DNA fingerprinting in botany: Past, present, future

Investigative Genetics

Volumn 5, Issue 1, 2014, Pages

  Nybom, Hilde ^a   Weising, Kurt ^b   Rotter, Björn ^c  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^b UNIVERSITY OF KASSEL   (Germany)

^c GENXPRO GMBH   (Germany)

Author keywords

DNA fingerprinting; Genetic mapping; Genotyping by sequencing; Microsatellites; Plants; Population genetics; Single nucleotide polymorphisms; Systematics

Indexed keywords

COMPLEMENTARY DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; BOTANY; CLEAVED AMPLIFIED POLYMORPHIC SEQUENCE; CULTIVAR; DNA FINGERPRINTING; DNA MARKER; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; FORENSIC SCIENCE; GENE FLOW; GENE MAPPING; GENETIC VARIABILITY; GENOTYPING TECHNIQUE; HIGH THROUGHPUT SEQUENCING; IN VITRO PROPAGATION; INTER SIMPLE SEQUENCE REPEAT; INTROGRESSION; LIFE HISTORY TRAIT; LONG TERMINAL REPEAT; MARKER ASSISTED BREEDING; MICROSATELLITE MARKER; MOLECULAR PHYLOGENY; NONHUMAN; OLIGONUCLEOTIDE PROBE; PHYLOGEOGRAPHY; POLYMERASE CHAIN REACTION; POLYPLOIDY; POPULATION DIFFERENTIATION; POPULATION STRUCTURE; PRIORITY JOURNAL; RANDOM AMPLIFIED POLYMORPHIC DNA; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVIEW; SEQUENCE CHARACTERIZED AMPLIFIED REGION; SIMPLE SEQUENCE REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC MUTATION; SOUTHERN BLOTTING; SPECIES DIFFERENTIATION; VEGETATIVE PROPAGATION; WILD PLANT;

EID: 84891603903     PISSN: None     EISSN: 20412223     Source Type: Journal    
DOI: 10.1186/2041-2223-5-1     Document Type: Review

References (355)

1. Hamrick JL, Godt MJW. Allozyme diversity in plant species. Plant Population Genetics, Breeding and Genetic Resources 1989, 43-63. Sunderland: Sinauer Associates, Brown AHD, Clegg MT, Kahler AL, Weir BS.
2. Tanksley SD, Young ND, Paterson AH, Bonierbale MW. RFLP mapping in plant breeding: new tools for an old science. Bio/Technology 1989, 7:257-264.
3. Hubbard M, Kelly J, Rajapakse S, Abbott A, Ballard R. Restriction fragment length polymorphisms in rose and their use for cultivar identification. HortScience 1992, 27:172-173.
4. Palmer JD, Herbon LA. Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. J Mol Evol 1988, 28:87-97. 10.1007/BF02143500, 3148746.
5. Mower JP, Touzet P, Gummow JS, Delph LF, Palmer JD. Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evol Biol 2007, 7:135. 10.1186/1471-2148-7-135, 1973135, 17688696.
6. Jeffreys AJ, Wilson V, Thein SL. Hypervariable " minisatellite" regions in human DNA. Nature 1985, 314:67-73. 10.1038/314067a0, 3856104.
7. Jeffreys AJ, Wilson V, Thein SL. Individual-specific " fingerprints" of human DNA. Nature 1985, 316:76-79. 10.1038/316076a0, 2989708.
8. Jeffreys AJ, Morton DB. DNA fingerprinting of dogs and cats. Anim Genet 1987, 18:1-15.
9. Burke T, Bruford MW. DNA fingerprinting in birds. Nature 1987, 327:149-152. 10.1038/327149a0, 3574475.
10. Dallas JF. Detection of DNA " fingerprints" of cultivated rice by hybridization with a human minisatellite DNA probe. Proc Natl Acad Sci U S A 1988, 85:6831-6835. 10.1073/pnas.85.18.6831, 282072, 2901106.
11. Ryskov AP, Jincharadze AG, Prosnyak MI, Ivanov PL, Limborska SA. M13 phage DNA as a universal marker for DNA fingerprinting of animals, plants and microorganisms. FEBS Letters 1988, 233:388-392. 10.1016/0014-5793(88)80467-8, 2838336.
12. Rogstad SH, Patton JC, Schaal BA. M13 repeat probe detects DNA minisatellite-like sequences in gymnosperms and angiosperms. Proc Natl Acad Sci U S A 1988, 85:9176-9178. 10.1073/pnas.85.23.9176, 282692, 3194419.
13. Rogstad SH, Nybom H, Schaal BA. The tetrapod DNA fingerprinting M13 repeat probe reveals genetic diversity and clonal growth in quaking aspen (Populus tremuloides, Salicaceae). Pl Syst Evol 1991, 175:115-123.
14. Nybom H, Schaal BA. DNA "fingerprints" reveal genotypic distributions in natural populations of blackberries and raspberries (Rubus, Rosaceae). Am J Bot 1990, 77:883-888.
15. Antonius K, Nybom H. DNA fingerprinting reveals significant amounts of genetic variation in a wild raspberry Rubus idaeus population. Mol Ecol 1994, 3:177-180.
16. Nybom H, Schaal BA, Rogstad SH. DNA "fingerprints" can distinguish cultivars of blackberries and raspberries. Acta Hortic 1989, 262:305-310.
17. Nybom H. DNA fingerprints in sports of 'Red Delicious' apples. HortScience 1990, 25:1641-1642.
18. Weising K, Weigand F, Driesel A, Kahl G, Zischler H, Epplen JT. Polymorphic simple GATA/GACA repeats in plant genomes. Nucleic Acids Res 1989, 17:10128-10128. 10.1093/nar/17.23.10128, 335264, 2602131.
19. Weising K, Kaemmer D, Weigand F, Epplen JT, Kahl G. Oligonucleotide fingerprinting reveals various probe-dependent levels of informativeness in chickpea (Cicer arietinum). Genome 1992, 35:436-442.
20. Kaemmer D, Afza R, Weising K, Kahl G, Nowak FJ. Oligonucleotide and amplification fingerprinting of wild species and cultivars of banana (Musa spp.). Bio/Technol 1992, 10:1030-1035.
21. Vosman B, Arens P, Ruskortekaas W, Smulders MJM. Identification of highly polymorphic DNA regions in tomato. Theor Appl Genet 1992, 85:239-244.
22. Kaemmer D, Weising K, Kahl G, Beyermann B, Börner T, Epplen JT. Oligonucleotide fingerprinting of tomato DNA. Plant Breed 1995, 114:12-17.
23. Ramakishana W, Lagu MD, Gupta VS, Ranjekar PK. DNA fingerprinting in rice using oligonucleotide probes specific for simple repetitive DNA sequences. Theor Appl Genet 1994, 88:402-406.
24. Schmidt T, Boblenz K, Metzlaff M, Kaemmer D, Weising K, Kahl G. DNA fingerprinting in sugar beet (Beta vulgaris) - identification of double haploid breeding lines. Theor Appl Genet 1993, 85:653-657.
25. Van Houten WHJ, Van Heusden AW, Rouppe Van Der Voort J, Raijmann L, Bachmann K. Hypervariable DNA fingerprint loci in Microseris pymaea (Asteraceae, Lactuceae). Bot Acta 1991, 104:252-255.
26. Weising K, Nybom H, Wolff K, Meyer W. DNA Fingerprinting in Plants and Fungi 1995, Boca Raton: CRC press.
27. Weising K, Nybom H, Wolff K, Kahl G. DNA Fingerprinting in Plants: Principles, Methods and Applications 2005, Boca Raton: Taylor & Francis/CRC press.
28. Weising K, Beyermann B, Ramser J, Kahl G. Plant DNA fingerprinting with radioactive and digoxigenated oligonucleotide probes complementary to simple repetitive DNA sequences. Electrophoresis 1991, 12:159-169. 10.1002/elps.1150120211, 2040264.
29. Parent JG, Pagé D. Identification of raspberry cultivars by nonradoactive DNA fingerprinting. HortScience 1992, 27:1108-1110.
30. Rogstad SH. Surveying plant genomes for variable number of tandem repeat loci. Molecular Evolution: Producing the Biochemical Data 1993, 224:278-294. [Methods in Enzymology, vol 224.].
31. Rogstad SH. Inheritance in turnip of variable number tandem-repeat genetic-markers revealed with synthetic repetitive DNA probes. Theor Appl Genet 1994, 89:824-830.
32. Kumar A, Rogstad SH. A hierarchical analysis of minisatellite DNA diversity in Gambel oak (Quercus gambelii Nutt.; Fagaceae). Mol Ecol 1998, 7:859-869.
33. Nybom H, Schaal BA. DNA "fingerprints" applied to paternity analysis in apples (Malus x domestica). Theor Appl Genet 1990, 79:763-768.
34. Kraft T, Nybom H, Werlemark G. Rubus vestervicensis (Rosaceae) - its hybrid origin revealed by DNA fingerprinting. Nord J Bot 1995, 15:237-242.
35. Nybom H. Evaluation of interspecific crossing experiments in facultatively apomictic blackberries (Rubus subgen. Rubus) using DNA fingerprinting. Hereditas 1995, 122:57-65.
36. Nei M, Li W-H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 1979, 76:5269-5273. 10.1073/pnas.76.10.5269, 413122, 291943.
37. Tzuri G, Hillel J, Lavi U, Haberfeld A, Vainstein A. DNA fingerprint analysis of ornamental plants. Plant Sci 1991, 76:91-97.
38. Vainstein A, Hillel J, Lavi U, Tzuri G. Assessment of genetic relatedness in carnation by DNA fingerprint analysis. Euphytica 1991, 56:225-229.
39. Nybom H, Hall HK. Minisatellite DNA "fingerprints" can distinguish Rubus cultivars and estimate their degree of relatedness. Euphytica 1991, 53:107-114.
40. Nybom H, Rogstad SH. DNA "fingerprints" detect genetic variation in Acer negundo. Pl Syst Evol 1990, 173:49-56.
41. Rogstad SH, Wolff K, Schaal BA. Geographical variation in Asimina triloba Dunal (Annonaceae) revealed by the M13 DNA fingerprinting probe. Am J Bot 1991, 78:1391-1396.
42. Wolff K, Schaal BA, Rogstad SH. Population and species variation of minisatellite DNA in Plantago. Theor Appl Genet 1994, 87:733-740.
