Abstract
During the past few decades, the employment of molecular markers to discover polymorphisms in DNA has been playing an increasing role in conservation strategies and use of plant genetic resources (PGR). Molecular markers are indispensable tools for determining the genetic variation and biodiversity with high levels of accuracy and reproducibility in short times. Different typologies of molecular markers exist, specific for the different applications in molecular genetic methods. Molecular tools have been successfully applied in the analysis of specific genes and gene pathways, as well as to increase understanding of gene action, to generate genetic maps and assist in the development of gene transfer technologies. Molecular markers have also had a critical role in studies of phylogeny and species evolution, and have been applied to increase our understanding of the distribution and extent of genetic variation within and between species. The main two groups of molecular markers can be classified on the basis of the analysis method used: polymerase chain reaction (PCR) and non-PCR-based. Recently, a new class of advanced techniques has emerged, primarily derived from a combination of earlier, more basic techniques. Advanced marker techniques tend to amalgamate advantageous features of several basic techniques, in order to increase the sensitivity and resolution to detect genetic discontinuity and distinctiveness. The past several years have seen revolutionary advances in DNA sequencing technologies with the advent of next-generation sequencing (NGS) techniques. NGS methods now allow millions of bases to be sequenced in one round, at moderate prices and in very short times. This paper is an overview of the diverse, predominantly molecular techniques, used in assessing plant genetic diversity, discussing about the most important and recent advances made in molecular marker techniques, their applications, advantages, and limitations applied to plant sciences in order to provide base platform information to the researchers working in the area.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Adam-Blondon A, Sevignac M, Bannerot H et al (1994) SCAR, RAPD and RFLP markers tightly linked to a dominant gene (Are) conferring resistance to anthracnose in common bean. Theor Appl Genet 88:865–870
Agrawal A, Eastmann Q, Schatz D (1998) Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394:744–751
Akbari M, Wenzl P, Caig V et al (2006) Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet 113:1409–1420
Alberte RS, Suba GK, Procaccini G et al (1994) Assessment of genetic diversity of seagrass populations using DNA fingerprinting: implications for population stability and management. Proc Nat Acad Sci USA 91:1049–1053
Ali IF, Neale DB, Marshall KA (1991) Chloroplast DNA restriction fragment length polymorphism in Sequoia sempervirens D. Don Endl., Pseudotsuga menzipsii (Mirb.) Franco, Calocedrus decurrens (Ton), and Pinus taeda. L. Theor Appl Genet 81:83–89
Althoff DM, Gitzendanner MA, Segraves KA (2007) The utility of amplified fragment length polymorphisms in phylogenetics: a comparison of homology within and between genomes. Syst Biol 56:477–484
Amaral AJ, Megens HJ, Crooijmans RPMA et al (2008) Linkage disequilibrium decay and haplotype block structure in the pig. Genetics 179:569–579
Antonious K, Nybom H (1994) DNA fingerprinting reveals significant amounts of genetic variation in a wild raspberry Rubus idaeus population. Mol Ecol 3:177–180
Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
Ayers NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD (1997) Microsatellites and a single nucleotidepolymorphism differentiate apparentamylose classes in an extended pedigree of US rice germplasm. Theor Appl Genet 94:773–781
Barcaccia G, Albertini E, Rosellini D (2000) Inheritance and mapping of 2n-egg production in diploid alfalfa. Genome 43:528–537
Bark OH, Havey MJ (1995) Similarities and relationships among populations of the bulb onion as estimated by RFLPs. Theor Appl Genet 90:407–414
Becker J, Vos P, Kuiper M et al (1995) Combined mapping of AFLP and RFLP markers in barley. Mol Gen Genet 249:65–73
