Abstract
Genetic markers have transformed the understanding of genetic studies which facilitate the implementation of gene mapping and molecular breeding in plants. The advancement of molecular markers from few decades has paved the way for highly stable and resistant crop varieties. Uses of highly polymorphic molecular markers such as single-nucleotide polymorphisms (SNPs) and simple sequence repeat (SSR) together with high-throughput technologies are preferred choice in quantitative trait loci (QTL) gene discovery and plant breeding. Next-generation sequencing is an important tool for discovery and validation of genetic markers. QTL and genome-wide association mapping providesĀ a detailed view of molecular markers and linked genes which inherit together in each generation. This chapter delivers an in-depth knowledge of molecular genetic markers, from their history to its application in the field of gene mapping, molecular breeding, and genetic diversity. Furthermore, comparisons of molecular markers are also discussed robustly.
References
Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant cell reports 27:617ā31
Allegre M, Argout X, Boccara M, Fouet O, Roguet Y, BĆ©rard A, ThĆ©venin JM, Chauveau A, Rivallan R, Clement D, Courtois B (2012) Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L. DNA Res 19:23ā35
Allentoft ME, Schuster S, Holdaway R, Hale M, McLay E, Oskam CL, Gilbert MT, Spencer P, Willerslev E, Bunce M (2009) Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data. BioTechniques 46:195ā200
Altshuler D, Pollara VJ, Cowles CR, Van Etten WJ, Baldwin J, Linton L, Lander ES (2000) An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407:513ā516
Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M (2011) The genome of Theobroma cacao. Nat Genet 43:101ā108
Ashkani S, Yusop MR, Shabanimofrad M, Azadi A, Ghasemzadeh A, Azizi P, Latif MA (2015) Allele mining strategies: principles and utilisation for blast resistance genes in rice (Oryza sativa L.) Curr Issues Mol Biol 17:57ā74
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376
Baldwin S, Pither-Joyce M, Wright K, Chen L, McCallum J (2012) Development of robust genomic simple sequence repeat markers for estimation of genetic diversity within and among bulb onion (Allium cepa L.) populations. Mol Breed 30:1401ā1411
Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A (2013) NCBI GEO: archive for functional genomics data setsāupdate. Nucleic Acids Res 41:D991āD995
Batley J, Edwards D (2016) The application of genomics and bioinformatics to accelerate crop improvement in a changing climate. Curr Opin Plant Biol 30:78ā81
Batley J, Barker G, OāSullivan H, Edwards KJ, Edwards D (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol 132:84ā91
Baxevanis AD, Ouellette BF (2004) Bioinformatics: a practical guide to the analysis of genes and proteins. Wiley, New York
Bernardo R (2008) Molecular markers and selection for complex traits in plants: learning from the last 20 years. Crop Sci 48:1649ā1664
Bhattramakki D, Dolan M, Hanafey M, Wineland R, Vaske D, Register Iii JC, Tingey SV, Rafalski A (2002) Insertion-deletion polymorphisms in 3ā² regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Mol Biol 48:539ā547
Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314
Brumfield RT, Beerli P, Nickerson DA, Edwards SV (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends Ecol Evol 18:249ā256
Ching AD, Caldwell KS, Jung M, Dolan M, Smith O, Tingey S, Morgante M, Rafalski AJ (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 3:1
Choi IY, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, Chase K, Lark KG, Reiter RS, Yoon MS, Hwang EY (2007) A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176:685ā696
Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, CistuƩ L, Corey A, Filichkina T, Johnson EA, Hayes PM (2011) Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC Genomics 12:4
Collins FS, Brooks LD, Chakravarti A (1998) A DNA polymorphism discovery resource for research on human genetic variation. Genome Res 8:1229ā1231
Condit R, Hubbell SP (1991) Abundance and DNA sequence of two-base repeat regions in tropical tree genomes. Genome 34:66ā71
Conkle MT (1981) Isozyme variation and linkage in six conifer species. Pacific Southwest Forest and Range Experiment Station. Berkeley, California
Dean A (2006) On a chromosome far, far away: LCRs and gene expression. Trends Genet 22:38ā45
Dieringer D, Schlƶtterer C (2003) Two distinct modes of microsatellite mutation processes: evidence from the complete genomic sequences of nine species. Genome Res 13:2242ā2251
Duran C, Appleby N, Clark T, Wood D, Imelfort M, Batley J, Edwards D (2009) AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants. Nucleic Acids Res 37:D951āD953
Edwards D, Batley J (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnol J 8:2ā9
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379
Eujayl I, Sorrells ME, Baum M, Wolters P, Powell W (2002) Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor Appl Genet 104:399ā407
FAO (2004) Scientific facts on genetically modified crops. GreenFacts, https://www.greenfacts.org/en/gmo/
Fischer SG, Lerman LS (1979) Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis. Cell 16:191ā200
Ganal MW, Altmann T, Rƶder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12:211ā217
Gao J, Zhang S, Qi L, Zhang Y, Wang C, Song W, Han S (2006) Application of ISSR markers to fingerprinting of elite cultivars (varieties/clones) from different sections of the genus Populus L. Silvae Genet 55:1ā6
Garg R, Patel RK, Tyagi AK, Jain M (2011) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res 18:53ā63
Gianfranceschi L, Seglias N, Tarchini R, Komjanc M, Gessler C (1998) Simple sequence repeats for the genetic analysis of apple. Theor Appl Genet 96:1069ā1076
Goldrick MM (2001) RNase cleavage-based methods for mutation/SNP detection, past and present. Hum Mutat 18:190ā204
Gompert Z, Forister ML, Fordyce JA, Nice CC, Williamson RJ, Alex BC (2010) Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies. Mol Ecol 19:2455ā2473
Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH (2009) A first-generation haplotype map of maize. Science 326:1115ā1117
Grimmer MK, Kraft T, Francis SA, Asher MJ (2008) QTL mapping of BNYVV resistance from the WB258 source in sugar beet. Plant Breed 127:650ā652
Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Gen Genomics 270:315ā323
Gupta PK, Langridge P, Mir RR (2010) Marker-assisted wheat breeding: present status and future possibilities. Mol Breed 26:145ā161
Guryev V, Berezikov E, Cuppen E (2005) CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences. BMC Genomics 6:1
Ha BK, Hussey RS, Boerma HR (2007) Development of SNP assays for marker-assisted selection of two southern root-knot nematode resistance QTL in soybean. Crop Sci 47:S-73
Hack C, Kendall G (2005) Bioinformatics: current practice and future challenges for life science education. Biochem Mol Biol Educ 33:82ā85
Hanover JW (1966) Genetics of terpenes. I. Gene control of monoterpene levels in Pinus monticola Dougl. Heredity 21:73ā84
Harry DE, Temesgen B, Neale DB (1998 Aug 1) Codominant PCR-based markers for Pinus taeda developed from mapped cDNA clones. Theor Appl Genet 97:327ā336
Hashimoto K, Hashimoto M, Mishiro S, Oota Y, inventors (2002) Method of detecting nucleic acid relating to disease. United States patent application US 10/070,415
