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Genome-wide characterization of the WRKY gene family in radish (Raphanus sativus L.) reveals its critical functions under different abiotic stresses

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Abstract

Key message

The radish WRKY gene family was genome-widely identified and played critical roles in response to multiple abiotic stresses.

Abstract

The WRKY is among the largest transcription factors (TFs) associated with multiple biological activities for plant survival, including control response mechanisms against abiotic stresses such as heat, salinity, and heavy metals. Radish is an important root vegetable crop and therefore characterization and expression pattern investigation of WRKY transcription factors in radish is imperative. In the present study, 126 putative WRKY genes were retrieved from radish genome database. Protein sequence and annotation scrutiny confirmed that RsWRKY proteins possessed highly conserved domains and zinc finger motif. Based on phylogenetic analysis results, RsWRKYs candidate genes were divided into three groups (Group I, II and III) with the number 31, 74, and 20, respectively. Additionally, gene structure analysis revealed that intron–exon patterns of the WRKY genes are highly conserved in radish. Linkage map analysis indicated that RsWRKY genes were distributed with varying densities over nine linkage groups. Further, RT-qPCR analysis illustrated the significant variation of 36 RsWRKY genes under one or more abiotic stress treatments, implicating that they might be stress-responsive genes. In total, 126 WRKY TFs were identified from the R. sativus genome wherein, 35 of them showed abiotic stress-induced expression patterns. These results provide a genome-wide characterization of RsWRKY TFs and baseline for further functional dissection and molecular evolution investigation, specifically for improving abiotic stress resistances with an ultimate goal of increasing yield and quality of radish.

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Abbreviations

aa:

Amino acids

BLAST:

Basic local alignment search tool

bp:

Base pair

Cd:

Cadmium

CDS:

Coding sequence

GO:

Gene ontology

HM:

Heavy metal

LG:

Linkage group

MW:

Molecular weight

Pb:

Lead

pI:

Isoelectric point

RT-qPCR:

Reverse transcription-quantitative polymerase chain reaction

TF:

Transcription factor

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Acknowledgements

The current work was partly funded by Grants from the Natural Science Foundation of China (31372064, 31501759, 31601766), National Key Technology Research and Development Program of China (2016YFD0100204-25), Key Technology R&D Program of Jiangsu Province (BE2016379), and Jiangsu Agricultural Science and Technology Innovation Fund (CX(16)1012).

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Authors and Affiliations

  1. National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China

    Bernard Kinuthia Karanja, Lianxue Fan, Liang Xu, Yan Wang, Mingjia Tang, Ronghua Wang, Fei Zhang, Everlyne M’mbone Muleke & Liwang Liu

  2. Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA

    Xianwen Zhu

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  1. Bernard Kinuthia Karanja
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  2. Lianxue Fan
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Communicated by Qiaochun Wang.

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299_2017_2190_MOESM1_ESM.tif

Fig. S1 Putative isoelectric points and molecular weights of WRKY proteins Group I, II and III in R. sativus (TIFF 248 kb)

299_2017_2190_MOESM2_ESM.tif

Fig. S2 The schematic diagram of the logo diagrams of ten motifs analyzed in all the 126 WRKY protein sequence in radish (TIFF 497 kb)

299_2017_2190_MOESM3_ESM.tif

Fig. S3 Gene ontology (GO) analysis and distribution of 126 RsWRKY genes into biological process, cellular component, and molecular functions (TIFF 410 kb)

299_2017_2190_MOESM4_ESM.tif

Fig. S4 Heat map showing WRKY genes expression pattern in radish expressed at various developmental stages in leaves, root, root tips, and cambium of radish. The heat map was created using Multi-Experiment Viewer (MeV 4.8) program (TIFF 2064 kb)

299_2017_2190_MOESM5_ESM.tif

Fig. S5 Heat map illustrating WRKY gene transcripts pattern from our radish lab data at different growth stages and biotic stresses. The heat map was created using Multi-Experiment Viewer (MeV 4.8) program (TIFF 1381 kb)

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Karanja, B.K., Fan, L., Xu, L. et al. Genome-wide characterization of the WRKY gene family in radish (Raphanus sativus L.) reveals its critical functions under different abiotic stresses. Plant Cell Rep 36, 1757–1773 (2017). https://doi.org/10.1007/s00299-017-2190-4

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