Skip to main content
SpringerLink
Log in

Genome-wide SNP discovery in mungbean by Illumina HiSeq

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Mungbean [Vigna radiata (L.) Wilczek], a self-pollinated diploid plant with 2n = 22 chromosomes, is an important legume crop with a high-quality amino acid profile. Sequence variation at the whole-genome level was examined by comparing two mungbean cultivars, Sunhwanokdu and Gyeonggijaerae 5, using Illumina HiSeq sequencing data. More than 40 billion bp from both mungbean cultivars were sequenced to a depth of 72×. After de novo assembly of Sunhwanokdu contigs by ABySS 1.3.2 (N50 = 9,958 bp), those longer than 10 kb were aligned with Gyeonggijaerae 5 reads using the Burrows–Wheeler Aligner. SAMTools was used for retrieving single nucleotide polymorphisms (SNPs) between Sunhwanokdu and Gyeonggijaerae 5, defining the lowest and highest depths as 5 and 100, respectively, and the sequence quality as 100. Of the 305,504 single-base changes identified, 40,503 SNPs were considered heterozygous in Gyeonggijaerae 5. Among the remaining 265,001 SNPs, 65.9 % (174,579 cases) were transitions and 34.1 % (90,422 cases) were transversions. For SNP validation, a total of 42 SNPs were chosen among Sunhwanokdu contigs longer than 10 kb and sharing at least 80 % sequence identity with common bean expressed sequence tags as determined with est2genome. Using seven mungbean cultivars from various origins in addition to Sunhwanokdu and Gyeonggijaerae 5, most of the SNPs identified by bioinformatics tools were confirmed by Sanger sequencing. These genome-wide SNP markers could enrich the current molecular resources and might be of value for the construction of a mungbean genetic map and the investigation of genetic diversity.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218

    Article  CAS  Google Scholar 

  • Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51:910–918

    Article  CAS  PubMed  Google Scholar 

  • Chaitieng B, Kaga A, Tomooka N, Isemura T, Kuroda Y, Vaughan DA (2006) Development of a black gram [Vigna mungo (L.) Hepper] linkage map and its comparison with an azuki bean [Vigna angularis (Willd.) Ohwi and Ohashi] linkage map. Theor Appl Genet 113:1261–1269

    Article  CAS  PubMed  Google Scholar 

  • Chankaew S, Somta P, Sorajjapinun W, Srinives P (2011) Quantitative trait loci mapping of Cercospora leaf spot resistance in mungbean, Vigna radiata (L.) Wilczek. Mol Breed 28:255–264

    Article  Google Scholar 

  • Childs KL, Hamilton JP, Zhu W, Cheung F, Wu H, Rabinowicz PD, Town CD, Buell CR, Chan AP (2007) The TIGR plant transcript assemblies database. Nucleic Acids Res 35(Database issue):D846–D851

    Article  CAS  PubMed  Google Scholar 

  • Choudhary S, Gaur R, Gupta S, Bhatia S (2012) EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea. Theor Appl Genet. doi:10.1007/s00122-012-1800-3

    PubMed  Google Scholar 

  • Datta S, Gupta S (2009) Use of genomic resources in improvement of Vigna species. J Food Legum 22:1–10

    Google Scholar 

  • Deschamps S, Rota ML, Ratashak JP, Biddle P, Thureen D, Farmer A, Luck S, Beatty M, Nagasawa N, Michael L (2010) Rapid genome-wide single nucleotide polymorphism discovery in soybean and rice via deep resequencing of reduced representation libraries with the Illumina genome analyzer. Plant Genome 3:53–68

    Article  CAS  Google Scholar 

  • Fatokun CA, Danesh D, Young ND, Stewart EL (1993) Molecular taxonomic relationships in the genus Vigna based on RFLP analysis. Theor Appl Genet 86:97–104

