Journal of Plant Biotechnology

The Korean Society of Plant Biotechnology (한국식물생명공학회)
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Development of InDel markers to identify Capsicum disease resistance using whole genome resequencing

  • Karna, Sandeep (Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration) ;
  • Ahn, Yul-Kyun (Deptartment of vegetable crops, Korea National College of Agriculture and Fisheries)
  • Received : 2017.12.14
  • Accepted : 2018.04.09
  • Published : 2018.09.30
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Abstract

In this study, two pepper varieties, PRH1 (powdery mildew resistance line) and Saengryeg (powdery mildew resistance line), were resequenced using next generation sequencing technology in order to develop InDel markers. The genome-wide discovery of InDel variation was performed by comparing the whole-genome resequencing data of two pepper varieties to the Capsicum annuum cv. CM334 reference genome. A total of 334,236 and 318,256 InDels were identified in PRH1 and Saengryeg, respectively. The greatest number of homozygous InDels were discovered on chromosome 1 in PRH1 (24,954) and on chromosome 10 (29,552) in Saengryeg. Among these homozygous InDels, 19,094 and 4,885 InDels were distributed in the genic regions of PRH1 and Saengryeg, respectively, and 198,570 and 183,468 InDels were distributed in the intergenic regions. We have identified 197,821 polymorphic InDels between PRH1 and Saengryeg. A total of 11,697 primers sets were generated, resulting in the discovery of four polymorphic InDel markers. These new markers will be utilized in order to identify disease resistance genotypes in breeding populations. Therefore, our results will make a one-step advancement in whole genome resequencing and add genetic resource datasets in pepper breeding research.

