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BioMed Research International
Volume 2018 (2018), Article ID 5646213, 7 pages
https://doi.org/10.1155/2018/5646213
Review Article

Next-Generation Sequencing Approaches in Genome-Wide Discovery of Single Nucleotide Polymorphism Markers Associated with Pungency and Disease Resistance in Pepper

1Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju 55365, Republic of Korea
2Department of Vegetable Crops, Korea National College of Agriculture and Fisheries, Jeonju 54874, Republic of Korea

Correspondence should be addressed to Yul-Kyun Ahn

Received 4 August 2017; Revised 23 October 2017; Accepted 26 October 2017; Published 9 January 2018

Academic Editor: Peter J. Oefner

Copyright © 2018 Abinaya Manivannan et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. S. Kim, M. Park, S.-I. Yeom et al., “Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species,” Nature Genetics, vol. 46, no. 3, pp. 270–278, 2014. View at Publisher · View at Google Scholar · View at Scopus
  2. E. A. Moscone, M. A. Scaldaferro, M. Grabiele et al., “The evolution of chili peppers (Capsicum-Solanaceae): a cytogenetic perspective,” Acta Horticulturae, vol. 745, pp. 137–169, 2007. View at Publisher · View at Google Scholar · View at Scopus
  3. P. Nimmakayala, V. L. Abburi, T. Saminathan et al., “Genome-wide divergence and linkage disequilibrium analyses for Capsicum baccatum revealed by genome-anchored single nucleotide polymorphisms,” Frontiers in Plant Science, vol. 7, article 1646, 2016. View at Publisher · View at Google Scholar · View at Scopus
  4. A. Marín, F. Ferreres, F. A. Tomás-Barberán, and M. I. Gil, “Characterization and quantitation of antioxidant constituents of sweet pepper (Capsicum annuum L.),” Journal of Agricultural and Food Chemistry, vol. 52, no. 12, pp. 3861–3869, 2004. View at Publisher · View at Google Scholar · View at Scopus
  5. H.-G. Kim, J.-H. Bae, Z. Jastrzebski et al., “Binding, antioxidant and anti-proliferative properties of bioactive compounds of sweet paprika (Capsicum annuum L.),” Plant Foods for Human Nutrition, vol. 71, no. 2, pp. 129–136, 2016. View at Publisher · View at Google Scholar · View at Scopus
  6. A. Allemand, B. F. Leonardi, A. R. Zimmer, S. Moreno, P. R. T. Romão, and G. Gosmann, “Red pepper (Capsicum baccatum) extracts present anti-inflammatory effects in vivo and inhibit the production of TNF-α and NO in vitro,” Journal of Medicinal Food, vol. 19, no. 8, pp. 759–767, 2016. View at Publisher · View at Google Scholar · View at Scopus
  7. J. Sung, H. S. Jeong, and J. Lee, “Effect of the capsicoside G-rich fraction from pepper (Capsicum annuum L.) seeds on high-fat diet-induced obesity in mice,” Phytotherapy Research, vol. 30, no. 11, pp. 1848–1855, 2016. View at Publisher · View at Google Scholar · View at Scopus
  8. J. Mammadov, R. Aggarwal, R. Buyyarapu, and S. Kumpatla, “SNP markers and their impact on plant breeding,” International Journal of Plant Genomics, vol. 2012, Article ID 728398, 11 pages, 2012. View at Publisher · View at Google Scholar · View at Scopus
  9. B. C. Meyers, S. V. Tingey, and M. Morgante, “Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome,” Genome Research, vol. 11, no. 10, pp. 1660–1676, 2001. View at Publisher · View at Google Scholar · View at Scopus
  10. D. Kuhn, “Design of an Illumina Infinium 6k SNPchip for genotyping two large avocado mapping populations,” in Proceedings of the 20th Conference on Plant and Animal Genome, San Diego, Calif, USA, January 2012.
  11. M. Trick, Y. Long, J. Meng, and I. Bancroft, “Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing,” Plant Biotechnology Journal, vol. 7, no. 4, pp. 334–346, 2009. View at Publisher · View at Google Scholar · View at Scopus
  12. E. Novaes, D. R. Drost, W. G. Farmerie et al., “High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome,” BMC Genomics, vol. 9, no. 1, article 312, 2008. View at Publisher · View at Google Scholar · View at Scopus
  13. W. B. Barbazuk, S. J. Emrich, H. D. Chen, L. Li, and P. S. Schnable, “SNP discovery via 454 transcriptome sequencing,” The Plant Journal, vol. 51, no. 5, pp. 910–918, 2007. View at Publisher · View at Google Scholar · View at Scopus
