Journal of Genetics

, 98:61 | Cite as

Translation initiation codon (ATG) or SCoT markers-based polymorphism study within and across various Capsicum accessions: insight from their amplification, cross-transferability and genetic diversity

  • Vibha Gupta
  • Pradeep Kumar Jatav
  • Shamshad Ul Haq
  • Kumar Sambhav Verma
  • Varsha Khurana Kaul
  • S. L. Kothari
  • Sumita KachhwahaEmail author
Research Article


Being an economical and nutritional crop, Capsicum appeases people’s peppery taste and is found to be widely distributed all over the world having vast diversity. In the present study, genetic polymorphism, cross transferability (CT) and genetic diversity were examined among the 54 different accessions of Capsicum species including 49 of Capsicum annuum, three of C. baccatum and two of Cfrutescens, using a set of 36 start codon targeted (SCoT) primers. Of the total, 35 SCoT markers showed successful amplification profile among chilli germplasms and an average primer polymorphism was reported as 81.52% which ranged from 50% (SCoT-6) to 100% (SCoT-11). A total of 365 amplicons were obtained with an average of 10.43 bands per primer and the length of the bands ranged from 150 bp to 1.2 kb. Further, polymorphic information content value of SCoT markers ranged from 0.42 (for SCoT-25) to 0.86 (SCoT-27) with an average of 0.78. The average value of CT of SCoT markers was 44.08% ranged from 14.25% to 57.26% among different chilli accessions. A dendrogram was constructed and established genetic relationship among 54 capsicum species, with the help of translation initiation codon polymorphisms or SCoT primer amplification. This study suggests the effectiveness of SCoT marker system for characterizing and assessing genetic diversity of Capsicum germplasm, which can be used for evolutionary studies and to identify agronomically important traits.


Capsicum start codon targeted primers genetic diversity cross amplification 



The authors express sincere thanks to Council of Scientific and Industrial Research (CSIR) and Indian Council of Medical Research (ICMR) for providing Junior Research Fellow (JRF). We are also grateful to UGC-UPE programme and Bioinformatics Infrastructure Facilities (BIF), University of Rajasthan for providing research facilities. CSIR-Research Associate programme is also acknowledged for providing fellowship. Our thanks are extended to Ms Raini Verma, Ms Prerna Dhingra and Ms Rakhi Poonia for their assistance in technical work.


