Molecular Breeding

, 36:128 | Cite as

Genome re-sequencing of two accessions and fine mapping the locus of lobed leaflet margins in mungbean

  • Keyuan Jiao
  • Xin Li
  • Wuxiu Guo
  • Xingxing Yuan
  • Xiaoyan Cui
  • Xin Chen


Mungbean (Vigna radiata L.) is a fast-growing warm-season legume crop widely distributed in Asia. A large amount of self-shading of mungbean plants could reduce its seed yield. Thus, modification of the leaflet type could affect the leaf canopy and improve yield. In this study, a classical locus, lobed leaflet margins (lma) in mungbean, was investigated, which was controlled by a semi-dominant allele. In order to map the lma, the whole genomes of AL127 carrying lma and another accession Sulu with oval leaflets were re-sequenced; 236,998 single nucleotide polymorphisms and 8896 insertion/deletions (InDels) were identified between the two accessions. Using the validated InDels and SNP markers, lma was mapped to a syntenic region about 376 kb on chromosome 3 in mungbean and on chromosome 1 in common bean, respectively. Our results provided a framework for map-based gene cloning in mungbean. Cloning the lma should shed light on the underlying molecular mechanism controlling leaf shape in legumes and further provide the molecular basis for genetic improvement on legume crops.


Mungbean lma Genome re-sequencing SNP InDel Synteny 



This work was supported by the National Natural Science Foundation of China (grant no. 31271786) and the Ministry of Agriculture of China for Transgenic Research (grant no. 2014ZX0800943B).

Supplementary material

11032_2016_552_MOESM1_ESM.xlsx (9 kb)
Table S1 The number of SNPs and InDels detected on the mungbean chromosomes and scaffold between AL127 and VC1973A, Sulu and VC1973A. (XLSX 8 kb)
11032_2016_552_MOESM2_ESM.xlsx (6.6 mb)
Table S2 The SNPs between AL127 and Sulu. (XLSX 6726 kb)
11032_2016_552_MOESM3_ESM.xlsx (1.3 mb)
Table S3 The InDels between AL127 and Sulu. (XLSX 1280 kb)
11032_2016_552_MOESM4_ESM.xlsx (11 kb)
Table S4 Developing new markers for fine mapping of the lma locus in mungbean. (XLSX 11 kb)
11032_2016_552_MOESM5_ESM.xlsx (24 kb)
Table S5 The SNP between AL127 and Sulu in the lma region. (XLSX 23 kb)
11032_2016_552_MOESM6_ESM.xlsx (9 kb)
Table S6 The InDels between AL127 and Sulu in the lma region. (XLSX 9 kb)
11032_2016_552_MOESM7_ESM.xlsx (15 kb)
Table S7 The homolog genes in the syntenic block. (XLSX 14 kb)


