Abstract
Markers are essential for categorising the living creatures. Starting from using visible features, science made the hidden characters visible, eventually using the material of inheritance, the DNA as source of markers. This chapter allows an insight into the different types of DNA based marker systems, guiding the reader through marker systems either with or without preliminary sequence information, with low and the nowadays so powerful high throughput technologies.
Communicated by Francisco M Cánovas
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References
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
Balsalobre TWA, da Silva Pereira G, Margarido GRA et al (2017) GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane. BMC Genomics 18:72. doi:10.1186/s12864-016-3383-x
Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51:910–918
Behjati S, Tarpey PS (2013) What is next generation sequencing? Arch Dis Child Educ Pract Ed 98:236–238. doi:10.1136/archdischild-2013-304340
Bendich AJ (1987) Why do chloroplasts and mitochondria contain so many copies of their genome? Bioessays 6:279–282
Caetano-Anollés G, Bassam BJ, Gresshoff PM (1991) DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Nat Biotechnol 9:553–557. doi:10.1038/nbt0691-553
Cao M, Shi J, Wang J, Hong J, Cui B, Ning G (2015) Analysis of human triallelic SNPs by next-generation sequencing. Ann Hum Genet 79:275–281. doi:10.1111/ahg.12114
Chen X, Sullivan PF (2003) Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. Pharmacogenomics J 3:77–96. doi:10.1038/sj.tpj.6500167
Davey JW, Blaxter ML (2010) RADSeq: next-generation population genetics. Brief Funct Genomics 9:416–423. doi:10.1093/bfgp/elq031
Demesure B, Sodzi N, Petit R (1995) A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Mol Ecol 4:129–134
Deschamps S, Llaca V, May GD (2012) Genotyping-by-sequencing in plants. Biology 1:460–483. doi:10.3390/biology1030460
Diekmann S (1989) The migration anomaly of DNA fragments in polyacrylamide gels allows the detection of small sequence-specific DNA structure variations. Electrophoresis 10:354–359
Ebert D, Peakall R (2009) Chloroplast simple sequence repeats (cpSSRs): technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species. Mol Ecol Resour 9:673–690. doi:10.1111/j.1755-0998.2008.02319.x
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. doi:10.1371/journal.pone.0019379
Evans TG (2015) Considerations for the use of transcriptomics in identifying the ‘genes that matter’ for environmental adaptation. J Exp Biol 218:1925–1935. doi:10.1242/jeb.114306
Fauré S, Noyer JL, Carreel F, Horry JP, Bakry F, Lanaud C (1994) Maternal inheritance of chloroplast genome and paternal inheritance of mitochondrial genome in bananas (Musa acuminata). Curr Genet 25:265–269
Fumagalli M, Vieira FG, Korneliussen TS, Linderoth T, Huerta-Sánchez E, Albrechtsen A, Nielsen R (2013) Quantifying population genetic differentiation from next-generation sequencing data. Genetics 195:979–992. doi:10.1534/genetics.113.154740
Ganal MW, Polley A, Graner EM, Plieske J, Wieseke R, Luerssen H, Durstewitz G (2012) Large SNP arrays for genotyping in crop plants. J Biosci 37(5):821–828
Gore MA, Wright MH, Ersoz ES, Bouffard P, Szekeres ES, Jarvie TP, Hurwitz BL, Narechania A, Harkins TT, Grills GS, Ware DH, Buckler ES (2009) Large-scale discovery of gene-enriched SNPs. Plant Gen 2:121–133
Hayden MJ, Sharp PJ (2001) Sequence-tagged microsatellite profiling (STMP): a rapid technique for developing SSR markers. Nucleic Acids Res 29:E43–E43
He J, Zhao X, Laroche A, Lu Z-X, Liu HK, Li Z (2014) Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci. doi:10.3389/fpls.2014.00484
Heinze B (2007) A database of PCR primers for the chloroplast genomes of higher plants. Plant Methods 3:4. doi:10.1186/1746-4811-3-4
Heslop-Harrison JS, Schmidt T (2012) Plant nuclear genome composition. In: eLS. Wiley Online Library. doi:10.1002/9780470015902.a0002014.pub2
Jiang Z, Wang H, Michal JJ, Zhou X, Liu B, Woods LCS, Fuchs RA (2016) Genome wide sampling sequencing for SNP genotyping: methods, challenges and future development. Int J Biol Sci 12:100–108. doi:10.7150/ijbs.13498
Liu J, Huang S, Sun M, Liu S, Liu Y, Wang W, Xiurong Zhang X, Wang H, Hua W (2012) An improved allele-specific PCR primer design method for SNP marker analysis and its application. Plant Methods 8:34. doi:10.1186/1746-4811-8-34