Hauge XY, Litt M (1993) A study of the origin of āshadow bandsā seen when typing dinucleotide repeat polymorphisms by the PCR. Hum Mol Genet 2:411ā415
Hayashi K, Hashimoto N, Daigen M, Ashikawa I (2004) Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theor Appl Genet 108:1212ā20
Hill M, Witsenboer H, Zabeau M, Vos P, Kesseli R, Michelmore R (1996) PCR-based fingerprinting using AFLPs as a tool for studying genetic relationships in Lactuca spp. Theor Appl Genet 93:1202ā1210
Horner DS, Pavesi G, CastrignanĆ² T, De Meo PD, Liuni S, Sammeth M, Picardi E, Pesole G (2009) Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief Bioinform 11:181ā197
Hu J, Vick BA (2003) Target region amplification polymorphism: a novel marker technique for plant genotyping. Plant Mol Biol Report 21:289ā294
Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, Weng Q, Huang T, Dong G (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068ā1076
Iannone MA, Taylor JD, Chen J, Li MS, Rivers P, Slentz-Kesler KA, Weiner MP (2000) Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry. Cytometry 39:131ā140
Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29:e25
Jones ES, Sullivan H, Bhattramakki D, Smith JS (2007) A comparison of simple sequence repeat and single nucleotide polymorphism marker technologies for the genotypic analysis of maize (Zea mays L.). Theor Appl Genet 115:361ā71
James KE, Schneider H, Ansell SW, Evers M, Robba L, Uszynski G, Pedersen N, Newton AE, Russell SJ, Vogel JC, Kilian A (2008) Diversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms. PLoS One 3:e1682
Joshi SP, Ranjekar PK, Gupta VS (1999) Molecular markers in plant genome analysis. Curr Sci 77:230ā240
Karp A (1997) Molecular tools in plant genetic resources conservation: a guide to the technologies. Bioversity Int. IPGRI Technical Bulletin No. 2, Rome, Italy
Kim KS, Bellendir S, Hudson KA, Hill CB, Hartman GL, Hyten DL, Hudson ME, Diers BW (2010a) Fine mapping the soybean aphid resistance gene Rag1 in soybean. Theor Appl Genet 120:1063ā1071
Kim KS, Hill CB, Hartman GL, Hyten DL, Hudson ME, Diers BW (2010b) Fine mapping of the soybean aphid-resistance gene Rag2 in soybean PI 200538. Theor Appl Genet 121:599ā610
Korbin MA, Kuras AN, Zurawicz E (2002) Fruit plant germplasm characterisation using molecular markers generated in RAPD and ISSR-PCR. Cell Mol Biol Lett 7:785ā794
Kozlowski TT, Pallardy SG (1979) Stomatal responses of Fraxinus pennsylvanica seedlings during and after flooding. Physiol Plant 46:155ā158
Kwok PY, Deng Q, Zakeri H, Taylor SL, Nickerson DA (1996) Increasing the information content of STS-based genome maps: identifying polymorphisms in mapped STSs. Genomics 31:123ā126
Kwon SJ, Hong SW, Son JH, Lee JK, Cha YS, Eun MY, Kim NS (2006) CACTA and MITE transposon distributions on a genetic map of rice using F 15 RILs derived from Milyang 23 and Gihobyeo hybrids. Mol Cells (Springer Science & Business Media BV) 21:360ā366
Leal SM (2003) Genetic maps of microsatellite and single-nucleotide polymorphism markers: are the distances accurate? Genet Epidemiol 24:243ā252
Lehmensiek A, Sutherland MW, McNamara RB (2008) The use of high resolution melting (HRM) to map single nucleotide polymorphism markers linked to a covered smut resistance gene in barley. Theor Appl Genet 117:721ā728
Levinson G, Gutman GA (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4:203ā221
Li H, Durbin R (2009) Fast and accurate short read alignment with BurrowsāWheeler transform. Bioinformatics 25:1754ā1760
Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet 103:455ā461