43. Keane B, Pelikan S, Toth GP, Smith MK, Rogstad SH. Genetic diversity of Typha latifolia (Typhaceae) and the impact of pollutants examined with tandem-repetitive DNA probes. Am J Bot 1999, 86:1226-1238. 10.2307/2656770, 10487810.
44. Lim HW, Pelikan S, Rogstad SH. Genetic diversity among populations and size classes of buckeyes (Aesculus: Hippocastanaceae) examined with multilocus VNTR probes. Pl Syst Evol 2002, 230:125-141.
45. Nybom H. Applications of DNA fingerprinting in plant breeding. DNA Fingerprinting: Approaches and Applications 1991, 294-311. Basel: Birkhäuser, Burke T, Dolph G, Jeffreys AJ, Wolff R.
46. Nybom H. Applications of DNA fingerprinting in plant population studies. DNA Fingerprinting: State of the Science 1993, 293-309. Basel: Birkhäuser, Pena SDJ, Chakraborty R, Epplen JT, Jeffreys AJ.
47. Rogstad SH. Assessing genetic diversity in plants with synthetic tandem repetitive DNA probes. Genomes of Plants and Animals: 21st Stadler Genetics Symposium 1996, 1-14. New York: Plenum Press Publ. Corp, Gustafson JP, Flavell RB.
48. Weising K, Kahl G. Hybridization-based microsatellite fingerprinting of plants and fungi. Markers: Protocols, Applications, and Overviews 1998, 27-54. New York: Wiley-VCH, Caetano-Anollés G, Gresshoff PM.
49. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 1988, 239:487-491. 10.1126/science.2448875, 2448875.
50. Welsh J, McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 1990, 18:7213-7218. 10.1093/nar/18.24.7213, 332855, 2259619.
51. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 1990, 18:6231-6235. 10.1093/nar/18.21.6231, 332486, 2243771.
52. Caetano-Anollés G, Bassam BJ, Gresshoff PM. High resolution DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Bio/Technology 1991, 9:553-557. 10.1038/nbt0691-553, 1367225.
53. Zabeau M, Vos P. Selective restriction fragment amplification: a general method for DNA fingerprinting. European Patent Office, publication (0 534 858 A1). bulletin 93/13.
54. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 1995, 23:4407-4414. 10.1093/nar/23.21.4407, 307397, 7501463.
55. Gupta M, Chyi YS, Romero-Severson J, Owen JL. Amplification of DNA markers from evolutionary diverse genomes using single primers of simple-sequence repeats. Theor Appl Genet 1994, 89:998-1006.
56. Zietkiewicz E, Rafalski A, Labuda D. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 1994, 20:176-183. 10.1006/geno.1994.1151, 8020964.
57. Li G, Quiros CF. 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 2001, 103:455-461.
58. Li G, McVetty PBE, Quiros CF. SRAP molecular marker technology in plant science. Plant Breeding from Laboratories to Fields 2013, Rijeka, Croatia: InTech, Andersen SB, DOI: 10.5772/54511.
59. Hu J, Vick BA. Target region amplification polymorphism: a novel marker technique for plant genotyping. Plant Mol Biol Rep 2003, 21:289-294.
60. Witsenboer H, Vogel J, Michelmore RW. Identification, genetic localization, and allelic diversity of selectively amplified microsatellite polymorphic loci in lettuce and wild relatives (Lactuca spp.). Genome 1997, 40:923-936. 10.1139/g97-119, 18464878.
61. Zhou Z, Bebeli PJ, Somers DJ, Gustafson JP. Direct amplification of minisatellite-region DNA with VNTR core sequences in the genus Oryza. Theor Appl Genet 1997, 95:942-949.
62. Chen XM, Line RF, Leung H. Genome scanning for resistance-gene analogs in rice, barley, and wheat by high-resolution electrophoresis. Theor Appl Genet 1998, 97:345-355.
63. Jaccoud D, Peng K, Feinstein D, Kilian A. Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 2001, 29:e25. 10.1093/nar/29.4.e25, 29632, 11160945.
64. Lezar S, Myburg AA, Berger DK, Wingfield MJ, Wingfield BD. Development and assessment of microarray-based DNA fingerprinting in Eucalyptus grandis. Theor Appl Genet 2004, 109:1329-1336. 10.1007/s00122-004-1759-9, 15290050.
65. Kilian A, Wenzl P, Huttner E, Carling J, Xia L, Blois H, Caig V, Heller-Uszynska K, Jaccoud D, Hopper C, Aschenbrenner-Kilian M, Evers M, Peng K, Cayla C, Hok P, Uszynski G. Diversity Arrays Technology: a generic genome profiling technology on open platforms. Meth Mol Biol 2012, 888:67-89.
66. James KE, Schneider H, Ansell SW, Evers M, Robba L, Uszynski G, Pedersen N, Newton AE, Russell SJ, Vogel J, Kilian A. Diversity Arrays Technology (DArT) for pan-genomic evolutionary studies of non-model organisms. PLoS One 2008, 3:e1682. 10.1371/journal.pone.0001682, 2244804, 18301759.
67. Schulman AH. Molecular markers to assess genetic diversity. Euphytica 2007, 158:313-321.
68. Kalendar R, Grob T, Regina M, Suoniemi A, Schulmann A. IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 1999, 98:704-711.
69. Provan J, Thomas WTB, Forster BP, Powell W. Copia-SSR: a simple marker technique which can be used on total genomic DNA. Genome 1999, 42:363-366.
70. Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BBT, Powell W. Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol Gen Genet 1997, 253:687-694. 10.1007/s004380050372, 9079879.
71. Casa A, Brouwer C, Nagel A, Wang L, Zhang Q, Kresovich S, Wessler SR. The MITE family Heartbreaker (Hbr): molecular markers in maize. Proc Natl Acad Sci U S A 2000, 97:10083-10089. 10.1073/pnas.97.18.10083, 27704, 10963671.
72. Park KC, Kim NH, Cho YS, Kang KH, Lee JK, Kim N-S. Genetic variations of AA genome Oryza species measured by MITE-AFLP. Theor Appl Genet 2003, 197:203-209.
73. Selkoe KA, Toonen RJ. Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol Lett 2006, 9:615-629. 10.1111/j.1461-0248.2006.00889.x, 16643306.
74. Guichoux E, Lagache L, Wagner S, Chaumeil P, Léger P, Lepais O, Lepoittevin C, Malausa T, Revardel E, Salin F, Petit RJ. Current trends in microsatellite genotyping. Mol Ecol Resources 2011, 11:591-611.
75. Akkaya MS, Bhagwat AA, Cregan PB. Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 1992, 132:1131-1139. 1205234, 1459432.
76. Squirrell J, Hollingsworth PM, Woodhead M, Russell J, Lowe AJ, Gibby M, Powell W. How much effort is required to isolate nuclear microsatellites from plants?. Mol Ecol 2003, 12:1339-1348. 10.1046/j.1365-294X.2003.01825.x, 12755865.
77. Tang S, Okashah RA, Cordonnier-Pratt MM, Pratt LH, Johnson VE, Taylor CA, Arnold ML, Knapp SJ. EST and EST-SSR marker resources for Iris. BMC Plant Biol 2009, 9:72. 10.1186/1471-2229-9-72, 2703627, 19515254.
78. Thiel T, Michalek W, Varshney RK, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 2003, 106:411-422.
79. Pashley CH, Ellis JR, McCauley DE, Burke JM. EST databases as a source for molecular markers: lessons from Helianthus. J Hered 2006, 97:381-388. 10.1093/jhered/esl013, 16840524.
80. Wöhrmann T, Weising K. In silico mining for simple sequence repeat (SSR) loci in a pineapple expressed sequence tag (EST) database and cross-species amplification of EST-SSR markers across Bromeliaceae. Theor Appl Genet 2011, 123:635-647. 10.1007/s00122-011-1613-9, 21625993.
81. Varshney RK, Graner A, Sorrells ME. Genic microsatellite markers in plants: principles, methods, and applications. Trends Biotechnol 2005, 23:48-55. 10.1016/j.tibtech.2004.11.005, 15629858.
82. Paran I, Michelmore RW. Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor Appl Genet 1993, 85:985-993.
83. Bautista R, Crespillo R, Cánovas FM, Claros MG. Identification of olive-tree cultivars with SCAR markers. Euphytica 2002, 129:33-41.
84. Turkec A, Sayar M, Heinze B. Identification of sweet cherry cultivars (Prunus avium L.) and analysis of their genetic relationships by chloroplast sequence-characterised amplified regions (cpSCAR). Genet Res Crop Evol 2006, 53:1635-1641.
85. Konieczny A, Ausubel FM. A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 1993, 4:403-410. 10.1046/j.1365-313X.1993.04020403.x, 8106085.
86. Appleby N, Edwards D, Batley J. New technologies for ultra-high throughput genotyping in plants. Methods Mol Biol 2009, 513:19-39. 10.1007/978-1-59745-427-8_2, 19347650.
87. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Rev Genet 2011, 12:499-510. 10.1038/nrg3012, 21681211.
88. Martin LB, Fei Z, Giovannoni JJ, Rose JK. Catalyzing plant science research with RNA-seq. Front Plant Sci 2013, 4:66. 3612697, 23554602.
89. Picoult-Newberg L, Ideker TE, Pohl MG, Taylor SL, Donaldson MA, Nickerson DA, Boyce-Jacino M. Mining SNPs from EST databases. Genome Res 1999, 9:167-174. 310719, 10022981.
90. Ganal MW, Altmann T, Röder MS. SNP identification in crop plants. Curr Opin Plant Biol 2009, 12:1-7. 10.1016/j.pbi.2008.12.005, 19112043.
91. Ganal MW, Polley A, Graner EM, Plieske J, Wieseke R, Luerssen H, Durstewitz G. Large SNP arrays for genotyping in crop plants. J Biosci 2012, 37:821-828. 10.1007/s12038-012-9225-3, 23107918.
92. Nelson JC, Wang S, Wu Y, Li X, Antony G, White FF, Yu J. Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum. BMC Genomics 2011, 12:352. 10.1186/1471-2164-12-352, 3146956, 21736744.
93. Dumolin-Lapègue S, Pemonge MH, Petit RJ. An enlarged set of consensus primers for the study of organelle DNA in plants. Mol Ecol 1997, 6:393-397. 10.1046/j.1365-294X.1997.00193.x, 9131816.
94. Shaw J, Lickey EB, Schilling EE, Small RL. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am J Bot 2007, 94:275-288. 10.3732/ajb.94.3.275, 21636401.
