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Identification of QTLs conferring resistance to begomovirus isolate of PepYLCIV in Capsicum chinense

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Abstract

Pepper yellow leaf curl disease caused by begomoviruses has emerged as a major limitation to the cultivation of pepper (Capsicum spp.) production in a number of regions around the world. Although begomovirus resistance has been reported in several accessions, pepy-1 derived from BaPep-5 (C. annuum) is the only begomovirus resistance gene cloned to date. In this study, we evaluated the resistance of a C. chinense accession GR1 against pepper yellow leaf curl Indonesia virus (PepYLCIV), which is one of the predominant begomovirus species infecting pepper plants in Indonesia. Infection of PepYLCIV to susceptible Habanero (C. chinense) plants induced typical yellowing symptoms, whereas the GR1 plant showed symptoms with very low severity. Moreover, the accumulation of viral DNA was restricted in GR1 compared to Habanero. Phenotypic analyses of F1 and F2 populations obtained by crossing Habanero with GR1 inferred that the resistance is a dominant trait controlled by multiple genes. Linkage analysis in the F2 population using restriction site-associated DNA sequencing data detected two significant quantitative trait loci (QTLs), one on chromosome 4 and another on chromosome 11, which explained 31.6 and 19.7% of the phenotypic variation, respectively. Moreover, QTL-seq conducted using F3 population partially confirmed the result of F2 population, which detected QTLs on chromosome 3 and 11, respectively. The QTLs identified for PepYLCIV resistance in this research are novel since no other resistance causing QTLs have ever been reported in these genomic regions. GR1 is a highly valuable genetic resource for the breeding of begomovirus resistance in peppers.

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Acknowledgements

We thank Satoko Kondo (Ryukoku University) for supporting RAD-seq library preparation. We thank Shinya Kanzaki (Kindai University) and Hiroki Saito (Japan International Research Center for Agricultural Sciences) for useful discussion.

Funding

This work was supported by JSPS KAKENHI Grant Number 19H02950 and 21KK0109 for S. Koeda, and JSPS-DG-RSTHE Joint Research Program for S. Koeda and E. Kesumawati.

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Authors and Affiliations

  1. Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan

    Namiko Mori & Sota Koeda

  2. Faculty of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan

    Shota Hasegawa, Ryota Takimoto, Ryo Horiuchi, Chiho Watanabe, Daiki Onizaki & Sota Koeda

  3. Takii & Co. Ltd, Konan, Shiga, 520-3231, Japan

    Hayato Shiragane

  4. Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan

    Atsushi J. Nagano

  5. Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2914, Japan

    Atsushi J. Nagano

  6. Faculty of Agriculture, Syiah Kuala University, Darussalam, Banda Aceh, 23111, Indonesia

    Elly Kesumawati

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  1. Namiko Mori
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  2. Shota Hasegawa
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  3. Ryota Takimoto
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  10. Sota Koeda
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Contributions

NM and SK designed experiment, interpreted the results, and wrote the manuscript. NM, SH, RT, RH, CW, and DO evaluated the begomovirus resistance. NM, HS, AJN, and SK conducted RAD-seq. EK provided the resources. All authors read and approved the final manuscript.

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Correspondence to Sota Koeda.

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Mori, N., Hasegawa, S., Takimoto, R. et al. Identification of QTLs conferring resistance to begomovirus isolate of PepYLCIV in Capsicum chinense. Euphytica 218, 20 (2022). https://doi.org/10.1007/s10681-022-02970-9

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