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Determination of R Gene Composition in a Ctv Locus Conferring Citrus Tristeza Virus Resistance from the Genetic Resources of Citrus and Its Relatives

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Determination of R Gene Composition in a Ctv Locus Conferring Citrus Tristeza Virus Resistance from the Genetic Resources of Citrus and Its Relatives Plant Breed. Biotech. 2018 (September) 6(3):245~256 Online ISSN: 2287-9366 https://doi.org/10.9787/PBB.2018.6.3.245 Print ISSN: 2287-9358 RESEARCH ARTICLE Determination of R Gene Composition in a Ctv Locus Conferring Citrus Tristeza Virus Resistance from the Genetic Resources of Citrus and Its Relatives 1† 1† 2 3 3 4 1 Jiyeon Jeong , Jin-Kyu Woo , Young Chul Park , Sukman Park , Su-Hyun Yun , Yi Lee , Gun-Hyoung Cho , 5,6 1,7 Kwan Jeong Song *, Ho Bang Kim * 1 Life Sciences Research Institute, Biomedic Co., Ltd., Bucheon 14548, Korea 2 Agricultural Research and Extension Services, Jeju Special Self-Governing Province, Seogwipo 63556, Korea 3 Citrus Research Institute, National Institute of Horticultural & Herbal Science, Seogwipo 63607, Korea 4 Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea 5 Major of Horticultural Science, Faculty of Bioscience and Industry, SARI, Jeju National University, Jeju 63243, Korea 6 Research Institute for Subtropical Agriculture & Biotechnology, Jeju National University, Jeju 63243, Korea 7 Major of Biomaterials, Faculty of Biotechnology, Jeju National University, Jeju 63243, Korea ABSTRACT Regardless of the importance of a viral pathogen, citrus tristeza virus (CTV), in citrus industry, molecular marker tools closely associated with its resistance trait have not been developed yet. Map-based cloning of a Ctv locus, one of at least two CTV-resistant loci, was previously reported from trifoliate orange. The genetic locus displayed a distinct feature of enriched composition of R genes that encode coiled-coil-nucleotide-binding site-leucine-rich repeat (CC-NBS-LRR) receptors. Based on the previous molecular characteristics of the genetic locus, we developed multiplex PCR marker sets to specifically detect seven R genes consisting of a Ctv locus. By using the multiplex PCR marker sets, we determined composition of seven R genes consisting of the genetic locus in a total of 155 citrus genetic resources including 12 of Korean landrace citrus. Genetic composition of seven R genes in the locus was variable among the genetic resources investigated. However, all of seven R genes were detected only in both trifoliate orange, Poncirus trifoliata and its derivative cultivar, P. trifoliata ‘Flying Dragon’, which have been reported to be resistant to CTV. Multiplex PCR marker sets established in this study would be an effective molecular tool to develop scion or rootstock cultivars with high resistance trait against CTV in citrus breeding program. Keywords Citrus tristeza virus, Ctv locus, R gene, CC-NBS-LRR, Molecular marker, Citrus genetic resources INTRODUCTION decreases tree vigor, fruit size and quality, and productivity regardless of rootstock (Gmitter et al. 2007). CTV has Citrus tristeza virus (CTV) is the most significant infected 100 million citrus trees, mainly in the Americas pathogenic virus in citrus worldwide, which causes two and Mediterranean (Donkersley et al. 2018). There are only major serious disease syndromes, that is, quick decline and three Citrus relatives which have been reported to be stem-pitting. The former causes tree death resulting from resistant to CTV; Severinia buxifolia (Poir.) Tenore, phloem necrosis below the graft union of infected scions on Swinglea glutinosa (Blanco) Merr., and Poncirus trifoliata sour orange (Citrus aurantium L.) rootstock. The latter (L.) Raf. (Garnsey et al. 1987; Garnsey et al. 1997; Mestre Received June 20, 2018; Revised August 12, 2018; Accepted August 14, 2018; Published September 1, 2018 *Corresponding author Kwan Jeong Song, [email protected], Tel: +82-64-754-3328, Fax: +82-64-725-4905 *Corresponding author Ho Bang Kim, [email protected], Tel: +82-32-218-1515, Fax: +82-32-218-1517 † These authors contributed equally. Copyright ⓒ 2018 by the Korean Society of Breeding Science This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. 246 ∙ Plant Breed. Biotech. 2018 (September) 6(3):245~256 et al. 1997a). In the genus Citrus, some of C. maxima could be strong Ctv candidates (US patent No. 7126044B2). (Burm.) Merrill are known to have resistance to CTV. The Rai (2006) introduced ten Ctv resistance candidates including CTV resistance gene was characterized as a single R genes into CTV-susceptible grapefruit variety, C. paradisi, dominant gene (Yoshida 1985, 1993) and designated Ctv by Agrobacterium-mediated transformation approach. Trans- (Gmitter et al. 1996). Fang and Roose (1999) subsequently genic lines displayed either an absence of initiation of identified another single dominant gene (Ctv2) conferring infection or its slow spread (R2 lines), or an initial CTV resistance from ʻChandlerʼ pumello [C. maxima appearance of infection and its subsequent obliteration (R1 (Burm.) Merrill], which was an independently