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Genome-wide association study of turnip mosaic virus resistance in non-heading Chinese cabbage

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Abstract

A genome-wide association study (GWAS) using 83 diverse non-heading Chinese cabbage (NHCC) accessions identified 42,526 high-quality single nucleotide polymorphism markers associated with turnip mosaic virus (TuMV) resistance. Seventeen associated loci were identified, along with the related genes that were differentially expressed between resistant and susceptible varieties, suggesting that they may be candidate genes for TuMV tolerance. Nine mutant genes of Arabidopsis were selected for inoculation with TuMV-GFP (green fluorescence protein) to further confirm the disease resistance of these genes. Quantitative polymerase chain reaction (qPCR) analysis showed that the virus content in the Arabidopsis mutants with the homologous genes of cell wall-associated proteins, pectin methyl-esterase (PME), transcription factors (TFs), resistance gene (R), VAN3/SFC protein and F-box gene were significantly higher than that in the mutants with the homologous genes of methylation and J protein. Our results provide the basis of further study of the potential function of these candidate TuMV resistance genes and demonstrate that the described diverse NHCC can be efficiently used for GWAS of various quantitative traits. Taken together, the findings of this study will be useful to improve TuMV resistance in NHCC breeding and to discover new genes related to TuMV resistance.

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Abbreviations

CMV:

Cucumber mosaic virus

CP:

Coat protein

CT:

Cycle threshold

FLA:

Fasciclin-like domains of AGPs

GFP:

Green fluorescence protein

GLM:

General linear model

GWAS:

Genome-wide association study

J protein:

J-domain protein

MLM:

Mixed linear model

NBS-LRR:

Nucleotide binding site-leucine-rich repeats

NHCC:

Non-heading Chinese cabbage

PRP:

Pathogenesis-related protein

qRT-PCR:

Quantitative real-time PCR-Polymerase chain reaction

QTL:

Quantitative trait locus

SNP:

Single-nucleotide polymorphism

S/TK:

Serine-threorine kinase

TF:

Transcription factors

TuMV:

Turnip mosaic virus

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Acknowledgements

The authors thank Jiangsu Agricultural Industry Technology System [JATS (2019) 416] and Natural science foundation of Jiangsu Province (BK20191308) for providing support to carrying out this research work.

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Authors and Affiliations

  1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People’s Republic of China

    Rujia Zhang, Chang Liu, Xiaoming Song, Dong Xiao, Yanping Wei, Xilin Hou & Changwei Zhang

  2. Nanjing Vegetable Science Research Institute, Nanjing, 210042, Jiangsu, People’s Republic of China

    Feifei Sun

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  1. Rujia Zhang
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  2. Chang Liu
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  3. Xiaoming Song
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  7. Xilin Hou
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  8. Changwei Zhang
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Contributions

RZ, CL, XS, FS, YW, XH and CZ conceived the study. RZ, CL, XS and YW completed the experiments. RZ, CL, XS and FS contributed to data analysis and manuscript preparation. XH and CZ participated in the planning of experiments and revising the manuscript. All authors had read and approved the final version of the manuscript.

Corresponding author

Correspondence to Changwei Zhang.

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Electronic supplementary material

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13205_2020_2344_MOESM1_ESM.docx

Supplementary file1 Fig.S1. The population structure and phylogenetic tree of non-heading Chinese cabbage (NHCC). (A) The population structure; each color represents one population, and K1to K6 are shown using STRUCTURE. The y-axis quantifies thesubgroup membership, and the x-axis shows the accessions.(B) The delta K was used to define the populationstructure of all NHCC accessions.(C) The neighbor-joining phylogenetic treeof the NHCCaccessions for each population were constructed using SNPs. (DOCX 355 kb)

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Zhang, R., Liu, C., Song, X. et al. Genome-wide association study of turnip mosaic virus resistance in non-heading Chinese cabbage. 3 Biotech 10, 363 (2020). https://doi.org/10.1007/s13205-020-02344-9

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