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QTL mapping for Fusarium wilt resistance based on the whole-genome resequencing and their association with functional genes in Raphanus sativus

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Abstract

Key message

Two major QTL associated with resistance to Fusarium wilt (FW) were identified using whole-genome resequencing. Sequence variations and gene expression level differences suggest that TIR-NBS and LRR-RLK are candidate genes associated with FW-resistance.

Abstract

Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. raphani is an important disease in radish, leading to severe decrease in yield and quality. YR4 as a novel genetic source to resistant to FW was confirmed through screening with five pathogen isolates. We have generated F2 and F2:3 populations segregated with FW resistance using YR4 and YR18 inbred lines. The disease symptom was evaluated in F2:3 population (n = 180) in three independent studies over two years. We identified 4 QTL including the two major QTL (FoRsR7.159A and FoRsR9.359A). FoRsR7.159A and FoRsR9.359A were detected in three replicated experiments. FoRsR7.159A was delimited to the 2.18-Mb physical interval on chromosome R07, with a high LOD value (5.17–12.84) and explained phenotypic variation (9.34%–27.97%). The FoRsR9.359A represented relatively low LOD value (3.38–4.52) and explained phenotypic variation (6.24%–8.82%). On the basis of the re-sequencing data for the parental lines, we identified five putative resistance-related genes and 13 unknown genes with sequence variations at the gene and protein levels. A semi-quantitative RT-PCR analysis revealed that Rs382940 (TIR-NBS) and Rs382200 (RLK) were expressed only in ‘YR4’ from 0 to 6 days after the inoculation. Moreover, Rs382950 (TIR-NBS-LRR) was more highly expressed in ‘YR4’ from 3 to 6 days after the inoculation. These three genes might be important for FW-resistance in radish. We identified several markers based on these potential candidate genes. The marker set should be useful for breeding system to introduce the FW resistance loci from ‘YR4’ to improve tolerance to FW.

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Acknowledgements

This research was supported by Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries through Golden Seed Project, funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA) (213006-05-5-SBO20, 213006-05-5-SB110).

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Authors and Affiliations

  1. Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon, 34134, Republic of Korea

    Yinbo Ma, Sushil Satish Chhapekar, Lu Lu, Xiaona Yu, Yong Pyo Lim & Su Ryun Choi

  2. Shandong Provincial Key Laboratory of Dryland Farming Technology, Shandong Peanut Industry Collaborative Innovation Center, College of Agronomy, Qingdao Agricultural University, Qingdao, 266000, China

    Xiaona Yu

  3. Neo Seed Co., 256-45 Jingeonjung-gil, Gongdo-eup, Anseong, Gyeonggi Province, 17565, Republic of Korea

    Seungho Kim

  4. Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea

    Soo Min Lee & Gyung Ja Choi

  5. JIREH Seed Co., 104 Dongtansunhwan-daero 20-gil, Hwaseong, Gyeonggi Province, 18484, Republic of Korea

    Tae Hyoung Gan

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  1. Yinbo Ma
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Contributions

SRC and YPL and designed the study. YM carried out experiments, generated data. SRC, YM analyzed all data, and drafted manuscript. SSC participated in candidate gene identification, writing and editing of the manuscript. LL did marker survey and genotyping. LL, SK, GJC, SML, THG were participated in phenotype evaluations. YPL provided plant materials, conceived the study, and finalized the manuscript. SRC conceived and designed the study, participated as a director, and modified the manuscript. All authors read and approved the final manuscript. All the authors declare that they have no conflicts of interest.

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Correspondence to Yong Pyo Lim or Su Ryun Choi.

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122_2021_3937_MOESM7_ESM.pdf

Symptoms of plants infected with Fusarium oxysporum f. sp. raphani pathotypes 59A, 57A, 147A, HN, JHW at 25 °C and 60% relative humidity, with a 12-h light condition cycle in a culture room at the Korea Research Institute of Chemical Technology (KRICT) (PDF 1194 kb)

Genetic map of radish showing nine linkage groups (PDF 150 kb)

122_2021_3937_MOESM9_ESM.pdf

QTL for Fusarium wilt resistant traits to Fusarium oxysporum f. sp. raphani pathotype 59A in F2:3 population of R. sativus by two different software, WinQTL 2.5 and IciMapping 4.1. (a), (b) represented the results of 9 chromosome scane overall radish genome. (c), (d) represented the QTL regions identified on R7 in two different analysis methods by WinQTL 2.5 based on Composite Interval Mappin (CIM) and Inclusive Composite Interval Mapping (ICIM). Tree different replicates were performed during 2 years in culture room and glasshouse (PDF 635 kb)

PCR amplification profiles of Rs382940 in ‘YR4’, ‘YR18’, and F1 plants (PDF 215 kb)

PCR amplification profiles of Rs382200 in ‘YR4’, ‘YR18’, and F1 plants (PDF 287 kb)

122_2021_3937_MOESM12_ESM.pdf

Box plots of disease index (DI) variation at different haplotypes of alleles. The central line of box means median, and box limits are the upper and lower quartiles. The significance of difference was analyzed with T-Test and one way ANOVA and in all haplotypes significant difference were observed (P<0.001) (PDF 771 kb)

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Ma, Y., Chhapekar, S.S., Lu, L. et al. QTL mapping for Fusarium wilt resistance based on the whole-genome resequencing and their association with functional genes in Raphanus sativus. Theor Appl Genet 134, 3925–3940 (2021). https://doi.org/10.1007/s00122-021-03937-5

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