  14. P. C. Bundock, F. G. Eliott, G. Ablett et al., “Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing,” Plant Biotechnology Journal, vol. 7, no. 4, pp. 347–354, 2009. View at Publisher · View at Google Scholar · View at Scopus
  15. J.-B. Fan, A. Oliphant, R. Shen et al., “Highly parallel SNP genotyping,” Cold Spring Harbor Symposium on Quantitative Biology, vol. 68, pp. 69–78, 2003. View at Publisher · View at Google Scholar · View at Scopus
  16. F. J. Steemers and K. L. Gunderson, “Whole genome genotyping technologies on the BeadArray™ platform,” Biotechnology Journal, vol. 2, no. 1, pp. 41–49, 2007. View at Publisher · View at Google Scholar · View at Scopus
  17. K. J. Livak, S. J. A. Flood, J. Marmaro, W. Giusti, and K. Deetz, “Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization,” Genome Research, vol. 4, no. 6, pp. 357–362, 1995. View at Publisher · View at Google Scholar · View at Scopus
  18. S. P. Kumpatla, R. Buyyarapu, I. Y. Abdurakhmonov, and J. A. Mammadov, “Genomics-assisted plant breeding in the 21st century: technological advances and progress,” in Plant Breeding, InTech, 2012. View at Google Scholar
  19. A. M. Hulse-Kemp, H. Ashrafi, J. Plieske et al., “A HapMap leads to a Capsicum annuum SNP infinium array: A new tool for pepper breeding,” Horticulture Research, vol. 3, Article ID 16036, 2016. View at Publisher · View at Google Scholar · View at Scopus
  20. F. Taranto, N. D'Agostino, B. Greco, T. Cardi, and P. Tripodi, “Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing,” BMC Genomics, vol. 17, no. 1, article no. 943, 2016. View at Publisher · View at Google Scholar · View at Scopus
  21. C. Qin, C. Yu, Y. Shen et al., “Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization,” Proceedings of the National Academy of Sciences, vol. 111, no. 14, pp. 5135–5140, 2014. View at Google Scholar
  22. S. Liu, W. Li, Y. Wu, C. Chen, and J. Lei, “De novo transcriptome assembly in chili pepper (Capsicum frutescens) to identify genes involved in the biosynthesis of capsaicinoids,” PLoS ONE, vol. 8, no. 1, Article ID e48156, 2013. View at Publisher · View at Google Scholar · View at Scopus
  23. Y.-K. Ahn, S. Tripathi, Y.-I. Cho et al., “De novo transcriptome assembly and novel microsatellite marker information in Capsicum annuum varieties Saengryeg 211 and Saengryeg 213,” Botanical Studies, vol. 54, no. 1, p. 58, 2013. View at Publisher · View at Google Scholar · View at Scopus
  24. H. J. Kim, K. H. Baek, S. W. Lee et al., “Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome,” BMC Plant Biology, vol. 8, article 101, 7 pages, 2008. View at Publisher · View at Google Scholar
  25. A. Garcés-Claver, S. M. Fellman, R. Gil-Ortega, M. Jahn, and M. S. Arnedo-Andrés, “Identification, validation and survey of a single nucleotide polymorphism (SNP) associated with pungency in Capsicum spp.,” Theoretical and Applied Genetics, vol. 115, no. 7, pp. 907–916, 2007. View at Publisher · View at Google Scholar · View at Scopus
  26. P. Nimmakayala, V. L. Abburi, T. Saminathan et al., “Genome-wide diversity and association mapping for capsaicinoids and fruit weight in Capsicum annuum L,” Scientific Reports, vol. 6, Article ID 38081, 2016. View at Publisher · View at Google Scholar · View at Scopus
  27. U. K. Reddy, A. Almeida, V. L. Abburi et al., “Identification of gene-specific polymorphisms and association with capsaicin pathway metabolites in Capsicum annuum L. collections,” PLoS ONE, vol. 9, no. 1, Article ID e86393, 2014. View at Publisher · View at Google Scholar · View at Scopus
  28. Y. Jang, E. Yang, M. Cho, Y. Um, K. Ko, and C. Chun, “Effect of grafting on growth and incidence of phytophthora blight and bacterial wilt of pepper (Capsicum annuum L.),” Horticulture, Environment, and Biotechnology, vol. 53, no. 1, pp. 9–19, 2012. View at Publisher · View at Google Scholar · View at Scopus
  29. P. Prior, C. Allen, and J. Elphinstone, Eds., Bacterial Wilt Disease: Molecular and Ecological Aspects, Springer Science & Business Media, 2013.
  30. G. Zhou, Q. Zhang, C. Tan, X.-Q. Zhang, and C. Li, “Development of genome-wide InDel markers and their integration with SSR, DArT and SNP markers in single barley map,” BMC Genomics, vol. 16, no. 1, 2015. View at Publisher · View at Google Scholar · View at Scopus
  31. Y.-K. Ahn, S. Karna, T.-H. Jun et al., “Complete genome sequencing and analysis of Capsicum annuum varieties,” Molecular Breeding, vol. 36, no. 10, article no. 140, 2016. View at Publisher · View at Google Scholar · View at Scopus