95. Weising K, Gardner RC. A set of conserved PCR primers for the analysis of simple sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiosperms. Genome 1999, 42:9-19. 10.1139/g98-104, 10207998.
96. Nybom H. Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol Ecol 2004, 13:1143-1155. 10.1111/j.1365-294X.2004.02141.x, 15078452.
97. Nybom H, Weising K. DNA-based identification of clonally propagated cultivars. Plant Breed Rev 2010, 34:221-295.
98. Jones ES, Sullivan H, Bhattramaki D, Smith JSC. A comparison of simple sequence repeat and single nucleotide polymorphism marker technologies for the genotypic analysis of maize (Zea mays L.). Theor Appl Genet 2007, 115:361-371. 10.1007/s00122-007-0570-9, 17639299.
99. Hoffmann P, Blaich R, Forneck A. Retrotransposon-based mutations in clones of 'Pinot' cultivars. Acta Hortic 2009, 827:83-86.
100. Hysing S-C, Säll T, Nybom H, Liljeroth E, Merker A, Orford S, Koebner RMD. Temporal diversity changes among 198 Nordic bread wheat landraces and cultivars detected by retrotransposon-based S-SAP analysis. Plant Genet Resour Charact Utilizat 2008, 6:113-125.
101. Wegscheider E, Benjak A, Forneck A. Clonal variation in Pinot noir revealed by S-SAP involving universal retrotransposon-based sequences. Am J Enol Vitic 2009, 60:104-109.
102. Sorkheh K, Shiran B, Gradziel TM, Epperson BK, Martínez-Gomez P, Asadi E. Amplified fragment length polymorphism as a tool for molecular characterization of almond germplasm: genetic diversity among cultivated genotypes and related wild species of almond, and its relationship with agronomic traits. Euphytica 2007, 156:327-344.
103. Koopman WJM, Kuiper I, Klein-Geltink DJA, Sabatino GJH, Smulders MJM. Botanical DNA evidence in criminal cases: knotgrass (Polygonum aviculare L.) as a model species. Forensic Sci Internat Genet 2012, 6:366-374.
104. Steinger T, Korner C, Schmid B. Long-term persistence in a changing climate: DNA analysis suggests very old ages of clones of alpine Carex curvula. Oecologia 1996, 105:94-99.
105. Hollingsworth ML, Bailey JP. Evidence for massive clonal growth in the invasive weed Fallopia japonica (Japanese knotweed). Bot J Linn Soc 2000, 133:463-472.
106. Xu CY, Zhang WJ, Fu CZ, Lu BR. Genetic diversity of alligator weed in China by RAPD analysis. Biodivers Conserv 2003, 12:637-645.
107. Ren MX, Zhang QG. Clonal diversity and structure of the invasive aquatic plant Eichhornia crassipes in China. Aquatic Bot 2007, 87:242-246.
108. Hämmerli A, Reusch TBH. Inbreeding depression influences genet size distribution in a marine angiosperm. Mol Ecol 2003, 12:619-629. 10.1046/j.1365-294X.2003.01766.x, 12675818.
109. Pfeiffer T, Klahr A, Peterson A, Levichev IG, Schnittler M. No sex at all? Extremely low genetic diversity in Gagea spathacea (Liliaceae) across Europe. Flora 2012, 207:372-378.
110. van der Hulst RGM, Mes THM, Den Nijs JCM, Bachmann K. Amplified fragment length polymorphism (AFLP) markers reveal that population structure of triploid dandelions (Taraxacum officinale) exhibits both clonality and recombination. Mol Ecol 2000, 9:1-8. 10.1046/j.1365-294x.2000.00704.x, 10652071.
111. Majeský L, Vasut RJ, Kitner M, Trávnicek B. The pattern of genetic variability in apomictic clones of Taraxacum officinale indicates the alternation of asexual and sexual histories of apomicts. PLoS One 2012, 7:e41868. 10.1371/journal.pone.0041868, 3411577, 22870257.
112. Paun O, Greilhuber J, Temsch E, Hörandl E. Patterns, sources and ecological implications of clonal diversity in apomictic Ranunculus carpaticola (Ranunculus auricomus complex, Ranunculaceae). Mol Ecol 2006, 15:897-910. 10.1111/j.1365-294X.2006.02800.x, 16599955.
113. Paun O, Hörandl E. Evolution of hypervariable microsatellites in apomictic polyploid lineages of Ranunculus carpaticola: directional bias at dinucleotide loci. Genetics 2006, 174:387-398. 10.1534/genetics.105.052761, 1569770, 16783024.
114. Drummond EBM, Vellend M. Genotypic diversity effects on the performance of Taraxacum officinale populations increase with time and environmental favorability. PLOS One 2012, 7:e30314. 10.1371/journal.pone.0030314, 3277588, 22348004.
115. McLeod KA, Scascitelli M, Vellend M. Detecting small-scale genotype-environment interactions in apomictic dandelion (Taraxacum officinale) populations. J Evol Biol 2012, 25:1667-1675. 10.1111/j.1420-9101.2012.02549.x, 22694090.
116. De Andres MT, Cabezas JA, Cervera MT, Borrego J, Martínez-Zapater JM, Jouve N. Molecular characterization of grapevine rootstocks maintained in germplasm collections. Am J Enol Viticult 2007, 58:75-86.
117. Cipriani G, Marrazzo MT, Di Gaspero G, Pfeiffer A, Morgante M, Testolin R. A set of microsatellite markers with long core repeat optimized for grape (Vitis spp.) genotyping. BMC Plant Biol 2008, 8:127. 10.1186/1471-2229-8-127, 2625351, 19087321.
118. Song QJ, Quigley CV, Carter TE, Nelson RL, Boerma HR, Strachan J, Cregan PB. A selected set of trinucleotide simple sequence repeat markers for soybean cultivar identification. Plant Varieties Seeds 1999, 12:207-220.
119. Zhang DP, Mischke S, Goenaga R, Hemeida AA, Saunders JA. Accuracy and reliability of high-throughput microsatellite genotyping for cacao clone identification. Crop Sci 2006, 46:2084-2092.
120. Vélez MD, Ibánez J. Evaluation of the uniformity and stability of microsatellite markers in grapevine. Acta Hortic 2009, 827:163-168.
121. Bracci T, Sebastiani L, Busconi M, Fogher C, Belaj A, Trujillo I. SSR markers reveal the uniqueness of olive cultivars from the Italian region of Liguria. Scientia Hortic 2009, 122:209-215.
122. Cabezas JA, Ibánez J, Lijavetzky D, Vélez D, Bravo G, Rodríguez V, Carreno I, Jermakow AM, Carreno J, Ruiz-García L, Thomas MR, Martinez-Zapater JM. A 48 SNP set for grapevine cultivar identification. BMC Plant Biol 2011, 11:153. 10.1186/1471-2229-11-153, 3221639, 22060012.
123. Fujii H, Shamada T, Nonaka K, Kita M, Kuniga T, Endo T, Ikoma Y, Omura M. High-throughput genotyping in Citrus accessions using an SNP genotyping array. Tree Genet Genom 2013, 9:145-153.
124. Chebotar S, Röder MS, Korzun V, Saal B, Weber WE, Börner A. Molecular studies on genetic integrity of open-pollinating species rye (Secale cereale L.) after long-term genebank maintenance. Theor Appl Genet 2003, 107:1469-1476. 10.1007/s00122-003-1366-1, 12898026.
125. Van Hintum TJL, van de Wiel CCM, Visser DL, Van Treuren R, Vosman B. The distribution of genetic diversity in a Brassica oleracea gene bank collection related to the effects of regeneration as measured with AFLPs. Theor Appl Genet 2007, 114:777-786. 10.1007/s00122-006-0456-2, 1913180, 17273846.
126. Kopecký D, Bartos J, Christelová P, Cernoch V, Kilian A, Dolezel J. Genomic constitution of Festuca x Lolium hybrids revealed by the DArTFest array. Theor Appl Genet 2011, 122:355-363. 10.1007/s00122-010-1451-1, 20872131.
127. Nelson RL. Managing self-pollinated germplasm collections to maximize utilization. Plant Genet Resour Charact Utilizat 2011, 9:123-133.
128. Chao S, Zhang W, Akhunov E, Sherman J, Ma Y, Luo MC, Dubcovsky J. Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars. Mol Breeding 2009, 23:23-33.
129. Franks T, Botta R, Thomas MR. Chimerism in grapevines: implications for cultivar identity, ancestry and genetic improvement. Theor Appl Genet 2002, 104:192-199. 10.1007/s001220100683, 12582686.
130. Moncada X, Hinrichsen P, Pelsy F, Medinoglu D. Microsatellite markers as reproducible tools to identify chimerical polymorphisms in 'Cabernet Sauvignon'. Acta Hortic 2009, 827:259-264.
131. Regner F, Hack R, Hanak K, Santiago JL. Variability in the cultivar 'Gruener Veltliner'. Acta Hortic 2009, 827:245-252.
132. Castro I, Leal F, Guedes-Pinto H, Eiras Dias J, Veloso M, Pinto-Carnide O. Genomic variability in grapevine cultivars assessed by molecular markers. Acta Hortic 2009, 827:187-192.
133. Venturi S, Dondini L, Donini P, Sansavini S. Retrotransposon characterisation and fingerprinting of apple clones by S-SAP markers. Theor Appl Genet 2006, 112:440-444. 10.1007/s00122-005-0143-8, 16328231.
134. Zhao G, Dai H, Chang L, Ma Y, Sun H, He P, Zhang Z. Isolation of two novel complete Ty1-copia retrotransposons from apple and demonstration of use of derived S-SAP markers for distinguishing bud sports of Malus domestica cv. Tree Fuji Genet Genom 2010, 6:149-159.
135. Bretó MP, Ruiz C, Pina JA, Asíns MJ. The diversification of Citrus clementina Hort. ex Tan., a vegetatively propagated crop species. Mol Phylogenet Evol 2001, 21:285-293. 10.1006/mpev.2001.1008, 11697922.
136. Liao Z-K, Zhang Q-M, Liu W-G, Ding W-P, Wang C-M. Identification of Citrus mutants by APLP technique. J Fruit Sci 2006, 23:486-488.
137. Gomes S, Martins-Lopes PJ, Lima-Brito J, Meirinhos J, Lopes A, Martins A, Guedes-Pinto H. Evidence for clonal variation in 'Verdeal-Transmontana' olive using RAPD, ISSR and SSR markers. J Hortic Sci Biotechnol 2008, 83:395-400.
