Biomics

The species identification and evaluation of intraspecific genetic polymorphism are the most important tasks of modern plant genetics. To solve these problems, a large number of various methods of searching and studying of taxonomically significant DNA fragments were developed, which are called molecular or DNA markers. This review is devoted to the most popular methods for studying DNA markers of wild plants based on the use of polymerase chain reaction (PCR), DNA microarray and sequencing technologies. Among the PCR based methods ISSR, RAPD, SSR, AFLP, IRAP and REMAP have been most widely used, and these methods are used for both genetic diversity assessment and species identification. More effective for studying intraspecific polymorphism is the SNP-analysis, which is usually carried out by the DNA microarray. The rapid growth of research related to SNP analysis suggests that this group of methods will soon probably completely replace the classical methods of PCR fingerprinting. For the species identification of wild plants, the method of sequencing of variable taxonomically significant DNA fragments is quite effective. To this end, chloroplast markers rpoB, rpoC1, rbcL, matK, psbK-psbI, trnH-psbA, atpF-atpH and nuclear markers ITS1 and ITS2 are most often used. None of these markers is not universal, however when using phylogenetic simultaneous analysis of multiple DNA markers, and wherein the supporting role can perform PCR fingerprinting techniques. Whole genome sequencing and computer analysis of the data, if their cost and complexity will reduce in the future, could replace all current PCR- and DNA-microarray-based methods of assessing the genetic polymorphism.

molecular markers, DNA markers, genetic polymorphism, species identification, fingerprinting, ISSR, RAPD, SSR, AFLP, IRAP, REMAP, chloroplast markers, ITS

1. Aleksandrov O.S., Divashuk M.G., Karlov G.I. Development of a sex-specific molecular marker for Japanese hop Humulus japonicus Siebold & Zucc. Russian Journal of Genetics. 2011. Т. 47. № 8. P. 1016–1020. DOI: 10.1134/S1022795411080023
2. Altukhov Yu.P., Salmenkova E.A. DNA polymorphism in population genetics. Russian Journal of Genetics. 2002. V. 38. P. 989–10 DOI: 10.1023/A:1020288812170
3. Andreev I.O., Spiridonova E.V., Kyryachenko S.S., Parnikoza I.Yu., Maidaniuk D.N., Volkov R.A., Kozeretska I.A., Kunakh V.A. Population genetic analysis of Deschampsia antarctica from two regions of maritime Antarctica. Bulletin of Moscow University. Series 16: Biology. № 4. P. 88–91.
4. Arif I.A., Khan H.A., Bahkali A.H., Homaidan A.A., Farhan A.A., Sadoon, M.A., Shobrakc M. DNA marker technology for wildlife conservation. Saudi J Biol Sci. 2011 V. 18. P. 219–225. DOI: 10.1016/j.sjbs.2011.03.002
5. Awasthi A., Nagaraja G., Naik G., Kanginakudru S., Thangavelu K., Nagaraju J. Genetic diversity and relationships in mulberry (genus Morus) as revealed by RAPD and ISSR marker assays. BMC Genetics. V. 5. P. 1–9. DOI: 10.1186/1471-2156-5-1
6. Baimuhametova E.A., Lashtabova S.V., Golovina V.Y., Kimsanbaev O.H., Kuluev B.R. Application of induced mutagenesis for increasing the genetic polymorphism of cotton. 2017. V.9. No. 4. P. 370–379.
7. Baumel A., Ainouche M., Kalendar R., Schulman A.H. Retrotransposons and genomic stability in populations of the young allopolyploid species Spartina anglicaE. Hubbard (Poaceae). Mol Biol Evol. 2002. V. 19. 1218–1227. DOI: 10.1093/oxfordjournals.molbev.a004182
8. Bayramgulova Z.Kh., Redkina N.N., Bayramgulov N.R. Features of the gene pool of licorice Korzhinsky in the south-east of Bashkortostan. Actual problems of genetics and molecular biology. Materials of the All-Russian Youth Conference in the framework of the federal target program "Scientific and scientific-pedagogical personnel of innovative Russia" for 2009-2013. FGBOU VPO "Bashkir State Agrarian University". 2010. P. 32–37.
9. Bhattacharyya P., van Staden J. Molecular insights into genetic diversity and population dynamics of five medicinal Eulophia species: a threatened orchid taxa of Africa. Physiol Mol Biol Plants. V. 24. P. 631–641. DOI: 10.1007/s12298-018-0523-6
10. Bitonti M.B., Cozza R., Wang G., Ruffini-Castiglione M., Mazzuca S., Castiglione S., Sala F., Innocenti A.M. Nuclear and genomic changes in floating and submerged buds and leaves of heterophyllous water chestnut (Trapa natans). Physiologia Plantarum. 1996. V. 97. P. 21–27.
