Молекулярные маркеры. МОЛЕКУЛЯРНЫЕ МАРКЕРЫ. ПРИЧИНЫ И ПОСЛЕДСТВИЯ ОШИБОК ГЕНОТИПИРОВАН. Молекулярные маркеры. Причины и последствия ошибок генотипирования
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ЗАКЛЮЧЕНИЕ За последние два десятилетия наблюдается экспоненциальный рост использования молекулярных маркеров в изучении разнообразных аспектов жизнедеятельности растительных организмов. Общее количество работ уже приближается к двум десяткам тысяч. В связи с этим очевидна не только значимость использования различных типов молекулярных маркеров, но и корректность оценки получаемых с их помощью результатов. Опираясь на огромный экспериментальный опыт, в целом ряде обзоров исследователями сформулированы преимущества и недостатки используемых молекулярных маркеров, основные требования при их выборе для того или иного рода исследований. Несмотря на разнообразие маркеров, существует ряд первоочередных общих требований и критериев, позволяющих повысить достоверность получаемых результатов. В их числе выбор адекватного типа маркеров для решения поставленной задачи; достаточно высокая полиморфность маркеров, высокая разрешающая способность, кодоминантность, частота и равномерность распределения по геному, высокая воспроизводимость. Не менее важным и существенным при генетическом анализе является минимизирование ошибок, которые разделены исследователями на категории. Главные из них: соответствующее качество и количество анализируемой ДНК; оценка и отбор оптимальных праймеров для повышения информативности соответствующих локусов; особенности Tag-полимеразы и оптимизация условий ПЦР; надлежащее использование повторностей и контролей, а также адекватность статистических подходов для оценки полученных результатов и выявления ошибок при анализе. Работа выполнена в рамках Гранта 0048/ГФ по подприоритету: «Исследования в области продовольственной безопасности» Бюджетной программы 055, финансируемой Государственным учреждением «Комитет науки Министерства образования и науки Республики Казахстан». ЛИТЕРАТУРА Ganal M.W., Polley A., Graner E.M., Plieske J., Wieseke R., Luerssen H., Durstewitz G. Large SNP arrays for genotyping in crop plants // J Biosci. – 2012. – Vol. 37. – P. 821-288. CrossRef Miedaner T., Korzun V. Marker-assisted selection for disease resistance in wheat and barley breeding // Phytopathology. – 2012. – Vol.102. – P. 560-566. CrossRef Paux E., Sourdille P., Mackay I., Feuillet C. Sequence-based marker development in wheat: advances and applications to breeding // Biotechnol Adv. – 2001. – Vol. 30. – P. 1071-1088. CrossRef Hall D., Tegström C., Ingvarsson P.K. Using association mapping to dissect the genetic basis of complex traits in plants // Brief Funct Genomics. – 2010. – Vol. 9. – P. 157-165. CrossRef Zimmer E.A., Wen J. Using nuclear gene data for plant phylogenetics: progress and prospects // Mol Phylogenet Evol. – 2012. – Vol. 65. – P. 774-785. CrossRef Kumar P., Gupta V.K., Misra A.K., Modi D. R., Pandey B. K. Potential of Molecular Markers in Plant Biotechnology // Plant Omics Journal. – 2009. – Vol. 2. – Р. 141-162. Woodhead M., Russell J., Squirrell J., Hollingsworth P. M., Mackenzie K., Gibb M., Powell W. Comparative analysis of population genetic structure in Athyrium distentifolium (Pteridophyta) using AFLPs and SSRs from anonymous and transcribed gene regions // Molecular Ecology. – 2005. – Vol. 14. – Р. 1681-1695. CrossRef Kuczmog A., Galambos A., Horváth S., Mátai A., Kozma P., Szegedi E., Putnoky P. Mapping of crown gall resistance locus Rcg1 in grapevine // Theor Appl Genet. – 2012. – Vol.125. – P. 1565-1574. CrossRef Ujihara