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Molecular marker information from de novo assembled transcriptomes of chilli pepper (Capsicum annuum L.) varieties based on next-generation sequencing technology

Published online by Cambridge University Press:  16 July 2014

Yul-Kyun Ahn ,
Swati Tripathi ,
Young-Il Cho ,
Jeong-Ho Kim ,
Hye-Eun Lee ,
Do-Sun Kim  and
Jong-Gyu Woo
Yul-Kyun Ahn*
Affiliation:
Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon 440-706, Republic of Korea
Swati Tripathi
Affiliation:
Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon 440-706, Republic of Korea
Young-Il Cho
Affiliation:
Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon 440-706, Republic of Korea
Jeong-Ho Kim
Affiliation:
Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon 440-706, Republic of Korea
Hye-Eun Lee
Affiliation:
Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon 440-706, Republic of Korea
Do-Sun Kim
Affiliation:
Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon 440-706, Republic of Korea
Jong-Gyu Woo
Affiliation:
Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon 440-706, Republic of Korea
*
* Corresponding author. E-mail: aykyun@korea.kr
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Abstract

Next-generation sequencing technique has been known as a useful tool for de novo transcriptome assembly, functional annotation of genes and identification of molecular markers. This study was carried out to mine molecular markers from de novo assembled transcriptomes of four chilli pepper varieties, the highly pungent ‘Saengryeg 211’ and non-pungent ‘Saengryeg 213’ and variably pigmented ‘Mandarin’ and ‘Blackcluster’. Pyrosequencing of the complementary DNA library resulted in 361,671, 274,269, 279,221, and 316,357 raw reads, which were assembled in 23,607, 19,894, 18,340 and 20,357 contigs, for the four varieties, respectively. Detailed sequence variant analysis identified numerous potential single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for all the varieties for which the primers were designed. The transcriptome information and SNP/SSR markers generated in this study provide valuable resources for high-density molecular genetic mapping in chilli pepper and Quantitative trait loci analysis related to fruit qualities. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.

Keywords

Capsicum annuumpyrosequencingsimple sequence repeatssingle-nucleotide polymorphismstranscriptome assembly
Type
Research Article
Information
Plant Genetic Resources , Volume 12 , Issue S1: Special issue on the 3rd International Symposium on “Genomics of Plant Genetic Resources” , July 2014 , pp. S83 - S86
Copyright
Copyright © NIAB 2014 

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References

Ahn, YK, Tripathi, S, Kim, JH, Cho, YI, Lee, HE, Kim, DS, Woo, JG and Cho, MC (2014) Transcriptome analysis of Capsicum annuum varieties Mandarin and Blackcluster: assembly, annotation and molecular marker discovery. Gene 533: 494–499.Google Scholar
Ashrafi, H, Hill, T, Stoffel, K, Kozik, A, Yao, JQ, Chin-Wo, SR and Deynze, AV (2012) De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes. BMC Genomics 13: 571.Google Scholar
Deschamps, S, Llaca, V and May, GD (2012) Genotyping by sequencing in plants. Biology 1: 460–483.Google Scholar
Hill, TA, Ashrafi, H, Chin-Wo, SR, Yao, J, Stoffel, K, Truco, MJ, Kozik, A, Michelmore, RW and Van Deynze, A (2013) Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30 K unigene pepper GeneChip. PLoS One 8: e56200.Google Scholar
Hyten, D, Cannon, S, Song, Q, Weeks, N, Fickus, E, Shoemaker, R, Specht, J, Farmer, A, May, G and Cregan, P (2010) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11: 38.CrossRefGoogle ScholarPubMed
Kim, HJ, Baek, KH, Lee, SW, Kim, JE, Lee, BW, Cho, HS, Kim, WT, Choi, D and Hur, CG (2008) Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome. BMC Plant Biology 8: 101.Google Scholar
Liu, S, Li, W, Wu, Y, Chen, C and Lei, J (2013) De novo transcriptome assembly in chilli pepper (Capsicum frutescens) to identify genes involved in the biosynthesis of capsaicinoids. PLoS One 8: e48156.CrossRefGoogle ScholarPubMed
Lu, FH, Cho, MC and Park, YJ (2012) Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68. Molecular Biology Reports 39: 3327–3335.Google Scholar
Novaes, E, Drost, DR, Farmerie, WG, Pappas, GJ Jr, Grattapaglia, D, Sederoff, RR and Kirst, M (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9: 312.Google Scholar
Sonah, H, Deshmukh, RK, Sharma, A, Singh, VP, Gupta, DK, Gacche, RN, Rana, JC, Singh, NK and Sharma, TR (2011) Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium . PLoS One 6: e21298.Google Scholar
Spindel, J, Wright, M, Chen, C, Cobb, J, Gage, J, Harrington, S, Lorieux, M, Ahmadi, N and McCouch, S (2013) Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Theoretical and Applied Genetics 126: 2699–2716.Google Scholar
Temnykh, S, DeClerck, G, Lukashova, A, Lipovich, L, Cartinhour, S and McCouch, S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Research 11: 1441–1452.Google Scholar
Van Tassell, CP, Smith, TP, Matukumalli, LK, Taylor, JF, Schnabel, RD, Lawley, CT, Haudenschild, CD, Moore, SS, Warren, WC and Sonstegard, TS (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods 5: 247–252.Google Scholar
Yang, T, Bao, SY, Ford, R, Jia, TJ, Guan, JP, He, YH, Sun, XL, Jiang, JY, Hao, JJ, Zhang, XY and Zong, XX (2012) High-throughput novel microsatellite marker of faba bean via next generation sequencing. BMC Genomics 13: 602.Google Scholar
Yu, JN, Won, C, Jun, J, Lim, Y and Kwak, M (2011) Fast and cost-effective mining of microsatellite markers using NGS technology: an example of a Korean water deer Hydropotes inermis argyropus . PLoS One 6: e26933.Google Scholar