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Discovery and Role of Molecular Markers Involved in Gene Mapping, Molecular Breeding, and Genetic Diversity

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 provides 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.

Keywords

  • Biochemical marker
  • Molecular marker
  • RFLP
  • RAPD
  • SSR
  • SNP
  • Population mapping
  • Plant breeding
  • QTL
  • GWAS

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References

  • Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant cell reports 27:617–31

    Google Scholar 

  • Allegre M, Argout X, Boccara M, Fouet O, Roguet Y, Bérard A, Thévenin 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 19:23–35

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 46:195–200

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 407:513–516

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 43:101–108

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 17:57–74

    PubMed  Google Scholar 

  • 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

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  • 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 30:1401–1411

    CAS  CrossRef  Google Scholar 

  • 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 sets—update. Nucleic Acids Res 41:D991–D995

    CAS  PubMed  CrossRef  Google Scholar 

  • Batley J, Edwards D (2016) The application of genomics and bioinformatics to accelerate crop improvement in a changing climate. Curr Opin Plant Biol 30:78–81

    PubMed  CrossRef  Google Scholar 

  • Batley J, Barker G, O’Sullivan H, Edwards KJ, Edwards D (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol 132:84–91

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Baxevanis AD, Ouellette BF (2004) Bioinformatics: a practical guide to the analysis of genes and proteins. Wiley, New York

    Google Scholar 

  • Bernardo R (2008) Molecular markers and selection for complex traits in plants: learning from the last 20 years. Crop Sci 48:1649–1664

    CrossRef  Google Scholar 

  • Bhattramakki D, Dolan M, Hanafey M, Wineland R, Vaske D, Register Iii JC, Tingey SV, Rafalski A (2002) Insertion-deletion polymorphisms in 3′ regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Mol Biol 48:539–547

    CAS  PubMed  CrossRef  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Brumfield RT, Beerli P, Nickerson DA, Edwards SV (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends Ecol Evol 18:249–256

    CrossRef  Google Scholar 

  • 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

    CrossRef  Google Scholar 

  • 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 176:685–696

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistué 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

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Collins FS, Brooks LD, Chakravarti A (1998) A DNA polymorphism discovery resource for research on human genetic variation. Genome Res 8:1229–1231

    CAS  PubMed  CrossRef  Google Scholar 

  • Condit R, Hubbell SP (1991) Abundance and DNA sequence of two-base repeat regions in tropical tree genomes. Genome 34:66–71

    CAS  PubMed  CrossRef  Google Scholar 

  • Conkle MT (1981) Isozyme variation and linkage in six conifer species. Pacific Southwest Forest and Range Experiment Station. Berkeley, California

    Google Scholar 

  • Dean A (2006) On a chromosome far, far away: LCRs and gene expression. Trends Genet 22:38–45

    CAS  PubMed  CrossRef  Google Scholar 

  • Dieringer D, Schlötterer C (2003) Two distinct modes of microsatellite mutation processes: evidence from the complete genomic sequences of nine species. Genome Res 13:2242–2251

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • 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:D951–D953

    CAS  PubMed  CrossRef  Google Scholar 

  • Edwards D, Batley J (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnol J 8:2–9

    CAS  PubMed  CrossRef  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • 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 104:399–407

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 16:191–200

    CAS  PubMed  CrossRef  Google Scholar 

  • Ganal MW, Altmann T, Röder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12:211–217

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 55:1–6

    CrossRef  Google Scholar 

  • 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 18:53–63

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Gianfranceschi L, Seglias N, Tarchini R, Komjanc M, Gessler C (1998) Simple sequence repeats for the genetic analysis of apple. Theor Appl Genet 96:1069–1076

    CAS  CrossRef  Google Scholar 

  • Goldrick MM (2001) RNase cleavage-based methods for mutation/SNP detection, past and present. Hum Mutat 18:190–204

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 19:2455–2473

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 326:1115–1117

    CAS  PubMed  CrossRef  Google Scholar 

  • Grimmer MK, Kraft T, Francis SA, Asher MJ (2008) QTL mapping of BNYVV resistance from the WB258 source in sugar beet. Plant Breed 127:650–652

    CrossRef  Google Scholar 

  • 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 270:315–323

    CAS  CrossRef  Google Scholar 

  • Gupta PK, Langridge P, Mir RR (2010) Marker-assisted wheat breeding: present status and future possibilities. Mol Breed 26:145–161

    CrossRef  Google Scholar 

  • Guryev V, Berezikov E, Cuppen E (2005) CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences. BMC Genomics 6:1

    CrossRef  CAS  Google Scholar 

  • 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

    CrossRef  CAS  Google Scholar 

  • Hack C, Kendall G (2005) Bioinformatics: current practice and future challenges for life science education. Biochem Mol Biol Educ 33:82–85

    CAS  PubMed  CrossRef  Google Scholar 

  • Hanover JW (1966) Genetics of terpenes. I. Gene control of monoterpene levels in Pinus monticola Dougl. Heredity 21:73–84