  1. Agarwal M., Shrivastava N. and Padh H. 2008 Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep. 27, 617–631.CrossRefGoogle Scholar
  2. Agarwal A., Gupta V., Haq S. U., Jatav P. K., Kothari S. and Kachhwaha S. 2018 Assessment of genetic diversity in 29 rose germplasms using SCoT marker. J. King Saud Univ.-Sci. (
  3. Aguilar-Meléndez A., Morrell P. L., Roose M. L. and Kim S. C. 2009 Genetic diversity and structure in semiwild and domesticated chillies (Capsicum annuum; Solanaceae) from Mexico. Am. J. Bot. 96, 1190–1202.CrossRefGoogle Scholar
  4. Akyavuz R., Taskin B., Koçak M. and Yildiz M. 2018 Exploring the genetic variations and population structure of Turkish pepper (Capsicum annuum L.) genotypes based on peroxidase gene markers. 3. Biotech. 8, 355.Google Scholar
  5. Al-Qurainy F., Khan S., Nadeem M. and Tarroum M. 2015 SCoT marker for the assessment of genetic diversity in Saudi Arabian date palm cultivars. Pak. J. Bot. 47, 637–643.Google Scholar
  6. Amirmoradi B., Talebi R. and Karami E. 2012 Comparison of genetic variation and differentiation among annual Cicer species using start codon targeted (SCoT polymorphism, DAMD-PCR, and ISSR markers. Plant Syst. Evol. 298, 1679–1688.CrossRefGoogle Scholar
  7. Andersen J. R. and Lübberstedt T. 2003 Functional markers in plants. Trends Plant Sci. 8, 554–560.CrossRefGoogle Scholar
  8. Arumuganathan K. and Earle E. 1991 Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 208–218.CrossRefGoogle Scholar
  9. Bhattacharyya P., Kumaria S., Kumar S. and Tandon P. 2013 Start codon targeted (SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl., an endangered medicinal orchid species. Gene 529, 21–26.CrossRefGoogle Scholar
  10. Botstein D., White R. L., Skolnick M. and Davis R. W. 1980 Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32, 314.PubMedPubMedCentralGoogle Scholar
  11. Bramley P. M. 2000 Is lycopene beneficial to human health?Phytochemistry 54, 233–236.CrossRefGoogle Scholar
  12. Cardoso R., Ruas C. F., Giacomin R. M., Ruas P. M., Ruas E. A., Barbieri R. L. et al. 2018 Genetic variability in Brazilian Capsicum baccatum germplasm collection assessed by morphological fruit traits and AFLP markers. PloS One 13, e0196468.CrossRefGoogle Scholar
  13. Chen C., Durand E., Forbes F. and François O. 2007 Bayesian clustering algorithms ascertaining spatial population structure, a new computer program and a comparison study. Mol. Ecol. Notes 7, 747–756.CrossRefGoogle Scholar
  14. Chen H., He X., Luo C., Zhu J. and Li F. 2010 Analysis on the genetic diversity of 24 longan (Dimocarpus longan) accessions by SCoT markers. Acta Hort. Sin. 37, 1651–1654.Google Scholar
  15. Collard B., Jahufer M., Brouwer J. and Pang E. 2005 An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement, the basic concepts. Euphytica 142, 169–196.CrossRefGoogle Scholar
  16. Collard B. C. and Mackill D. J. 2009 Start codon targeted (SCoT) polymorphism, a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol. Biol. Rep. 27, 86.CrossRefGoogle Scholar
  17. Csilléry G. 2006 Pepper taxonomy and the botanical description of the species. Acta Agron. Hung. 54, 151–166.CrossRefGoogle Scholar
  18. Dagnoko S., Yaro-Diarisso N., Sanogo P. N., Adetula O., Dolo-Nantoumé A., Gamby-Touré K. et al. 2013 Overview of pepper (Capsicum spp.) breeding in West Africa. Afr. J. Agric. Res. 8, 1108–1114.CrossRefGoogle Scholar
  19. Deng L., Liang Q., He X., Luo C., Chen H. and Qin Z. 2015 Investigation and analysis of genetic diversity of diospyros germplasms using SCoT molecular markers in Guangxi. PloS One 10, e0136510.CrossRefGoogle Scholar
  20. Dhaliwal M., Yadav A. and Jindal S. 2014 Molecular characterization and diversity analysis in chilli pepper using simple sequence repeats (SSR) markers. Afr. J. Biotechnol. 13, 3137–3143.CrossRefGoogle Scholar
