Abstract
Transposable element (TE) marker system was developed considering the useful properties of the transposable elements such as their large number in the animal and plant genomes, high rate of insertion polymorphism, and ease of detection. Various methods have been employed for developing a large number of TE markers in several crop plants for genomics studies. Here we describe some of these methods including the recent whole genome search. We also review the application of TE markers in molecular breeding.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Bertioli DJ, Cannon SB, Froenicke L, Huang G, Farmer AD, Cannon EK, Liu X, Gao D, Clevenger J, Dash S, Ren L, Moretzsohn MC, Shirasawa K, Huang W, Vidigal B, Abernathy B, Chu Y, Niederhuth CE, Umale P, Araujo AC, Kozik A, Do Kim K, Burow MD, Varshney RK, Wang X, Zhang X, Barkley N, Guimaraes PM, Isobe S, Guo B, Liao B, Stalker HT, Schmitz RJ, Scheffler BE, Leal-Bertioli SC, Xun X, Jackson SA, Michelmore R, Ozias-Akins P (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat Genet 48(4):438–446. https://doi.org/10.1038/ng.3517
Consortium IBGS (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491(7426):711
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326(5956):1112–1115
Wessler SR (2006) Transposable elements and the evolution of eukaryotic genomes. Proc Natl Acad Sci 103(47):17600–17601
Kumar A, Hirochika H (2001) Applications of retrotransposons as genetic tools in plant biology. Trends Plant Sci 6(3):127–134
Casa AM, Brouwer C, Nagel A, Wang L, Zhang Q, Kresovich S, Wessler SR (2000) The MITE family Heartbreaker (Hbr): molecular markers in maize. Proc Natl Acad Sci 97(18):10083–10089. https://doi.org/10.1073/pnas.97.18.10083
Izsvak Z, Ivics Z, Shimoda N, Mohn D, Okamoto H, Hackett PB (1999) Short inverted-repeat transposable elements in teleost fish and implications for a mechanism of their amplification. J Mol Evol 48(1):13–21
Chen ZJ, Ni Z (2006) Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. BioEssays 28(3):240–252
Lu C, Chen J, Zhang Y, Hu Q, Su W, Kuang H (2012) Miniature inverted–repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa. Mol Biol Evol 29(3):1005–1017
Casacuberta JM, Santiago N (2003) Plant LTR-retrotransposons and MITEs: control of transposition and impact on the evolution of plant genes and genomes. Gene 311:1–11
Marcon HS, Domingues DS, Silva JC, Borges RJ, Matioli FF, de Mattos Fontes MR, Marino CL (2015) Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic. BMC Plant Biol 15(1):198
Purugganan M, Wessler S (1995) Transposon signatures: species-specific molecular markers that utilize a class of multiple-copy nuclear DNA. Mol Ecol 4(2):265
Waugh R, McLean K, Flavell A, Pearce S, Kumar A, Thomas B, Powell W (1997) Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol Gen Genet 253(6):687–694
Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98(5):704–711
Antonius-Klemola K, Kalendar R, Schulman AH (2006) TRIM retrotransposons occur in apple and are polymorphic between varieties but not sports. Theor Appl Genet 112(6):999–1008
Du D, Du X, Mattia MR, Wang Y, Yu Q, Huang M, Yu Y, Grosser JW, Gmitter FG (2018) LTR retrotransposons from the Citrus x clementina genome: characterization and application. Tree Genet Genomes 14(4):43
Belyayev A, Kalendar R, Brodsky L, Nevo E, Schulman AH, Raskina O (2010) Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat. Mob DNA 1(1):6
Nasri S, Mandoulakani BA, Darvishzadeh R, Bernousi I (2013) Retrotransposon insertional polymorphism in Iranian bread wheat cultivars and breeding lines revealed by IRAP and REMAP markers. Biochem Genet 51(11–12):927–943
Smýkal P, Bačová-Kerteszová N, Kalendar R, Corander J, Schulman AH, Pavelek M (2011) Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers. Theor Appl Genet 122(7):1385–1397