11. Blackmore T., Thomas I., McMahon R., Powell W., Hegarty M. Genetic-geographic correlation revealed across a broad European ecotypic sample of perennial ryegrass (Lolium perenne) using array-based SNP genotyping. Theor Appl Genet. 2015. V. 128. P. 1917–1932. DOI: 10.1007/s00122-015-2556-3
12. Blouin M.S., Parsons M., Lacaille V., Lotz S. Use of microsatellite loci to classify individuals by relatedness. Molecular Ecology. 1996. V. 5. P. 393–401.
13. Boboshina I.V., Boronnikova S.V. Studying of genetic polymorphism of some grades Triticum aestivum with use of ISSR-markers. Agrarian Bulletin of the Urals. 2012. No. 5. P. 19–20.
14. Boronnikova S.V. Genetic certification of populations of rare species of plants of the genus Adonis using ISSR- and IRAP markers. Izvestia of Timiryazev Agricultural Academy. 1. 2009. P. 82–88.
15. Boronnikova S.V. Genetic certification of rare and endangered species of plants as basis for their gene pool preservation optimization. Questions of modern science and practice. Vernadsky University. 2009. No. 3. P. 8–17.
16. Boronnikova S.V., Kokaeva Z.G., Tikhomirova N.N., Smirnova A. V., Boikova A. A. Molecular-genetic analysis of a rare medicinal plant species (Adonis sibirica) based on polymorphism of ISSR markers. Uspekhi Sovremennoi Biologii. 2010. V. 130. No. 5. P. 481–486.
17. Boronnikova S.V., Nechaeva Yu.S. The molecular-genetic identification and sertification of rare species of plants of Perm krai Adenophora lilifolia (L.) А. DC. Bulletin of Perm University. 2012. P. 41–44.
18. Boronnikova S.V. Molecular genetic analysis and assessment of the state of the gene pools of plant species of the Perm region: monograph. Perm State National Research University. 2013. 239 p.
19. Devyatova N.M., Beltyukova N.N., Nazarov A.V. Analysis of the genetic diversity of Poa pratensis L. under conditions of oil pollution of soils using IRAP markers. Agrarian Bulletin of the Urals. 2011. No. 1. P. 18–20.
20. Dizkirici A., Kansu C., Onde S. Molecular phylogeny of Triticum and Aegilops genera based on its and MatK sequence data. Pakistan Journal of Botany. V. 48. P. 143–153.
21. Dymshakova O.S., Semerikov V.L., Lascoux M. AFLP analysis to estimate the genetic contribution of parents to progeny from hybridization between Saxifraga sibirica and S. cernua L. Russian Journal of Ecology. 2012. V. 43. No. 5. P. 347–351. DOI: 10.1134/S1067413612050062
22. Ebadi M., Eghbali M. Study of different wheat cultivars using the ISSR marker. World Family Medicine. 2017. V. 10. P. 296–301. DOI: 10.5742/MEWFM.2017.93178
23. Eruult Ch., Naranhazhid M., Choizhamts G., Purevdorzh I. Molecular genetic study of Dasiphora fruticosa growing in Mongolia. Siberian Medical Journal (Irkutsk). V. 119. No. 4. P. 106–110.
24. Evdokimov I.Yu. Molecular phylogeny of the Ranunculaceae family based on rbcL and trnL-F chloroplast DNA sequences. Problems of botany of Southern Siberia and Mongolia. 2017. No. 16. P. 240–245.
25. Fedorov N.I., Redkina N.N., Yanbaev Yu.A., Mikhaylenko O.I. Comparative analysis of the variability of isozyme loci of Thalictrum species in the Southern Urals. Actual problems of genetics and molecular biology. Materials of the All-Russian Youth Conference in the framework of the federal target program "Scientific and Scientific-Pedagogical Personnel of Innovative Russia" for 2009-2013. Ministry of Agriculture of the Russian Federation. Bashkir State Agrarian University ". 2012. P. 90–92.
26. Flavell A.J., Knox M.R., Pearce S.R., Ellis T.H. Retrotransposon-Based Insertion Polymorphisms (RBIP) for high throughput marker analysis. Plant 1998. V. 16. P. 643–650.
27. Foster T.F., Allan G.J., Chan A.P., Rabinowicz P.D., Ravel J., Jackson P.J., Keim P. Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis). BMC Plant Biol. 2010. DOI: 10.1186/1471-2229-10-13
28. Frolova L.L., Sabirov M.S., Firsova S.S. Phylogenetic analysis of rbcL, cpcA and cpcB, psaA, atpB genes of indicating phytoplankton organisms. Georesources. 2012. No. 6. P. 45–48.