Bell CJ, Ecker JR (1994) Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 19:137–144
Besse P, Seguin M, Lebrun P et al (1994) Genetic diversity among wild and cultivated populations of Hevea brasiliensis assessed by nuclear RFLP analysis. Theor Appl Genet 88:199–207
Botstein D, White RL, Skolnick M et al (1980) Construction of a genetic map in man using restriction fragment length polymorphisms. Amer J Hum Genet 32:314–331
Bouck A, Vision T (2007) The molecular ecologist’s guide to expressed sequence tags. Mol Ecol 16:907–924
Brooks SA, Gabreski N, Miller D et al (2010) Whole-genome SNP association in the horse: identification of a deletion in myosin Va responsible for lavender foal syndrome. PLoS Genet 6:e1000909
Broquet T, Petit E (2004) Quantifying genotyping errors in noninvasive population genetics. Mol Ecol 13:3601–3608
Brown AHD (1979) Enzyme polymorphism in plant populations. Theor Pop Biol 15:1–42
Brubaker CL, Wendel JF (1994) Reevaluating the origin of domesticated cotton (Gossypium hirsutum; Malvaceae) using nuclear restriction fragment length polymorphisms (RFLPs). Amer J Bot 81:1309–1326
Bucci G, Anzidei M, Madaghiele A et al (1998) Detection of haplotypic variation and natural hybridization in halepensiscomplex pine species using chloroplast simple sequence repeat (SSR) markers. Mol Ecol 7:1633–1643
Caetano-Anolles G (1994) MAAP: a versatile and universal tool for genome analysis. Plant Mol Biol 25:1011–1026
Caetano-Anolles G, Bassam BJ, Gresshoff PM (1991) DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Biotech 9:553–557
Castagna R, Maga G, Perenzin M, Heun M (1994) RFLP-based genetic relationships of Einkorn wheats. Theor Appl Genet 88:818–823
Cho RJ, Mindrinos M, Richards DR et al (1999) Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nature Genet 23:203–207
Clark CM, Wentworth TM, Malley DMO (2000) Genetic discontinuity revealed by chloroplast microsatellites in eastern North American Abies (Pinaceae). Am J Bot 87:774–778
Clausen AM, Spooner DM (1998) Molecular support for the hybrid origin of the wild potato species Solanum × rechei. Crop Sci 38:858–865
Cordeiro GM, Casu R, McIntyre CL, Manners JM, Henry RJ et al (2001) Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant Sci 160:1115–1123
D’Hont A, Paulet F, Glaszmann JC (2002) Oligoclonal interspecific origin of “North Indian” and “Chinese” sugarcanes. Chromosome Res 10:253–262
Dubreuil P, Dufour P, Krejci E et al (1996) Organization of RFLP diversity among inbred lines of maize representing the most significant heterotic groups. Crop Sci 36:790–799
Deu M, Gonzales-de Leon JC, Glaszmann I, Degremont J et al (1994) RFLP diversity in cultivated sorghum in relation to racial differentiation. Theor Appl Genet 88:838–844
Dietrich W, Katz H, Lincoln SE et al (1992) A genetic map of mouse suitable for typing intraspecific crosses. Genetics 131:423–447
Eujayl I, Sorrells M, Baum M, Wolters P, Powell W (2001) Assessment of genotypic variation among cultivated durum wheat based on EST-SSRs and genomic SSRs. Euphytica 119:39–43
Fang DQ, Roose ML, Krueger RR et al (1997) Fingerprinting trifoliate orange germplasm accessions with isozymes, RFLPs, and inter-simple sequence repeat markers. Theor Appl Genet 95:211–219
Ferguson-Smith MA (1997) Genetic analysis by chromosome sorting and painting: Phylogenetic and diagnostic applications. Eur J Hum Genet 5:253–265
Finnegan DJ (1989) Eukaryotic transposable elements and genome evolution. Trend Genet 5:103–107
Flavell A, Smith D, Kumar A et al (1992) Extreme heterogenity of Ty1-copia group retrotransposons in plants. Mol Genet Genom 231:233–242
Girard L, Freeling M (1999) Regulatory changes as a consequence of transposon insertion. Dev Genet 25:291–296
Goff SA, Ricke D, Lan TH et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100
Gonzalez AA, Wong A, Delgado-Salinas R, Gepts P (2005) Assessment of inter simple sequence repeat markers to differentiate sympatric wild and domesticated populations of common bean. Crop Sci 45:606–615
Gray Y (2000) It takes two transposon to tango. Trends Genet 16:461–468