138. Martins-Lopes P, Gomes S, Lima-Brito J, Lopes J, Guedes-Pinto H. Assessment of clonal genetic variability in Olea europaea L. 'Cobrançosa' by molecular markers. Scientia Hortic 2009, 123:82-89.
139. Guimaraes NCC, Torga PP, De Resende EC, Chalfun A, Paiva E, Paiva LV. Identification of somaclonal variants in 'Prata Ana' banana using molecular and cytogenetic techniques [In Portuguese]. Ciencia e Agrotecnologia 2009, 33:448-454.
140. Sheidai M, Aminpoor H, Noormohammadi Z, Farahani F. RAPD analysis of somaclonal variation in banana (Musa acuminata L.) cultivar Valery. Acta Biol Szeged 2008, 52:307-311.
141. Perrini R, Alba V, Ruta C, Morone-Fortunato I, Blanco A, Montemurro C. An evaluation of a new approach to the regeneration of Helichrysum italicum (Roth) G. Don, and the molecular characterization of the variation among sets of differently derived regenerants. Cell Molec Biol Lett 2009, 14:377-394.
142. Al-Kaabi HH, Zaid A, Shephard H, Ainsworth C. AFLP variation in tissue culture-derived date palm (Phoenix dactylifera L.) plants. Acta Hortic 2007, 736:135-159.
143. Osipova ES, Lysenko EA, Troitsky AV, Dolgikh YI, Shamina ZB, Gostimskii SA. Analysis of SCAR marker nucleotide sequences in maize (Zea mays L.) somaclones. Plant Science 2011, 180:313-322. 10.1016/j.plantsci.2010.10.004, 21421376.
144. Carrier G, Le Cunff L, Dereeper A, Legrand D, Sabot F, Bouchez O, Audeguin L, Boursiquot JM, This P. Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. PLoS One 2012, 7:e32973. 10.1371/journal.pone.0032973, 3299709, 22427919.
145. Yoon CK. Botanical witness for the prosecution. Science 1993, 260:894-895.
146. Korpelainen H, Virtanen V. DNA fingerprinting of mosses. J Forensic Sci 2003, 48:804-807.
147. Virtanen V, Korpelainen H, Kostamo K. Forensic botany: usability of bryophyte material in forensic studies. Forensic Sci Int 2007, 172:161-163. 10.1016/j.forsciint.2006.11.012, 17300893.
148. Rodriguez-Plaza P, Gonzalez R, Moreno-Arribas MV, Polo MC, Bravo G, Martínez-Zapater JM, Martínez MC, Cifuentes A. Combining microsatellite markers and capillary gel electrophoresis with laser-induced fluorescence to identify the grape Vitis vinifera cultivar of musts. Eur Food Res Technol 2006, 223:625-631.
149. Faria MA, Nunes E, Oliveira MBPP. Relative quantification of Vitis vinifera L. cultivars in musts by microsatellite DNA analysis. Eur Food Res Technol 2008, 227:845-850.
150. Spaniolas S, Tsachaki M, Bennett MJ, Tucker GA. Toward the authentication of wines of Nemea denomination of origin through cleaved amplified polymorphic sequence (CAPS)-based assay. J Agric Food Chem 2008, 56:7667-7671. 10.1021/jf801036f, 18698791.
151. Martins-Lopes P, Gomes S, Santos E, Guedes-Pinto H. DNA markers for Portuguese olive oil fingerprinting. J Agric Food Chem 2008, 56:11786-11791. 10.1021/jf801146z, 19053397.
152. Montemurro C, Pasqualone A, Simeone R, Sabetta W, Blanco A. AFLP molecular markers to identify virgin olive oils from single Italian cultivars. Eur Food Res Technol 2008, 226:1439-1444.
153. Archak S, Lakshminarayanareddy V, Nagaraju J. High-throughput multiplex microsatellite marker assay for detection and quantification of adulteration in Basmati rice (Oryza sativa). Electrophoresis 2007, 28:2396-2405. 10.1002/elps.200600646, 17577195.
154. Melchlade D, Foroni I, Corrado G, Santangelo I, Rao R. Authentication of the 'Annurca' apple in agro-food chain by amplification of microsatellite loci. Food Biotechnol 2007, 21:33-43.
155. Yamamoto T, Kimura T, Hayashi T, Ban Y. DNA profiling of fresh and processed fruits in pear. Breed Sci 2006, 56:165-171.
156. Ding G, Zhang DZ, Feng ZY, Fan WJ, Ding XY, Li XX. SNP, ARMS and SSH authentication of medicinal Dendrobium officinale Kimura et Migo and application for identification of Fengdou drugs. Biol Pharmaceut Bull 2008, 31:553-557.
157. Nybom H, Weising K. DNA profiling of plants. Medicinal Plant Biotechnology 2007, 73-95. Weinheim: Wiley-VCH Publishers, Kayser O, Quax WJ.
158. Sarwat M, Nabi G, Das S, Srivastava PS. Molecular markers in medicinal plant biotechnology: past and present. Crit Rev Biotechnol 2012, 32:74-92. 10.3109/07388551.2011.551872, 21649550.
159. Kumar LD, Kathirvei M, Rao GV, Nagaraju J. DNA profiling of disputed chilli samples (Capsicum annum) using ISSR-PCR and FISSR-PCR marker assays. Forensic Sci Int 2001, 116:63-68. 10.1016/S0379-0738(00)00350-9, 11118756.
160. Gilmore S, Peakall R, Robertson J. Short tandem repeat (STR) DNA markers are hypervariable and informative in Cannabis sativa: implications for forensic investigations. Forensic Sci Internat 2003, 131:65-74.
161. Köhnemann S, Nedele J, Schwotzer D, Morzfeld J, Pfeiffer H. The validation of a 15 STR multiplex PCR for Cannabis species. Int J Legal Med 2012, 126:601-606. 10.1007/s00414-012-0706-6, 22573357.
162. Höltken AM, Schröder H, Wischnewski N, Degen B, Magel E, Fladung M. Development of DNA-based methods to identify CITES-protected timber species: a case study in the Meliaceae family. Holzforschung 2012, 66:97-104.
163. Nybom H, Bartish IV. Effects of life history traits and sampling strategies on genetic diversity estimates obtained with RAPD markers in plants. Persp Plant Evol Ecol Syst 2000, 3:93-114.
164. Gabrielsen TM, Bachmann K, Jakobsen KS, Brochmann C. Glacial survival does not matter: RAPD phylogeography of Nordic Saxifraga oppositifolia. Mol Ecol 1997, 6:831-842.
165. Williams DA, Muchugu E, Overholt WA, Cuda JP. Colonization patterns of the invasive Brazilian peppertree, Schinus terebinthifolius, in Florida. Heredity 2007, 98:284-293. 10.1038/sj.hdy.6800936, 17245420.
166. Forrest CN, Ottewell KM, Whelan RJ, Ayre DJ. Tests for inbreeding and outbreeding depression and estimation of population differentiation in the bird-pollinated shrub Grevillea mucronulata. Ann Bot 2011, 108:185-195. 10.1093/aob/mcr100, 3119612, 21546431.
167. Fahima T, Sun GL, Beharav A, Krugman T, Beiles A, Nevo E. RAPD polymorphism in wild emmer wheat populations, Triticum dicoccoides, in Israel. Theor Appl Genet 1999, 98:434-447.
168. Torres E, Iriondo JM, Escudero A, Pérez C. Analysis of within-population spatial genetic structure in Antirrhinum microphyllum (Scrophulariaceae). Am J Bot 2003, 90:1688-1695. 10.3732/ajb.90.12.1688, 21653345.
169. Meeus S, Honnay O, Jacquemyn H. Strong differences in genetic structure across disjunct, edge, and core populations of the distylous forest herb Pulmonaria officinalis (Boraginaceae). Am J Bot 2012, 99:1809-1818. 10.3732/ajb.1200223, 23092991.
170. Pandey M, Rajora OP. Higher fine-scale genetic structure in peripheral than in core populations of a long-lived and mixed-mating conifer - eastern white cedar (Thuja occidentalis L.). BMC Evol Biol 2012, 12:48. 10.1186/1471-2148-12-48, 3359246, 22480185.
171. Volis S, Zaretsky M, Shulgina I. Fine-scale spatial genetic structure in a predominantly selfing plant: role of seed and pollen dispersal. Heredity 2010, 105:384-393. 10.1038/hdy.2009.168, 19953120.
172. Ennos RA. Estimating the relative rates of pollen and seed migration among plant populations. Heredity 1994, 72:250-259.
173. Beebee T, Rowe G. An Introduction to Molecular Ecology 2004, Oxford: Oxford University Press.
174. Barluenga M, Austerlitz F, Elzinga JA, Texeira S, Goudet J, Bermasconi G. Fine-scale spatial genetic structure and gene dispersal in Silene latifolia. Heredity 2011, 106:13-24. 10.1038/hdy.2010.38, 3183859, 20389310.
175. Fievet V, Touzet P, Arnaud J-F, Cuguen J. Spatial analysis of nuclear and cytoplasmic DNA diversity in wild sea beet (Beta vulgaris ssp. maritima) populations: do marine currents shape the genetic structure?. Mol Ecol 2007, 16:1847-1864. 10.1111/j.1365-294X.2006.03208.x, 17444897.
176. White GM, Boshier DH, Powell W. Genetic variation within a fragmented population of Swietenia humilis Zucc. Mol Ecol 1999, 8:1899-1909. 10.1046/j.1365-294x.1999.00790.x, 10620233.
177. Aldrich PR, Hamrick JL. Reproductive dominance of pasture trees in a fragmented tropical forest mosaic. Science 1998, 281:103-105.
178. Quinteros-Casaverde N, Flores-Negrón CF, Williams DA. Low genetic diversity and fragmentation in a wind-pollinated tree, Polylepis multijuga Plige (Rosaceae) in the high Andes. Conserv Genet 2012, 13:593-603.
179. Gerber S, Mariette S, Streiff R, Bodénès C, Kremer A. Comparison of microsatellites and amplified fragment length polymorphism markers for parentage analysis. Mol Ecol 2000, 9:1037-1048. 10.1046/j.1365-294x.2000.00961.x, 10964223.
180. Streiff R, Ducousso A, Lexer C, Steinkellner H, Gloessl J, Kremer A. Pollen dispersal inferred from paternity analysis in a mixed oak stand of Quercus robur L. and Q. petraea (Matt.) Liebl. Mol Ecol 1999, 8:831-841.