29. Gaweł M., Wisniewska I., Rafalski A. Semi-specific PCR for the evaluation of diversity among cultivars of wheat and triticale. Cell Mol Biol Lett. 2002. V. 7. P. 577–582.
30. Gilani S.A., HiranoH., Fujii Y., Watanabe K. AFLP and PBA polymorphisms in an endangered medicinal plant, Rhazya stricta, in Pakistan. Plant Genetic Resources. 2014. V. 12. P. 199–206.
31. Golovnina K.A., Glushkov S.A., Blinov A.G., Mayorov V.I., Adkison L.R., Goncharov N.P. Molecular phylogeny of genus Triticum Plant Syst Evol. 2007. V. 264. P. 195–216. DOI: 10.1007/s00606-006-0478-x
32. Grushetskaya Z.E., Nikitinskaya T.V., Kubrak S.V., Dzyuban O.V., Kukhareva L.V., Poliksenova V.D., Titok V.V., Lemesh V.A., Parfenov V.I., Khotyleva L.V. Using ISSR-analysis to study intra- and interspecific genetic polymorphism of various taxa of higher plants. Bulletin of BSU. 2013. No. 3. P. 50–56.
33. Grzebelus D., Stawujak K., Mitoraj J., Szklarczyk M. Dynamics of vulmar/vulmite group of transposable elements in Chenopodiaceae subfamily Betoideae. 2011. V. 139. P. 1209–1216. DOI: 10.1007/s10709-011-9622-9
34. Guchetl S.Z., Chelyustnikova T.A., Antonova T.S. Optimization of broomrape DNA extraction (Orobanche cumana) and identification of polymorphic RAPD and SSR loci for genotyping the oilseed parasite. Scientific and technical bulletin of the All-Russian Scientific Research Institute of Oilseeds. Krasnodar. 2013. No. 2. P. 17.
35. Gui F.R., Wan F.H., Guo J.Y. Determination of the population genetic structure of the invasive weed Ageratina adenophora using ISSR-PCR markers. Russ J Plant Physiol. 2009. V. 56. P. 410–416. DOI: 10.1134/S1021443709030157
36. Gustafsson A.L., Skrede I., Rowe H.C., Gussarova G., Borgen L., Rieseberg L.H., Brochmann C., Parisod C. Genetics of cryptic speciation within an Arctic mustard, Draba nivalis. PLoS One. 2014. V. 9(4): e93834. DOI: 10.1371/journal.pone.0093834
37. He R.L., Han Y.L., Wang F., Liu J.Q., Wang L.H. Analysis on SSR information in transcriptome of Astragalus membranaceus mongholicus and its polymorphism. Zhongguo Zhong Yao Za Zhi. 2018. V. 43. P. 1838–1843. DOI: 10.19540/j.cnki.cjcmm.20180307.002
38. Huang S., Sirikhachornkit A., Faris J.D., Su X., Gill B.S., Haselkorn R., Gornicki P. Phylogenetic analysis of the acetyl-CoA carboxylase and 3-phosphoglycerate kinase loci in wheat and other grasses. Plant Mol Biol. 2002. V. 48. P. 805–820. DOI: 10.1023/A:1014868320552
39. Huang Q., Wang Z., Wang T., Su Y. Development and characterization of 23 polymorphic microsatellite loci for Amentotaxus argotaenia (Taxaceae), a relict vulnerable species. Appl Plant Sci. 2018. V. 23. 6(5):e01149. DOI: 10.1002/aps3.1149
40. Ievina B., Syed N.H., Flavell A.J., Ievinsh G., Rostoks N. Development of retrotransposon-based SSAP molecular marker system for study of genetic diversity in sea holly (Eryngium maritimum ). Plant Genetic Resources: Characterization and Utilization. 2010. V. 8. P. 258–266. DOI: 10.1017/s1479262110000316
41. Jarne P., Lagoda P.J. Microsatellites, from molecules to populations and back. Trends in Ecology & Evolution. V.11 P. 424–429.
42. Ji F., Wei W., Liu Y., Wang G., Zhang Q., Xing Y., Zhang S., Liu Z., Cao Q., Qin L. Construction of a SNP-based high-density genetic map using genotyping by sequencing (GBS) and QTL analysis of nut traits in Chinese chestnut (Castanea mollissima Blume). Front Plant Sci. 2018. V. 14. 816. DOI: 10.3389/fpls.2018.00816
43. Jing E., Gesta S., Kahn C.R. SIRT2 regulates adipocyte differentiation through FoxO1 acetylation/deacetylation. Cell Metab. 2007. V. 6. P. 105–114.