  21. Djian-Caporalino C., Lefebvre V., Sage-Daubèze A. and Palloix A. 2007 Capsicum, genetic resources, chromosome engineering, and crop improvement, CRC Press, Boca Raton, pp. 185–243.CrossRefGoogle Scholar
  22. Doyle J. J. 1990 Isolation of plant DNA from fresh tissue. Focus 12, 13–15.Google Scholar
  23. Evanno G., Regnaut S. and Goudet J. 2005 Detecting the number of clusters of individuals using the software structure, a simulation study. Mol. Ecol. 14, 2611–2620.CrossRefGoogle Scholar
  24. Falush D., Stephens M. and Pritchard J. K. 2003 Inference of population structure using multilocus genotype data, linked loci and correlated allele frequencies. Genetics 164, 1567–1587.PubMedPubMedCentralGoogle Scholar
  25. Farooq S. and Azam F. 2002 Molecular markers in plant breeding-II. Some pre-requisites for use. Pak. J. Biol. Sci. 5, 1141–1147.CrossRefGoogle Scholar
  26. Feng S., He R., Yang S., Chen Z., Jiang M., Lu J. et al. 2015 Start codon targeted (SCoT) and target region amplification polymorphism (TRAP) for evaluating the genetic relationship of Dendrobium species. Gene 567, 182–188.CrossRefGoogle Scholar
  27. Gaikwad A. B., Archak S. and Gautam D. 2013 DNA profiling of Capsicum annuum L. Cultivars based on AFLP and ISSR markers. Geneconserve 12, 4–12.Google Scholar
  28. González-Pérez S., Garcés-Claver A., Mallor C., de MieraL. E. S., Fayos O., Pomar F. et al. 2014 New insights into Capsicum spp relatedness and the diversification process of Capsicum annuum in Spain. PloS One 9, e116276.CrossRefGoogle Scholar
  29. Gorji A. M., Poczai P., Polgar Z. and Taller J. 2011 Efficiency of arbitrarily amplified dominant markers (SCoT, ISSR and RAPD) for diagnostic fingerprinting in tetraploid potato. Am. J. Potato. Res. 88, 226–237.CrossRefGoogle Scholar
  30. Guerra M. 2008 Chromosome numbers in plant cytotaxonomy, concepts and implications. Cytogenet. Genome Res. 120, 339–350.CrossRefGoogle Scholar
  31. Gulsen O., Sever-Mutlu S., Mutlu N., Tuna M., Karaguzel O., Shearman R. C. et al. 2009 Polyploidy creates higher diversity among Cynodon accessions as assessed by molecular markers. Theor. Appl. Genet. 118, 1309–1319.CrossRefGoogle Scholar
  32. Guo D.-L., Zhang J.-Y. and Liu C.-H. 2012 Genetic diversity in some grape varieties revealed by SCoT analyses. Mol. Biol. Rep. 39, 5307–5313.CrossRefGoogle Scholar
  33. Gupta P. and Rustgi S. 2004 Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct. Integr. Genomics 4, 139–162.CrossRefGoogle Scholar
  34. Haq S., Jain R., Sharma M., Kachhwaha S. and Kothari S. 2014 Identification and characterization of microsatellites in expressed sequence tags and their cross transferability in different plants. Intl. J. Genomics 2014, 863948, 12 pages.Google Scholar
  35. Hill T. A., Ashrafi H., Reyes-Chin-Wo S., Yao J., Stoffel K., Truco M.-J. et al. 2013 Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene pepper GeneChip. PloS One 8, e56200.CrossRefGoogle Scholar
  36. Kim S., Park M., Yeom S.-I., Kim Y.-M., Lee J. M., Lee H.-A. et al. 2014 Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat. Genet. 46, 270.CrossRefGoogle Scholar
  37. Knapp S., Bohs L., Nee M. and Spooner D. M. 2004 Solanaceae – a model for linking genomics with biodiversity. Int. J. Genomics 5, 285–291.Google Scholar
  38. Kothari S., Joshi A., Kachhwaha S. and Ochoa-Alejo N. 2010 Chilli peppers – a review on tissue culture and transgenesis. Biotechnol. Adv. 28, 35–48.CrossRefGoogle Scholar
  39. Luo C., He X.-H., Chen H., Ou S.-J. and Gao M.-P. 2010 Analysis of diversity and relationships among mango cultivars using start codon targeted (SCoT) markers. Biochem. Syst. Ecol. 38, 1176–1184.CrossRefGoogle Scholar
