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Genomics and Molecular Markers in Cannabis sativa L.

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Abstract

Over the last twenty years, the development of molecular markers in Cannabis sativa significantly contributed to the advancement of knowledge of the genome structure of the species. Male-associated markers have contributed to the understanding of chromosome structure and composition of sexual chromosomes; microsatellites have highlighted the extent of the genetic variation of Cannabis; research on chemotype-associated markers has been of great relevance in the development of an increasingly refined view of the biochemistry and physiology of the chemotype determinants in Cannabis. Moreover, the application of extensive sequencing, which enabled the determination of the first Cannabis genomes and transcriptomes, has boosted the availability of sequences associated to specific traits. In this chapter, the development of different types of molecular markers and their application to the most relevant traits for Cannabis breeding are described and discussed.

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References

  • Alghanim HJ, Almirall JR (2003) Development of microsatellite markers in Cannabis sativa for DNA typing and genetic relatedness analyses. Anal Bioanal Chem 376:1225–1233

    Article  CAS  PubMed  Google Scholar 

  • Beherec O (2000) FNPC hemp breeding and CCPSC seeds production (France). In: Proceedings of Bioresource hemp, Wolfsburg, Germany, 13–16 September 2000

    Google Scholar 

  • Bocsa I (1958) Beiträge zur Züchtung eines ungarischen monözischen Hanfes und zur Kenntnis der Inzuchterscheinungen beim Hanf (Cannabis sativa L.) Z. Pflanzenzüchtg 39:11–34

    Google Scholar 

  • Bocsa I, Mathé P, Hangyel L (1997) Effect of nitrogen on tetrahydrocannabinol (THC) content in hemp (Cannabis sativa L.) leaves at different positions. J Int Hemp Assoc 4:80–81

    Google Scholar 

  • Bocsa I, Karus M (1998) The cultivation of hemp: botany, varieties, cultivation and harvesting. Chapter 4 ‘the breeding of hemp varieties’, pp 47–71, Hemptec, Sebastopol

    Google Scholar 

  • Bredemann G (1938) Züchtung des Hanfes auf Fasergehalt. Die Ergebnisse des Jahres 1937. Faserforschung 13:81–87

    Google Scholar 

  • Datwyler SL, Weiblen GD (2006) Genetic variation in hemp and marijuana (Cannabis sativa L.) according to amplified fragment length polymorphisms. J Forensic Sci 51:371–375

    Article  CAS  PubMed  Google Scholar 

  • Dias VHG, Ribeiro ASD, Mello ICT, Silva R, Sabino BD, Garrido RG, Seldin L, Moura-Neto RS et al (2015) Genetic identification of Cannabis sativa using chloroplast trnL-F gene. Forensic Sci Int: Genet 14:201–202

    Article  CAS  Google Scholar 

  • Divashuk MG, Alexandrov OS, Razumova OV, Kirov IV, Karlov GI (2014) Molecular cytogenetic characterization of the dioecious Cannabis sativa with an XY chromosome sex determination system. PLoS ONE 9(1):e85118

    Article  PubMed  PubMed Central  Google Scholar 

  • de Meijer EPM (2014) The chemical phenotypes (chemotypes) of Cannabis. In: Pertwee RG (editor). Handbook of Cannabis. Handbooks in Psychopharmacology: Oxford University Press, pp 89–110

    Google Scholar 

  • de Meijer EPM, Hammond KM (2005) The inheritance of chemical phenotype in Cannabis sativa L. (II): cannabigerol predominant plants. Euphytica 145:189–198

    Article  Google Scholar 

  • de Meijer EPM, van der Kamp HJ, van Eeuwijk FA (1992) Characterisation of Cannabis accessions with regard to cannabinoid content in relation to other plant characters. Euphytica 62:187–200

    Article  Google Scholar 

  • de Meijer EPM, Bagatta M, Carboni A, Crucitti P, Moliterni VMC, Ranalli P, Mandolino G (2003) The inheritance of chemical phenotype in Cannabis sativa L. Genetics 163:334–335

    Google Scholar 

  • de Meijer EPM, Hammond KM, Micheler M (2009) The inheritance of chemical phenotype in Cannabis sativa L. (III): variation in cannabichromene proportion. Euphytica 165:293–311

    Article  CAS  Google Scholar 

  • Ellis JR, Burke JM (2007) EST-SSRs as a resource for population genetic analyses. Heredity 99:125–132

    Article  CAS  PubMed  Google Scholar 

  • Faeti V, Mandolino G, Ranalli P (1996) Genetic diversity of Cannabis sativa germplasm based on RAPD markers. Plant Breed 115:367–370