Greene SL, Morris JB (2001) The case for multiple-use plant Germplasm collections and a strategy for implementation. Crop Sci 41:886–892
Guarino L (1999) Approaches to measuring genetic erosion. Proceedings of the technical meeting on the methodology of the FAO World Information and Early Warning System on Plant Genetic Resources, Prague June 1999
Gynheung A, Dong-Hoon J, Ki-Hong J, Sichul L (2005) Reverse genetic approaches for functional genomics of rice. Plant Mol Biol 59:111–123
Hadrys H, Balick M, Schierwater B (1992) Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. Mol Ecol 1:55–63
Hajibabaei M, Janzen DH, Burns JM (2006) DNA barcodes distinguish species of tropical Lepidoptera. Proc Nat Acad Sci USA 103:968–971
Hamrick JL, Godt MJW (1997) Allozyme diversity in cultivated crops. Crop Sci 37:26–30
Harlan JR, de Wet JMJ (1971) Toward a rational classification of cultivated plants. Taxon 20(4):509–517
Hearne CM, Ghosh S, Todd JA (1992) Microsatellites for linkage analysis of genetic traits. Tren Genet 8:288–294
Hebert PDN, Cywinska A, Ball SL et al (2003) Biological identifications through DNA barcodes. Proc R Soc Biol Sci 270:313–321
Hebert PDN, Penton EH, Burns JM (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptesfulgerator. Proc Nat Acad Sci USA 101:14812–14817
Hemmat M, Weeden NF, Manganaris AG et al (1994) Molecular Marker linkage map for apple. J Hered 85:4–11
Herselman L (2003) Genetic variation among Southern African cultivated peanut (Arachis hypogaea L.) genotypes as revealed by AFLP analysis. Euphytica 133(3):319–327
Heun M, Schäfer-Pregl R, Klawan D et al (1997) Site of Einkorn wheat domestication identified by DNA fingerprinting. Science 278:1312–1314
Huang J, Xu Q, Sun ZJ (2007) Identifying earthworms through DNA barcodes. Pedobiologia 51:301–309
Jaccoud D, Peng K, Feinstein D et al (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucl Acid Res 29:25
James D, Schmidt A, Wall E et al (2003) Reliable detection and identification of genetically modified maize, soybean, and canola by multiplex PCR analysis. J Agric Food Chem 51(20):5829–5834
Jarne P, Lagoda PJ (1996) Microsatellites, from molecules to populations and back. Trends Ecol Evol 11(10):424–429
Karaiskou N (2008) High degree of transferability of 86 newly developed zebra finch EST-linked microsatellite markers in 8 bird species. J Hered 99:688–693
Karp A, Seberg O, Buiatti M (1996) Molecular techniques in the assessment of botanical diversity. Ann Bot 78:143–149
Katsiotis A, Schmidt T, Heslop-Harrison J (1996) Chromosomal and genomic organization of Ty1-copia-like retrotransposon sequences in the genus Avena. Genome 39:410–417
Kiss G, Csanadi G, Kalman K et al (1993) Construction of a basis genetic map for alfalfa using RFLP, RAPD, isozyme and morphological markers. Mol Gen Genet 238:129–137
La Rota M, Sorrells ME (2004) Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat. Funct Int Genom 4:34–46
Landegren U, Kaiser R, Sanders J, Hood L (1988) A ligase-mediated gene detection technique. Science 241:1077–1080
Lanner HC, Gustafsson M, Falt AS et al (1996) Diversity in natural populations of wild Brassica oleracea as estimated by isozyme and RAPD analysis. Genet Resour Crop Evol 43:13–23
Laurent V, Risterucci AM, Lanaud C (1994) Genetic diversity in cocoa revealed by cDNA probes. Theor Appl Genet 88:193–198
Lübberstedt TH, Melchinger AE, Dussle D et al (2000) Relationships among early European maize inbreds: Genetic diversity revealed with AFLP markers and comparison with RFLP, RAPD, and pedigree data. Crop Sci 40:783–791
Lynch M (1990) The similarity index and DNA finger printing. Mol Biol Evol 7:478–484
Mackill DJ, Zhang Z, Redoña ED et al (1996) Level of polymorphism and genetic mapping of AFLP markers in rice. Genome 39:969–977
Martin GB, Williams JGK, Tanksley SD (1991) Rapid identification of markers linked to a Pseudomonas resistance gene in tomato by using random primers and near-isogenic lines. Proc Natl Acad Sci USA 88:2336–2340
May BP, Dellaporta SL (1998) Transposon sequences drive tissue-specific expression of the maize regulatory gene R-s. Plant J 13:241–248