44. Kachare S., Tiwari S., Tripathi N. Morphological and molecular assessment of genetic diversity of water chestnut (Trapa natans) from different ponds of central India. World Research Journal of Cell Biology. 2013. V. 1. P. 028–031.
45. Kalaev V.N., Zemlyanukhina O.A., Karpechenko I.Yu., Karpechenko KA, Kondratieva A.M., Veprintsev V.N., Karpechenko N.A., Karpova S.S., Moiseeva E.V., Baranova T.V. Using the methods of molecular genetic analysis to study the DNA polymorphism of plants of the genus Rhododendron for the purpose of their certification. Basic research. Publishing House "Academy of Natural Sciences." Penza. 2012. No. 6. P. 323–328.
46. Kalendar R.N., Grob T., Regina M., Suoniemi A., Schulman A.H. IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Appl Genet. 1999. V. 98. P. 704–711.
47. Kalendar R.N., Glazko V.I. Types of molecular-genetic markers and their application. Physiology and Biochemistry of Cultivated Plants. 2002. V. 34. P. 279–296.
48. Kalendar R.N., Schulman A.H. IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nature Protoc. 2006. V. 1. P. 2478–2484.
49. Kalko G.V. The DNA markers for exploring of genetic resources of spruce and pine. Proceedings of the Saint Petersburg Forestry Research Institute. No. 4. P. 19–34.
50. Kalko G.V. The testing of nuclear microsatellite markers of Scots pine. Proceedings of the Saint Petersburg Forestry Research Institute. No. 1. P. 23–34.
51. Kanazin V., Blake T., Shoemaker R. Organization of the histone H3 genes in soybean, barley and wheat. Gen. Genet. 1996. V. 250. P. 137–147.
52. Karp A., Edwards K., Bruford M., Vosman B., Morgante M., Seberg O.,Kremer A., Boursot P., Arctander P., Tautz D., Hewitt G. Newer molecular technologies for biodiversity evaluation: opportunities and challenges. Nature Biotechnol. 1997. V. 15. P. 625–628.
53. Khlestkina E.K. Molecular markers in genetic studies and breeding. Russian Journal of Genetics: Applied Research. 2014. Т. 4. No. 3. P. 236–244. DOI: 10.1134/S2079059714030022
54. Kochieva E.Z., Oganisyan A.G. Molecular analysis of RAPD markers of the potato genome. Agricultural biotechnology. Selected works. Under. Ed. Shevelukha V.S. Eurasia. 2000. T. 1. P. 24–32.
55. Kuhn B.C., Mangolin C.A., Souto E.R., Vicient C.M., Machado M.F. Development of retrotransposon-based markers IRAP and REMAP for cassava (Manihot esculenta). Genet Mol Res. 2016. V. 15. DOI: 10.4238/gmr.15027149
56. Kuluev B.R., Artyukhin A.E., Shevchenko A.M., Mikhaylova E.V. 2017. Water caltrop Trapa: biology, habitat and the study of Its isolated populations in the lakes of Nurimanovsky district in the Republic of Bashkortostan. Biomics. 2017. V. 9. No. 2. P. 101–118.
57. Kuluev B.R., Fateryga A.V., Kuluev A.R., Mikhaylova E.V., Chemeris A.V. The molecular genetic study of krim-saghyz (Taraxacum hybernum Steven) using SSR, RAPD and ISSR markers. Vavilov Journal of Genetics and Breeding. 2018a. V. 22. P. 102–107. DOI 10.18699/VJ18.337
58. Kuluev B.R., Baymiev An.Kh., Gerashchenkov G.A., Chemeris D.A., Zubov V.V., Kuluev A.R., Baymiev Al.Kh., Chemeris A.V. Random priming PCR strategies for identification of multilocus DNA polymorphism in eukaryotes. Russian Journal of Genetics. 2018b. V. 54. No. 5. P. 499–513. DOI: 10.1134/S102279541805006X
59. Kuluev A.R., Matnijazov R.T., Kuluev B.R., Chemeris A.V. A molecular genetic research of the Triticum sinskajae Filat. et Kurk. by RAPD analysis and by comparing the nucleotide sequences of the variable intergenic region of the petN-trnC-GCA chloroplast genome and intron of the histone H3.2 gene. Ecological Genetics. 2018c. V. 16. P. 53–59. DOI: 10.17816/ecogen16153-59
60. Kuluev R., Shvets D.Yu., Golovanov Ya.M., Probatova N.S. Thladiantha dubia (Cucurbitaceae) in Republic of Bashkortostan - a dangerous weed with high invasive potential. Russian Journal of Biological Invasions. 2018d. No. 4. In press.