Lidholm J, Gustafsson P (1991) Homologues of the green algal gidA gene and the liverwort frxC gene are present on the chloroplast genomes of conifers. Plant Mol Biol 17:787ā798
Liu CJ, Witcombe JR, Pittaway TS, Nash M, Hash CT, Busso CS, Gale MD (1994) An RFLP-based genetic map of pearl millet (Pennisetum glaucum). Theor Appl Genet 89:481ā487
Lyamichev V, Mast AL, Hall JG, Prudent JR, Kaiser MW, Takova T, Kwiatkowski RW, Sander TJ, de Arruda M, Arco DA, Neri BP (1999) Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat Biotechnol 17:292ā296
Machugh DE, Loftus RT, Bradley DG, Sharp PM, Cunningham P (1994) Microsatellite DNA variation within and among European cattle breeds. Proc R Soc Lond B Biol Sci 256:25ā31
Malik A (2016) Genomics resources for plants. In Hakeem KR, TombuloÄlu H, TombuloÄlu G (eds) Plant omics: trends and applications. Springer Switzerland, 29ā57Ā Ā
Mammadov JA, Chen W, Ren R, Pai R, Marchione W, YalƧin 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 121:577ā588
Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S (2012) SNP markers and their impact on plant breeding. Int J Plant Genomics 2012:1ā11
Maphosa M, Talwana H, Tukamuhabwa P (2012) Enhancing soybean rust resistance through Rpp2, Rpp3 and Rpp4Ā pair wiseĀ gene pyramiding. Afr J Agric Res 30:4271ā4277
Marcel TC, Varshney RK, Barbieri M, Jafary H, De Kock MJ, Graner A, Niks RE (2007) A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues. Theor Appl Genet 114:487ā500
Maroof MS, Biyashev RM, Yang GP, Zhang Q, Allard RW (1994) Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations, and population dynamics. Proc Natl Acad Sci 91:5466ā5470
Matus IA, Hayes PM (2002) Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats. Genome 45:1095ā1106
McCouch SR, Zhao K, Wright M, Tung CW, Ebana K, Thomson M, Reynolds A, Wang D, DeClerck G, Ali ML, McClung A (2010) Development of genome-wide SNP assays for rice. Breed Sci 60:524ā535
McDermott JM, Brandle U, Dutly F, Haemmerli UA, Keller S, Muller KE, Wolfe MS (1994) Genetic variation in powdery mildew of barley: development of RAPD, SCAR, and VNTR markers. Phytopathology 84:1316ā1321
Miller MR, Atwood TS, Eames BF, Eberhart JK, Yan YL, Postlethwait JH, Johnson EA (2007a) RAD marker microarrays enable rapid mapping of zebrafish mutations. Genome Biol 8:1
Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007b) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17:240ā248
Moose SP, Mumm RH (2008) Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol 147:969ā977
Morgante M, Rafalski A, Biddle P, Tingey S, Olivieri AM (1994) Genetic mapping and variability of seven soybean simple sequence repeat loci. Genome 37:763ā769
Mueller UG, Wolfenbarger LL (1999) AFLP genotyping and fingerprinting. Trends Ecol Evol 14:389ā394
Murray V, Monchawin C, England PR (1993) The determination of the sequences present in the shadow bands of a dinucleotide repeat PCR. Nucleic Acids Res 21:2395ā2398
Nordborg M, Weigel D (2008) Next-generation genetics in plants. Nature 456:720ā723
Okii D, Chilagane LA, Tukamuhabwa P, Maphosa M (2014) Application of bioinformatics in crop improvement: annotating the putative soybean rust resistance gene Rpp3 for enhancing marker assisted selection. J Proteomics Bioinforma 7:1
Orita M, Iwahana H, Kanazawa H, Hayashi K, Sekiya T (1989) Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci 86:2766ā2770
Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N (2010) ArrayExpress updateāan archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res 39(suppl_1):D1002āD1004
Perry DJ, Bousquet J (1998) Sequence-tagged-site (STS) markers of arbitrary genes: the utility of black spruce-derived STS primers in other conifers. Theor Appl Genet 97:735ā743