181. Gaiotto FA, Grattapaglia D, Vencovsky R. Genetic structure, mating system, and long distance gene flow in heart of palm (Euterpe edulis Mart.). J Hered 2003, 94:399-406. 10.1093/jhered/esg087, 14557393.
182. Ziegenhagen B, Scholz F, Madaghiele A, Vendramin GG. Chloroplast microsatellites as markers for paternity analysis in Abies alba. Can J Forest Res 1998, 28:317-321.
183. Korecký J, Klápste J, Lstiburek M, Kobliha J, Nelson CD, El-Kassaby YA. Comparison of genetic parameters from marker-based relationship, sibship, and combined models in Scots pine multi-site open-pollinated tests. Tree Genet Genom 2013, 9:1227-1235. doi:10.1007/s11295-013-0630-z.
184. Soleimani VD, Baum BR, Johnson DA. Analysis of genetic diversity in barley cultivars reveals incongruence between S-SAP, SNP and pedigree data. Genet Resour Crop Evol 2007, 54:83-97.
185. Coart E, Vekemans X, Smulders MJM, Wagner I, Van Huylenbroeck J, Van Bockstaele E, Roldán-Ruiz I. Genetic variation in the endangered wild apple (Malus sylvestris (L.) Mill.) in Belgium as revealed by amplified fragment length polymorphism and microsatellite markers. Mol Ecol 2003, 12:845-857. 10.1046/j.1365-294X.2003.01778.x, 12753206.
186. Coart E, Van Glabeke S, De Loose M, Larsen AS, Roldán-Ruiz I. Chloroplast diversity in the genus Malus: new insights into the relationship between the European wild apple (Malus sylvestris (L.) Mill.) and the domesticated apple (Malus domestica Borkh.). Mol Ecol 2006, 15:2171-2182. 10.1111/j.1365-294X.2006.02924.x, 16780433.
187. Patocchi A, Fernández-Fernández F, Evans K, Gobbin D, Rezzonico F, Boudichevskaia A, Dunemann F, Stankiewicz-Kosyl M, Mathis-Jeanneteau F, Durel CE, Gianfranceschi L, Vosta F, Toller C, Cova V, Mott D, Komjanc M, Barbaro E, Kodde L, Rikkerink E, Gessler C, van de Weg WE. Development and test of 21 multiplex PCRs composed of SSRs spanning most of the apple genome. Tree Genet Genom 2009, 5:211-223.
188. Escribano P, Viruel MA, Hormaza JL. Comparison of different methods to construct a core germplasm collection in woody perennial species with simple sequence repeat markers. A case study in cherimoya (Annona cherimola, Annonaceae), an underutilized subtropical fruit tree species. Ann Appl Biol 2008, 153:25-32.
189. Escribano P, Viruel MA, Hormaza JL. Establishment of a core collection to optimise the conservation of cherimoya (Annona cherimola Mill.) genetic resources using SSR information. Acta Hortic 2009, 814:67-70.
190. Le Cunff L, Fournier-Level A, Laucou V, Vezzulli S, Lacombe T, Adam-Blondon A-F, Boursiquot JM, This P. Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp. sativa. BMC Plant Biol 2008, 8:31. 10.1186/1471-2229-8-31, 2375891, 18384667.
191. Rieseberg LH. The role of hybridisation in evolution: old wine in new skin. Am J Bot 1995, 82:944-953.
192. Arnold ML, Bennett BD, Zimmer EA. Natural hybridisation between Iris fulva and Iris hexagona: pattern of ribosomal DNA variation. Evolution 1990, 44:1512-1521.
193. Nason JD, Ellstrand NC, Arnold ML. Patterns of hybridization and introgression in populations of oaks, manzanitas and irises. Am J Bot 1992, 79:101-111.
194. Arnold ML. Iris nelsonii (Iridaceae): origin and genetic composition of a homoploid hybrid species. Am J Bot 1993, 80:577-583.
195. Rieseberg LH. Homology among RAPD fragments in interspecific comparisons. Mol Ecol 1996, 5:99-105.
196. Yatabe Y, Kane NC, Scotti-Saintagne C, Rieseberg LH. Rampant gene exchange across a strong reproductive barrier between the annual sunflowers, H. annuus and H. petiolaris. Genetics 2007, 175:1883-1893. 10.1534/genetics.106.064469, 1855124, 17277373.
197. Whitney KD, Randell RA, Rieseberg LH. Adaptive introgression of adaptive herbivore traits in the weedy sunflower Helianthus annuus. Am Nat 2006, 167:794-807. 10.1086/504606, 16649157.
198. Whitney KD, Randell RA, Rieseberg LH. Adaptive introgression of abiotic tolerance traits in the sunflower Helianthus annuus. New Phytol 2010, 187:230-239. 10.1111/j.1469-8137.2010.03234.x, 20345635.
199. Scascitelli M, Whitney KD, Randell RA, King M, Buerkle CA, Rieseberg LH. Genome scan of hybridizing sunflowers from Texas (Helianthus annuus and H. debilis) reveals asymmetric patterns of introgression and small islands of genomic differentiation. Mol Ecol 2010, 19:521-541. 10.1111/j.1365-294X.2009.04504.x, 20355258.
200. Dumolin-Lapègue S, Demesure B, Fineschi S, Le Corre V, Petit RJ. Phylogeographic structure of white oaks throughout the European continent. Genetics 1997, 146:1475-1487. 1208090, 9258689.
201. McKinnon GE, Vaillancourt RE, Jackson HD, Potts BM. Chloroplast sharing in the Tasmanian eucalypts. Evolution 2001, 55:703-711. 10.1554/0014-3820(2001)055[0703:CSITTE]2.0.CO;2, 11392388.
202. Bänfer G, Moog U, Fiala B, Mohamed M, Weising K, Blattner FR. A chloroplast genealogy of myrmecophytic Macaranga species (Euphorbiaceae) in Southeast Asia reveals hybridization, vicariance and long-distance dispersals. Mol Ecol 2006, 15:4409-4424. 10.1111/j.1365-294X.2006.03064.x, 17107473.
203. Tsitrone A, Kirkpatrick M, Levin DA. A model for chloroplast capture. Evolution 2003, 57:1776-1782.
204. Harris SA, Robinson JP, Juniper BE. Genetic clues to the origin of the apple. Trends Genet 2002, 18:426-430. 10.1016/S0168-9525(02)02689-6, 12142012.
205. Richards CM, Volk GM, Reilley AA, Henk AD, Lockwood DR, Reeves PA, Forsline PL. Genetic diversity and population structure in Malus sieversii, a wild progenitor species of domesticated apple. Tree Genet Genomes 2009, 5:339-347.
206. Cornille A, Gladieaux P, Smulders MJM, Roldán-Ruiz I, Lauren F, Le Cam B, Nersesyan A, Clavel J, Olonova M, Feugey L, Gabrielyan I, Zhang XG, Tenaillon MI, Giraud T. New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS Genetics 2012, 8:e1002703. 10.1371/journal.pgen.1002703, 3349737, 22589740.
207. Muranishi S, Tamaki I, Setsuko S, Tomaru N. Asymmetric introgression between Magnolia stellata and M. salicifolia at a site where the two species grow sympatrically. Tree Genet Genomes 2013, 9:1005-1015. doi:10.1007/s11295-013-0612-1.
208. Beck JB, Allison JR, Pryer KM, Windham MD. Identifying multiple origins of polyploid taxa: a multilocus study of the hybrid cloak fern (Astrolepis integerrima; Pteridaceae). Am J Bot 2012, 99:1857-1865. 10.3732/ajb.1200199, 23108464.
209. Ritz CM, Schmuths H, Wissemann V. Evolution by reticulation: European dogroses originated by multiple hybridization across the genus Rosa. J Hered 2005, 96:4-14. 10.1093/jhered/esi011, 15618309.
210. Nair AS, Teo CH, Schwarzacher T, Heslop-Harrison P. Genome classification of banana cultivars from South India using IRAP markers. Euphytica 2005, 144:285-290.
211. Ning A-P, Xu L-B, Lu Y, Huang B-Z, Ge X-J. Genome composition and genetic diversity of Musa germplasm from China revealed by PCR-RFLP and SSR markers. Scientia Hortic 2007, 114:281-288.
212. Sales EK, Butardo NG, Paniagua HG, Jansen H, Dolezei J. Assessment of ploidy and genome constitution of some Musa balbisiana cultivars using DArT markers. Philippine J Crop Sci 2011, 36:11-18.
213. Kardolus JP, Van Eck HJ, Van den Berg RG. The potential of AFLPs in biosystematics: a first application in Solanum taxonomy (Solanaceae). Plant Syst Evol 1998, 210:87-103.
214. Korbecka G, Rymer PD, Harris SA, Pannell JR. Solving the problem of ambiguous paralogy for marker loci: microsatellite markers with diploid inheritance in allohexaploid Mercurialis annua (Euphorbiaceae). J Hered 2010, 101:504-511. 10.1093/jhered/esq026, 20219887.
215. Fu Y-B, Peterson GW, Richards KW, Tarn TR, Percy JE. Genetic diversity of Canadian and exotic potato germplasm revealed by simple sequence repeat markers. Am J Potato Res 2009, 86:38-48.
216. Cosendai AC, Rodewald J, Hörandl E. Origin and distribution of autopolyploids via apomixis in the alpine species Ranunculus kuepferi (Ranunculaceae). Taxon 2011, 60:355-364.
217. Esselink GD, Nybom H, Vosman B. Assignment of allelic configuration in polyploids using the MAC-PR (Microsatellite DNA Allele Counting - Peak Ratios) method. Theor Appl Genet 2004, 109:402-408.
218. Nybom H, Esselink DG, Werlemark G, Vosman B. Microsatellite DNA marker inheritance indicates preferential pairing between highly homologous genomes in polyploid and hemisexual dog-roses Rosa L. sect. Caninae. Heredity 2004, 92:139-150. 10.1038/sj.hdy.6800332, 14981531.
219. Nybom H, Esselink GD, Werlemark G, Leus L, Vosman B. Unique genomic configuration revealed by microsatellite DNA in polyploid dogroses. Rosa sect. Caninae. J Evol Biol 2006, 19:635-648. 10.1111/j.1420-9101.2005.01010.x, 16599938.
220. Babaei A, Tabaei-Aghdaei SR, Khosh-Khui M, Omidbaigi R, Naghavi MR, Esselink GD, Smulders MJM. Microsatellite analysis of Damask rose (Rosa damascena Mill.) accessions from various regions in Iran reveals multiple genotypes. BMC Plant Biol 2007, 7:12. 10.1186/1471-2229-7-12, 1832195, 17346330.