    CAS  CrossRef  Google Scholar 

  • Harry DE, Temesgen B, Neale DB (1998 Aug 1) Codominant PCR-based markers for Pinus taeda developed from mapped cDNA clones. Theor Appl Genet 97:327–336

    CAS  CrossRef  Google Scholar 

  • 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

    Google Scholar 

  • Hauge XY, Litt M (1993) A study of the origin of ‘shadow bands’ seen when typing dinucleotide repeat polymorphisms by the PCR. Hum Mol Genet 2:411–415

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 108:1212–20

    Google Scholar 

  • 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 93:1202–1210

    CAS  PubMed  CrossRef  Google Scholar 

  • Horner DS, Pavesi G, Castrignanò 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 11:181–197

    PubMed  CrossRef  CAS  Google Scholar 

  • Hu J, Vick BA (2003) Target region amplification polymorphism: a novel marker technique for plant genotyping. Plant Mol Biol Report 21:289–294

    CAS  CrossRef  Google Scholar 

  • 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 19:1068–1076

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • 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 39:131–140

    CAS  PubMed  CrossRef  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • 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 115:361–71

    Google Scholar 

  • 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

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  • Joshi SP, Ranjekar PK, Gupta VS (1999) Molecular markers in plant genome analysis. Curr Sci 77:230–240

    CAS  Google Scholar 

  • Karp A (1997) Molecular tools in plant genetic resources conservation: a guide to the technologies. Bioversity Int. IPGRI Technical Bulletin No. 2, Rome, Italy

    Google Scholar 

  • 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 120:1063–1071

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 121:599–610

    CAS  PubMed  CrossRef  Google Scholar 

  • Korbin MA, Kuras AN, Zurawicz E (2002) Fruit plant germplasm characterisation using molecular markers generated in RAPD and ISSR-PCR. Cell Mol Biol Lett 7:785–794

    CAS  PubMed  Google Scholar 

  • Kozlowski TT, Pallardy SG (1979) Stomatal responses of Fraxinus pennsylvanica seedlings during and after flooding. Physiol Plant 46:155–158

    CrossRef  Google Scholar 

  • 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 31:123–126

    CAS  PubMed  CrossRef  Google Scholar 

  • 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) 21:360–366

    CAS  Google Scholar 

  • Leal SM (2003) Genetic maps of microsatellite and single-nucleotide polymorphism markers: are the distances accurate? Genet Epidemiol 24:243–252

    PubMed  CrossRef  Google Scholar 

  • 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 117:721–728

    CAS  PubMed  CrossRef  Google Scholar 

  • Levinson G, Gutman GA (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4:203–221

    CAS  PubMed  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • 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 103:455–461

    CAS  CrossRef  Google Scholar 

  • 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 17:787–798

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 89:481–487

    CAS  PubMed  Google Scholar 

  • 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 17:292–296

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 256:25–31

    CAS  CrossRef  Google Scholar 

  • Malik A (2016) Genomics resources for plants. In Hakeem KR, Tombuloğlu H, Tombuloğlu G (eds) Plant omics: trends and applications. Springer Switzerland, 29–57  

    Google Scholar 

  • Mammadov JA, Chen W, Ren R, Pai R, Marchione W, Yalçin 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 121:577–588

    CAS  PubMed  CrossRef  Google Scholar 

  • Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S (2012) SNP markers and their impact on plant breeding. Int J Plant Genomics 2012:1–11

    CrossRef  CAS  Google Scholar 

  • Maphosa M, Talwana H, Tukamuhabwa P (2012) Enhancing soybean rust resistance through Rpp2, Rpp3 and Rpp4 pair wise gene pyramiding. Afr J Agric Res 30:4271–4277

    Google Scholar 

  • 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 114:487–500

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 91:5466–5470

    CAS  CrossRef  Google Scholar 

  • Matus IA, Hayes PM (2002) Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats. Genome 45:1095–1106

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 60:524–535

    CrossRef  Google Scholar 

  • 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 84:1316–1321

    CAS  CrossRef  Google Scholar 

  • 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

    Google Scholar 

  • 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 17:240–248

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Moose SP, Mumm RH (2008) Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol 147:969–977

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Morgante M, Rafalski A, Biddle P, Tingey S, Olivieri AM (1994) Genetic mapping and variability of seven soybean simple sequence repeat loci. Genome 37:763–769

    CAS  PubMed  CrossRef  Google Scholar 

  • Mueller UG, Wolfenbarger LL (1999) AFLP genotyping and fingerprinting. Trends Ecol Evol 14:389–394

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 21:2395–2398

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Nordborg M, Weigel D (2008) Next-generation genetics in plants. Nature 456:720–723

    CAS  PubMed  CrossRef  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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 86:2766–2770

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N (2010) ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res 39(suppl_1):D1002–D1004

    Google Scholar 

  • 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 97:735–743

    CAS  CrossRef  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Pop M, Salzberg SL (2008) Bioinformatics challenges of new sequencing technology. Trends Genet 24:142–149