Cheraghi A, Rahmani F, Hassanzadeh-Ghorttapeh A (2018) IRAP and REMAP based genetic diversity among varieties of Lallemantia iberica. Mol Biol Res Commun 7(3):125–132. https://doi.org/10.22099/mbrc.2018.29924.1327
Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH (2000) Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci 97(12):6603–6607
Sorkheh K, Dehkordi MK, Ercisli S, Hegedus A, Halász J (2017) Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species. Sci Rep 7(1):5966
Flavell AJ, Knox MR, Pearce SR, Ellis TN (1998) Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J 16(5):643–650
Konovalov FA, Goncharov NP, Goryunova S, Shaturova A, Proshlyakova T, Kudryavtsev A (2010) Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats. Mol Gen Genomics 283(6):551–563
Lou Q, Chen J (2007) Ty1-copia retrotransposon-based SSAP marker development and its potential in the genetic study of cucurbits. Genome 50(9):802–810
Melnikova NV, Kudryavtseva AV, Speranskaya AS, Krinitsina AA, Dmitriev AA, Belenikin MS, Upelniek VP, Batrak ER, Kovaleva IS, Kudryavtsev AM (2012) The FaRE1 LTR-retrotransposon based SSAP markers reveal genetic polymorphism of strawberry (Fragaria × ananassa) cultivars. J Agric Sci 4(11):111
Petit M, Guidat C, Daniel J, Denis E, Montoriol E, Bui Q, Lim K, Kovarik A, Leitch A, Grandbastien MA (2010) Mobilization of retrotransposons in synthetic allotetraploid tobacco. New Phytol 186(1):135–147
Syed N, Sureshsundar S, Wilkinson M, Bhau B, Cavalcanti J, Flavell A (2005) Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.). Theor Appl Genet 110(7):1195–1202
Hirano R, Naito K, Fukunaga K, Watanabe KN, Ohsawa R, Kawase M (2011) Genetic structure of landraces in foxtail millet (Setaria italica (L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet. Genome 54(6):498–506
Karki S, Tsukiyama T, Okumoto Y, Rizal G, Naito K, Teraishi M, Nakazaki T, Tanisaka T (2009) Analysis of distribution and proliferation of mPing family transposons in a wild rice (Oryza rufipogon Griff.). Breed Sci 59(3):297–307
Shan X, Ou X, Liu Z, Dong Y, Lin X, Li X, Liu B (2009) Transpositional activation of mPing in an asymmetric nuclear somatic cell hybrid of rice and Zizania latifolia was accompanied by massive element loss. Theor Appl Genet 119(7):1325
Takagi K, Ishikawa N, Maekawa M, Tsugane K, Iida S (2007) Transposon display for active DNA transposons in rice. Genes Genet Syst 82(2):109–122
Van den Broeck D, Maes T, Sauer M, Zethof J, De Deukeleire P, D’hauw M, Van Montagu M, Gerats T (1998) Transposon display identifies individual transposable elements in high copy number lines. Plant J 13(1):121–129
Zhang X, Feschotte C, Zhang Q, Jiang N, Eggleston WB, Wessler SR (2001) P instability factor: an active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases. Proc Natl Acad Sci 98(22):12572–12577
Kalendar R, Antonius K, Smýkal P, Schulman AH (2010) iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor Appl Genet 121(8):1419–1430
Xu JY, Zhu Y, Yi Z, Wu G, Xie GY, Qin MJ (2018) Molecular diversity analysis of Tetradium ruticarpum (WuZhuYu) in China based on inter-primer binding site (iPBS) markers and inter-simple sequence repeat (ISSR) markers. Chin J Nat Med 16(1):1–9. https://doi.org/10.1016/S1875-5364(18)30024-4
Coutinho JP, Carvalho A, Martin A, Lima-Brito J (2018) Molecular characterization of Fagaceae species using inter-primer binding site (iPBS) markers. Mol Biol Rep 45(2):133–142. https://doi.org/10.1007/s11033-018-4146-3
Monden Y, Fujii N, Yamaguchi K, Ikeo K, Nakazawa Y, Waki T, Hirashima K, Uchimura Y, Tahara M (2014) Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site. Genome 57(5):245–252
Monden Y, Yamaguchi K, Tahara M (2014) Application of iPBS in high-throughput sequencing for the development of retrotransposon-based molecular markers. Curr Plant Biol 1:40–44