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References

  1. Albert VA, Chang TH (2014) Evolution of a hot genome. Proc Natl Acad Sci U S A 111:5069-5070 https://doi.org/10.1073/pnas.1402378111
  2. Allendorf FW, Hohenlohe PA, Luikart G (2010) Genomics and the future of conservation genetics. Nat Rev Genet 11:697-709
  3. Cox MP, Peterson DA, Biggs PJ (2010) SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11:485 https://doi.org/10.1186/1471-2105-11-485
  4. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11-15
  5. Fakrudin B, Vijaykumar, Kambalpally KB. Patil BV, Kuruvinashetti MS (2006) DNA-based marker systems and their utility in entomology. Entomologica Fennica 17
  6. Hou X, Li L, Peng Z, Wei B, Tang S, Ding M, Liu J, Zhang F, Zhao Y, Gu H, Qu LJ (2010) A platform of high-density INDEL/ CAPS markers for map-based cloning in Arabidopsis. Plant J 63:880-888 https://doi.org/10.1111/j.1365-313X.2010.04277.x
  7. Jiang GQ, Yao XF, Liu CM (2013) A Simple CELI Endonuclease- Based Protocol for Genotyping both SNPs and InDels. Plant Molecular Biology Reporter 31:1325-1335 https://doi.org/10.1007/s11105-013-0606-z
  8. Kim S, Park M, Yeom SI, Kim YM et al. (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46:270-278 https://doi.org/10.1038/ng.2877
  9. Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26:589-595 https://doi.org/10.1093/bioinformatics/btp698
  10. Li H, Handsaker B, Wysoker A, Fennell T et al (2009) Genome Project Data Processing: The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079 https://doi.org/10.1093/bioinformatics/btp352
  11. Liu J, Qu J, Yang C, Tang D, Li J, Lan H, Rong T (2015) Development of genome-wide insertion and deletion markers for maize, based on next-generation sequencing data. BMC Genomics 16:601 https://doi.org/10.1186/s12864-015-1797-5
  12. Marin A, Ferreres F, Tomas-Barberan FA, Gil MI (2004) Characterization and quantitation of antioxidant constituents of sweet pepper (Capsicum annuum L.). J Agric Food Chem 52:3861-3869 https://doi.org/10.1021/jf0497915
  13. McCouch SR, Chen X, Panaud O, Temnykh S, Xu Y, Cho YG, Huang N, Ishii T, Blair M (1997) Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol Biol 35:89-99 https://doi.org/10.1023/A:1005711431474
  14. Mejia LA, Hudson E, deMejia EG, Vazquez F (1998) Carotenoid content and vitamin-A activity of some common cultivars of Mexican peppers (Capsicum annuum) as determined by HPLC. J. Food Sci. 53:1448-1451
  15. Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, Devine SE (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res 16:1182-1190 https://doi.org/10.1101/gr.4565806
  16. Montgomery SB, Goode DL, Kvikstad E, Albers CA et al. (2013) The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Res 23:749-761 https://doi.org/10.1101/gr.148718.112
  17. Nagaraju J, Kathirvel M, Kumar RR, Siddiq EA, Hasnain SE (2002) Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by using fluorescence-based ISSR-PCR and SSR markers. Proc Natl Acad Sci U S A 99:5836-5841 https://doi.org/10.1073/pnas.042099099
  18. Neuman JA, Isakov O, Shomron N (2013) Analysis of insertiondeletion from deep-sequencing data: software evaluation for optimal detection. Brief Bioinform 14:46-55 https://doi.org/10.1093/bib/bbs013
  19. Ollitrault F, Terol J, Martin AA, Pina JA, Navarro L, Talon M, Ollitrault P (2012) Development of indel markers from Citrus clementina (Rutaceae) BAC-end sequences and interspecific transferability in Citrus. Am J Bot 99:e268-273 https://doi.org/10.3732/ajb.1100569
  20. Pacurar DI, Pacurar ML, Street N, Bussell JD, Pop TI, Gutierrez L, Bellini C (2012) A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions. J Exp Bot 63:2491-2501 https://doi.org/10.1093/jxb/err422
  21. Pena HB, Pena SD (2012) Automated Genotyping of a Highly Informative Panel of 40 Short Insertion-Deletion Polymorphisms Resolved in Polyacrylamide Gels for Forensic Identification and Kinship Analysis. Transfus Med Hemother 39:211-216 https://doi.org/10.1159/000338854
  22. Pickersgill B (1997) Genetic resources and breeding of Capsicum spp. Euphytica. 96:129-133 https://doi.org/10.1023/A:1002913228101
  23. Primmer CR (2009) From conservation genetics to conservation genomics. Ann N Y Acad Sci 1162:357-368 https://doi.org/10.1111/j.1749-6632.2009.04444.x
  24. Stenson PD, Ball EV, Mort M, Phillips AD, Shaw K, Cooper DN (2012) The Human Gene Mutation Database (HGMD) and its exploitation in the fields of personalized genomics and molecular evolution. Curr Protoc Bioinformatics Chapter 1:Unit 13
  25. Sun T, Xu Z, Wu CT, Janes M, Prinyawiwatkul W, No HK (2007) Antioxidant activities of different colored sweet bell peppers (Capsicum annuum L.). J Food Sci 72:S98-102 https://doi.org/10.1111/j.1750-3841.2006.00245.x
  26. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441-52 https://doi.org/10.1101/gr.184001
  27. Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3-new capabilities and interfaces. Nucleic Acids Res 40:e115 https://doi.org/10.1093/nar/gks596
  28. Vali U, Brandstrom M, Johansson M, Ellegren H (2008) Insertion-deletion polymorphisms (indels) as genetic markers in natural populations. BMC Genet 9:8
  29. Vasemagi A, Gross R, Palm D, Paaver T, Primmer CR (2010) Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon. BMC Genomics 11:156 https://doi.org/10.1186/1471-2164-11-156
  30. Vos P, Hogers R, Bleeker M, Reijans M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407-4414 https://doi.org/10.1093/nar/23.21.4407
  31. Wu DH, Wu HP, Wang CS, Tseng HY, Hwu KK (2013) Genomewide InDel marker system for application in rice breeding and mapping studies. Euphytica. Euphytica: 131-143