    Article  Google Scholar 

  • Faux AM, Bertin P (2014) Modelling approach for the quantitative variation of sex expression in monoecious hemp (Cannabis sativa L.). Plant Breed 133:782–787

    Article  Google Scholar 

  • Faux AM, Draye X, Lambert R, d’Andrimont R, Raulier P, Bertin P (2013) The relationship of stem and seed yields to flowering phenology and sex expression in monoecious hemp (Cannabis sativa L.). Eur J Agron 47:11–22

    Article  Google Scholar 

  • Faux AM, Berhin A, Dauguet N, Bertin P (2014) Sex chromosomes and quantitative sex expression in monoecious hemp (Cannbis sativa L.). Euphytica 196:183–197

    Article  Google Scholar 

  • Faux AM, Draye X, Flamand MC, Occre A, Bertin P (2016) Identification of QTLs for sex expression in dioecious and monoecious hemp (Cannabis sativa L.) Euphytica 209:357−376

    Google Scholar 

  • Flachowsky H, Schumann E, Weber WE, Peil A (2001) Application of AFLP for the detection of sex-specific markers in hemp. Plant Breed 120:305–309

    Article  CAS  Google Scholar 

  • Forapani S, Carboni A, Paoletti C, Moliterni VMC, Ranalli P, Mandolino G (2001) Comparison of hemp varieties using random amplified polymorphic DNA markers. Crop Sci 41:1682–1689

    Article  CAS  Google Scholar 

  • Fournier G (1981) Les chemiotypes du chanvre (Cannabis sativa L.). Interet pour un programme de selection. Agronomie 1:679–688

    Article  Google Scholar 

  • Fournier G, Paris M (1980) Determination de chimiotypes a partir des cannabinoıdes chez le chanvre a fibres monoıque (Cannabis sativa L.). Possibilites de selection. Physiol Veg 18:349–356

    CAS  Google Scholar 

  • Fournier G, Richez-Dumanois C, Duvezin J, Mathieu JP, Paris M (1987) Identification of a new chemotype in Cannabis sativa: cannabigerol-dominant plants, biogenetic and agronomic prospects. Plant Med 53:277–280

    Article  CAS  Google Scholar 

  • Gao C, Xin P, Cheng C, Tang Q, Chen P, Wang C, Zang G, Zhao L (2014) Diversity analysis in Cannabis sativa based on large-scale development of expressed sequence tag-derived simple sequence repeat markers. PLoS ONE 9:e110638

    Article  PubMed  PubMed Central  Google Scholar 

  • Giacoppo S, Mandolino G, Galuppo M, Bramanti P, Mazzon E (2014) Cannabinoids: new promising agents in the treatment of neurological diseases. Molecules 19:18781–18816

    Article  PubMed  Google Scholar 

  • Gillan R, Cole MD, Linacre A, Thorpe JW, Watson ND (1995) Comparison of Cannabis sativa by random amplification of polymorphic DNA (RAPD) and HPLC of cannabinoids: a preliminary study. Sci Justice 35:169–177

    Article  CAS  PubMed  Google Scholar 

  • Gilmore S, Peakall R, Robertson J (2003) Short tandem repeat (STR) DNA markers are hypervariable and informative in Cannabis sativa implications for forensic investigations.Forensic Sci Intl 131:65−74

    Article  CAS  Google Scholar 

  • Hillig K (2005) Genetic evidence for speciation in Cannabis (Cannabaceae). Genet Res Crop Evol 52:161–180

    Article  CAS  Google Scholar 

  • Hsieh HM, Hou RJ, Tsai LC, Wei CS, Liu SW, Huang LH, Kuo YC, Linacre A, Lee JC (2003) A highly polymorphic STR locus in Cannabis sativa. Forensic Sci Int 9:53–58

    Article  Google Scholar 

  • Jagadish V, Robertson J, Gibbs A (1996) RAPD analysis distinguishes Cannabis sativa samples from different sources. Forensic Sci Int 79:113–121

    Article  CAS  Google Scholar 

  • Kojoma M, Iida O, Makino Y, Sekita S, Satake M (2002) DNA fingerprinting of Cannabis sativa using inter-simple sequence repeat (ISSR) amplification. Planta Med 68(1):60–63

    Article  CAS  PubMed  Google Scholar 

  • Kojoma M, Seki H, Yoshida S, Muranaka T (2006) DNA polymorphisms in the tetrahydrocannabinolic acid (THCA) synthase gene in “drug-type” and “fiber-type” Cannabis sativa L. Forensic Sci Int 159:132–140

