

Comparison of differential genes of DS1 vs DXY in different periods A: Volcano plot of differential genes; B: Statistical plot of number of differential genes; C: Venn plot of differential genes. Da-De represent the samples of DS1 were taken at 25 days, 40 days, 61 days, 82 days, and 103 days after planting the seedlings, respectively; Xa-Xe represent the samples of DXY were taken at 25 days, 40 days, 61 days, 82 days, and 103 days after planting the seedlings, respectively."

Fig. 4

Enrichment analysis of differential genes of DS1 vs DXY A: GO classification of the differentially expressed genes; B: the top 20 most significant enrichment KEGG pathways."

Fig. 5

KEGG enrichment analysis of differential genes of DS1 vs DXY in different periods Da-De represent the samples of DS1 were taken at 25 days, 40 days, 61 days, 82 days and 103 days after planting the seedlings, respectively; Xa-Xe represent the samples of DXY were taken at 25 days, 40 days, 61 days, 82 days, and 103 days after planting the seedlings, respectively."

Fig. 6

Heat map of differential gene expression associated with starch and sucrose metabolic pathways at different times The relative expression of each gene is determined using DESeq2 log2 (DS1 vs DXY). Light blue and dark blue indicate upward adjustment and downward adjustment, respectively. Da-De: the samples of DS1 were taken at 25 days, 40 days, 61 days, 82 days, and 103 days after planting the seedlings, respectively; Xa-Xe: the samples of DXY were taken at 25 days, 40 days, 61 days, 82 days, and 103 days after planting the seedlings, respectively."

Fig. 7

Heat map of differential gene expression associated with starch and sucrose metabolic pathways at different times The amount of gene expression was determined by log2 (FPKM). Red means high expression and blue means low expression. Da-De: the samples of DS1 were taken at 25 days, 40 days, 61 days, 82 days, and 103 days after planting the seedlings, respectively; Xa-Xe: the samples of DXY were taken at 25 days, 40 days, 61 days, 82 days, and 103 days after planting the seedlings, respectively."

Fig. 8

qRT-PCR validation of differentially expressed genes A: the comparison of RT-PCR and RNA seq, B: the correlation analysis between qRT-PCR and RNA-seq. Da-De: the samples of DS1 were taken at 25 days, 40 days, 61 days, 82 days, and 103 days after planting the seedlings, respectively; Xa-Xe: the samples of DXY were taken at 25 days, 40 days, 61 days, 82 days, and 103 days after planting the seedlings, respectively."

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