assorting and R4 lines). These previous findings suggest that four R gene from Ctv. genes (R1 through R4) might play major roles in CTV For the map-based cloning (MBC) of Ctv gene, many resistance. Asins et al. (2012) reported that the position of molecular markers associated with CTV resistance have the major QTL for CTV resistance is conserved among C. been developed from the bulked segregant analysis (BSA) grandis, C. aurantium, and P. trifoliata, and located on for the genetic cross or backcross population using trifoliate linkage group 4b. These previous results strongly suggest orange (P. trifoliata); random amplified polymorphic DNA that R genes in Ctv locus could be useful gene markers for (RAPD), inter simple sequence repeat (ISSR), sequence MAS in citrus breeding program. characterized amplified regions (SCAR), and restriction Regardless of the importance of CTV resistance trait in fragment length polymorphism (RFLP). Many efforts have citrus industry, molecular breeding programs to produce been further focused on the construction of genetic linkage CTV resistant cultivars have not been systematically maps for the CTV resistance locus and marker-assisted operated due to the absence of robust molecular markers selection (MAS) by using the developed molecular tightly linked to the agronomic traits (Kim et al. 2016). Up markers (Gmitter et al. 1996; Deng et al. 1997; Mestre et al. to now, systematic molecular surveys of a Ctv locus in 1997b; Fang et al. 1998). citrus have not been performed yet, although molecular Bacterial artificial chromosome (BAC) libraries were cloning and characterization of a Ctv locus have been constructed for MBC of Ctv gene (Deng et al. 2001a; Yang reported (Yang et al. 2003; Rai 2006). In this report, in et al. 2001). BAC contig map covering Ctv locus was order to make early selection of CTV resistant cultivars constructed from chromosome walking using molecular possible, we developed molecular marker sets to efficiently markers closely linked to Ctv and BAC clone searches by detect whole R gene sets in a Ctv locus and comprehensively resistance gene candidate (RGC) markers (Deng et al. explored distribution of the CTV resistant locus in the 2001b; Yang et al. 2001). Finally, Yang et al. (2003) genetic resources of citrus and its relatives. determined nucleotide sequences of 282 kb of BAC contigs covering Ctv region and performed gene prediction. They found that the contig contained R gene cluster consisted of MATERIALS AND METHODS seven coiled-coil-nucleotide-binding site-leucine-rich repeat (CC-NBS-LRR) genes and suggested that one of the R Citrus genetic resources and genomic DNA isolation genes may be a Ctv gene conferring broad spectrum Citrus genetic resources of two public research institutes resistance against CTV. Two BAC contig sequences in Jeju, Korea, were used in this study; Agricultural containing either resistant (Ctv) or susceptible allele (ctv) Research and Extension Services, Jeju Special Self- were isolated from BAC libraries of ‘Thong Dee’ pumello Governing Province, and Citrus Research Institute, (C. grandis L.) and CTV-resistant USDA 17-47 line National Institute of Horticultural & Herbal Science, Rural (‘Thong Dee’ pumello x P. trifoliata). Comparison between Development Administration. Citrus leaf tissues were Ctv and ctv contig sequences revealed that two CC-NBS-LRR collected from the accessions growing in the experimental genes, R2 and R3, were found only in the contig sequence research plantation. The leaves were rinsed with running containing resistant allele, indicating that these two R genes tap water and then were kept at ‒80°C until use. Genomic R Gene Composition in a Ctv Locus Conferring CTV Resistance ∙ 247 ® DNA was extracted from leaf tissues using Biomedic 1.5 (R4/CTV#11): 2 (R6/CTV#18): 1 (R7/CTV#21). The Plant gDNA Extraction Kit (Biomedic Co., Ltd., Korea; PCR mixtures included 1 µL of genomic DNA (10 ng/µL), TM www.ibiomedic.co.kr) according to the manufacturer's 4 µL of primer mixtures, 10 µL of 2x HS Taq mix protocol. DNA quantity and quality were determined using (Dongsheng Biotech.), and 5 µL of distilled water. Multiplex DeNovix DS-11+ Spectrophotometer (DeNovix, Wilmington, PCR condition was the same as described above. DE, USA) and agarose gel electrophoresis, respectively. PCR amplification RESULTS Primers to specifically amplify seven R genes encoding CC-NBS-LRR receptors are listed in Table 1. The PCR Establishment of multiplex PCR sets specifically Ctv mixtures included 1 µL of genomic DNA (10 ng/µL), each detecting a locus 0.5 µL of forward and reverse primers (each 10 pmol/µL), In order to develop DNA-based molecular markers TM 5 µL of 2x HS Taq mix (Dongsheng Biotech., Guangzhou, specifically detecting a Ctv locus, we performed multiple China), and 3 µL of distilled water. PCR condition to amplify nucleotide sequence alignment using genic sequences for the individual R genes was as follows; 95°C, 5 minutes for seven R genes, which were obtained from a public database initial denaturation, followed by 95°C for 30 seconds, 55°C (GenBank accession No.
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