    Article  CAS  PubMed  Google Scholar 

  • Lata H, Chandra S, Techen N, Khan IA, ElSohly MA (2010) Assessment of the genetic stability of micropropagated plants of Cannabis sativa by ISSR markers. Planta Med 76:97–100

    Article  CAS  PubMed  Google Scholar 

  • Lata H, Chandra S, Techen N, Khan IA, ElSohly MA (2011) Molecular analysis of genetic fidelity in Cannabis sativa L. plants grown from synthetic (encapsulated) seeds following in vitro storage. Biotechnol Lett 33:2503–2508

    Article  CAS  PubMed  Google Scholar 

  • Linacre A, Thorpe J (1998) Detection and identification of Cannabis by DNA. Forensic Sci Int 91:71–76

    Article  CAS  PubMed  Google Scholar 

  • Mandolino G (2007) Marker assisted selection and genomics of industrial plants. Improv Crop Plants Ind End Uses 5:59–82

    Article  Google Scholar 

  • Mandolino G, Carboni A (2004) Potential of marker-assisted selection in hemp genetic improvement. Euphytica 140:107–120

    Article  Google Scholar 

  • Mandolino G, Ranalli P (2002) The applications of molecular markers in genetics and breeding of hemp. J Ind Hemp 7:7–23

    Article  CAS  Google Scholar 

  • Mandolino G, Carboni A, Forapani S, Faeti V, Ranalli P (1999) Identification of DNA markers linked to the male sex in dioecious hemp (Cannabis sativa L.). Theor Appl Genet 98:86–92

    Article  CAS  Google Scholar 

  • Mandolino G, Carboni A, Bagatta M, Moliterni VMC, Ranalli P (2002) Occurrence and frequency of putatively Y chromosome linked DNA markers in Cannabis sativa L. Euphytica 126:211–218

    Article  CAS  Google Scholar 

  • McKernan KJ, Helbert Y, Tadigotla V, McLaughlin S, Spangler J, Zhang L, Smith D (2015) Single molecule sequencing of THCA synthase reveals copy number variation in modern drug-type Cannabis sativa L. doi:10.1101/028654

    Google Scholar 

  • Mendoza MA, Mills DK, Lata H, Chandra S, ElSohly MA, Almirall JR (2009) Genetic individualization of Cannabis sativa by a short tandem repeat multiplex system. Anal Bioanal Chem 393:719–726

    Article  CAS  PubMed  Google Scholar 

  • Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ming R, Bendahmane A, Renner SS (2011) Sex chromosomes in land plants. Annu Rev Plant Biol 62:485–514

    Article  CAS  PubMed  Google Scholar 

  • Mohan Ram HY, Jaiswal VS (1970) Induction of female flowers on male plants of Cannabis sativa L. by 2-chloroethanephosphonic acid. Experientia 23:214–216

    Google Scholar 

  • Mohan Ram HY, Sett R (1982a) Modification of growth and sex expression in Cannabis sativa by aminoethoxyvinyl glycine and ethephon. Zeitschrift Fuer Pflanzenphysiologie 105:165–172

    Article  Google Scholar 

  • Mohan Ram HY, Sett R (1982b) Induction of fertile male flowers in genetically female Cannabis sativa plants by silver nitrate and silver thiosulphate anionic complex. Theor Appl Genet 62:369–375

    CAS  PubMed  Google Scholar 

  • Morimoto S, Komatsu K, Taura F, Shoyama Y (1997) Enzymological evidence for cannabichromenic acid biosynthesis. J Nat Prod 60:854–857

    Article  CAS  Google Scholar 

  • Morimoto S, Komatsu K, Taura F, Shoyama Y (1998) Purification and characterization of cannabichromenic acid synthase from Cannabis sativa. Phytochemistry 49:1525–1529

    Article  CAS  PubMed  Google Scholar 

  • Ober D (2005) Seeing double: gene duplication and diversification in plant secondary metabolism. Trends Plant Sci 10:444–449

    Article  CAS  PubMed  Google Scholar 

  • Oh H, Seo B, Lee S, Ahn D-H, Jo E, Park J-K, Min G-S (2015) Two complete chloroplast genome sequences of Cannabis sativa varieties. Mitochondrial DNA. doi:10.3109/19401736.2015.1053117

    Google Scholar 

  • Onofri C, de Meijer EPM, Mandolino G (2015) Sequence heterogeneity of cannabidiolic- and tetrahydrocannabinolic acid-synthase in Cannabis sativa L. and its relationship with chemical phenotype. Phytochemistry 116:57–68