Monden Y, Takai T, Tahara M (2014) Characterization of a novel retrotransposon TriRe-1 using nullisomic-tetrasomic lines of hexaploid wheat. Sci Rep Fac Agric 103:21–30
Yamane F, Hirashima Y, Shindo A, Tahara M, Fujii N, Ikeo K, Yamashita Y (2012) Cultivar identification markers of common beans based on the retrotransposon insertion site sequences obtained by next-generation DNA sequencing. DNA Test 4:67–74
Monden Y, Takai T, Tahara M, Umeno Y, Nakamura R (2014) High-throughput development of DNA markers for wheat cultivar discrimination based on an active retrotransposon TriRe-1 insertion polymorphism. DNA Polymorph 22:60–65
Monden Y, Yamamoto A, Shindo A, Tahara M (2014) Efficient DNA fingerprinting based on the targeted sequencing of active retrotransposon insertion sites using a bench-top high-throughput sequencing platform. DNA Res 21(5):491–498
Paz RC, Kozaczek ME, Rosli HG, Andino NP, Sanchez-Puerta MV (2017) Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum. Genetica 145(4–5):417–430. https://doi.org/10.1007/s10709-017-9977-7
Metcalfe CJ, Oliveira SG, Gaiarsa JW, Aitken KS, Carneiro MS, Zatti F, Van Sluys M-A (2015) Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane. J Exp Bot 66(14):4239–4250
Wenke T, Seibt KM, Döbel T, Muders K, Schmidt T (2015) Inter-SINE amplified polymorphism (ISAP) for rapid and robust plant genotyping. In: Plant genotyping. Springer, New York, NY, pp 183–192
Mamedov IZ, Arzumanyan ES, Amosova AL, Lebedev YB, Sverdlov ED (2005) Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach. Nucleic Acids Res 33(2):e16–e16
Zhang Q, Arbuckle J, Wessler SR (2000) Recent, extensive and preferential insertion of members of the miniature inverted-repeat transposable element family Heartbreaker into genic regions of maize. Proc Natl Acad Sci 97(3):1160–1165
Johal GS, Briggs SP (1992) Reductase activity encoded by the HM1 disease resistance gene in maize. Science 258(5084):985–987
Grzebelus D, Simon PW (2009) Diversity of DcMaster-like elements of the PIF/Harbinger superfamily in the carrot genome. Genetica 135(3):347–353
Grzebelus D, Lasota S, Gambin T, Kucherov G, Gambin A (2007) Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula. BMC Genomics 8(1):409
Grzebelus D, Stawujak K, Mitoraj J, Szklarczyk M (2011) Dynamics of Vulmar/VulMITE group of transposable elements in Chenopodiaceae subfamily Betoideae. Genetica 139(9):1209–1216
Takahashi H, Akagi H, Mori K, Sato K, Takeda K (2006) Genomic distribution of MITEs in barley determined by MITE-AFLP mapping. Genome 49(12):1616–1620
Lyons M, Cardle L, Rostoks N, Waugh R, Flavell AJ (2008) Isolation, analysis and marker utility of novel miniature inverted repeat transposable elements from the barley genome. Mol Gen Genomics 280(4):275–285
Hřibová E, Neumann P, Matsumoto T, Roux N, Macas J, Doležel J (2010) Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing. BMC Plant Biol 10(1):204
Wanjugi H, Coleman-Derr D, Huo N, Kianian SF, Luo M-C, Wu J, Anderson O, Gu YQ (2009) Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat. Genome 52(6):576–587
Yadav CB, Bonthala VS, Muthamilarasan M, Pandey G, Khan Y, Prasad M (2015) Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database. DNA Res 22(1):79–90
Patel M, Jung S, Moore K, Powell G, Ainsworth C, Abbott A (2004) High-oleate peanut mutants result from a MITE insertion into the FAD2 gene. Theor Appl Genet 108(8):1492–1502
Bhat RS, Patil VU, Chandrashekar TM, Sujay V, Gowda MVC, Kuruvinashetti MS (2008) Recovering flanking sequence tags of miniature inverted-repeat transposable element by thermal asymmetric interlaced-PCR in peanut. Curr Sci 95(4):452–453
Gowda MVC, Bhat RS, Motagi BN, Sujay V, Varshakumari BS (2010) Association of high-frequency origin of late leaf spot resistant mutants with AhMITE1 transposition in peanut. Plant Breed 129(5):567–569