Poland JA, Brown PJ, Sorrells ME, Jannink JL (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7:e32253
Pop M, Salzberg SL (2008) Bioinformatics challenges of new sequencing technology. Trends Genet 24:142ā149
Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215ā222
Pratap A, Gupta SK, Kumar J, Solanki RK (2012) Soybean. In: Technological innovations in major world oil crops, vol 1. Springer, New York, p 293ā321
Pushpendra KG, Harindra SB, Pawan LK, Neeraj K, Ajay K, Reyazul RM, Amita M, Jitendra K (2007) QTL analysis for some quantitative traits in bread wheat. J Zhejiang Univ Sci B 8:807ā814
Ramkumar G, Biswal A, Mohan KM, Sakthivel K, Sivaranjani A, Neeraja CN, Ram T, Balachandran SM, Sundaram RM, Prasad MS, Viraktamath BC (2010) Identifying novel alleles of rice blast resistance genes Pikh and Pita through allele mining. Intl Rice Res Notes 117:185
Rostoks N, Mudie S, Cardle L, Russell J, Ramsay L, Booth A, Svensson JT, Wanamaker SI, Walia H, Rodriguez EM, Hedley PE (2005) Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol Gen Genomics 274:515ā527
Roy JK, Smith KP, Muehlbauer GJ, Chao S, Close TJ, Steffenson BJ (2010) Association mapping of spot blotch resistance in wild barley. Mol Breed 26:243ā256
Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A (2003) TM4: a free, open-source system for microarray data management and analysis. BioTechniques 34:374
Sallaud C, Lorieux M, Roumen E, Tharreau D, Berruyer R, Svestasrani P, Garsmeur O, GhesquiĆØre A, Notteghem JL (2003) Identification of five new blast resistance genes in the highly blast-resistant rice variety IR64 using a QTL mapping strategy. Theor Appl Genet 106:794ā803
Saxena RK, Cui X, Thakur V, Walter B, Close TJ, Varshney RK (2011) Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea (Cajanus spp.) Funct Integr Genomics 11:651ā657
Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723ā726
Semagn K, BjĆørnstad Ć , Ndjiondjop MN (2006) An overview of molecular marker methods for plants. Afr J Biotechnol 5:2540
Slavov GT, Howe GT, Gyaourova AV, Birkes DS, Adams WT (2005) Estimating pollen flow using SSR markers and paternity exclusion: accounting for mistyping. Mol Ecol 14:3109ā3121
Squillace AE (1971) Inheritance of monoterpene composition in cortical oleoresin of slash pine. For Sci 17:381ā387
Stoehr MU, Orvar BL, Vo TM, Gawley JR, Webber JE, Newton CH (1998) Application of a chloroplast DNA marker in seed orchard management evaluations of Douglas-fir. Can J For Res 28:187ā195
Strauss SH, Palmer JD, Howe GT, Doerksen AH (1988) Chloroplast genomes of two conifers lack a large inverted repeat and are extensively rearranged. Proc Natl Acad Sci 85:3898ā3902
SyvƤnen AC (1999) From gels to chips: āminisequencingā primer extension for analysis of point mutations and single nucleotide polymorphisms. Hum Mutat 13:1ā0
Tang J, Vosman B, Voorrips RE, van der Linden CG, Leunissen JA (2006) QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species. BMC Bioinforma 7:438
Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127ā4138
Temesgen B, Neale DB, Harry DE (2000) Use of haploid mixtures and heteroduplex analysis enhance polymorphisms revealed by denaturing gradient gel electrophoresis. BioTechniques 28:114ā116
Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441ā1452
Terwilliger JD, Haghighi F, Hiekkalinna TS, Gƶring HH (2002) A bias-ed assessment of the use of SNPs in human complex traits. Curr Opin Genet Dev 12:726ā734
Tohme J, Gonzalez D, Beebe S, Duque MC (1996) AFLP analysis of gene pools of a wild bean core collection. Crop Sci 36:1375ā1384
TĆ³th G, GĆ”spĆ”ri Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10:967ā981