  40. Luo C., He X.-H., Chen H., Hu Y. and Ou S.-J. 2012 Genetic relationship and diversity of Mangifera indica L., revealed through SCoT analysis. Genet. Resour. Crop. Evol. 59, 1505–1515.CrossRefGoogle Scholar
  41. Makari H., Patil H. R., Abhilash M. and Kumar H. M. 2009 Genetic diversity in commercial varieties of chilli as revealed by RAPD method. Indian J. Sci. Technol. 2, 91–94.Google Scholar
  42. Misra S., Lal R. K., Darokar M. P. and Khanuja S. P. S. 2011 Genetic variability in germplasm accessions of Capsicum annuum L. Am. J. Plant Sci. 2, 629.CrossRefGoogle Scholar
  43. Monna L., Miyao A., Inoue T., Fukuoka S., Yamazaki M., Zhong H. S. et al. 1994 Determination of RAPD markers in rice and their conversion into sequence tagged sites (STSs) and STS-specific primers. DNA Res. 1, 139–148.CrossRefGoogle Scholar
  44. Moscone E. A., Baranyi M., Ebert I., Greilhuber J., Ehrendorfer F. and Hunziker A. T. 2003 Analysis of nuclear DNA content in Capsicum (Solanaceae) by flow cytometry and Feulgen densitometry. Ann. Bot. 92, 21–29.CrossRefGoogle Scholar
  45. Mulpuri S., Muddanuru T. and Francis G. 2013 Start codon targeted (SCoT) polymorphism in toxic and non-toxic accessions of Jatropha curcas L. and development of a codominant SCAR marker. Plant Sci. 207, 117–127.CrossRefGoogle Scholar
  46. Nath V. S., Hegde V. M., Jeeva M. L., Misra R. S., Veena S. S., Raj M. et al. 2015 Genetic diversity of Phytophthora colocasiae causing taro leaf blight, analysis using start codon targeted (SCoT) polymorphism. J. Root Crops 39, 168–177.Google Scholar
  47. Navarro J. M., Flores P., Garrido C. and Martinez V. 2006 Changes in the contents of antioxidant compounds in pepper fruits at different ripening stages, as affected by salinity. Food Chem. 96, 66–73.CrossRefGoogle Scholar
  48. Page R. 1996 TREEVIEW, An application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12, 357–358.PubMedGoogle Scholar
  49. Paran I. and Michelmore R. 1993 Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor. Appl. Genet. 85, 985–993.CrossRefGoogle Scholar
  50. Paran I., Aftergoot E. and Shifriss C. 1998 Variation in Capsicum annuum revealed by RAPD and AFLP markers. Euphytica 99, 167–173.CrossRefGoogle Scholar
  51. Pavlicek A., Hrda S. and Flegr J. 1999 Free-tree–freeware program for construction of phylogenetic trees on the basis of distance data and bootstrap/jackknife analysis of the tree robustness. Application in the RAPD analysis of genus Frenkelia. Folia. Biol. (Krakow) 45, 97.Google Scholar
  52. Pickersgill B. 1977a Chromosomes and evolution in Capsicum. In: E. Pochard (Ed). Capsicum 77, C.R. 36me Congres EU- CARPIA Piment, INRA, Avignon-Montfavet.Google Scholar
  53. Pickersgill B. 1997b Genetic resources and breeding of Capsicum spp. Euphytica 96, 129–133.CrossRefGoogle Scholar
  54. Portis E., Nagy I., Sasvari Z., Stagel A., Barchi L. and Lanteri S. 2007 The design of Capsicum spp. SSR assays via analysis of in silico DNA sequence, and their potential utility for genetic mapping. Plant Sci. 172, 640–648.CrossRefGoogle Scholar
  55. Pritchard J. K., Stephens M. and Donnelly P. 2000 Inference of population structure using multilocus genotype data. Genet. 155, 945–959.Google Scholar
  56. Purkayastha J., Alam S., Gogoi H. and Singh L. 2012 Capsicum assamicum sp. nov. (Solanaceae), from Assam, northeastern India. Ozean J. Appl. Sci. 5, 55–66.Google Scholar
  57. Rai V. P., Kumar R., Kumar S., Rai A., Kumar S., Singh M. et al. 2013 Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers. Physiol. Mol. Biol. Plants 19, 575–586.CrossRefGoogle Scholar
  58. Rathore N. S., Rai M. K., Phulwaria M., Rathore N. and Shekhawat N. 2014 Genetic stability in micropropagated Cleome gynandra revealed by SCoT analysis. Acta. Physiol. Plant. 36, 555–559.CrossRefGoogle Scholar