61. Kostyukova E.E., Zayakin VV, Nam I.Ya. Molecular genetic analysis of rare orchid species of the Bryansk region. Bulletin of the Bryansk branch of the RBO. 2013. No. 1. P. 51–55.
62. Li S.F, Wang L.J, Deng C.L, Gao W.J. Identification of male-specific AFLP and scar markers in the Dioecious plant Humulus scandens. Mol Cell Probes. 2017. V. 34. P. 68–70. DOI: 10.1016/j.mcP.2017.05.007
63. Li W., Gao Z., Xiao W., Wei Y., Liu Y., Chen G., Pu Z., Chen H., Zheng Y. Molecular diversity of restriction enzyme sites, indels and upstream open reading frames (uORFs) of 5' untransalted regions (UTRs) of Waxy genes in Triticum and Aegilops L. species. Genetic Resources and Crop Evolution. 2012. V. 59. P. 1625–1647.
64. Li X.L., Fan X.R., Chu H.J., Wei Li., Chen Y.Y. Genetic delimitation and population structure of three Trapa taxa from the Yangtze River, China. Aquatic Botany. 2017. V. 136. P. 61–70.
65. Li-Na G., Xue-Li Z., Xin-Fen G. De novo assembly and characterization of leaf transcriptome for the development of EST-SSR markers of the non-model species Indigofera szechuensis. Biochemical Systematics and Ecology. 2016. V. 68. P. 36–43.
66. Liu X., Zhang X., Shi Y., Tang D. Genetic diversity analysis of nine narcissus based on morphological characteristics and random amplified polymorphic DNA markers. Hortscience. 2017. V. 52. No. 2. P. 212–220. DOI: 10.21273/HORTSCI11171-16
67. Logacheva M.D., Penin A.A., Samigullin T.H., Vallejo-Roman C.M., Antonov A.S. Phylogeny of flowering plants by the chloroplast genome sequences: In search of a "lucky gene". Biochemistry (Moscow). 2007. V. 72. No. 12. P. 1324–1330. DOI: 10.1134/S0006297907120061
68. Luzhanin V.G., Rodionov A.V., Yakovlev G.P. Molecular-phylogenetic study of the genus Ononis(Fabaceae) in the flora of Russia and adjacent countries. Botanicheskii Zhurnal. 2013. V. 98. No. 5. P. 629–637.
69. Nadot S., Bajon R., Lejeune B. The chloroplast gene rps4 as a tool for the study of Poaceae phylogeny. Plant Syst. Evol. 1994. V. 191. P. 27–38.
70. Nagy E.D., Molnár I., Schneider A., Kovács G., Molnár-Láng M. Characterization of chromosome-specific S-SAP markers and their use in studying genetic diversity in Aegilops Genome. 2006. V. 49. P. 289–296.
71. Nguyen T.X., Lee S.I., Rai R., Kim N.S., Kim J.H. Ribosomal DNA locus variation and REMAP analysis of the diploid and triploid complexes of Lilium lancifolium. Genome. 2016. V. 59. P. 551–564. DOI: 10.1139/gen-2016-0011
72. Mahatma M.K., Srivashtav V.S., Jha S. Genetic diversity analysis of date palm using Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeat (ISSR). Methods Mol Biol. 2017. V. 1638. P. 105–112. DOI: 10.1007/978-1-4939-7159-6_10
73. Marwal A., Sahu A.K., Choudhary D.K., Gaur R.K. Complete nucleotide sequence of a begomovirus associated with satellites molecules infecting a new host tagetes patula in India. Virus Genes. 2014. V. 47. P. 194–198. DOI: 10.1007/s11262-013-0914-2
74. Matveeva T.V., Simonova A.V., LutovaL.A. Molecular markers of inbred radish (Raphanus sativus var. Radicola pers) lines. Cell and Mol. Biol. Lett. 2002. V. 7. P. 845–848.
75. Matveeva T. V., Pavlova O. A., Bogomaz D. I., Lutova L. A., Demkovich A. E. Molecular markers for plant species identification and phylogenetics. Ecological Genetics. 2011. V. 9. No. 1. P. 32–43.
76. McAssey E.V., Gudger E.G., Zuellig M.P., Burke J.M. Population genetics of the rubber-producing Russian dandelion (Taraxacum kok-saghyz). PLoS One. 2016. V. 11. DOI 10.1371/journal.pone.0146417
77. Melnikova N.V., Spranskaya A.S., Dariy M.V., Belenikin M., Dmitriev A.A., Kudryavtseva A.V. The use of molecular markers based on retrotransposons for studying the genetic diversity of plants. Bulletin of the Russian State Agrarian Correspondence University. No. 14. P. 32–35.