    Article  CAS  PubMed  Google Scholar 

  • Pacifico D, Miselli F, Micheler M, Carboni A, Ranalli P, Mandolino G (2006) Genetics and marker-assisted selection of the chemotype in Cannabis sativa L. Mol Breed 17:257–268

    Article  CAS  Google Scholar 

  • Pacifico D, Miselli F, Carboni A, Moschella A, Mandolino G (2008) Time course of cannabinoid accumulation and chemotype development during the growth of Cannabis sativa L. Euphytica 160:231–240

    Article  CAS  Google Scholar 

  • Parker JS, Clark MS (1991) Dosage sex-chromosome systems in plants. Plant Sci 80:79–92

    Article  Google Scholar 

  • Peil A, Schumann E, Flachowsky H, Kriese U, El Ghani M, Riedel M, Weber WE (2000) AFLP markers for male plantsof hemp (Cannabis sativa L.). In: Proceedings of the biore-source hemp, 13–18 September, Wolfsburg, Germany. On line at www.nova-institut.de/bioresource-hemp/op.htm

  • Peil A, Flachowsky H, Schumann E, Weber WE (2001) In: Proceedings of the International Conference on “Bast Fibrous Plants on the Turn of the Second and Third Millennium”, 18–22 September, Shenyang, China. pp 1–7

    Google Scholar 

  • Peil A, Flachowsky H, Schumann E, Weber WE (2003) Sex-linked AFLP markers indicate a pseudoautosomal region in hemp (Cannabis sativa L.). Theor Appl Genet 107:102–109

    Article  CAS  PubMed  Google Scholar 

  • Razumova OV, Alexandrov OS, Divashuk MG, Sukhorada TI, Karlov GI (2015) Molecular cytogenetic analysis of monoecious hemp (Cannabis sativa L.) cultivars reveals its karyotype variations and sex chromosomes constitution. Protoplasma. doi:10.1007/s00709-015-0851-0

  • Rotherham D, Harbison SA (2011) Differentiation of drug and non-drug Cannabis using a single nucleotide polymorphism (SNP) assay. Forensic Sci Int 207:193–197

    Article  CAS  PubMed  Google Scholar 

  • Sakamoto K, Shimomura K, Komeda H, Satoh S (1995) A male associated DNA sequence in a dioecious plant, Cannabis sativa L. Plant Cell Physiol 36:1549–1554

    CAS  PubMed  Google Scholar 

  • Sakamoto K, Akiyama Y, Fukui K, Kamada H, Satoh S (1998) Characterization; genome sizes and morphology of sex chromosomes in hemp (Cannabis sativa L.). Cytologia 63:459–464

    Article  Google Scholar 

  • Sakamoto K, Ohmido N, Fukui K, Kamada H, Satoh S (2000) Site-specific accumulation of a LINE-like retrotransposon in a sex chromosome of the dioecious plant Cannabis sativa. Plant Mol Boil 44:723–732

    Article  CAS  Google Scholar 

  • Sakamoto K, Abe T, Matsuyama T, Yoshida S, Ohmido N, Fukui K, Satoh S (2005) RAPD markers encoding retrotransposable elements are linked to the male sex in Cannabis sativa L. Genome 48:931–936

    Article  CAS  PubMed  Google Scholar 

  • Sawler J, Stout JM, Gardner KM, Hudson D, Vidmar J, Butler L, Page JE, Myles S (2015) The genetic structure of marijuana and hemp. PLoS ONE 10(8):e0133292. doi:10.1371/journal.pone.0133292

    Article  PubMed  PubMed Central  Google Scholar 

  • Shao H, Song S, Clarke R (2003) Female-associated DNA polymorphisms of hemp (Cannabis sativa L.). J Ind Hemp 8: 5–9

    Google Scholar 

  • Shephard HL, Parker JS, Darby P, Ainsworth CC (2000) Sexual development and sex chromosomes in hop. New Phytol 148:397–411

    Article  Google Scholar 

  • Siniscalco Gigliano G (1998) Identification of Cannabis sativa L. (Cannabaceae) using restriction profiles of the Internal Transcribed Spacer II (ITS2). Sci Justice 38:225–230

    Article  Google Scholar 

  • Siniscalco Gigliano G, Caputo P, Cozzolino S (1997) Ribosomal DNA analysis as a tool to identify specimens of Cannabis sativa L. of forensic interest. Sci Justice 37:171–174

