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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (7): 1769-1784.doi: 10.3724/SP.J.1006.2023.24180


Evolution and relative expression pattern of LRRII-RLK gene family in sugarcane Saccharum spontaneum

DING Hong-Yan1,2(), FENG Xiao-Xi3, WANG Bai-Yu2, ZHANG Ji-Sen1,2,*()   

  1. 1College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
    2State Key Laboratory of Conservation and Utilization of Agric-Biological Resources, Guangxi University, Nanning 530004, Guangxi, China
    3College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
  • Received:2022-08-03 Accepted:2022-11-25 Online:2023-07-12 Published:2022-12-14
  • Contact: *E-mail: zjisen@126.com E-mail:hyding2020@163.com;zjisen@126.com
  • Supported by:
    The National Key Research and Development Program of China(2021YFF1000100);The Science and Technology Planting Project of Guangdong Province(2019B020238001)


It is well-known that LRRII-RLK gene family widely exists in plants. These genes are receptor like kinase (RLK), which play a significant role in plant development and biological stress. Up till now, there is no systematic identification and analysis of the LRRII-RLK gene family in sugarcane. Here, we identified 27 LRRII-RLK genes in Saccharum spontaneum, which were distributed on 17 chromosomes. Phylogenetic tree showed the classification of these genes into three different branches including NIK, SERK, and LRRII-C. Furthermore, we observed the significant amplification in the LRRII-C branch. Next, we characterized the cis-regulatory elements, which identified 32 different types of cis elements in the gene promoters, primarily involved in light response, stress response, regulation of hormone mechanism, and plant growth. Interestingly, SsLRRII-RLK genes were detected to be conserved with 35 collinear gene pairs and multiple conserved motifs. These genes were mainly amplified by segmental replication and had undergone strict purification selection during the evolution, according to their Ka/Ks ratios. Furthermore, the relative expression level of SsLRRII-RLK genes varied in different tissues of sugarcane. Additionally, some genes expressed differently during distinct periods of day and night, suggesting that they were associated with plant growth regulation and photosynthesis. Noticeably, the relative expression pattern of SsLRRII-RLK genes varied significantly under different disease conditions (sugarcane pokkah boeng disease and mosaic disease). In conclusion, these genes might play a role in pathogenesis and viral replication. The results of this study are helpful to further understand the evolutionary process of LRRII-RLK gene in sugarcane. This data provides a preliminary theoretical basis for the functional study of LRRII-RLK gene during photosynthesis, growth and development, and disease conditions in sugarcane.

Key words: Saccharum spontaneum, LRRII-RLK genes, transcriptomics, gene expression analysis, phylogenetic analysis

Table 1

Primers for qPCR study"

Gene name
Forward sequence (5'-3')
Reverse sequence (5'-3')

Table 2

Information of LRRII-RLK gene family in Saccharum spontaneum"

No. of genes
Gene name
MW (kD)
Grand average of hydropathicity
Sspon.01G0025910-4D SsLRRII-RLK-1 1D 629 69.86 5.31 31.89 -0.130 4
Sspon.01G0025910-2B SsLRRII-RLK-1-2 1B 384 41.90 6.83 30.59 0.105 4
Sspon.03G0036270-1B SsLRRII-RLK-2 3B 417 45.56 8.85 35.51 -0.022 4
Sspon.03G0036270-2C SsLRRII-RLK-2-2 3C 417 45.51 8.85 35.15 -0.021 4
Sspon.03G0036270-3D SsLRRII-RLK-2-3 3D 410 44.65 7.10 26.89 -0.053 4
Sspon.04G0004390-1A SsLRRII-RLK-3 4A 661 72.62 7.87 38.30 -0.010 4
Sspon.04G0004390-2D SsLRRII-RLK-3-2 4D 626 68.61 7.25 39.69 -0.037 4
Sspon.04G0009850-1A SsLRRII-RLK-4 4A 578 63.63 5.57 44.60 -0.181 4
Sspon.04G0009850-3D SsLRRII-RLK-4-2 4D 625 68.62 5.57 44.03 -0.147 4
Sspon.04G0013270-1A SsLRRII-RLK-5 4A 606 67.54 5.13 35.40 -0.184 4
Sspon.04G0014480-3D SsLRRII-RLK-6 4D 715 79.13 5.68 38.88 -0.107 4
Sspon.05G0010060-2C SsLRRII-RLK-7 5C 458 50.37 5.98 46.82 -0.237 4
Sspon.05G0010060-1A SsLRRII-RLK-7-2 5A 543 60.94 7.06 45.11 -0.243 4
Sspon.06G0005550-1A SsLRRII-RLK-8 6A 982 105.55 10.63 46.16 -0.211 4
Sspon.06G0010230-1A SsLRRII-RLK-9 6A 580 64.21 5.84 43.90 -0.243 4
Sspon.06G0010230-2B SsLRRII-RLK-9-2 6B 586 64.37 5.66 44.92 -0.166 4
Sspon.06G0010230-3C SsLRRII-RLK-9-3 6C 584 64.62 5.77 43.86 -0.221 3
Sspon.06G0016870-1A SsLRRII-RLK-10 6A 581 65.10 5.89 38.07 -0.211 4
Sspon.06G0016880-1A SsLRRII-RLK-11 6A 925 102.95 8.20 45.98 -0.382 4
Sspon.06G0016880-2B SsLRRII-RLK-11-2 6B 619 69.48 5.57 38.08 -0.120 2
Sspon.06G0016880-1P SsLRRII-RLK-12 6B 624 70.00 5.64 38.47 -0.107 4
Sspon.06G0005060-3C SsLRRII-RLK-13 6C 591 66.41 6.35 34.31 -0.092 4
Sspon.06G0035390-1D SsLRRII-RLK-14 6D 473 52.30 8.63 32.14 -0.084 4
Sspon.07G0011930-3D SsLRRII-RLK-15 7D 497 54.79 5.45 39.04 -0.049 4
Sspon.08G0009990-1A SsLRRII-RLK-16 8A 336 37.00 8.70 33.67 -0.025 4
Sspon.08G0009990-2C SsLRRII-RLK-16-2 8C 581 63.95 6.89 39.18 -0.130 1
Sspon.08G0009990-3D SsLRRII-RLK-16-3 8D 551 60.66 7.95 39.71 -0.132 4