78. Ming-na L., Rui-cai L., Zi-rong F., Feng-qi L., Yan S., Kun Z., Jun-mei K., Zhen W., Shi-hao C. Transcriptome analysis of salt-responsive genes and SSR marker exploration in Carex rigescens using RNA-seq. Journal of Integrative Agriculture. 2018. V. 17. P. 184–196.
79. Mukrimin M., Kovalchuk A., Neves L.G., Jaber E.H.A., Haapanen M., Kirst M., Asiegbu F.O. Genome-wide exon-capture approach identifies genetic variants of Norway spruce genes associated with susceptibility to Heterobasidion parviporum Front Plant Sci. 2018. V. 9. 793. DOI: 10.3389/fpls.2018.00793
80. Nechaeva Yu.S., Boronnikova S.V., Vidyakin A.I., Prishnivskaya Ya.V., Yusupov R.R. Molecular genetic analysis of populations of coniferous plants in the Urals and the east of the European part of Russia for the conservation and renewal of forest resources. Proceedings of the Samara Scientific Center of the Russian Academy of Sciences. 2014. V. 16. No. 1-3. P. 878–882.
81. Nikulin V. Yu., Gontcharov A.A. Molecular-phylogenetic characterization of Sedum (Crassulaceae) and closely related genera based on cpDNA gene matK and ITS rDNA sequence comparisons. Botanicheskii Zhurnal. V. 102. No. 3. P. 309–328.
82. Nimbal S., Behl R.K., Chhabra A.K. RAPD analysis for genetic polymorphism in bread wheat (Triticum aestivum ) genotypes varying for grain protein content. The South Pacific J. Nat. Sci. 2009. V. 27. P. 49–56. DOI: 10.1071/SP09009
83. Novikova A.A., Sheykina O.V., Novikov P.S., Doronina G.U. Evaluation of the possibility of using ISSR-markers for the systematization and genetic certification of plants of the genus Rhododendron. Polythematic network electronic scientific journal of the Kuban State Agrarian University. 2012. No. 82. P. 79–89.
84. Olmstead R.G., Sweere J.A. Combining data in phylogenetic systematics: An empirical approach using three molecular data sets in the Solanaceae. Syst. Biol. V. 43. P. 467–481.
85. Ouyang P., Kang D., Mo X., Tian E., Hu Y., Huang R. Development and characterization of high-throughput EST-based SSR markers for Pogostemon cablin using transcriptome sequencing. Molecules. 2018. V. 23. pii: E2014. DOI: 10.3390/molecules23082014
86. Pakhrou O., Medraoui L., Yatrib C., Alami M., Filali-Maltouf A., Belkadi B. Assessment of genetic diversity and population structure of an endemic Moroccan tree (Argania spinosa) based in IRAP and ISSR markers and implications for conservation. Physiol Mol Biol Plants. 2017. V. 23. P. 651–661. DOI: 10.1007/s12298-017-0446-7
87. Palombi M.A., Damiano C. Comparison between RAPD and SSR molecular markers in detecting genetic variation in kiwifruit (Actinidia deliciosa Chev). Plant Cell Reports. 2002. V. 20. P. 1061–1066.
88. Pandotra P., Gupta A., Khan S., Ram G., Gupta S. A comparative assessment of ISSR, RAPD, IRAP, & REMAP molecular markers in Zingiber officinale germplasm characterization. Scientia Horticulturae. 2015. V. 194. P. 201–207.
89. Paux E., Faure S., Choulet F., Roger D., Gauthier V., Martinant J., Sourdille P., Balfourier F., Le Paslier M., Chauveau A., Cakir M., Gandon B., Feuillet C. Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat. Plant Biotechnol. 2010. V. 8. P. 196–210. DOI: 10.1111/j.1467-7652.2009.00477.x
90. Polanco C., Ruiz M. AFLP analysis of somaclonal variationin Arabidopsis thaliana regenerated plants. Plant Sci. 2002. V. 162. P. 817–824.
91. Prażak R. Paczos-Grzęda E. Genetic similarity among Aegilops kotschyi with Triticum aestivum L. hybrid lines. Romanian Agricultural Research. 2017. Vol. 34. P. 15–23.