Maughan PJ, Yourstone SM, Jellen EN, Udall JA (2009) SNP discovery via genomic reduction, barcoding and 454-pyrosequencing in amaranth. Plant Gen 2:260–270
Maughan PJ, Yourstone SM, Byers RL, Smith SM, Udall JA (2010) Single-nucleotide polymorphism genotyping in mapping populations via genomic reduction and next-generation sequencing: proof of concept. Plant Gen. doi:10.3835/plantgenome2010.07.0016
Mullaney JM, Mills RE, Pittard WS, Devine SE (2010) Small insertions and deletions (INDELs) in human genomes. Hum Mol Genet 19:R131–R136. doi:10.1093/hmg/ddq400
Oda K, Yamato K, Ohta E, Nakamura Y, Takemura M, Nozato N, Akashi K, Kanegae T, Ogura Y, Kohchi T, Ohyama K (1992) Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. J Mol Biol 223:1–7. doi:10.1016/0022-2836(92)90708-R
Pootakham W, Shearman JR, Ruang-areerate P et al (2014) Large-scale SNP discovery through RNA sequencing and SNP genotyping by targeted enrichment sequencing in cassava (Manihot esculenta Crantz). PLoS One 9(12):e116028. doi:10.1371/journal.pone.0116028
Rabinowicz PD, Citek R, Budiman MA et al (2005) Differential methylation of genes and repeats in land plants. Genome Res 15:1431–1440
Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100. doi:10.1016/S1369-5266(02)00240-6
Rasmusson AG, Møller IM (2015) The genetic system in plant mitochondria has several special features. In: Taiz L, Zeiger E, Møller IM, Murphy A (eds) Plant physiology and development, 6th edn. Topic 12.6 published by Sinauer Associates
Reddy MP, Sarla N, Siddiq EA (2002) Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica 128:9–17
Rogers SM, Payton M, Allen RW, Melcher U, Carver J, Fletcher J (2012) Method: a single nucleotide polymorphism genotyping method for wheat streak mosaic virus. Investigative Genet 3:10. doi:10.1186/2041-2223-3-10
Shen R, Fan J-B, Campbell D, Jing W, Chang W, Chen J, Doucet D, Yeakley J, Bibikova M, Wickham Garcia ME, McBride C, Steemers F, Garcia F, Kermani BG, Gunderson K, Oliphant A (2005) High-throughput SNP genotyping on universal bead arrays. Mutat Res 573:70–82. doi:10.1016/j.mrfmmm.2004.07.022
Syed NH, Flavell AJ (2006) Sequence-specific amplification polymorphisms (SSAPs): a multi-locus approach for analyzing transposon insertions. Nat Protoc 1:2746–2752
Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109
Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471
Twyford AD, Ennos RA (2012) Next-generation sequencing as a tool for plant ecology and evolution. Plant Ecol Divers 5:411–413. doi:10.1080/17550874.2012.754513
Vartia S, Villanueva-Cañas JS, Finarelli J, Farrell ED et al (2016) A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding. R Soc Open Sci 3:150565. doi:10.1098/rsos.150565
Verma S, Gupta S, Bandhiwal N, Kumar T, Bharadwaj C, Bhatia S (2015) High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using genotyping-by-sequencing (GBS). Sci Rep 5:17512. doi:10.1038/srep17512
Vos P, Hogers R, Bleeker M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414. doi:10.1093/nar/23.21.4407
Wang Z, Gerstein M, Snyder M (2009) RNA-seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63. doi:10.1038/nrg2484
Weising K, Nybom H, Wolff K, Kahl G (2005) Properties of RAPD markers. In: DNA fingerprinting in plants. CRC Press, Taylor & Francis Group, p 37
Williams JGK, 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
Wischnitzki E, Sehr EM, Hansel-Hohl K, Berenyi M, Burg K, Fluch S (2015) How to isolate a plant’s hypomethylome in one shot. Biomed Res Int 2015:570568. doi:10.1155/2015/570568
Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, McCown B, Harbut R, Simon P (2012) Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot 99:193–208. doi:10.3732/ajb.1100394
Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176–183
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Burg, K. (2017). Molecular Markers for Genetic Diversity. In: Cánovas, F., Lüttge, U., Matyssek, R. (eds) Progress in Botany Vol. 79. Progress in Botany, vol 79. Springer, Cham. https://doi.org/10.1007/124_2017_9
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DOI: https://doi.org/10.1007/124_2017_9
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