221. Catalán P, Segarra-Moragues JG, Palop-Esteban M, Moreno C, González-Candelas F. A Bayesian approach for discriminating among alternative inheritance hypotheses in plant polyploids: the allotetraploid origin of genus Borderea (Dioscoreaceae). Genetics 2006, 172:1939-1953. 1456289, 16322527.
222. Van Dijk T, Noordijk Y, Dubos T, Bink MCAM, Meulenbroek BJ, Visser RGF, van de Weg E. Microsatellite allele dose and configuration establishment (MADCE): an integrated approach for genetic studies in allopolyploids. BMC Plant Biol 2012, 12:25. 10.1186/1471-2229-12-25, 3338383, 22340438.
223. Liao W-J, Zhu B-R, Zeng Y-F, Zhang D-Y. TETRA: an improved program for population genetic analysis of allotetraploid microsatellite data. Mol Ecol Resources 2008, 8:1260-1262.
224. Clark LV, Jasieniuk M. POLYSAT: an R package for polyploid microsatellite analysis. Mol Ecol Resources 2011, 11:562-566.
225. Voorrips R, Gort G, Vosman B. Genotype calling in tetraploid species from bi-allelic marker data using mixture models. BMC Bioinformatics 2011, 12:172. 10.1186/1471-2105-12-172, 3121645, 21595880.
226. Gidskehaug L, Kent M, Hayes BJ, Lien S. Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array. Bioinformatics 2011, 27:303-310. 10.1093/bioinformatics/btq673, 21149341.
227. Bruvo R, Michiels NK, D'Souza TG, Schulenburg H. A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level. Mol Ecol 2004, 13:2101-2106. 10.1111/j.1365-294X.2004.02209.x, 15189230.
228. Obbard DJ, Harris SA, Pannell JR. Simple allelic-phenotype diversity and differentiation statistics for allopolyploids. Heredity 2006, 97:296-303. 10.1038/sj.hdy.6800862, 16823402.
229. Assoumane A, Zoubeirou AM, Rodier-Goud M, Favreau B, Bezançon G, Verhaegen D. Highlighting the occurrence of tetraploidy in Acacia senegal (L.) Willd. and genetic variation patterns in its natural range revealed by DNA microsatellite markers. Tree Genet Genom 2013, 9:93-106.
230. Lexer C, Widmer C. The genic view of plant speciation: recent progress and emerging questions. Phil Trans R Soc 2008, B363:3023-3036.
231. Strasburg JL, Sherman NA, Wright KM, Moyle LC, Willis JH, Rieseberg LH. What can patterns of differentiation across plant genomes tell us about adaptation and speciation?. Phil Trans Roy Soc Series B 2012, 367:364-373.
232. Scotti-Saintagne C, Mariette S, Porth I, Goicoechea PG, Barreneche T, Bodénès C, Burg K, Kremer A. Genome scanning for interspecific differentiation between two closely related oak species [Quercus robur L. and Q. petraea (Matt.) Liebl.]. Genetics 2004, 168:1615-1626. 10.1534/genetics.104.026849, 1448783, 15579711.
233. Despres L, Gielly L, Redoutet B, Taberlet P. Using AFLP to resolve phylogenetic relationships in a morphologically diversified plant species complex when nuclear and chloroplast sequences fail to reveal variability. Mol Phylogenet Evol 2003, 27:185-196. 10.1016/S1055-7903(02)00445-1, 12695084.
234. Bänfer G, Fiala B, Weising K. AFLP analysis of phylogenetic relationships among myrmecophytic species of Macaranga (Euphorbiaceae) and their allies. Pl Syst Evol 2004, 249:213-231.
235. Aggarwal RK, Brar DS, Khush GS. Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization. Mol General Genet 1997, 254:1-12.
236. Aggarwal RK, Brar DS, Nandi S, Huang N, Khush GS. Phylogenetic relationships among Oryza species revealed by AFLP markers. Theor Appl Genet 1999, 98:1320-1328.
237. Zou XH, Zhang FM, Zhang JG, Zang LL, Tang L, Wang L, Sang T, Ge S. Analysis of 142 genes resolves the rapid diversification of the rice genus. Genome Biol 2008, 9:R49. 10.1186/gb-2008-9-3-r49, 2397501, 18315873.
238. Zou XH, Yang Z, Doyle JJ, Ge S. Multilocus estimation of divergence times and ancestral effective population sizes of Oryza species and implications for the rapid diversification of the genus. New Phytol 2013, 198:1155-1164. 10.1111/nph.12230, 23574344.
239. Scariot V, Akkak A, Botta R. Characterization and genetic relationships of wild species and old garden roses based on microsatellite analysis. J Am Soc Hort Sci 2006, 131:66-73.
240. Koopman WJM, Vosman B, Sabatino GJH, Visser D, Van Huylenbroeck J, De Riek J, De Cock K, Wissemann V, Ritz CM, Maes B, Werlemark G, Nybom H, Debener T, Linde M, Smulders MJM. AFLP markers as a tool to reconstruct complex relationships in the genus Rosa (Rosaceae). Am J Bot 2008, 95:353-366. 10.3732/ajb.95.3.353, 21632360.
241. De Riek J, De Cock K, Smulders MJM, Nybom H. AFLP-based population structure analysis as a means to validate the complex taxonomy of dogroses (Rosa section Caninae). Mol Phylogenet Evol 2013, 67:547-559. 10.1016/j.ympev.2013.02.024, 23499615.
242. Kovarik A, Werlemark G, Leitch AR, Souckova-Skalicka K, Lim KY, Khaitová L, Koukalova B, Nybom H. The asymmetric meiosis in pentaploid dogroses (Rosa sect. Caninae) is associated with a skewed distribution of rRNA gene families in the gametes. Heredity 2008, 101:359-367. 10.1038/hdy.2008.63, 18648391.
243. Meerow AW, Francisco-Ortega J, Calonje M, Griffith MP, Ayala-Silva T, Stevenson DW, Nakamura K. Zamia (Cycadales: Zamiaceae) on Puerto Rico: asymmetric genetic differentiation and the hypothesis of multiple introductions. Am J Bot 2012, 99:1828-1839. 10.3732/ajb.1200494, 23125434.
244. Koppolu R, Upadhyaya HD, Dwivedi SL, Hoisington DA, Varshney RK. Genetic relationships among seven sections of genus Arachis studied by using SSR markers. BMC Plant Biol 2010, 10:15. 10.1186/1471-2229-10-15, 2826335, 20089171.
245. Richard M, Thorpe RS. Can microsatellites be used to infer phylogenies? Evidence from population affinities of the Western Canary Island Lizard (Gallotia galloti). Mol Phylogenet Evol 2001, 20:351-360. 10.1006/mpev.2001.0981, 11527463.
246. Avise JC. Phylogeography: The History and Formation of Species 2000, Cambridge, MA: Harvard University Press.
247. Schaal BA, Hayworth DA, Olsen KM, Rauscher JT, Smith WA. Phylogeographic studies in plants: problems and prospects. Mol Ecol 1998, 7:465-474.
248. Posada D, Crandall KA. Intraspecific gene genealogies: trees grafting into networks. Trends Ecol Evol 2001, 16:37-45. 10.1016/S0169-5347(00)02026-7, 11146143.
249. Lascoux M, Palmé AE, Cheddadi R, Latta RG. Impact of the Ice Ages on the genetic structure of trees and shrubs. Phil Trans R Soc Lond 2004, B359:197-207.
250. Burban C, Petit RJ. Phylogeography of maritime pine inferred with organelle markers having contrasted inheritance. Mol Ecol 2003, 12:1487-1495. 10.1046/j.1365-294X.2003.01817.x, 12755877.
251. Marchelli P, Baier C, Mengel C, Ziegenhage B, Gallo LA. Biogeographic history of the threatened species Araucaria araucana (Molina) K. Koch and implications for conservation: a case study with organellar DNA markers. Conserv Genet 2010, 11:951-963.
252. Cornille A, Giraud T, Bellard C, Tellier A, Le Cam B, Smulders MJM, Kleinschmit J, Roldán-Ruiz I, Gladieux P. Postglacial recolonization history of the European crabapple (Malus sylvestris Mill.), a wild contributor to the domesticated apple. Mol Ecol 2013, 22:2249-2263. 10.1111/mec.12231, 23402276.
253. Kadereit JW, Arafeh R, Somogyi G, Westberg E. Terrestrial growth and marine dispersal? Comparative phylogeography of five coastal plant species at a European scale. Taxon 2005, 54:861-876.
254. Schönswetter P, Tribsch A, Niklfeld H. Phylogeography of the high Alpine cushion plant Androsace alpina (Primulaceae) in the European Alps. Plant Biol 2003, 5:623-630.
255. Guicking D, Blattner FR, Fiala B, Slik F, Mohamed M, Weising K. Comparative chloroplast DNA phylogeography of two tropical pioneer tree species, Macaranga gigantea and M. pearsonii (Euphorbiaceae). Tree Genet Genomes 2011, 7:573-585.
256. Clement M, Posada D, Crandall KA. TCS: a computer program to estimate gene genealogies. Mol Ecol 2000, 9:1657-1659. 10.1046/j.1365-294x.2000.01020.x, 11050560.
257. Collevatti RG, Grattapaglia D, Hay JD. Evidences for multiple maternal lineages of Caryocar brasiliense populations in the Brazilian Cerrado based on the analysis of chloroplast DNA sequences and microsatellite haplotype variation. Mol Ecol 2003, 12:105-115.
258. Vachon N, Freeland JR. Phylogeographic inferences from chloroplast DNA: quantifying the effects of mutations in repetitive and non-repetitive sequences. Mol Ecol Resources 2011, 11:279-285.
259. Grivet D, Petit RJ. Chloroplast DNA phylogeography of the hornbeam in Europe: evidence for a bottleneck at the outset of postglacial colonization. Cons Genet 2003, 4:47-56.
260. Valtuena FJ, Preston CD, Kadereit JW. Phylogeography of a Tertiary relict plant, Meconopsis cambrica (Papaveraceae), implies the existence of northern refugia for a temperate herb. Mol Ecol 2012, 21:1423-1437. 10.1111/j.1365-294X.2012.05473.x, 22320448.
261. Shafer ABA, Cullingham CI, Coté SC, Coltman DW. Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Mol Ecol 2010, 19:4589-4621. 10.1111/j.1365-294X.2010.04828.x, 20849561.