  1. Bajaj D, Das S, Badoni S, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK (2015) Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea. Sci Rep 5:12468–12484CrossRefPubMedPubMedCentralGoogle Scholar
  2. 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 28:255–264CrossRefGoogle Scholar
  3. Chen HL, Wang LX, Wang SH, Liu CJ, Blair MW, Cheng XZ (2015) Transcriptome sequencing of mung bean (Vigna radiate L.) genes and the identification of EST-SSR markers. PLoS One 10:e0120273CrossRefPubMedPubMedCentralGoogle Scholar
  4. Cheng X, Wen J, Tadege M, Ratet P, Mysore KS (2011) Reverse genetics in Medicago truncatula using Tnt1 insertion mutants. Methods Mol Biol 678:179–190CrossRefPubMedGoogle Scholar
  5. Chhabra AK (1990) Inheritance of lobed and pentafoliate leaf in mungbean. Indian J Pulses Res 3:69–72Google Scholar
  6. Constantin GD, Krath BN, MacFarlane SA, Nicolaisen M, Johansen IE, Lund OS (2004) Virus-induced gene silencing as a tool for functional genomics in a legume species. Plant J 40:622–631CrossRefPubMedGoogle Scholar
  7. Gao Q, Yue G, Li W, Wang J, Xu J, Yin Y (2012) Recent progress using high-throughput sequencing technologies in plant molecular breeding. J Integr Plant Biol 54:215–227CrossRefPubMedGoogle Scholar
  8. 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 42:961–967CrossRefPubMedGoogle Scholar
  9. 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 44:32–39CrossRefGoogle Scholar
  10. Isemura T, Kaga A, Tabata S, Somta P, Srinives P, Shimizu T, Jo U, Vaughan DA, Tomooka N (2012) Construction of a genetic linkage map and genetic analysis of domestication related traits in mungbean (Vigna radiata). PLoS One 7:e41304CrossRefPubMedPubMedCentralGoogle Scholar
  11. Jain M, Moharana KC, Shankar R, Kumari R, Garg R (2014) Genome-wide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance. Plant Biotechnol J 12:253–264CrossRefPubMedGoogle Scholar
  12. Kang YJ, Kim SK, Kim MY, Lestari P, Kim KH, Ha BK, Jun TH, Hwang WJ, Lee T, Lee J, Shim S, Yoon MY, Jang YE, Han KS, Taeprayoon P, Yoon N, Somta P, Tanya P, Kim KS, Gwag JG, Moon JK, Lee YH, Park BS, Bombarely A, Doyle JJ, Jackson SA, Schafleitner R, Srinives P, Varshney RK, Lee SH (2014) Genome sequence of mungbean and insights into evolution within Vigna species. Nat Commun 5:443–5451Google Scholar
  13. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–1645CrossRefPubMedPubMedCentralGoogle Scholar
  14. 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 42:1027–1030CrossRefPubMedGoogle Scholar
  15. 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 SS, Zhang G (2010) Resequencing of 31 wild and cultivated soybean genomes identified patterns of genetic diversity and selection. Nat Genet 12:1053–1059CrossRefGoogle Scholar
  16. Lambrides CJ, Godwin ID (2007) Mungbean. In: Kole C (ed) Genome mapping and molecular breeding in plants. Pulses, sugar and tuber crops, vol 3. Springer, Berlin, pp 69–90CrossRefGoogle Scholar
  17. Lawn RJ (1979) Agronomic studies on Vigna spp. in southeastern Queensland I. Phenological response of cultivars to sowing date. Aust J Agric Res 30:855–870CrossRefGoogle Scholar
  18. Lee YS, Lee JY, Kim DK, Yoon CY, Bak GC, Park IJ, Bang GP, Moon JK, Oh YJ, Min KS (2004) A new high-yielding mungbean cultivar, “Samgang” with lobed leaflet. Korean J Breed 36:183–184Google Scholar
  19. Li X, Zhuang LL, Ambrose M, Rameau C, Hu XH, Yang J, Luo D (2010) Genetic analysis of ele mutants and comparative mapping of ele1 locus in the control of organ internal asymmetry in garden pea. J Integr Plant Biol 52:528–535CrossRefPubMedGoogle Scholar
  20. Liu B, Wang Y, Zhai W, Deng J, Wang H, Cui Y, Cheng F, Wang X, Wu J (2013) Development of InDel markers for Brassica rapa based on whole-genome re-sequencing. Theor Appl Genet 126:231–239CrossRefPubMedGoogle Scholar
  21. Lü Y, Cui X, Li R, Huang P, Zong J, Yao D, Li G, Zhang D, Yuan Z (2015) Development of genome-wide insertion/deletion markers in rice based on graphic pipeline platform. J Integr Plant Biol. doi: 10.1111/jipb.12354 Google Scholar
  22. Moe KT, Chung JW, Cho Y, Moon JK, Ku JH, Jung JK, Lee J, Park YJ (2011) Sequence information on simple sequence repeats and single nucleotide polymorphisms through transcriptome analysis of mungbean. J Integr Plant Biol 53:63–73CrossRefPubMedGoogle Scholar
  23. Moe KT, Gwag JG, Park YJ (2012) Efficiency of POWERCORE in core set development using amplified fragment length polymorphic markers in mungbean. Plant Breed 131:110–117CrossRefGoogle Scholar