92. Prince L.M. Plastid primers for angiosperm phylogenetics and phylogeography. Appl Plant Sci. 2015. V. 3. pii: apps.1400085. DOI: 10.3732/apps.1400085
93. Prishnivska Ya.V., Nechayeva Yu.S., Krasilnikov VP, Boronnikova S.V. Molecular genetic analysis of four populations of Pinus silvestris L. in the east of the Russian plain based on ISSR-marker polymorphism. Bulletin of the Orenburg State University. 2016. No. 2. P. 88–93.
94. Protopopova M.V., Pavlichenko V.V., Gnutikov A.A., Adelshin R.V., Chepinoga V.V. The use of genetic markers to assess the state of relict plant species of the Baikal Siberia. Bulletin of Peoples' Friendship University of Russia. Series: Ecology and Life Safety. No. 4. P. 28–36.
95. Queller D.C., Strassmann J.E., Hughes C.R. Microsatellites and kinship. Trends in Ecology and Evolution. 1993. V. 8. P. 285–288.
96. Rani V., Parida A., Raina S.N. Random amplified polymorphic DNA (RAPD) markers for genetic analysis in micropropagated plants of Populus deltoides Plant Cell Rep. 1995. V. 14. P.459–462. DOI: 10.1007/bf00234055
97. Reddy, R.P., Sarla, N., Siddiq, E.A. Inter Simple Sequence Repeat (ISSR) polymorphism and its application in plant breeding. Euphytica. V. 128. P. 9–17.
98. Reunova G.D., Kats I.L., Muzarok T.I., Zhuravlev Y.N. Polymorphism of RAPD, ISSR and AFLP markers of the Panax ginseng C. A. Meyer (Araliaceae) genome. Russian Journal of Genetics. V. 46. No. 8. P. 938–947. DOI: 10.1134/S1022795410080053
99. Rohlf F.J. NTSYSpc numerical taxonomy and multivariate analysis system. Version 5.1. Exeter Publishing Ltd., Setauket, N.Y.2001.
100. Romero G., Adeva C., Battad Z. Genetic fingerprinting: advancing the frontiers of crop biology research. Phil Sci Lett. 2009. V. 2. P. 8–13.
101. Ronikier M. The use of AFLP markers in conservation genetics - a case study on Pulsatilla vernalis in the polish lowlands. Cell Mol Biol Lett. 2002 V. 7. P. 677–684.
102. Roy N.S., Lee S.I., Nkongolo K., Kim N.S. Retrotransposons in Betula nana, and interspecific relationships in the Betuloideae, based on Inter-Retrotransposon Amplified Polymorphism (IRAP) markers. Genes Genomics. 2018. V. 40. P. 511–519. DOI: 10.1007/s13258-018-0655-7
103. Sagyndykova MS, Imanbaeva A.A., Sarsenbayev K.N. Study of the medicinal plant Ferula foetida using RAPD-PCR DNA analysis in natural populations of Mangystau. In collection: Biological features of medicinal and aromatic plants and their role in medicine collection of scientific papers of the International Scientific and Practical Conference dedicated to the 85th anniversary of VILAR. 2016. P. 149–152.
104. Savelkoul P.H, Aarts H.J., De Haas J., Dijkshoorn L., Duim B., Otsen M., Rademaker J.l., Schouls L., Lenstra J.A. Amplified-fragment length polymorphism analysis: the state of an art. J Clin Microbiol. 1999. V. 37. P. 3083–3091.
105. Senerchia N., Felber F., Parisod C. Contrasting evolutionary trajectories of multiple retrotransposons following independent allopolyploidy in wild wheats. New Phytol. 2014. V. 202. P. 975–985. DOI: 10.1111/nph.12731
106. Simchuk A.P., Ivashov A.V., Oberemok V.V., Gurbuz M.F. Influence of genetic variability of oak fluffy oak and green oak moth on the components of fitness of its parasite Brachimeria intermedia (Hymenoptera: chalcididae). Ecosystems, their optimization and protection. 2015. V. 6. P. 115–120.
107. Sobrino B., Briоn M., Carracedo A. SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int. 2005. V. 154. P. 181–194.
108. Sorkheh K., Amirbakhtiar N., Ercisli S. Potential start codon targeted (SCoT) and Inter-Retrotransposon Amplified Polymorphism (IRAP) markers for evaluation of genetic diversity and conservation of wild Pistacia species population. Biochem Genet. 2016. V. 54. P. 368–387. DOI: 10.1007/s10528-016-9725-1
109. Sorkheh K., Dehkordi M.K., Ercisli S., Hegedus A., Halász J. Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species. Sci Rep. 2017. V. 7. P. 5966. DOI: 10.1038/s41598-017-06084-4
110. Spiridovich E.V., Fomenko T.I., Vlasova AB, Mazur T.V., Yukhimuk A.N. Biochemical and molecular genetic analysis of Agastache rugosa (Fisch. et Mey.) Kuntze in the culture in vitro. Bulletin of pharmacy. 2012. No. 4. 75–87.