262. Soltis DE, Morris AB, McLachlan JS, Manos PS, Soltis PS. Comparative phylogeography of unglaciated eastern North America. Mol Ecol 2006, 15:4261-4293. 10.1111/j.1365-294X.2006.03061.x, 17107465.
263. Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T. A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 1998, 148:479-494. 1459786, 9475757.
264. Wenzl P, Li H, Carling J, Zhou M, Raman H, Paul E, Hearnden P, Maier C, Xia L, Caig V, Ovesná J, Cakir M, Poulsen D, Wang J, Raman R, Smith KP, Muehlbauer GJ, Chalmers KJ, Kleinhofs A, Huttner E, Kilian A. A high-density consensus map of barley linking DArT markers to SSR. RFLP and STS loci and agricultural traits. BMC Genomics 2006, 7:206. 10.1186/1471-2164-7-206, 1564146, 16904008.
265. Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES. A first-generation haplotype map of maize. Science 2009, 326:1115-1117. 10.1126/science.1177837, 19965431.
266. Pollard DA. Design and construction of recombinant inbred lines. Methods Mol Biol 2012, 871:31-39. 10.1007/978-1-61779-785-9_3, 22565831.
267. Michelmore RW, Paran I, Kesseli RV. 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 U S A 1991, 88:9828-9832. 10.1073/pnas.88.21.9828, 52814, 1682921.
268. Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Tar'an B, Millan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo MC, Thudi M, Gowda CL, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, Singh KB, Datta SK, Jackson SA, Wang J, Cook DR. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnol 2013, 31:240-246.
269. Abdurakhmonov IY, Abdukarimov A. Application of association mapping to understanding the genetic diversity of plant germplasm resources. Int J Plant Genomics 2008, 2008:574927. 2423417, 18551188.
270. Soto-Cerda BJ, Cloutier S. Association Mapping in Plant Genomes. Genetic Diversity in Plants 2012, Mahmut Çalişkan: InTech, DOI: 10.5772/33005.
271. Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, McClung AM, Bustamante CD, McCouch SR. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2011, 2:467. 3195253, 21915109.
272. Strigens A, Freitag NM, Gilbert X, Grieder C, Riedelsheimer C, Schrag TA, Messmer R, Melchinger AE. Association mapping for chilling tolerance in elite flint and dent maize inbred lines evaluated in growth chamber and field experiments. Plant Cell Environ 2013, 36:1871-1887. 10.1111/pce.12096, 23488576.
273. Sork VL, Aitken SN, Dyer RJ, Eckert AJ, Legendre P, Neale DB. Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate. Trees Genet Genomes 2013, 9:901-911.
274. Pavy N, Gagnon F, Rigault P, Blais S, Deschênes A, Boyle B, Pelgas B, Deslauriers M, Clément S, Lavigne P, Lamothe M, Cooke JE, Jaramillo-Correa JP, Beaulieu J, Isabel N, Mackay J, Bousquet J. Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners. Ecol Resour 2013, 13:324-336.
275. Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, Micheletti D, Rosyara UR, Cattonaro F, Vendramin E, Main D, Aramini V, Blas AL, Mockler TC, Bryant DW, Wilhelm L, Troggio M, Sosinski B, Aranzana MJ, Arús P, Iezzoni A, Morgante M, Peace C. Development and evaluation of a 9 K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS One 2012, 7:e35668. 10.1371/journal.pone.0035668, 3334984, 22536421.
276. Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, Velasco R, Main D, Rees JD, Iezzoni A, Mockler T, Wilhelm L, Van de Weg E, Gardiner SE, Bassil N, Peace C. Genome-wide SNP detection, validation, and development of an 8 K SNP array for apple. PLoS One 2012, 7:e31745. 10.1371/journal.pone.0031745, 3283661, 22363718.
277. Peace C, Bassil N, Main D, Ficklin S, Rosyara UR, Stegmeir T, Sebolt A, Gilmore B, Lawley C, Mockler TC, Bryant DW, Wilhelm L, Iezzoni A. Development and evaluation of a genome-wide 6 K SNP array for diploid sweet cherry and tetraploid sour cherry. PLoS One 2012, 7:e48305. 10.1371/journal.pone.0048305, 3527432, 23284615.
278. Yu J, Holland JB, McMullen MD, Buckler ES. Genetic design and statistical power of nested association mapping in maize. Genetics 2008, 178:539-551. 10.1534/genetics.107.074245, 2206100, 18202393.
279. Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R. A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet 2009, 5:e1000551. 10.1371/journal.pgen.1000551, 2700969, 19593375.
280. Cook JP, McMullen MD, Holland JB, Tian F, Bradbury P, Ross-Ibarra J, Buckler ES, Flint-Garcia SA. Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels. Plant Physiol 2012, 158:824-834. 10.1104/pp.111.185033, 3271770, 22135431.
281. Poland JA, Bradbury PJ, Buckler ES, Nelson RJ. Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc Natl Acad Sci U S A 2011, 108:6893-6898. 10.1073/pnas.1010894108, 3084105, 21482771.
282. Peiffer JA, Flint-Garcia SA, De Leon N, McMullen MD, Kaeppler SM, Buckler ES. The genetic architecture of maize stalk strength. PLoS One 2013, 8:e67066. 10.1371/journal.pone.0067066, 3688621, 23840585.
283. Khan MA, Zhao YF, Korban SS. Identification of genetic loci associated with fire blight resistance in Malus through combined use of QTL and association mapping. Physiol Plant 2013, 148:344-353. 10.1111/ppl.12068, 23627651.
284. Jiang G-L. Molecular markers and marker-assisted breeding in plants. Plant Breeding from Laboratories to Fields 2013, InTech, Andersen SB, DOI: 10.5772/52583.
285. Guo Z, Tucker DM, Lu J, Kishore V, Gay G. Evaluation of genome-wide selection efficiency in maize nested association mapping populations. Theor Appl Genet 2012, 124:261-275. 10.1007/s00122-011-1702-9, 21938474.
286. Meuwissen TH, Hayes BJ, Goddard ME. Prediction of total genetic value using genome-wide dense marker maps. Genetics 2001, 157:1819-1829. 1461589, 11290733.
287. Cabrera-Bosquet L, Crossa J, Von Zitzewitz J, Serret MD, Araus JL. High-throughput phenotyping and genomic selection: the frontiers of crop breeding converge. J Integr Plant Biol 2012, 54:312-320. 10.1111/j.1744-7909.2012.01116.x, 22420640.
288. Zou W, Zeng ZB. Statistical Methods for Mapping Multiple QTL. Int J Plant Genomics 2008, 2008:286561. 2423007, 18551187.
289. Reed GH, Kent JO, Wittwer CT. High-resolution DNA melting analysis for simple and efficient molecular diagnostics. Pharmacogenomics 2007, 8:597-608. 10.2217/14622416.8.6.597, 17559349.
290. Li J, Wang X, Dong R, Yang Y, Zhou J, Yu C, Cheng Y, Yan C, Chen J. Evaluation of high-resolution melting for gene mapping in rice. Plant Mol Biol Rep 2011, 29:979-985.
291. Ganopoulos I, Tsaballa A, Xanthopoulou A, Madesis P, Tsaftaris A. Sweet cherry cultivar identification by high-resolution-melting (HRM) analysis using gene-based SNP markers. Plant Mol Biol Rep 2013, 31:763-768.
292. Dang X-D, Kelleher CT, Howard-Wiiliams E, Meade CV. Rapid identification of chloroplast haplotypes using High Resolution Melting analysis. Mol Ecol Resources 2012, 12:894-908.
293. Holland PM, Abramson RD, Watson R, Gelfand DH. Detection of specific polymerase chain reaction product by utilizing the 5′-3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc Natl Acad Sci U S A 1991, 88:7276-7280. 10.1073/pnas.88.16.7276, 52277, 1871133.
294. Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008, 9:387-402. 10.1146/annurev.genom.9.081307.164359, 18576944.
295. Metzker ML. Sequencing technologies - the next generation. Nature Rev Genet 2010, 11:31-46. 10.1038/nrg2626, 19997069.
296. Rothberg JM, Leamon JH. The development and impact of 454 sequencing. Nature Biotechnol 2008, 26:1117-1124.
297. Byrne S, Czaban A, Studer B, Panitz F, Bendixen C, Asp T. Genome wide allele frequency fingerprints (GWAFFs) of populations via genotyping by sequencing. PLoS One 2013, 8:e57438. 10.1371/journal.pone.0057438, 3587605, 23469194.
298. Davey JW, Cezard T, Fuentes-Utrilla P, Eland C, Gharbi K, Blaxter ML. Special features of RAD sequencing data: implications for genotyping. Mol Ecol 2013, 11:3151-3164.
299. Abdelkrim J, Robertson BC, Stanton J-AL, Gemmell NJ. Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. BioTechniques 2009, 46:185-192. 10.2144/000113084, 19317661.
300. Santana QC, Coetzee MPA, Steenkamp ET, Mlonyeni OX, Hammond GNA, Wingfield MJ, Wingfield BD. Microsatellite discovery by deep sequencing of enriched genomic libraries. BioTechniques 2009, 46:217-223. 10.2144/000113085, 19317665.
301. Allentoft ME, Schuster SC, Holdaway RN, Hale ML, McLay E, Oskam C, Gilbert TP, Spencer P, Willerslev E, Bunce M. Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data. BioTechniques 2009, 46:195-200. 10.2144/000113086, 19317662.
302. Csencsics D, Brodbeck S, Holderegger R. Cost-effective, species-specific microsatellite development for the endangered dwarf bulrush (Typha minima) using next generation sequencing technology. J Hered 2010, 101:789-793. 10.1093/jhered/esq069, 20562212.
303. Lee R, Thimmapuram J, Thinglum KA, Gong G, Hernandez AG, Wright CL, Kim RW, Mikel MA, Tranel PJ. Sampling the waterhemp (Amaranthus tuberculatus) genome using pyrosequencing technology. Weed Sci 2009, 57:463-469.
304. Tangphatsornruang S, Somta P, Uthaipaisanwong P, Chanprasert J, Sangsakru D, Seehalak W, Sommanas W, Trangoonrung S, Srinives P. Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek). BMC Plant Biol 2009, 9:137. 10.1186/1471-2229-9-137, 2788553, 19930676.
305. Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, McCown B, Harbut R, Simon P. Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot 2012, 99:193-208. 10.3732/ajb.1100394, 22186186.
306. Castoe TA, Poole AW, De Koning APJ, Jones KL, Tomback DF, Oyler-McCance SJ, Fike JA, Lance SL, Streicher JW, Smith EN, Pollock DD. Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake. PLoS One 2012, 7:e30953. 10.1371/journal.pone.0030953, 3279355, 22348032.