    Article  CAS  Google Scholar 

  • Feuillet C, Leach JE, Rogers J, Schnable PS, Eversole K (2011) Crop genome sequencing: lessons and rationales. Trends Plant Sci 16:77–88

    Article  CAS  PubMed  Google Scholar 

  • Gelvin SB, Schilperoort RA (1995) Plant molecular biology manual. Kluwer Academic Publishers, Norwell

    Google Scholar 

  • Gwag JG, Chung JW, Chung HK, Lee JH, Ma KH, Dixit A, Park YJ, Cho EG, Kim TS, Lee SH (2006) Characterization of new microsatellite markers in mungbean, Vigna radiata (L.). Mol Ecol Notes 6:1132–1134

    Article  CAS  Google Scholar 

  • Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, Frazer KA (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 10:R32

    Article  PubMed  Google Scholar 

  • Hong EH, Lee YH, Kim SD, Hwang YH, Moon YH, Ham YS (1983) New disease resistant and high yielding mungbean variety “Seonhwanogdu”. Res Rept ORD 25:178–180

    Google Scholar 

  • Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967

    Article  CAS  PubMed  Google Scholar 

  • Huang X, Zhao Y, Wei X, Li C, Wang A, Zhao Q, Li W, Guo Y, Deng L, Zhu C, Fan D, Lu Y, Weng Q, Liu K, Zhou T, Jing Y, Si L, Dong G, Huang T, Lu T, Feng Q, Qian Q, Li J, Han B (2012) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 44:32–39

    Article  Google Scholar 

  • Humphry ME, Konduri V, Lambrides CJ, Magner T, McIntyre CL, Aitken EAB, Liu CJ (2002) Development of a mungbean (Vigna radiata) RFLP linkage map and its comparison with lablab (Lablab purpureus) reveals a high level of colinearity between the two genomes. Theor Appl Genet 105:160–166

    Article  CAS  PubMed  Google Scholar 

  • Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8:R143

    Article  PubMed  Google Scholar 

  • Hyten DL, Cannon SB, Song Q, Weeks N, Ficks EW, Shoemaker RC, Specht JE, Farmer AD, May GD, Cregan PB (2010a) 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

    Article  PubMed  Google Scholar 

  • Hyten DL, Song Q, Fickus EW, Quigley CV, Lim JS, Choi IY, Hwang EY, Pastor-Corrales M, Cregan PB (2010b) High-throughput SNP discovery and assay development in common bean. BMC Genomics 11:475

    Article  PubMed  Google Scholar 

  • Imrie BC (1996) Mungbean. In: Hyde K (ed) The new rural industries. A handbook for farmers and investors. Rural Industries Research and Development Corporation, Canberra, pp 355–360

    Google Scholar 

  • Iqbal MJ, Mamidi S, Ahsan R, Kianian SF, Coyne CJ, Hamama AA, Narina SS, Bhardwaj HL (2012) Population structure and linkage disequilibrium in Lupinus albus L. germplasm and its implication for association mapping. Theor Appl Genet 125:517–530

    Article  CAS  PubMed  Google Scholar 

  • Isemura T, Kaga A, Konishi S, Ando T, Tomooka N, Han OK, Vaughan DA (2007) Genome dissection of traits related to domestication in azuki bean (Vigna angularis) and comparison with other warm-season legumes. Ann Bot 100:1053–1071

    Article  PubMed  Google Scholar 

  • Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M, Jiao Y, Ni P, Zhang J, Li D, Guo X, Ye K, Jian M, Wang B, Zheng H, Liang H, Zhang X, Wang S, Chen S, Li J, Fu Y, Springer NM, Yang H, Wang J, Dai J, Schnable PS, Wang J (2010) Genome-wide patterns of genetic variation among elite maize inbreds. Nat Genet 42:1027–1030

    Article  CAS  PubMed  Google Scholar 

  • Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sun SSM, Zhang G (2010) Resequencing of 31 wild and cultivated soybean genomes identified patterns of genetic diversity and selection. Nat Genet 12:1053–1059