  24. Nair RM, Yang RY, Easdown WJ, Thavarajah D, Thavarajah P, Hughes JD, Keatinge JD (2013) Biofortification of mungbean (Vigna radiata) as a whole food to enhance human health. J Sci Food Agric 9:1805–1813CrossRefGoogle Scholar
  25. Pflieger S, Blanchet S, Meziadi C, Richard MM, Thareau V, Mary F, Mazoyer C, Geffroy V (2014) The “one-step” bean pod mottle virus (BPMV)-derived vector is a functional genomics tool for efficient overexpression of heterologous protein, virus-induced gene silencing and genetic mapping of BPMV R-gene in common bean (Phaseolus vulgaris L.). BMC Plant Biol 14:232–247CrossRefPubMedPubMedCentralGoogle Scholar
  26. Ramamoorthi N, Veerabadhiran P, Ramasamy A, Jehangir K (1994) Inheritance of lobed leaf in mungbean. Madras Agric J 81:685Google Scholar
  27. Sindhu A, Ramsay L, Sanderson LA, Stonehouse R, Li R, Condie J, Shunmugam AS, Liu Y, Jha AB, Diapari M, Burstin J, Aubert G, Tar’an B, Bett KE, Warkentin TD, Sharpe AG (2014) Gene-based SNP discovery and genetic mapping in pea. Theor Appl Genet 127:2225–2241CrossRefPubMedPubMedCentralGoogle Scholar
  28. Soehendi R, Chanprame T, Toojinda T, Srenives P (2006a) Inheritance and AFLP tagging of leaflet mutants in mungbean (Vigna radiate (L.) Wilczek). Kasetsart J Nat Sci 40:566–572Google Scholar
  29. Soehendi R, Chanprame S, Toojinda T, Ngampongsai S, Srenives P (2006b) Genetics, agromic and molecular study of leaflet mutants in mungbean (Vigna radiata (L.) Wilczek). J Crop Sci Biotechnol 10:193–200Google Scholar
  30. Somta P, Srinives P (2007) Genome research in mungbean (Vigna radiata (L.) Wilczek) and blackgram (V. mungo (L.) Hepper). Sci Asia 33(Suppl. 1):69–74CrossRefGoogle Scholar
  31. Steiner JJ, Banuelos GS (2003) Registration of ARS-NLT-SALT and ARS-NLT-SALT/B saline tolerant narrow-leaf trefoil germplasm. Crop Sci 43:1888–1889CrossRefGoogle Scholar
  32. Sung F, Chen J (1989) Changes in photosynthesis and other chloroplast traits in lanceolate leaflet isoline of soybean. Plant Physiol 90:773–777CrossRefPubMedPubMedCentralGoogle Scholar
  33. 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 9:137–148CrossRefPubMedPubMedCentralGoogle Scholar
  34. Tomooka N, Vaughan DA, Moss H, Maxted N (2002) The Asian Vigna: genus Vigna subgenus ceratotropis genetic resources. Kluwer, Dordrecht, p 270CrossRefGoogle Scholar
  35. Urbański DF, Małolepszy A, Stougaard J, Andersen SU (2013) High-throughput and targeted genotyping of Lotus japonicus LORE1 insertion mutants. Methods Mol Biol 1069:119–146CrossRefPubMedGoogle Scholar
  36. Van K, Kang YJ, Han KS, Lee YH, Gwag JG, Moon JK, Lee SH (2013) Genome-wide SNP discovery in mungbean by Illumina HiSeq. Theor Appl Genet 126:2017–2027CrossRefPubMedGoogle Scholar
  37. Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621–630CrossRefPubMedGoogle Scholar
  38. Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27:522–530CrossRefPubMedGoogle Scholar
  39. Wang Z, Luo Y, Li X, Wang L, Xu S, Yang J, Weng L, Sato S, Tabata S, Ambrose M, Rameau C, Feng X, Hu X, Luo D (2008) Genetic control of floral zygomorphy in pea (Pisum sativum L.). Proc Natl Acad Sci USA 105:10414–10419CrossRefPubMedPubMedCentralGoogle Scholar
  40. Webb A, Cottage A, Wood T, Khamassi K, Hobbs D, Gostkiewicz K, White M, Khazaei H, Ali M, Street D, Duc G, Stoddard FL, Maalouf F, Ogbonnaya FC, Link W, Thomas J, O’Sullivan DM (2015) A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.). Plant Biotechnol. doi: 10.1111/pbi.12371 Google Scholar
  41. Yadav CB, Bhareti P, Muthamilarasan M, Mukherjee M, Khan Y, Rathi P, Prasad M (2015) Genome-wide SNP identification and characterization in two soybean cultivars with contrasting mungbean yellow mosaic India virus disease resistance traits. PLoS One 10:e0123897CrossRefPubMedPubMedCentralGoogle Scholar
  42. Zhuang LL, Ambrose M, Rameau C, Yang J, Hu X, Luo D, Li X (2012) LATHYROIDES, encoding a WUSCHEL-related homeobox1 transcriptional factor, controls organ lateral growth and regulates tendril and dorsal petal identities in garden pea (Pisum sativum L.). Mol Plant 5:1333–1345CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Keyuan Jiao
    • 1
    • 2
  • Xin Li
    • 2
  • Wuxiu Guo
    • 1
  • Xingxing Yuan
    • 2
    • 3
  • Xiaoyan Cui
    • 3
  • Xin Chen
    • 3
  1. 1.Guangdong Key Laboratory of Plant Resources, School of Life SciencesSun Yat-Sen UniversityGuangzhouChina
  2. 2.College of Life Sciences, Laboratory Center of Life SciencesNanjing Agricultural UniversityNanjingChina
  3. 3.Institute of Vegetable CropsJiangsu Academy of Agricultural SciencesNanjingChina

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