Travis SE, Maschinski J, Keim P (1996) An analysis of genetic variation in Astragalus cremnophylax var. cremnophylax, a critically endangered plant, using AFLP markers. Mol Ecol 5:735ā745
Tsumura Y, Suyama Y, Yoshimura K, Shirato N, Mukai Y (1997) Sequence-tagged-sites (STSs) of cDNA clones in Cryptomeria japonica and their evaluation as molecular markers in conifers. Theor Appl Genet 94:764ā772
Van Eijk MJ, Broekhof JL, van der Poel HJ, Hogers RC, Schneiders H, Kamerbeek J, Verstege E, van Aart JW, Geerlings H, Buntjer JB, van Oeveren AJ (2004) SNPWaveTM: a flexible multiplexed SNP genotyping technology. Nucleic Acids Res 32:e47
Varshney RK (2010) Gene-based marker systems in plants: high throughput approaches for marker discovery and genotyping. In Molecular techniques in crop improvement. Springer Netherlands, 119ā142
Vassilev D, Leunissen J, Atanassov A, Nenov A, Dimov G (2005) Application of bioinformatics in plant breeding. Biotechnol Biotechnol Equip 19:139ā152
Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T, Hornes M, Friters A, Pot J, Paleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407ā4414
Voss-Fels K, Snowdon RJ (2015) Understanding and utilizing crop genome diversity via high-resolution genotyping. Plant Biotechnol J 14:1086ā1094
Vuylsteke M, Mank R, Antonise R, Bastiaans E, Senior ML, Stuber CW, Melchinger AE, LĆ¼bberstedt T, Xia XC, Stam P, Zabeau M (1999) Two high-density AFLPĀ® linkage maps of Zea mays L.: analysis of distribution of AFLP markers. Theor Appl Genet 99:921ā935
Wang Z, Weber JL, Zhong G, Tanksley SD (1994) Survey of plant short tandem DNA repeats. Theor Appl Genet 88:1ā6
Wang L, Li P, Brutnell TP (2010) Exploring plant transcriptomes using ultra high-throughput sequencing. Brief Funct Genomics 9:118ā128
Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388
van de Wiel C, Arens P, Vosman B (1999) Microsatellite retrieval in lettuce (Lactuca sativa L.) Genome 42:139ā149
Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531ā6535
Wu KS, Tanksley SD (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genetics MGG 241:225ā235
Xiao W, Oefner PJ (2001) Denaturing high-performance liquid chromatography: a review. Hum Mutat 17:439ā474
Yahyaa M, Matsuba Y, Brandt W, Doron-Faigenboim A, Bar E, McClain A, Davidovich-Rikanati R, Lewinsohn E, Pichersky E, Ibdah M (2015) Identification, functional characterization, and evolution of terpene synthases from a basal dicot. Plant Physiol 169:1683ā1697
Yang W, Kang X, Yang Q, Lin Y, Fang M (2013) Review on the development of genotyping methods for assessing farm animal diversity. J Anim Sci Biotechnol 4:2
Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79ā92
Yu H, Xie W, Wang J, Xing Y, Xu C, Li X, Xiao J, Zhang Q (2011) Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers. PLoS One 6:e17595
Zhang Z, Guo X, Liu B, Tang L, Chen F (2011) Genetic diversity and genetic relationship of Jatropha curcas between China and Southeast Asian revealed by amplified fragment length polymorphisms. Afr J Biotechnol 10:2825
Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176ā183
Zimmermann P, Laule O, Schmitz J, Hruz T, Bleuler S, Gruissem W (2008) Genevestigator transcriptome meta-analysis and biomarker search using rice and barley gene expression databases. Mol Plant 1:851ā857
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Singh, A.K. (2017). Discovery and Role of Molecular Markers Involved in Gene Mapping, Molecular Breeding, and Genetic Diversity. In: Hakeem, K., Malik, A., Vardar-Sukan, F., Ozturk, M. (eds) Plant Bioinformatics. Springer, Cham. https://doi.org/10.1007/978-3-319-67156-7_12
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