    Article  Google Scholar 

  • Lambrides CJ, Godwin ID (2007) Mungbean. In: Kole C (ed) Genome mapping and molecular breeding in plants, vol 3., Pulses, sugar and tuber cropsSpringer, Germany, pp 69–90

    Google Scholar 

  • Lawn RJ (1979) Agronomic studies on Vigna spp. in southeastern Queensland I. Phenological response of cultivars to sowing date. Aust J Agric Res 30:855–870

    Article  Google Scholar 

  • Li H, DurbIn R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760

    Article  CAS  PubMed  Google Scholar 

  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) 1000 genome project data processing subgroup. The sequence alignment/map (SAM) format and SAM tools. Bioinformatics 25:2078–2079

    Article  PubMed  Google Scholar 

  • Lu Y, Yan J, Guimaraes CT, Taba S, Hao Z, Gao S, Chen S, Li J, Zhang S, Vivek BS, Magorokosho C, Mugo S, Makumbi D, Parentoni SN, Shah T, Rong T, Crouch JH, Xu Y (2009) Molecualr characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms. Theor Appl Genet 120:93–115

    Article  CAS  PubMed  Google Scholar 

  • Mammadov JA, Chen W, Ren R, Pai R, Marchione W, Yalcin F, Witsenboer H, Greene TW, Thompson SA, Kumpatla SP (2010) Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.] genome for use in marker-assisted breeding. Theor Appl Genet 121:577–588

    Article  CAS  PubMed  Google Scholar 

  • Menancio-Hautea D, Fatokun CA, Kumar L, Danesh D, Young ND (1993) Comparative genome analysis of mungbean (Vigna radiata L. Wilczek) and cowpea (V. unguiculata L. Walpers) using RFLP mapping data. Theor Appl Genet 86:797–810

    Article  CAS  Google Scholar 

  • Moe KT, Chung J-W, Cho Y-I, Moon J-K, Ku J-H, Jung J-K, Lee J, Park Y-J (2011) Sequence information on simple sequence repeats and single nucleotide polymorphisms through transcriptome analysis of mungbean. J Integr Plant Biol 53:63–73

    Article  CAS  PubMed  Google Scholar 

  • Murray MG, Palmer JD, Cuellar RE, Thompson WF (1979) Deoxyribonucleic acid sequence organization in the mungbean genome. Biochem 18:5259–5266

    Article  CAS  Google Scholar 

  • Novaes E, Drost DR, Farmerie WG, Pappas GJ Jr, Grattapaglia D, Sederoff RR, Kirst M (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9:312

    Article  PubMed  Google Scholar 

  • Peace C, Bassil N, Main D, Ficklin S, Rosyara UR, Stegmeir T, Sebolt A, Gilmore B, Lawley C, Mockler TC, Bryant DW, Wilhelm L, Iezzoni A (2012) Development and evaluation of a genome-wide 6 K SNP array for diploid sweet cherry and tetraploid sour cherry. PLoS ONE 7:e48305

    Article  CAS  PubMed  Google Scholar 

  • Rafalski A (2002) Application of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100

    Article  CAS  PubMed  Google Scholar 

  • Semagn K, Magorokosho C, Vivek BS, Makumbi D, Beyene Y, Mugo S, Prasanna BM, Warburton ML (2012) Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers. BMC Genomics 13:113

    Article  CAS  PubMed  Google Scholar 

  • Shirasawa K, Isobe S, Hirakawa H, Asamizu E, Fukuoka H, Just D, Rothan C, Sasamoto S, Fujishiro T, Kishida Y, Kohara M, Tsuruoka H, Wada T, Nakamura Y, Sato S, Tabata S (2010) SNP discovery and linkage map construction in cultivated tomato. DNA Res 17:381–391