McCauley DE (1994) Contrasting the distribution of chloroplast DNA and allozyme polymorphisms among local populations of Silene alba: implications for studying gene flow in plants. Proc Nat Acad Sci 17:8127–8131
Miller JC, Tanksley SD (1990) RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor Appl Genet 80:437–448
Miller W, McDonald J, Pinsker W et al (1997) Molecular domestication of mobile elements. Genetica 100:261–270
Mochida K, Yamazaki Y, Ogihara Y (2004) Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags. Mol Genet Genom 270:371–377
Mohammadi SA, Prasanna BM (2003) Analysis of genetic diversity in crop plants-salient statistical tools and considerations. Crop Sci 43(4):1235–1248
Morgante M, Olivieri AM (1993) PCR-amplified microsatelites as markers in plant genetics. Plant J 3:175–182
Mullis KB, Faloona FA, Scharf SJ et al (1986) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harbor Symp Quant Biol 51:263–273
Nandi S, Subudhi PK, Senadhira D et al (1997) Mapping QTLs for submergence tolerance in rice by AFLP analysis and selective genotyping. Mol Gen Genet 255:1–8
Neale DB, Williams CG (1991) Restriction fragment length polymorphism mapping in conifers and applications to forest genetics and tree improvement. Can J Fors Res 21:545–554
Paran I, Kesseli R, Michelmore R (1991) Identification of restriction-fragment-length-polymorphisms and random amplified polymorphic DNA markers linked to downy mildew resistance genes in lettuce, using near isogenic lines. Genome 34:1021–1027
Parducci L, Szmidt AE, Madaghiele A et al (2001) Genetic variation at chloroplast microsatellites (cpSSRs) in Abies nebrodensis (Lojac.) Mattei and three neighboring Abies species. Theor Appl Genet 102:733–740
Peter G (2001) An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. Int J Legal Med 114:204–210
Powell W, Thomas WTB, Baird E et al (1996) Analysis of quantitative traits in barley by the use of amplified fragment length polymorphisms. Heredity 79:48–59
Primack RB (1993) Essentials of conservation biology. Sinauer Associates, Sunderland, MA, USA
Provan J, Russell JR, Booth A et al (1999a) Polymorphic chloroplast simple-sequence repeat primers for systematic and population studies in the genus Hordeum. Mol Ecol 8:505–511
Provan J, Soranzo N, Wilson NJ et al (1999b) Low mutation rate for chloroplast microsatellites. Genetics 153:943–947
Putney SD, Herlihy WC, Schimmel P (1983) A new troponin T and cDNA clones for 13 different muscle protein, found shot gun sequencing. Nature 302:718–721
Qi X, Stam P, Lindhout P (1998) Use of locus-specific markers to construct a high density map in barley. Theor Appl Genet 96:376–384
Reed DH, Frankham R (2003) Correlation between fitness and genetic diversity. Cons Biol 17:230–237
Richard I, Beckman JS (1995) How neutral are synonymous codon mutations? Nat Genet 10:259
Russell J, Booth A, Fuller J, Harrower B, Hedley P, Machray G, et al (2004) A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome. Genome 47:389–398
Saideswara Y, Rao S, Rao SA et al (1989) New evidence on the phylogeny basic chromosome number in Pennisetum. Curr Sci 58:869–872
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467
Schlotterer C, Tautz D (1992) Slippage synthesis of simple sequence DNA. Nucleic Acids Res 20:2211–2215
Shaw J, Lickey EB, Beck JT et al (2005) The tortoise and Hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot 92:142–166
Simons G, Van der Lee T, Diergaarde P et al (1997) AFLP-based fine mapping of the Mlo gene to a 30-kb DNA segment of the barley genome. Genomics 44:61–70
Sobrino B, Briona M, Carracedoa A (2005) SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int 154:181–194
Song Y, Wang Z, Bo W et al (2012) Transcriptional profiling by cDNA-AFLP analysis showed differential transcript abundance in response to water stress in Populus hopeiensis. BMC Genom 13:286
Southern E (1975) Detection of specific sequences among DNA fragments separated by gel-electrophoresis. J Mol Biol 98:503
Spooner D, Van Treuren R, De Vicente MC (2005) Molecular markers for Genebank Management. IPGRI Technical Bulletin No. 10, 2005
Stoecklem M (2003) Taxonomy, DNA, and the bar code of life. Bioscience 53:796–797
Sumner AT (1990) Chromosome banding. Unwin Hyman, London UK