T, Taniguchi F, Tanaka J, Hayashi N. Development of Expressed Sequence Tag (EST)-based Cleaved Amplified Polymorphic Sequence (CAPS) markers of tea plant and their application to cultivar identification // J Agric Food Chem. – 2011. – Vol. 59. – P. 1557-1564. CrossRef Segatto A.L.A., Caze A.L.R., Turchetto C., Klahre U., Kuhlemeier C., Bonatto S.L., Freitas L.B. Nuclear and plastid markers reveal the persistence of genetic identity: A newperspective on the evolutionary history of Petunia exserta // Molecular Phylogenetics and Evolution. - 2014. – Vol.70. – P. 504–512. CrossRef Cui Y., Lee M.Y., Huo N., Bragg J., Yan L., Yuan C., Li C., Holditch S.J., Xie J., Luo M.C., Li D., Yu J., Martin J., Schackwitz W., Gu Y.Q., Vogel J.P., Jackson A.O., Liu Z., Garvin D.F. Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon // PLoS One. – 2012. – Vol. 7:e38333. Jo K.-R., Arens M., Kim T.-Y., Jongsma M.A., Visser R.G.F., Jacobsen E., Vossen H.J. Mapping of the S. demissum late blight resistance gene R8 to a new locus on chromosome IX // Theor Appl Genet. – 2011. – Vol. 123. – P. 1331–1340. CrossRef Shu Q.Y., Liu G.S., Qi D.M., Chu C.C., Liu .J, Li H.J. An effective method for axillary bud culture and RAPD analysis of cloned plants in tetraploid black locust // Plant Cell Rep. – 2003. – Vol. 22. – P. 1751-1780. CrossRef Sreedhar R.V., Venkatachalam L., Bhagyalakshmi N. Genetic fidelity of long-term micropropagated shoot cultures of vanilla (Vanilla planifolia Andrews) as assessed by molecular markers // Biotechnol. J. – 2007. – Vol. 2. – P. 1007–1013. CrossRef Rai G.K, Singh M., Rai N.P., Bhardwaj D.R., Kumar S. In vitro propagation of spine gourd (Momordica dioica Roxb.) and assessment of genetic fidelity of micropropagated plants using RAPD analysis // Physiol Mol Biol Plants. – 2012. – Vol. 18. – P. 273-280. CrossRef Kim J.K., An G.H., Ahn S.H., Moon Y.H., Cha Y.L., Bark S.T., Choi Y.H., Suh S.J., Seo S.G., Kim S.H., Koo B.C. Development of SCAR marker for simultaneous identification of Miscanthus sacchariflorus, M. sinensis and M. x giganteus // Bioprocess Biosyst Eng. – 2012. – Vol.35. – P. 55-59. CrossRef Pankin A.A., Khavkin E.E. Genome-specific SCAR markers help solve taxonomy issues: a case study with Sinapis arvensis (Brassiceae, Brassicaceae) // Am J Bot. – 2011. – Vol. 98:e54-7. CrossRef Ray T., Roy S.C. Genetic diversity of Amaranthus species from the Indo-Gangetic plains revealed by RAPD analysis leading to the development of ecotype-specific SCAR marker // J Hered. – 2009. – Vol. 100. – P. 338-347. CrossRef Osipova E.S., Lysenko E.A., Troitsky A.V., Dolgikh Y.I., Shamina Z.B., Gostimskii S.A. Analysis of SCAR marker nucleotide sequences in maize (Zea mays L.) somaclones // Plant Sci. – 2011. – Vol. 180. – P. 313-322. CrossRef Rahman M., Sun Z., McVetty P.B., Li G. High throughput genome-specific and gene-specific molecular markers for erucic acid genes in Brassica napus (L.) for marker-assisted selection in plant breeding // Theor Appl Genet. – 2008. – Vol. 117. – P. 895-904. CrossRef Naeimi S., Kocsubé S., Antal Z., Okhovvat S.M., Javan-Nikkhah M., Vágvölgyi C., Kredics L. Strain-specific SCAR markers for the detection of Trichoderma harzianum AS12-2, a biological control agent against Rhizoctonia solani, the causal agent of rice sheath blight // Acta Biol Hung. – 2011, Mar. - №62(1). – Р. 73-84. CrossRef Falush D., Stephens M., Pritchard J.K. Inference of population structure using multilocus genotype data: dominant markers and null alleles // Molecular Ecology Notes. – 2007. – Vol. 7. – P. 574–578. CrossRef Powel l W., Machray G.C., Provan J. Polymorphism revealed by simple sequence repeats // Trends Plant Sci. – 1996. – Vol. 1. – P. 215-222. Chung A.M., Staub J.E., Chen J.F. Molecular phylogeny of Cucumis species as revealed by consensus chloroplast SSR marker length and sequence variation // Genome. – 2006. – Vol. 49. CrossRef Rajendrakumar P., Biswal A.K., Balachandran S.M., Srinivasarao K., Sundaram R.M. Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions // Bioinformatics. – 2007. – Vol. 23. – P.1-4. CrossRef Kalia R.K. Rai M.K, Kalia S., Singh R., Dhawan A.K. Microsatellite markers: an overview of the recent progress in plants // Euphytica. – 2011. – Vol.177. – P.309–334 CrossRef Hoffman J.I., and Amos W. Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion // Molecular Ecology. – 2005. – Vol. 14. – P.599-612. CrossRef Varshney R.K., Graner A., Sorrells M.E. Genic microsatellite markers in plants: features and applications // TRENDS in Biotechnology. – 2005. – Vol. 23. – P.48-55. CrossRef Ellis R., JM Burke. EST-SSRs as a resource for population genetic analyses // Heredity. – 2007. – Vol. 99. – P.125-132. CrossRef Saunders I.W., Brohede J., Hannan G.N. Estimating genotyping error rates from Mendelian errors in SNP array genotypes and their impact on inference // Genomics. – 2007. –Vol. 90. – P. 291-296. CrossRef Guichoux E., Lagache L., Wagner S., Chaumeil P., Le. Ger P., Lepais O., Lepoittevin C., Malausa E., Revardel E., Salin F., Petit R.J. Current trends in microsatellite genotyping // Molecular Ecology Resources. – 2011. – Vol. 11. – P. 591–611. CrossRef Schulman A.H., Flavell A.J., Ellis T.H. The application of LTR retrotransposons as molecular markers in plants // Methods in Molecular Biology. – 2004. – Vol. 260. – Р.145–173. Kalendar R., Antonius K., Smykal P., Schulman A.H. iPBS: a universal method for DNA Wngerprinting and retrotransposon isolation // Theor Appl Genet. – 2010. –121. – Р.1419–1430. CrossRef Castro I., D’Onofrio C., Martin J.P., Ortiz J.M., De Lorenzis G., Ferreira V.O. Pinto-Carnide. Effectiveness of AFLPs and Retrotransposon-Based Markers for the Identification of Portuguese Grapevine Cultivars and Clones Mol Biotechnol. – 2012. - Vol. 52. – Р. 26–39. Nakatsuka T., Yamada E., Saito M., Hikage T., Ushiku Y., Nishihara M. Construction of the first genetic linkage map of Japanese gentian (Gentianaceae) // BMC Genomics. – 2012. –Vol. 13. – Р. 672. CrossRef Bonin A., Bellemain E., Bronken Eidesen P., Pompanon F., Brochmann C., Taberlet P. How to track and assess genotyping errors in population genetics studies // Mol Ecol. – 2004. – Vol. 13. – P.3261-3273. CrossRef Pompanon F., Bonin A., Bellemain E.,Pierre Taberlet. Genotyping Errors: Causes, Consequences And Solutions. Genetics. – 2005. – Vol. 6. – P.847-859. CrossRef Morin P.A., Leduc R. G., Archer F. I., Martien K. K., Huebinger R., Bickham J.W., Taylor B.L. Significant deviations from Hardy–Weinberg equilibrium caused by low levels of microsatellite genotyping errors // Molecular Ecology Resources. – 2009. – Vol. 9. – P.498-504. CrossRef Gordon D., Heath S.C., Ott J. True pedigree errors more frequent than apparent errors for single nucleotide polymorphisms // Hum Hered. – 1999. – Vol.49. – P.65–70. Gordon D., Finch S.J., Nothnagel M., Ott J. Power and sample size calculations for case–control genetic association tests when errors are present: application to single nucleotide polymorphisms // Human Heredity. – 2002. – Vol. 54. – P.22–33. Sobel E., Papp J. C., Lange K. Detection and integration of genotyping errors in statistical genetics Am. J. Hum. Genet. – 2002. – Vol. 270. – P.496–508. Navidi W., Arnheim N., Waterman M.S. A multiple-Tubes Approach for Accurate genotyping of very Small DNA samples by using PCR: Statistical considerations // Am. J. Hum. Genet. – 1992. – Vol. 50. – P.347-359. Ghosh, S. et al. Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers // Genome Res. – 1997. – Vol. 7. – P.165–178. CrossRef Hosking L., Lumsden S., Lewis K., Yeo A., McCarthy L., Bansal A., Riley J., Purvis I., a Xu Ch-F. Detection of genotyping errors by Hardy–Weinberg equilibrium testing // European Journal of Human Genetics. – 2004. – Vol. 12. – P.395–399. CrossRef Ewen K.R., Bahlo M., Treloar S.A., Levinson D.F., Mowry B., Barlow J.W., S.J. Foote. Identification and Analysis of Error Types in High-Throughput Genotyping // Am. J. Hum. Genet. – 2000. – Vol. 67. – P.727–736. Gomes I., Collins A., Lonjou C. et al. Hardy–Weinberg quality control. Annals of Human Genetics. – 1999. – Vol. 63. – P.535–538. Callen D.F., Thompson A.D., Shen Y., Phillips H., Richards Rl., Mulley J.C., Sutherland G.R. Incidence and origin of 'null' alleles in the (AC)n microsatellite markers // Americun Jounrnl of Human genetics. – 1993. – Vol. 52. – P.922-927. Pemberton J.M., Slate J., Bancroftt ‘D.R, Barrett J.A. Nonamplifying alleles at microsatellite a caution for parentage and population loci: studies // Molecular Ecology. – 1995. – Vol. 4. – P.249-252. Van Oosterhout C., Weetman D., Hutchinson W. F. Estimation and adjustment of microsatellite null alleles in nonequilibrium populations // Molecular Ecology Notes. – 2006. – Vol. 6. – P.255–256. CrossRef Chapuis M.-P., Estoup A. Microsatellite Null Alleles and Estimation of Population Differentiation // Mol. Biol. Evol. – 2007. – Vol. 24. – P.621–631. CrossRef Dewoody J., Nason J.D., Hipkins V.D. Mitigating scoring errors in microsatellite data from wild populations // Molecular Ecology Notes. – 2006. – Vol. 6. – P.951–957. CrossRef Dakin E.E., Avise J.C. Microsatellite null alleles in parentage analysis // Heredity. –2004. – Vol. 93. – P.504-509. CrossRef Rungi D., Berube Y., Zhang J., Ralph S., Ritland C.E., Ellis B E., Douglas C., Bohlmann J., Ritland K. Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags // Theor Appl Genet. –2004. – Vol. 109. – P.1283–1294. CrossRef Wake D.B., Wake M.H., Specht C.D. Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution // Science. – 2011. – Vol. 331. – P.1032-1035. Estoup A., Jarne P., Cornuet J.-M. Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis // Molecular Ecology. – 2002. – Vol. 11. – P.1591–1604. O’hanlon P.C., Peakall R. A Simple method for the detection of size homoplasy among amplified fragment length polymorphism fragments // Molecular Ecology. – 2000. – Vol.9. – P.815–816. Vekemans X., Beauwens T., Lemaire M., Roldcn-Ruiz I. Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size // Molecular Ecology. – 2002. – Vol. 11. – P.139-151. Caballero A., Quesada H. Homoplasy and Distribution of AFLP Fragments: An Analysis In Silico of the Genome of Different Species // Mol. Biol. Evol. – 2010. – Vol. 27. – P.1139–1151. CrossRef Herrmann D., Poncet B.N., Manel S., Rioux D., Gielly .L, Taberlet P. Gugerli F. Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates // Genome. – 2010. – Vol. 53. – P.302–310. CrossRef Whitlock R., Hipperson H., Mannarelli M.,. Butlin R .K, Burke T. An objective, rapid and reproducible method for scoring AFLP peak-height data that minimizes genotyping error // Molecular Ecology Resources. – 2008. – Vol. 8. – P.725–735. CrossRef Zhang H., Hare M.P. Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters // Heredity. –2012. – Vol. 108. – P. 616–625. CrossRef |