    Article  CAS  PubMed  Google Scholar 

  • Smartt J (1984) Gene pools in grain legumes. Econ Bot 38:24–35

    Article  Google Scholar 

  • Somta P, Srinives P (2007) Genome research in mungbean (Vigna radiata (L.) Wilczek) and blackgram (V. mungo (L.) Hepper). ScienceAsia 33(Suppl 1):69–74

    Article  Google Scholar 

  • Somta P, Musch W, Kongsamai B, Chanprame S, Nakasathien S, Toojinda T, Sorajjapinun W, Seehalak W, Tragoonrung S, Srinives P (2008) New microsatellite markers isolated from mungbean (Vigna radiata (L.) Wilczek). Mol Ecol Res 8:1155–1157

    Article  CAS  Google Scholar 

  • Tangphatsornruang S, Somta P, Uthaipaisanwong P, Chanprasert J, Sangsrakru D, Seehalak W, Sommanas W, Tragoonrung S, Srinives P (2009) Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek). BMC Plant Biol 9:137

    Article  PubMed  Google Scholar 

  • Van K, Hwang E-Y, Kim MY, Kim Y-H, Cho Y-I, Cregan PB, Lee S-H (2004) Discovery of single nucleotide polymorphisms in soybean using primers designed from ESTs. Euphytica 139:147–157

    Article  CAS  Google Scholar 

  • Van K, Kim DH, Shin JH, Lee S-H (2011) Genomics of plant genetic resources: past, present and future. Plant Genet Resour 9:155–158

    Article  Google Scholar 

  • Van K, Kang YJ, Shim SR, Lee S-H (2012) Genome-wide scan of the soybean genome using degenerate oligonucleotide primed PCR: an example for studying large complex genome structure. Genes Genomics 34:467–474

    Article  CAS  Google Scholar 

  • Verdcourt B (1970) Studies in the Leguminosae–Papilionoideae for the flora of tropical East Africa. IV. Kew Bull 24:507–569

    Article  Google Scholar 

  • Vishnu-Mittre A (1974) Palaeobotanical evidence in India. In: Hutchison J (ed) Evolutionary studies in world crops. Cambridge University Press, Cambridge, pp 3–30

    Google Scholar 

  • Xu Y, Lu Y, Xie C, Gao S, Wan J, Prasanna BM (2012) Whole-genome strategies for marker-assisted plant breeding. Mol Breed 29:833–854

    Article  Google Scholar 

  • You FM, Huo N, Deal KR, Gu YQ, Luo M-C, McGuire PE, Dvorak J, Anderson OD (2011) Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. BMC Genomics 12:59

    Article  CAS  PubMed  Google Scholar 

  • Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young N, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134

    CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This research was supported by a grant from the Next Generation BioGreen 21 Program (Code No. PJ00811701), Rural Development Administration, Republic of Korea.

Author information

Authors and Affiliations

  1. Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea

    Kyujung Van, Yang Jae Kang, Kwang-Soo Han, Yeong-Ho Lee & Suk-Ha Lee

  2. National Agrobiodiversity Center, National Academy of Agricultural Science, Suwon, 441-707, Korea

    Jae-Gyun Gwag

  3. Upland Crop Division, National Institute of Crop Science, Suwon, 441-857, Korea

    Jung-Kyung Moon

  4. Plant Genomics and Breeding Research Institute, Seoul National University, Seoul, 151-921, Korea

    Suk-Ha Lee

Authors
  1. Kyujung Van
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yang Jae Kang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kwang-Soo Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yeong-Ho Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jae-Gyun Gwag
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jung-Kyung Moon
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Suk-Ha Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Suk-Ha Lee.

Additional information

Communicated by B. Diers.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Van, K., Kang, Y.J., Han, KS. et al. Genome-wide SNP discovery in mungbean by Illumina HiSeq. Theor Appl Genet 126, 2017–2027 (2013). https://doi.org/10.1007/s00122-013-2114-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-013-2114-9

Keywords

Search

Navigation