All Issue

2017 Vol.35, Issue 4 Preview Page
Development of Fluidigm SNP Type Genotyping Assays for Marker-assisted Breeding of Chili Pepper (Capsicum annuum L.)
Haein Kim1
,
Jae Bok Yoon2
,
>Jundae Lee2*
,
,
1Department of Horticulture, Chonbuk National University
2Research and Development Unit, Pepper and Breeding Institute
*교신저자. *Corresponding Author. 
31 August 2017. pp. 465-479
PDF XML Citation
Abstract

Chili pepper (Capsicum annuum L.) is an economically important horticultural crop in Korea; however, various diseases, including Phytophthora root rot, anthracnose, powdery mildew, Cucumber mosaic virus (CMV), Pepper mild mottle virus (PMMoV), and Pepper mottle virus (PepMoV), severely affect their productivity and quality. Therefore, pepper varieties with resistance to multiple diseases are highly desired. In this study, we developed 20 SNP type assays for three pepper populations using Fluidigm nanofluidic dynamic arrays. A total of 4,608 data points can be produced with a 192.24 dynamic array consisting of 192 samples and 24 SNP markers. The assays were converted from previously developed sequence-tagged-site (STS) markers and included markers for resistance to Phytophthora root rot (M3-2 and M3-3), anthracnose (CcR9, CA09g12180, CA09g19170, CA12g17210, and CA12g19240), powdery mildew (Ltr4.1-40344, Ltr4.2-56301, and Ltr4.2-585119), bacterial spot (Bs2), CMV (Cmr1- 2), PMMoV (L4), and PepMoV (pvr1 and pvr2-123457), as well as for capsaicinoids content (qcap3.1-40134, qcap6.1-299931, qcap6.1-589160, qdhc2.1-1335057, and qdhc2.2-43829). In addition, 11 assays were validated through a comparison with the corresponding data of the STS markers. Furthermore, we successfully applied the assays to commercial F1 cultivars and to our breeding lines. These 20 SNP type assays will be very useful for developing new superior pepper varieties with resistance to multiple diseases and a higher content of capsaicinoids for increased pungency.

Keywords
disease resistance
foreground selection
high-throughput genotyping
molecular marker
SNP
References
1
Aza-González C, Núñez-Palenius HG, Ochoa-Alejo N (2011) Molecular biology of capsaicinoid biosynthesis in chili pepper (Capsicum spp.). Plant Cell Rep 30:695-706. doi:10.1007/s00299-010-0968-8
2
Boukema IW (1984) Resistance to TMV in Capsicum chacoense Hunz. is governed by allele of the L-locus. Capsicum Newsl 3:47-48
3
Charron C, Nicolai M, Gallois JL, Robaglia C, Moury B, Palloix A, Caranta C (2008) Natural variation and functional analyses provide evidence for co-evolution between plant eIF4E and potyviral VPg. Plant J 54:56-68. doi:10.1111/j.1365-313X.2008.03407.x
4
Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and markerassisted selection for crop improvement: The basic concepts. Euphytica 142:169-196. doi:10.1007/s10681-005-1681-5
5
Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Phil Trans R Soc B 363:557-572. doi:10.1098/rstb.2007.2170
6
Eun MH, Han JH, Yoon JB, Lee J (2016) QTL mapping of resistance to the Cucumber mosaic virus P1 strain in pepper using a genotyping-by-sequencing analysis. Hortic Environ Biotechnol 57:589-597. doi:10.1007/s13580-016-0128-3
7
Kang BC, Yeam I, Frantz JD, Murphy JF, Jahn MM (2005) The pvr1 locus in Capsicum encodes a translation initiation factor eIF4E that interacts with Tobacco etch virus VPg. Plant J 42:392-405. doi:10.1111/j.1365-313X.2005.02381.x
8
Kang WH, Hoang NH, Yang HB, Kwon JK, Jo SH, Seo JK, Kim KH, Choi D, Kang BC (2010) Molecular mapping and characterization of a single dominant gene controlling CMV resistance in peppers (Capsicum annuum L.). Theor Appl Genet 120:1587-1596. doi:10.1007/s00122-010-1278-9