  59. Rodriguez J., Berke T., Engle L. and Nienhuis J. 1999 Variation among and within Capsicum species revealed by RAPD markers. Theor. Appl. Genet. 99, 147–156.CrossRefGoogle Scholar
  60. Sambrook J. and Russell D. W. 2001 Molecular cloning, A laboratory manual. 2001, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.Google Scholar
  61. Satya P., Karan M., Jana S., Mitra S., Sharma A., Karmakar P. et al. 2015 Start codon targeted (Scot) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producing species. Meta. Gene. 3, 62–70.CrossRefGoogle Scholar
  62. Slattery M. L., Benson J., Curtin K., Ma K.-N., Schaeffer D. and Potter J. D. 2000 Carotenoids and colon cancer. Am. J. Clin. Nutr. 71, 575–582.CrossRefGoogle Scholar
  63. Smith J., Chin E., Shu H., Smith O., Wall S., Senior M. et al. 1997 An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.), comparisons with data from RFLPs and pedigree. Theor. Appl. Genet. 95, 163–173.CrossRefGoogle Scholar
  64. Taranto F., D’Agostino N., Greco B., Cardi T. and Tripodi P. 2016 Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing. BMC Genomics 17, 943.CrossRefGoogle Scholar
  65. Thul S., Lal R., Shasany A., Darokar M., Gupta A., Gupta M. et al. 2009 Estimation of phenotypic divergence in a collection of Capsicum species for yield-related traits. Euphytica 168, 189–196.CrossRefGoogle Scholar
  66. Toquica S. P., Rodríguez F., Martínez E., Duque M. C. and Tohme J. 2003 Molecular characterization by AFLPs of Capsicum germplasm from the Amazon department in Colombia. Genet. Resour. Crop Evol. 50, 639–647.CrossRefGoogle Scholar
  67. USDA-ARS 2011 Grin species records of Capsicum. National 2063 Germplasm Resources Laboratory, Beltsville, Maryland.Google Scholar
  68. Votava E. J., Nabhan G. P. and Bosland P. W. 2002 Genetic diversity and similarity revealed via molecular analysis among and within an in situ population and ex situ accessions of chiltepin (Capsicum annuum var. glabriusculum). Conserv. Genet. 3, 123–129.CrossRefGoogle Scholar
  69. Votava E. J., Baral J. B. and Bosland P. W. 2005 Genetic diversity of Chile (Capsicum annuum var. annuum L.) landraces from northern New Mexico, Colorado, and Mexico. Econ. Bot. 59, 8–17.CrossRefGoogle Scholar
  70. Wu J.-M., Li Y.-R., Yang L.-T., Fang F.-X., Song H.-z., Tang H.-Q. et al. 2013 cDNA-Scot, a novel rapid method for analysis of gene differential expression in sugarcane and other plants. Aust. J. Crop Sci. 7, 659.Google Scholar
  71. Xiong F., Zhong R., Han Z., Jiang J., He L., Zhuang W. et al. 2011 Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (Arachis hypogaea L.) genotypes. Mol. Biol. Rep. 38, 3487–3494.CrossRefGoogle Scholar
  72. Yatung T., Dubey R. K., Singh V. and Upadhyay G. 2014 Genetic diversity of chilli (‘Capsicum annuum’ l.) genotypes of India based on morpho-chemical traits. Aust. J. Crop Sci. 8, 97.Google Scholar
  73. Zeng B., Zhang Y., Huang L., Jiang X., Luo D. and Yin G. 2014 Genetic diversity of orchardgrass (Dactylis glomerata L.) germplasms with resistance to rust diseases revealed by start codontargeted (SCoT) markers. Biochem. Syst. Ecol. 54, 96–102.CrossRefGoogle Scholar

Copyright information

© Indian Academy of Sciences 2019

Authors and Affiliations

  • Vibha Gupta
    • 1
  • Pradeep Kumar Jatav
    • 1
  • Shamshad Ul Haq
    • 1
  • Kumar Sambhav Verma
    • 2
  • Varsha Khurana Kaul
    • 1
  • S. L. Kothari
    • 2
  • Sumita Kachhwaha
    • 1
    • 3
    Email author
  1. 1.Department of BotanyUniversity of RajasthanJaipurIndia
  2. 2.Amity Institute of BiotechnologyAmity UniversityJaipurIndia
  3. 3.Bioinformatics Infrastructure FacilityUniversity of RajasthanJaipurIndia

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