Sunyaev S, Hanke J, Aydin A et al (1999) Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes. J Mol Med 77:754–760
Suoniemi A, Anamthawat-Jonsson K, Arna T et al (1996) Retrotransposon BARE-1 is a major, dispersed component of the barley (Hordeum vulgare L.) genome. Plant Mol Biol 30:1321–1329
Syvänen AC (2001) Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet 2:930–942
Taberlet P, Griffin S, Goossens B et al (1996) Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res 24(16):3189–3194
Tautz D, Arctander P, Minelli A et al (2002) DNA points the way ahead in taxonomy. Nature 418:479
Torres AM, Millan T, Cubero JI (1993) Identifying rose cultivars using random amplified polymorphic DNA markers. Hort Sci 28:333–334
Ude GN, Kenworthy WJ, Costa JM et al (2003) Genetic diversity of soybean cultivars from China, Japan, North America and North American ancestral lines determined by Amplified Fragment Length Polymorphism. Crop Sci 43:1858–1867
Vasemagi A (2005) Expressed sequence tag (EST) linked microsatellites as a source of gene associated polymorphisms for detecting signatures of divergent selection in Atlantic salmon (Salmo salar L.). Mol Biol Evol 22:1067–1076
Viegas-P´equignot E, Dutrillaux B (1978) Une methode simple pour obtenir des prophases et des prom´etaphases. Ann Genet 21:122–125
Volis S, Mendlinger S, Turuspekov Y et al (2001) Allozyme variation in Turkmenistan populations of wild barley, Hordeum spontaneum. Koch Ann Bot 87:435–446
Vos P, Hogers R, Bleeker M, Reijans M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414
Voytas DF, Cummings MP, Konieczny A et al (1992) Copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USA 89:7124–7128
Waugh R, Bonar N, Baird E et al (1997) Homology of AFLP products in three mapping populations of barley. Mol Gen Genet 255:311–321
Weising K, Nybom H, Wolff K, Meyer W (1995) In: Arbor A (ed) DNA finger printing in plants and fungi. CRC Press, Boca Raton, p 1–3
Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218
Wenzl P, Carling J, Kudrna D et al (2004) Diversity array technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci USA 101:9915–9920
Werner M, Herbon N, Gohlke H et al (2004) Asthma is associated with single-nucleotide polymorphisms in ADAM33. Clin Exp Allergy 34:26–31
Werner M, Sych M, Herbon N et al (2002) Large-scale determination of SNP allele frequencies in DNA pools using MALDI-TOF mass spectrometry. Hum Mutat 20:57–64
Williams JGK, Kubelik AR, Livak KJ et al (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl Acids Res 18:6531–6535
Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1991) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535
Xiao X, Li H, Tang C (2009) A silver-staining cDNA-AFLP protocol suitable for transcript profiling in the latex of Hevea brasiliensis (para rubber tree). Mol Biotechnol 42:91–99
Yang F, Alkalaeva EZ, Perelman PL et al (2003) Reciprocal chromosome painting among human, aardvark and elephant (superorder Afrotheria) reveals likely eutherian ancestral karyotype. Proc Natl Acad Sci USA 100:1062–1066
Yu J, Hu S, Wang J et al (2002) A draft sequence of the rice Genome (Oryza sativa L. ssp. indica. Science 296:79–92
Zabeau M, Vos P (1992) Selective restriction fragment amplification: a general method for DNA fingerprinting. European Patent EP0534858
Zalapa JE, Cuevas H, Zhu H et al (2012) Using next-generation sequencing approaches for the isolation of simple sequence repeat (SSR) loci in the plant sciences. Am J Bot 99:193–208
Zouros E, Foltz DW (1987) The use of allelic isozyme variation for the study of heterosis. Isozymes 13:1–59
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Mondini, L., Pagnotta, M.A. (2015). Using Molecular Techniques to Dissect Plant Genetic Diversity. In: Ahuja, M., Jain, S. (eds) Genetic Diversity and Erosion in Plants. Sustainable Development and Biodiversity, vol 7. Springer, Cham. https://doi.org/10.1007/978-3-319-25637-5_6
Download citation
DOI: https://doi.org/10.1007/978-3-319-25637-5_6
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-25635-1
Online ISBN: 978-3-319-25637-5
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)