111. Sukhareva A.S., Kuluev B.R. DNA markers for genetic analysis of crops. Biomics. 2018. V. 10. No. 1. P. 69–84. DOI: 10.31301/2221-6197.bmcs.2018-15
112. Sulimova G.E. DNK-markers in genetic studies: types of markers, their characteristics and application. Uspekhi Sovremennoy Biologii. 2011. V. 9. P. 32–43.
113. Svetlakova T.N., Boboshina I.V., Boronnikova S.V., Nechaeva Yu.S. Ecological and genetic analysis of population structure of Populus tremula in Perm region. Ecological Genetics. 2012. V. 10. No. 3. P. 22–27.
114. Taberlet P., Gielly L., Pautou G., Bouvet J. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol. 1991. V. 17. P. 1105–1109.
115. Tang S., Dai W., Li M., Zhang Y., Geng Y., Wang L., Zhong Y. Genetic diversity of relictual and endangered plant Abies ziyuanensis (Pinaceae) revealed by AFLP and SSR markers. Genetica. 2007. V. 133 P. 21–30.
116. Tsuchihashi Z., Dracopoli N. Progress in high throughput SNP genotyping methods. Pharmacogenomics. 2002. V. 2. P. 103–110.
117. Tukhvatullina L.A., Abramova L.M. Rare resource bows wild flora of Bashkortostan in the conditions of introduction. Bulletin of the Orenburg State Agrarian University. 2012. No. 1. P. 33–35.
118. Vakhitov V.A., Chemeris A.V., Sabirzhanov B.E., Akhunov E.D., Kulikov A.M., Nikonorov Yu.M., Gimalov F.R., Bikbulatova S.M., Baymiev Al.Kh. The phylogeny of Triticum L. and Aegilops L. inferred from comparative analysis of nucleotide sequences in rDNA promoter regions. Russian Journal of Genetics. V. 39. No. 1. P. 1–11. DOI: 10.1023/A:1022095224123
119. Van de Peer Y. Treecon for Windows: a software package for the construction and drawing evolutionary trees for the Microsoft Windows environment. Computer Application in the Biosciences. 1994. V.10. No. 5. P. 569–570.
120. Vos P.R., Hogers M., Bleeker M. T Van De Lee, Hornes M., Frijters A., Pot J., Peleman J., Kuiper M. AFLP: a new technique for DNA fingerprinting. Acids Res. 1995. V. 23. P. 4407–4414.
121. Waugh R., Mclean K., Flavell J., Pearce S.R., Kumar A., Thomas B., Powell W. Genetic distribution of bare-1-like retrotransposable elements in the barley genome revealed by Sequence-Specific Amplification Polymorphisms (S-SAP). Gen. Genet. 1997. V. 253. P.687–694.
122. Williams J.G., Kubelik A.R., Livak K.J., Rafalski J.A., Tingey S.V. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 1990. V. 8. P. 6531–6535.
123. Yanbaev R.Yu., Gabitova A.A., Sultanova R.R., Boronnikova S.V., Yanbaev Yu.A. ISSR analysis of DNA polymorphism of pedunculate oak: arguments in favor of using local plantations for reforestation of seeds. Proceedings of the Orenburg State Agrarian University. 2017. No. 1. P. 220–222.
124. Yang M., Han N., Li H., Meng L. Transcriptome analysis and microsatellite markers development of a traditional Chinese medicinal herb Halenia elliptica Don (Gentianaceae). Evol Bioinform Online. 2018. V. 14. DOI: 10.1177/1176934318790263
125. Zabeau M., Vos P. Selective restriction fragment amplification: a general method for DNA fingerprinting. European patent application 92402629.7 (publ. n. 0 534 858 a1). 1993.
126. Zaretskaya M.V., Fedorenko O.M. Genetic diversity and population structure of the species Arabidopsis thaliana (L.) Heynh. on Valaam island. Transactions of Karelian Research Centre of the Russian Academy of Sciences. No. 11 P. 9–16.
127. Zawko G., Krauss S., Dixon K.W., Sivasithamparam K. Conservation genetics of the rare and endangered Leucopogon obtectus (Ericaceae). Ecol. 2001 V. 10 P. 2389–2396.
128. Ziętkiewicz , Rafalski A., Labuda D. Genome fingerprinting by simple-sequence repeat (SSR) - anchored polymerase chain reaction amplification. Genomics. 1994. V. 20. P. 176–183.