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222

    CrossRef  Google Scholar 

  • Pratap A, Gupta SK, Kumar J, Solanki RK (2012) Soybean. In: Technological innovations in major world oil crops, vol 1. Springer, New York, p 293–321

    Google Scholar 

  • 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 8:807–814

    PubMed  PubMed Central  CrossRef  Google Scholar 

  • 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

    Google Scholar 

  • 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 274:515–527

    CAS  CrossRef  Google Scholar 

  • Roy JK, Smith KP, Muehlbauer GJ, Chao S, Close TJ, Steffenson BJ (2010) Association mapping of spot blotch resistance in wild barley. Mol Breed 26:243–256

    PubMed  PubMed Central  CrossRef  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Sallaud C, Lorieux M, Roumen E, Tharreau D, Berruyer R, Svestasrani P, Garsmeur O, Ghesquière 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 106:794–803

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 11:651–657

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • 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 100:723–726

    CAS  CrossRef  Google Scholar 

  • Semagn K, Bjørnstad Å, Ndjiondjop MN (2006) An overview of molecular marker methods for plants. Afr J Biotechnol 5:2540

    CAS  Google Scholar 

  • 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 14:3109–3121

    CAS  PubMed  CrossRef  Google Scholar 

  • Squillace AE (1971) Inheritance of monoterpene composition in cortical oleoresin of slash pine. For Sci 17:381–387

    CAS  Google Scholar 

  • 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 28:187–195

    CAS  CrossRef  Google Scholar 

  • 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 85:3898–3902

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Syvänen AC (1999) From gels to chips: “minisequencing” primer extension for analysis of point mutations and single nucleotide polymorphisms. Hum Mutat 13:1–0

    PubMed  CrossRef  Google Scholar 

  • 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

    CrossRef  CAS  Google Scholar 

  • Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127–4138

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Temesgen B, Neale DB, Harry DE (2000) Use of haploid mixtures and heteroduplex analysis enhance polymorphisms revealed by denaturing gradient gel electrophoresis. BioTechniques 28:114–116

    CAS  PubMed  Google Scholar 

  • 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 11:1441–1452

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Terwilliger JD, Haghighi F, Hiekkalinna TS, Göring HH (2002) A bias-ed assessment of the use of SNPs in human complex traits. Curr Opin Genet Dev 12:726–734

    CAS  PubMed  CrossRef  Google Scholar 

  • Tohme J, Gonzalez D, Beebe S, Duque MC (1996) AFLP analysis of gene pools of a wild bean core collection. Crop Sci 36:1375–1384

    CAS  CrossRef  Google Scholar 

  • Tóth G, Gáspári Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10:967–981

    PubMed  PubMed Central  CrossRef  Google Scholar 

  • 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 5:735–745

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 94:764–772

    CAS  CrossRef  Google Scholar 

  • 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

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  • 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, 119–142

    Google Scholar 

  • Vassilev D, Leunissen J, Atanassov A, Nenov A, Dimov G (2005) Application of bioinformatics in plant breeding. Biotechnol Biotechnol Equip 19:139–152

    CrossRef  Google Scholar 

  • 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 23:4407–4414

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Voss-Fels K, Snowdon RJ (2015) Understanding and utilizing crop genome diversity via high-resolution genotyping. Plant Biotechnol J 14:1086–1094

    Google Scholar 

  • Vuylsteke M, Mank R, Antonise R, Bastiaans E, Senior ML, Stuber CW, Melchinger AE, Lübberstedt T, Xia XC, Stam P, Zabeau M (1999) Two high-density AFLP® linkage maps of Zea mays L.: analysis of distribution of AFLP markers. Theor Appl Genet 99:921–935

    CAS  CrossRef  Google Scholar 

  • Wang Z, Weber JL, Zhong G, Tanksley SD (1994) Survey of plant short tandem DNA repeats. Theor Appl Genet 88:1–6

    CAS  PubMed  Google Scholar 

  • Wang L, Li P, Brutnell TP (2010) Exploring plant transcriptomes using ultra high-throughput sequencing. Brief Funct Genomics 9:118–128

    CAS  PubMed  CrossRef  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • van de Wiel C, Arens P, Vosman B (1999) Microsatellite retrieval in lettuce (Lactuca sativa L.) Genome 42:139–149

    PubMed  CrossRef  Google Scholar 

  • 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 18:6531–6535

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Wu KS, Tanksley SD (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genetics MGG 241:225–235

    Google Scholar 

  • Xiao W, Oefner PJ (2001) Denaturing high-performance liquid chromatography: a review. Hum Mutat 17:439–474

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 169:1683–1697

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    PubMed  PubMed Central  CrossRef  Google Scholar 

  • 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 296:79–92

    CAS  PubMed  CrossRef  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • 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

    CAS  CrossRef  Google Scholar 

  • Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176–183

    CAS  PubMed  CrossRef  Google Scholar 

  • 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 1:851–857

    CAS  PubMed  CrossRef  Google Scholar 

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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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