307. Jennings TN, Knaus BJ, Mullins TD, Haig SM, Cronn RC. Multiplexed microsatellite recovery using massively parallel sequencing. Mol Ecol Resources 2011, 11:1060-1067.
308. Lepais O, Bacles CFE. Comparison of random and SSR-enriched shotgun pyrosequencing for microsatellite discovery and single multiplex PCR optimization in Acacia harpophylla F. Muell. Ex Benth. Mol Ecol Resources 2011, 11:711-724.
309. Binladen J, Gilbert MTP, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One 2007, 2:e97.
310. Takayama K, López P, König C, Kohl G, Novak J, Stuessy TF. A simple and cost-effective approach for microsatellite isolation in non-model plant species using small-scale 454 pyrosequencing. Taxon 2011, 60:1442-1449.
311. Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Phillippy AM. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnol 2012, 30:693-700.
312. Travers KJ, Chin C-S, Rank DR, Eid JS, Turner SW. A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res 2010, 38:e159. 10.1093/nar/gkq543, 2926623, 20571086.
313. Grohme MA, Soler RF, Wink M, Frohme M. Microsatellite marker discovery using single molecule real-time circular consensus sequencing on the Pacific Biosciences RS. BioTechniques 2013, 55:253-256.
314. Krapp F, Wöhrmann T, Pinangé D, Benko-Iseppon A, Huettel B, Weising K. A set of plastid microsatellite loci for the genus Dyckia (Bromeliaceae) derived from 454 pyrosequencing. Am J Bot Primer Notes & Protocols 2012, 99:e470-e473.
315. Cao J, Schneeberger K, Ossowski S, Günther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C, Wang X, Ott F, Müller J, Alonso-Blanco C, Borgwardt K, Schmid KJ, Weigel D. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 2011, 43:956-963. 10.1038/ng.911, 21874002.
316. Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, Weng Q, Huang T, Dong G, Sang T, Han B. High-throughput genotyping by whole-genome resequencing. Genome Res 2009, 19:1068-1076. 10.1101/gr.089516.108, 2694477, 19420380.
317. Bevan MW, Uauy C. Genomics reveals new landscapes for crop improvement. Genome Biol 2013, 14:206. 10.1186/gb-2013-14-6-206, 23796126.
318. Andolfatto P, Davison D, Erezyilmaz D, Hu TT, Mast J, Sunayama-Morita T, Stern DL. Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res 2011, 21:610-617. 10.1101/gr.115402.110, 3065708, 21233398.
319. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 2008, 3:e3376. 10.1371/journal.pone.0003376, 2557064, 18852878.
320. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 2011, 6:e19379. 10.1371/journal.pone.0019379, 3087801, 21573248.
321. Li W, Zhang J, Mou Y, Geng J, McVetty PB, Hu S, Li G. Integration of Solexa sequences on an ultradense genetic map in Brassica rapa L. BMC Genomics 2011, 12:249. 10.1186/1471-2164-12-249, 3125265, 21595929.
322. Uitdewilligen JG, Wolters AM, D'hoop BB, Borm TJ, Visser RG, Van Eck HJ. A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS One 2013, 8:e62355. 10.1371/journal.pone.0062355, 3648547, 23667470.
323. van Orsouw NJ, Hogers RC, Janssen A, Yalcin F, Snoeijers S, Verstege E, Schneiders H, van der Poel H, Van Oeveren J, Verstegen H, Van Eijk MJ. Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS One 2007, 2:e1172. 10.1371/journal.pone.0001172, 2048665, 18000544.
324. Van Tassell CP, Smith TP, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstegard TS. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods 2008, 5:247-252. 10.1038/nmeth.1185, 18297082.
325. Altshuler D, Pollara VJ, Cowles CR, Van Etten WJ, Baldwin J, Linton L, Lander ES. A SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 2000, 407:513-516. 10.1038/35035083, 11029002.
326. Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE. Double Digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 2012, 7:e37135. 10.1371/journal.pone.0037135, 3365034, 22675423.
327. Etter PD, Johnson E. RAD paired-end sequencing for local de novo assembly and SNP discovery in non-model organisms. Meth Mol Biol 2012, 888:135-151.
328. Willing E-M, Hoffmann M, Klein JD, Weigel D, Dreyer C. Paired-end RAD-seq for de-novo assembly and marker design without available reference. Bioinformatics 2011, 27:2187-2193. 10.1093/bioinformatics/btr346, 21712251.
329. Bus A, Hecht J, Huettel B, Reinhardt R, Stich B. High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing. BMC Genomics 2012, 13:281. 10.1186/1471-2164-13-281, 3442993, 22726880.
330. Scaglione D, Acquadro A, Portis E, Tirone M, Knapp SJ, Lanteri S. RAD tag sequencing as a source of SNP markers in Cynara cardunculus L. BMC Genomics 2012, 13:3. 10.1186/1471-2164-13-3, 3269995, 22214349.
331. Pfender WF, Saha MC, Johnson EA, Slabaugh MB. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theor Appl Genet 2011, 122:1467-1480. 10.1007/s00122-011-1546-3, 21344184.
332. Baxter SW, Davey JW, Johnston JS, Shelton AM, Heckel DG, Jiggins CD, Blaxter ML. Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PLoS ONE 2011, 6:e19315. 10.1371/journal.pone.0019315, 3082572, 21541297.
333. Catchen J, Amores A, Hohenlohe P, Cresko W, Postlethwait J. Stacks: building and genotyping loci de novo from short-read sequences. Genes, Genomes, Genetics 2011, 1:171-182. 3276136, 22384329.
334. Lu F, Lipka AE, Glaubitz J, Elshire R, Cherney JH, Casler MD, Buckler ES, Costich DE. Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet 2013, 9:e1003215. 10.1371/journal.pgen.1003215, 3547862, 23349638.
335. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 2007, 23:2633-2635. 10.1093/bioinformatics/btm308, 17586829.
336. Chong Z, Ruan J, Wu C-I. Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads. Bioinformatics 2012, 28:2732-2737. 10.1093/bioinformatics/bts482, 22942077.
337. Poland JA, Rife TW. Genotyping-by-sequencing for plant breeding and genetics. The Plant Genome 2012, 5:92-102.
338. Yang H, Tao Y, Zheng Z, Li C, Sweetingham M, Howieson J. Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L. BMC Genomics 2012, 13:318. 10.1186/1471-2164-13-318, 3430595, 22805587.
339. Wolf JBW. Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial. Mol Ecol Resources 2013, 13:559-572.
340. Harper AL, Trick M, Higgins J, Fraser F, Clissold L, Wells R, Hattori C, Werner P, Bancroft I. Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nature Biotechnol 2012, 30:798-802.
341. Trick M, Adamski NM, Mugford SG, Jiang CC, Febrer M, Uauy C. Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat. BMC Plant Biol 2012, 12:14. 10.1186/1471-2229-12-14, 3296661, 22280551.
342. Liu S, Yeh C-T, Tang HM, Nettleton D, Schnable PS. Gene mapping via bulked segregant RNA-seq (BSR-seq). PloS One 2012, 7:e36406. 10.1371/journal.pone.0036406, 3346754, 22586469.
343. Kahl G, Molina C, Rotter B, Jüngling R, Frank A, Krezdorn N, Hoffmeier K, Winter P. Reduced representation sequencing of plant stress transcriptomes. J Plant Biochem Biotechnol 2012, 21(Suppl 1):119-127.
344. Ruge-Wehling B, Wojacki J, Fischer K, Rotter B, Wehling P. Introgression of an effective resistance against BYDV from Hordeum bulbosum to cultivated barley [in German]. Tagungsband der 63. Jahrestagung der Vereinigung der Pflanzenzüchter und Saatgutkaufleute Österreichs 19-21 November 2012 2013, 3-6. Raumberg-Gumpenstein, Austria. Resistenz gegen biotischen Stress in der Pflanzenzüchtung.
345. Ekblom R, Galindo J. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 2010, 107:1-15. 3186121, 21139633.
346. Seeb JE, Carvalho G, Hauser L, Naish K, Roberts S, Seeb LW. Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Mol Ecol Resour 2011, 11(Suppl 1):1-8.
347. Lasky JR, Des Marais DL, McKay JK, Richards JH, Juenger TE, Keitt TH. Characterizing genomic variation of Arabidopsis thaliana: the roles of geography and climate. Mol Ecol 2012, 21:5512-5529. 10.1111/j.1365-294X.2012.05709.x, 22857709.
348. Stölting KN, Nipper R, Lindtke D, Caseys C, Waeber S, Castiglione S, Lexer C. Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species. Mol Ecol 2013, 22:842-855. 10.1111/mec.12011, 22967258.
349. Narum SR, Buerkle CA, Davey JW, Miller MR, Hohenlohe PA. Genotyping-by-sequencing in ecological and conservation genomics. Mol Ecol 2013, 22:2841-2847. 10.1111/mec.12350, 23711105.
350. McCormack JE, Faircloth BC. Next-generation phylogenetics takes root. Mol Ecol 2013, 22:19-21. 10.1111/mec.12050, 23383410.
351. Givnish TJ, Ames M, McNeal JR, McKain MR, Steele PR, DePamphilis CW, Graham SW, Pires JC, Stevenson DW, Zomlefer WB, Briggs BG, Duvall MR, Moore MJ, Heaney JM, Soltis DE, Soltis PS, Thiele K, Leebens-Mack JH. Assembling the tree of the monocotyledons: plastome sequence phylogeny and evolution of Poales. Ann Missouri Bot Gard 2010, 97:584-616.
352. Griffin P, Robin C, Hoffmann A. A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. BMC Biol 2011, 9:19. 10.1186/1741-7007-9-19, 3078099, 21429199.
353. Duarte JM, Wall PK, Edger PP, Landherr LL, Ma H, Pires JC, Leebens-Mack J, DePamphilis CW. Identification of shared single-copy nuclear genes in Arabidopsis, Populus, Vitis, and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evol Biol 2010, 10:61. 10.1186/1471-2148-10-61, 2848037, 20181251.
354. Harrison N, Kidner CA. Next-generation sequencing and systematics: what can a billion base pairs of DNA sequence data do for you?. Taxon 2011, 60:1552-1566.
355. Buerkle CA, Gompert Z. Population genomics based on low coverage sequencing: how low should we go?. Mol Ecol 2013, 22:3028-3035. 10.1111/mec.12105, 23174005.