9
Kim HJ, Han JH, Kim S, Lee HR, Shin JS, Kim JH, Cho J, Kim YH, Lee HJ, Kim BD, Choi D (2011) Trichome density of main stem is tightly linked to PepMoV resistance in chili pepper (Capsicum annuum L.). Theor Appl Genet 122:1051-1058. doi:10.1007/s00122-010-1510-7
10
Kim SB, Kang WH, Huy HN, Yeom SI, An JT, Kim S, Kang MY, Kim HJ, Jo YD, Ha Y, Choi D, Kang BC (2017) Divergent evolution of multiple virus-resistance genes from a progenitor in Capsicum spp. New Phytologist 213:886-899. doi:10.1111/nph.14177
11
Kumar S, Banks TW, Cloutier S (2012) SNP discovery through next-generation sequencing and its application. Int J Plant Genomics 831460. doi:10.1155/2012/831460
12
Lee J, Do JW, Yoon JB (2011) Development of STS markers linked to the major QTLs for resistance to the pepper anthracnose caused by Colletotrichum acutatum and C. capsici. Hortic Environ Biotechnol 52:596-601. doi:10.1007/s13580-011-0178-5
13
Lee J, Hong JH, Do JW, Yoon JB (2010) Identification of QTLs for resistance to anthracnose to two Colletotrichum species in pepper. J Crop Sci Biotechnol 13:227-233. doi:10.1007/s12892-010-0081-0
14
Lee J, Park SJ, Hong SC, Han JH, Choi D, Yoon JB (2016a) QTL mapping for capsaicin and dihydrocapsaicin content in a population of Capsicum annuum ‘NB1’ x Capsicum chinense ‘Bhut Jolokia’. Plant Breeding 135:376-383. doi:10.1111/pbr.12355
15
Lee SH, Lee JB, Kim SM, Choi HS, Park JW, Lee JS, Lee KW, Moon JS (2004) The incidence and distribution of viral diseases in pepper by cultivation types. Res Plant Dis 10:231-240. doi:10.5423/RPD.2004.10.4.231
16
Lee WP, Lee J, Han JH, Kang BC, Yoon JB (2012) Validity test for molecular markers associated with resistance to Phytophthora root rot in chili pepper (Capsicum annuum L.). Korean J Hortic Sci Technol 30:64-72. doi:10.7235/hort.2012.11112
17
Lee YR, Yoon JB, Lee J (2016b) A SNP-based genetic linkage map of Capsicum baccatum and its comparison to the Capsicum annuum reference physical map. Mol Breeding 36:61. doi:10.1007/s11032-016-0485-8
18
Lefebvre V, Daubèze AM, Rouppe van der Voort J, Peleman J, Bardin M, Palloix A (2003) QTLs for resistance to powdery mildew in pepper under natural and artificial infections. Theor Appl Genet 107:661-666. doi:10.1007/s00122-003-1307-z
19
Liu WY, Kang JH, Jeong HS, Choi HJ, Yang HB, Kim KT, Choi D, Choi GJ, Jahn M, Kang BC (2014) Combined use of bulked segregant analysis and microarrays reveals SNP markers pinpointing a major QTL for resistance to Phytophthora capsici in pepper. Theor Appl Genet 127:2503-2513. doi:10.1007/s00122-014-2394-8
20
Mahasuk P, Struss D, Mongkolporn O (2016) QTLs for resistance to anthracnose identified in two Capsicum sources. Mol Breed 36:10. doi:10.1007/s11032-016-0435-5
21
Mimura Y, Kageyama T, Minamiyama Y, Hirai M (2009) QTL analysis for resistance to Ralstonia solanacearum in Capsicum accession ‘LS2341’. J Jpn Soc Hort Sci 78:307-313. doi:10.2503/jjshs1.78.307
22
Park SK, Kim SH, Park HG, Yoon JB (2009) Capsicum germplasm resistant to pepper anthracnose differentially interact with Colletotrichum isolates. Hortic Environ Biotechnol 50:17-23
23
Poland JA, Rife TW (2012) Genotyping-by-sequencing for plant breeding and genetics. Plant Genome 5:92-102. doi:10.3835/ plantgenome2012.05.0005
24
Quirin EA, Ogundiwin EA, Prince JP, Mazourek M, Briggs MO, Chlanda TS, Kim KT, Falise M, Kang BC, Jahn MM (2005) Development of sequence characterized amplified region (SCAR) primers for the detection of Phyto.5.2 , a major QTL for resistance to Phytophthora capsici Leon. in pepper. Theor Appl Genet 110:605-612. doi:10.1007/s00122-004-1874-7
25
Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94-100. doi:10.1016 /S1369-5266(02)00240-6
26
Römer P, Hahn S, Jordan T, Strauβ T, Bonas U, Lahaye T (2007) Plant pathogen recognition mediated by promoter activation of the pepper Bs3 resistance gene. Science 318:645-648. doi:10.1126/science.1144958
27
Römer P, Jordan T, Lahaye T Identification and application of a DNA-based marker that is diagnostic for the pepper (Capsicum annuum) bacterial spot resistance gene Bs3. Plant Breeding 129:737-740. doi:10.1111/j.1439-0523.2009.01750.x
28
Stall RE, Jones JB, Minsavage GV (2009) Durability of resistance in tomato and pepper to Xanthomonads causing bacterial spot. Annu Rev Phytopathol 47:265-284. doi:10.1146/annurev-phyto-080508-081752
29
Tai T, Dahlbeck D, Stall RE, Peleman J, Staskawicz BJ (1999a) High-resolution genetic and physical mapping of the region containing the Bs2 resistance gene of pepper. Theor Appl Genet 99:1201-1206. doi:10.1007/s001220051325
30
Tai TH, Dahlbeck D, Clark ET, Gajiwala P, Pasion R, Whalen MC, Stall RE, Staskawicz BJ (1999b) Expression of the Bs2 pepper gene confers resistance to bacterial spot disease in tomato. Proc Natl Acad Sci 96:14153-14158. doi:10.1073/pnas.96.24.14153
31
Thomson MJ (2014) High-throughput SNP genotyping to accelerate crop improvement. Plant Breeding Biotech 2:195-212. doi:10.9787/ PBB.2014.2.3.195
32
Tomita R, Sekine KT, Mizumoto H, Sakamoto M, Murai J, Kiba A, Kikichi Y, Suzuki K, Kobayashi K (2011) Genetic basis for the hierarchical interaction between Tobamovirus spp. and L resistance gene alleles from different pepper species. Mol Plant Microbe Interact 24:108-117. doi:10.1094/MPMI-06-10-0127
33
Truong HTH, Kim KT, Kim S, Cho MC, Kim HR, Woo JG (2011) Development of gene-based markers for the Bs2 bacterial spot resistance gene for marker-assisted selection in pepper (Capsicum spp.). Hortic Environ Biotechnol 52:65-73. doi:10.1007/ s13580-011-0142-4
34
Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27:522-530. doi:10.1016/j.tibtech.2009.05.006
35
Wang J, Lin M, Crenshaw A, Hutchinson A, Hicks B, Yeager M, Berndt S, Huang WY, Hayes RB, Chanock SJ, Jones RC, Ramakrishnan R (2009) High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays. BMC Genomics 10:561. doi:10.1186/1471-2164-10-561
36
Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391-407. doi:10.2135/ cropsci2007.04.0191
37
Yang HB, Liu WY, Kang WH, Kim JH, Cho HJ, Yoo JH, Kang BC (2012) Development and validation of L allele-specific markers in Capsicum. Mol Breeding 30:819-829. doi:10.1007/s11032-011-9666-7
38
Yeam I, Kang BC, Lindeman W, Frantz JD, Faber N, Jahn MM (2005) Allele-specific CAPS markers based on point mutations in resistance alleles at the pvr1 locus encoding eIF4E in Capsicum. Theor Appl Genet 112:178-186. doi:10.1007/s00122-005-0120-2
39
Yoon JB (2003) Identification of genetic resources, interspecific hybridization and inheritance analysis for breeding pepper (Capsicum annuum) resistant to anthracnose. PhD Diss., Seoul National Univ., Seoul, Korea
Information
  • Publisher :KOREAN SOCIETY FOR HORTICULTURAL SCIENCE
  • Publisher(Ko) :원예과학기술지
  • Journal Title :Horticultural Science and Technology
  • Journal Title(Ko) :원예과학기술지
  • Volume : 35
  • No :4
  • Pages :465-479
  • Received Date :2016. 04. 04
  • Revised Date :2017. 05. 27
  • Accepted Date : 2017. 05. 26
  • DOI :https://doi.org/10.12972/kjhst.20170050
Journal Informaiton Horticultural Science and Technology Horticultural Science and Technology
Online Submission
  • scopus
  • NRF
  • KOFST
  • KISTI Current Status
  • KISTI Cited-by
  • crosscheck
  • orcid
  • open access
  • ccl
Journal Informaiton Journal Informaiton - close