  32. L. Emboulé, F. Daigle, D. F. Meyer et al., “Innovative approach for transcriptomic analysis of obligate intracellular pathogen: Selective capture of transcribed sequences of Ehrlichia ruminantium,” BMC Molecular Biology, vol. 10, article no. 111, 2009. View at Publisher · View at Google Scholar · View at Scopus
  33. L. H. Leonian, “Stem and fruit blight of peppers caused by Phytophthora capsici sp. nov,” Phytopathology, vol. 12, no. 9, 1922. View at Google Scholar
  34. T. H. Barksdale, G. C. Papavizas, and S. A. Johnston, “Resistance to foliar blight and crown rot of pepper caused by Phytophthora capsici [Breeding for disease resistance, New Jersey],” Plant Diseases, vol. 68, pp. 506–509, 1984. View at Google Scholar
  35. F.-H. Lu, M.-Y. Yoon, Y.-I. Cho et al., “Transcriptome analysis and SNP/SSR marker information of red pepper variety YCM334 and Taean,” Scientia Horticulturae, vol. 129, no. 1, pp. 38–45, 2011. View at Publisher · View at Google Scholar · View at Scopus
  36. P. Palukaitis, M. J. Roossinck, R. G. Dietzgen, and R. I. B. Francki, “Cucumber MOSAIC virus,” Advances in Virus Research, vol. 41, no. C, pp. 281–348, 1992. View at Publisher · View at Google Scholar · View at Scopus
  37. C. Caranta, A. Palloix, V. Lefebvre, and A. M. Daubèze, “QTLs for a component of partial resistance to cucumber mosaic virus in pepper: Restriction of virus installation in host-cells,” Theoretical and Applied Genetics, vol. 94, no. 3-4, pp. 431–438, 1997. View at Publisher · View at Google Scholar · View at Scopus
  38. M. Lapidot, I. Paran, R. Ben-Joseph et al., “Tolerance to cucumber mosaic virus in pepper: Development of advanced breeding lines and evaluation of virus level,” Plant Disease, vol. 81, no. 2, pp. 185–188, 1997. View at Publisher · View at Google Scholar · View at Scopus
  39. R. C. Grube, Y. Zhang, J. F. Murphy et al., “New source of resistance to Cucumber mosaic virus in Capsicum frutescens,” Plant Disease, vol. 84, no. 8, pp. 885–891, 2000. View at Publisher · View at Google Scholar · View at Scopus
  40. A. B. Chaim, R. C. Grube, M. Lapidot, M. Jahn, and I. Paran, “Identification of quantitative trait loci associated with resistance to cucumber mosaic virus in Capsicum annuum,” Theoretical and Applied Genetics, vol. 102, no. 8, pp. 1213–1220, 2001. View at Publisher · View at Google Scholar · View at Scopus
  41. K. Suzuki, T. Kuroda, Y. Miura, and J. Murai, “Screening and field trials of virus resistant sources in Capsicum spp.,” Plant Disease, vol. 87, no. 7, pp. 779–783, 2003. View at Publisher · View at Google Scholar · View at Scopus
  42. R. Nono‐Womdim, K. Gebre‐Selassie, A. Palloix, E. Pochard, and G. Marchoux, “Study of multiplication of cucumber mosaic virus in susceptible and resistant Capsicum annuuum lines,” Annals of Applied Biology, vol. 122, no. 1, pp. 49–56, 1993. View at Publisher · View at Google Scholar · View at Scopus
  43. R. Nono-Womdim, A. Palloix, K. Gébré-Selassié, and G. Marchoux, “Partial resistance of bell pepper to cucumber mosaic virus movement within plants: field evaluation of its efficiency in southern France,” Journal of Phytopathology, vol. 137, no. 2, pp. 125–132, 1993. View at Publisher · View at Google Scholar
  44. W.-H. Kang, N. H. Hoang, H.-B. Yang et al., “Molecular mapping and characterization of a single dominant gene controlling CMV resistance in peppers (Capsicum annuum L.),” Theoretical and Applied Genetics, vol. 120, no. 8, pp. 1587–1596, 2010. View at Publisher · View at Google Scholar · View at Scopus
  45. C. Kole, Ed., Wild Crop Relatives: Genomic and Breeding Resources: Cereals, vol. 1, Springer Science & Business Media, 2011.
  46. P. Mahasuk, N. Khumpeng, S. Wasee, P. W. J. Taylor, and O. Mongkolporn, “Inheritance of resistance to anthracnose (Colletotrichum capsici) at seedling and fruiting stages in chili pepper (Capsicum spp.),” Plant Breeding, vol. 128, no. 6, pp. 701–706, 2009. View at Publisher · View at Google Scholar · View at Scopus
  47. P. Mahasuk, D. Struss, and O. Mongkolporn, “QTLs for resistance to anthracnose identified in two Capsicum sources,” Molecular Breeding, vol. 36, no. 1, article no. 10, pp. 1–10, 2016. View at Publisher · View at Google Scholar · View at Scopus