Fig. 1

Phylogenetic tree of LRRII-RLKs inform Saccharum spontaneum (Ss) and presentative species including Arabidopsis thaliana (AT), Oryza sativa (Os), and Sorghum bicolor (Sb)"

Fig. 2

Phylogenetic relationships of LRRII-RLK proteins in 17 plant species Linear scale Time Mya (millions of years ago) was shown at the tree’s bottom. Seventeen plants including Saccharum spontaneum, Oryza sativa, Brachypodium distachyon, Sorghum bicolor, Solanum tuberosum, Solanum lycopersicum, Gossypium hirsutum, Arabidopsis thaliana, Raphanus sativus, Citrus sinensis, Citrus clementina, Cucumis sativus, Fragaria vesca, Pyrus bretschneideri, Malus domestica, Prunus mume, and Prunus persica."

Fig. 3

Analysis of conserved motifs and gene structure of LRRII-RLK gene family in Saccharum spontaneum A: SsLRRII-RLK genes structure analysis, different colored boxes indicate different gene structures, black lines indicate introns. B: SsLRRII-RLK proteins conserved motif analysis, different colored boxes indicate different conserved motifs, and black lines indicate amino acid sequences."

Fig. 4

Cis-elements analysis of LRRII-RLK genes in Saccharum spontaneum"

Fig. 5

Distribution and syntenic analysis of SsLRRII-RLK genes in Saccharum spontaneum The internal line indicates the collinearity within SsLRRII-RLK genes."

Fig. 6

Synteny analysis between Saccharum spontaneum and Sorghum bicolor species The grey lines in the background indicate the collinear blocks within two genomes. The red lines indicate the LRRII-RLK syntenic gene pairs."

Fig. 7

Ka/Ks value distribution of all LRRII-RLK orthologous gene pairs between Saccharum spontaneum and Sorghum bicolor * and ** mean significant difference at the 0.05 and 0.01 probability levels, respectively."

Table 3

Divergence time based on Ks estimation for the orthologous genes of LRRII-RLK from Sorghum bicolor and Saccharum spontaneum"

Number of genes
Gene name
Divergence time (Mya)
Sspon.03G0036270-1B-Sobic.003G051100 SsLRRII-RLK-2-SbLRRII-RLK1 0.1065600 4.512
Sspon.03G0036270-2C-Sobic.003G051100 SsLRRII-RLK-2-2-SbLRRII-RLK1 0.1075050 8.270
Sspon.04G0004390-2D-Sobic.004G252200 SsLRRII-RLK-3-2-SbLRRII-RLK5 0.0616391 4.741
Sspon.04G0009850-3D-Sobic.004G189900 SsLRRII-RLK-4-2-SbLRRII-RLK4 0.0675914 5.199
Sspon.04G0013270-1A-Sobic.004G128200 SsLRRII-RLK-5-SbLRRII-RLK3 0.0586529 4.512
Sspon.04G0014480-3D-Sobic.004G104800 SsLRRII-RLK-6-SbLRRII-RLK2 0.0743093 5.716
Sspon.06G0005550-1A-Sobic.007G142900 SsLRRII-RLK-8-SbLRRII-RLK12 0.2812260 21.633
Sspon.06G0010230-1A-Sobic.007G059600 SsLRRII-RLK-9-SbLRRII-RLK9 0.0693491 5.335
Sspon.06G0010230-2B-Sobic.007G059600 SsLRRII-RLK-9-2-SbLRRII-RLK9 0.1305250 10.040
Sspon.06G0016880-1A-Sobic.005G182400 SsLRRII-RLK-11-SbLRRII-RLK7 0.0387034 2.977
Sspon.06G0016880-2B-Sobic.005G182400 SsLRRII-RLK-11-2-SbLRRII-RLK7 0.0373593 2.874
Sspon.08G0009990-2C-Sobic.010G115300 SsLRRII-RLK-16-2-SbLRRII-RLK15 0.0964024 7.416
Sspon.08G0009990-3D-Sobic.010G115300 SsLRRII-RLK-16-3-SbLRRII-RLK15 0.0919244 7.071
Sspon.06G0035390-1D-Sobic.005G182400 SsLRRII-RLK-14-SbLRRII-RLK7 0.1044750 8.037

Fig. 8

Relative expression profiles of SsLRRII-RLK genes in different tissues, leaf gradients, and day-night rhythms in sugarcane Sd: seedling stage; PM: pre-mature; M: mature; SL: seeding leaf; SS: seeding stem; LR: leaf roll; LF: leaf; BZ: basal zone; TZ: translational zone; MZ1: maturing zone 1; MZ2: maturing zone 2."

Fig. 9

Verification for the relative expression pattern of SsLRRII-RLKs genes by qRT-PCR"

Fig. 10

Heat map of LRRII-RLK genes in sugarcane infected with different diseases (pokkah boeng disease and sugarcane mosaic disease) P1: CK; P2: inchoate; P3: advanced. S1: CK; S2: CK detoxify; S3: post-infection."

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