    Article  CAS  PubMed  Google Scholar 

  • Sirikantaramas S, Morimoto S, Shoyama Y, Ishikawa Y, Wada Y, Shoyama Y, Taura F (2004) The gene controlling marijuana psychoactivity. Molecular cloning and heterologous expression of Δ1-tetrahydrocannabinolic acid synthase from Cannabis sativa L. J Biol Chem 279:39767–39774

    Article  CAS  PubMed  Google Scholar 

  • Small E, Beckstead HD (1973) Common cannabinoid phenotypes in 350 stocks of Cannabis. Lloydia 36:144–165

    CAS  PubMed  Google Scholar 

  • Small E, Cronquist A (1976) A practical and natural taxonomy for Cannabis. Taxon 25:405–435

    Article  Google Scholar 

  • Staginnus C, Zörntlein S, de Meijer E (2014) A PCR marker linked to a THCA synthase polymorphism is a reliable tool to discriminate potentially THC-rich plants of Cannabis sativa L. J Forensic Sci 59:919–926

    Article  CAS  PubMed  Google Scholar 

  • Taura F, Sirikantaramas S, Shoyama Y, Yoshikai K, ShoyamaY Morimoto S (2007) Cannabidiolic-acid synthase, the chemotype-determining enzyme in the fiber-type Cannabis sativa. FEBS Lett 581:2929–2934

    Article  CAS  PubMed  Google Scholar 

  • Techen N, Chandra S, Lata H, Elsohly MA, Khan IA (2010) Genetic identification of female Cannabis sativa plants at early developmental stage. Planta Med 76:1938–1939

    Article  CAS  PubMed  Google Scholar 

  • Törjék O, Bucherna N, Kiss E, Homoki H, Finta-Korpelová Z et al (2002) Novel male-specific molecular markers (MADC5, MADC6) in hemp. Euphytica 127:209–218

    Article  Google Scholar 

  • Vergara D, White KH, Keepers KG, Kane NC (2015) The complete chloroplast genomes of Cannabis sativa and Humulus lupulus. Mitochondrial DNA. doi:10.3109/19401736.2015.1079905

    PubMed  Google Scholar 

  • van Bakel H, Stout JM, Cote AG, Tallon CM, Sharpe AG, Hughes TR, Page JE (2011) The draft genome and transcriptome of Cannabis sativa. Genome Biol 12:R102

    Article  PubMed  PubMed Central  Google Scholar 

  • Von Sengbusch R (1952) Ein weiterer Beitrag zur Vererbung des Geschlechts bei Hanf als Grundlage für die Züchtung eines monözischen Hanfes. Zeitschrift für Pflanzenzüchtung 31:319–338

    Google Scholar 

  • Virovets VG (1998) Interview. J Int Hemp Assoc 5:32–34

    Google Scholar 

  • Vogelmann AF, Turner JC, Mahlberg PG (1988) Cannabinoid composition in seedlings compared to adult plants of Cannabis sativa. J Nat Prod 51:1075–1079

    Article  CAS  Google Scholar 

  • Vyskot B, Hobza R (2004) Gender in plants: sex chromosomes are emerging from the fog. Trends Genet 20:432–438

    Article  CAS  PubMed  Google Scholar 

  • Weiblen GD, Wenger JP, Craft KJ, ElSohly MA, Mehmedic Z, Treiber EL, Marks MD (2015) Gene duplication and divergence affecting drug content in Cannabis sativa. New Phytol 208:1241–1250

    Article  CAS  PubMed  Google Scholar 

  • Westergaard M (1958) The mechanism of sex determination in dioecious flowering plants. Adv Genet 9:217–281

    CAS  PubMed  Google Scholar 

  • Wilkinson M, Linacre AM (2000) The detection and persistence of Cannabis sativa DNA on skin. Sci Justice 40:11–14

    Article  CAS  PubMed  Google Scholar 

  • Zhang LG, Chang Y, Zhang XF, Guan FZ, Yuan HM, Yu Y, Zhao LJ (2014) Analysis of the genetic diversity of Chinese native Cannabis sativa cultivars by using ISSR and chromosome markers. Genet Mol Res 13:10490–10500

    Article  CAS  PubMed  Google Scholar 

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Onofri, C., Mandolino, G. (2017). Genomics and Molecular Markers in Cannabis sativa L.. In: Chandra, S., Lata, H., ElSohly, M. (eds) Cannabis sativa L. - Botany and Biotechnology. Springer, Cham. https://doi.org/10.1007/978-3-319-54564-6_15

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