Crops ›› 2024, Vol. 40 ›› Issue (3): 13-22.doi: 10.16035/j.issn.1001-7283.2024.03.003

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Transcriptome Analysis of Different Foxtail Millet (Setaria italica L.) Varieties Treated with Imazapic Herbicide

Song Hui1(), Wang Tao2, Xing Lu1, Liu Junfang1, Zhang Yang1, Liu Jinrong1, Chen Hongqi1(), Feng Baili3   

  1. 1Anyang Academy of Agricultural Sciences, Anyang 455000, Henan, China
    2College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
    3College of Agriculture, Northwest Agriculture and Forestry University / State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling 712100, Shaanxi, China
  • Received:2023-01-27 Revised:2023-03-30 Online:2024-06-15 Published:2024-06-18

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Abstract:

Imidazolinone herbicides can effectively control monocotyledonous and dicotyledonous weeds in foxtail millet fields. In order to explore the molecular mechanism of millet resistance to imidazolinone herbicides, after the emergence of resistant varieties (R) and sensitive varieties (S) differentially expressed genes and metabolic pathways in resistant and susceptible foxtail millet cultivars were analyzed by high-throughput RNA-Seq sequencing after 15 d of uniform spraying with methamphetamine nicotinic acid. The results showed that genes related to photosynthesis and metabolic pathways were down-regulated after herbicide treatment in both cultivars. However, the down-regulation was more significant in the sensitive cultivar. Similarly, fatty acid elongation genes were significantly down-regulated after herbicide treatment in the sensitive cultivar. Quantitative real-time PCR (qRT-PCR) results of five candidate genes showed excellent agreement with those deep sequencing. These genes may play an important role in the imidazolinone herbicide resistance.

Key words: Imazapic, Transcriptome, Differentially expressed genes, Foxtail millet

Table 1

Primers used for qRT-PCR"

引物名称
Primer name		 引物序列
Primer sequence (5′-3′)
SiACTIN7-F GGCAAACAGGGAGAAGATGA
SiACTIN7-R GAGGTTGTCGGTAAGGTCACG
LOC101765996-F CATTCACAGCCTGAGGTGTTTCC
LOC101765996-R CCATCTCCGACATCTCGCATT
LOC101784847-F GACATCCCGGAGGTGCTCAA
LOC101784847-R CGTCAGGCTCGGCATTCAA
LOC101759205-F AGACATCACCGACCTGTTCCAA
LOC101759205-R GCCCAGCACTTGTTCTCACG
LOC101765796-F ACGCCATCAACTTCCCCATC
LOC101765796-R GCCTTGTAGACGACGACCCA
LOC101782898-F AGACAACCGAAAATCAGCAGACAG
LOC101782898-R TGCCCTCAGGTATGCCCAGT

Table 2

Transcriptome summary of foxtail millet transcriptome"

样本
Sample		 有效数据
Clean reads		 映射数据
Mapped reads		 映射率
Mapped rate (%)		 唯一映射率
Unique mapped rate (%)		 GC
(%)		 Q20
(%)		 Q30
(%)
R0_1 35 066 474 31 574 750 90.04 87.36 56.00 96.67 91.78
R0_2 27 620 386 25 642 394 92.84 89.43 54.00 97.23 92.65
R0_3 30 454 968 28 403 582 93.26 89.87 55.50 97.36 92.86
S0_1 32 637 848 29 758 054 91.18 87.40 55.00 96.75 92.06
S0_2 32 213 222 29 246 420 90.79 86.69 55.00 96.76 92.11
S0_3 30 212 562 27 707 582 91.71 86.30 54.50 96.91 92.26
RT_1 41 040 330 38 384 804 93.53 90.81 53.50 97.48 93.26
RT_2 32 272 636 29 688 540 91.99 88.97 54.00 97.19 92.74
RT_3 31 474 482 28 009 464 88.99 86.24 53.50 96.55 91.90
ST_1 31 395 192 28 837 638 91.85 89.42 53.00 96.82 92.31
ST_2 32 216 306 29 179 166 90.57 87.82 53.50 96.92 92.42
ST_3 38 151 776 35 326 060 92.59 89.61 53.00 97.26 92.91
WRT_1 30 168 990 26 748 998 88.66 82.49 54.00 96.40 91.63
WRT_2 41 280 980 38 641 026 93.60 89.58 55.00 97.75 93.49
WRT_3 33 018 182 30 868 352 93.49 89.25 55.00 97.66 93.26
WST_1 42 602 542 38 785 788 91.04 87.82 55.50 97.80 93.64
WST_2 38 116 254 33 591 880 88.13 84.78 55.50 97.78 93.60
WST_3 45 776 540 41 381 022 90.40 87.53 56.50 97.85 93.66

Table 3

Number of differentially expressed genes"

比较组
Comparison group		 DEG数
DEG number		 上调
Up-regulated		 下调
Down-regulated
RT vs R0 1413 983 430
ST vs S0 7453 3566 3887
RT vs WRT 743 615 128
ST vs WST 5298 2396 2902
WRT vs R0 186 71 115
WST vs S0 920 453 467

Fig.1

Venn diagram of differentially expressed genes in resistant (a) and sensitive (b) cultivars under 0 h and 48 h of herbicide or water treatments"

Fig.2

GO classifications of foxtail millet differentially expressed genes after treatment"

Fig.3

Scatter plot of 20 signi?cantly enriched KEGG pathways (a) RT vs WRT; (b) ST vs WST. Rich factor is the DEG numbers ratio annotated in this pathway term to all gene numbers annotated in this pathway term. Greater rich factor means greater intensiveness. q-value is corrected p-value ranging from 0 to 1. The lower the q value, the more significant the enrichment."

Fig.4

Heatmap analysis of DEGs related to branched chain amino acid synthesis The bar represents the scale of each gene's expression levels (log2 TPM) in the heat map. The expression level of the genes is denoted using different colours. Red denotes high expression while blue denotes low expression."

Fig.5

Heatmap analysis of DEGs related to photosynthesis (a) DEGs associated with antenna protein; (b) DEGs associated with photosystem; (c) DEGs related to carbon fixation. The bar represents the scale of each gene's expression levels (log2 TPM) in the heat map. The expression level of the genes is denoted using different colours. Red denotes high expression while blue denotes low expression.The same below."

Fig.6

Heatmap analysis of DEGs involved in the metabolic pathway The bar represents the expression level of each gene (log2 TPM) in the heat map."

Fig.7

Heatmap analysis of DEGs related to very-long-chain fatty acid elongases"

Fig.8

qRT-PCR analysis of RNA-Seq sequencing data"

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