Gowda MVC, Bhat RS, Sujay V, Kusuma P, Varshakumari BS, Varshney RK (2011) Characterization of AhMITE1 transposition and its association with the mutational and evolutionary origin of botanical types in peanut (Arachis spp.). Plant Syst Evol 291(3–4):153–158
Shirasawa K, Hirakawa H, Tabata S, Hasegawa M, Kiyoshima H, Suzuki S, Sasamoto S, Watanabe A, Fujishiro T, Isobe S (2012) Characterization of active miniature inverted-repeat transposable elements in the peanut genome. Theor Appl Genet 124(8):1429–1438. https://doi.org/10.1007/s00122-012-1798-6
Shirasawa K, Koilkonda P, Aoki K, Hirakawa H, Tabata S, Watanabe M, Hasegawa M, Kiyoshima H, Suzuki S, Kuwata C, Naito Y, Kuboyama T, Nakaya A, Sasamoto S, Watanabe A, Kato M, Kawashima K, Kishida Y, Kohara M, Kurabayashi A, Takahashi C, Tsuruoka H, Wada T, Isobe S (2012) In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut. BMC Plant Biol 12(1):80. https://doi.org/10.1186/1471-2229-12-80
Gayathri M, Shirasawa K, Varshney RK, Pandey MK, Bhat RS (2018) Development of new AhMITE1 markers through genome-wide analysis in peanut (Arachis hypogaea L.). BMC Res Notes 11(1):10. https://doi.org/10.1186/s13104-017-3121-8
Nunome T, Negoro S, Miyatake K, Yamaguchi H, Fukuoka H (2006) A protocol for the construction of microsatellite enriched genomic library. Plant Mol Biol Rep 24(3–4):305
Grzebelus D, Jagosz B, Simon PW (2007) The DcMaster transposon display maps polymorphic insertion sites in the carrot (Daucus carota L.) genome. Gene 390(1):67–74
Kwon S-J, Park K-C, Kim J-H, Lee JK, Kim N-S (2005) Rim 2/Hipa CACTA transposon display: a new genetic marker technique in Oryza species. BMC Genet 6(1):15
Goerner-Potvin P, Bourque G (2018) Computational tools to unmask transposable elements. Nat Rev Genet 19:688–704
Hake AA, Shirasawa K, Yadawad A, Nadaf HL, Gowda MVC, Bhat RS (2018) Genome-wide structural mutations among the lines resulting from genetic instability in peanut (Arachis hypogaea L.). Plant Gene 13(March):1–7. https://doi.org/10.1016/j.plgene.2017.11.001
Kang H, Zhu D, Lin R, Opiyo SO, Jiang N, Shiu S-H, Wang G-L (2016) A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads. DNA Res 23(3):241–251. https://doi.org/10.1093/dnares/dsw011
Nadeem MA, Nawaz MA, Shahid MQ, Doğan Y, Comertpay G, Yıldız M, Hatipoğlu R, Ahmad F, Alsaleh A, Labhane N (2018) DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnol Biotechnol Equip 32(2):261–285
Monden Y, Tahara M (2015) Plant transposable elements and their application to genetic analysis via high-throughput sequencing platform. Hort J 84(4):283–294
Shirasawa K, Bhat RS, Khedikar YP, Sujay V, Kolekar RM, Yeri SB, Sukruth M, Cholin S, Asha B, Pandey MK, Varshney RK, Gowda MVC (2018) Sequencing analysis of genetic loci for resistance for late leaf spot and rust in peanut (Arachis hypogaea L.). Front Plant Sci:9. https://doi.org/10.3389/fpls.2018.01727. https://www.frontiersin.org/articles/10.3389/fpls.2018.01727/abstract
Takai T, Tahara M (2011) Discovery of the retrotransposon showing genome insertion polymorphisms among wheat cultivars. DNA Polymorph 20:80–90
Monden Y, Yamamoto A, Tahara M (2013) Development of DNA markers for anthocyanin content purple sweet potato using active retrotransposon insertion polymorphisms. DNA Polymorph 21:47–54
Tahara M, Yamashita H, Ooe N (2007) Cultivar identification based on retrotransposon insertion polymorphisms applied for sweet potato products. DNA Polymorph 15:122–125
Nakagawa A, Yamashita H, Tahara M, Ooyama Y (2009) Retrotransposon DNA marker for Azuki cultivar Shumari identification. DNA Polymorph 17:85–91
Yamashita H (2008) Retrotransposon DNA marker for Azuki cultivar identification. DNA Polymorph 16:82–87
Akitake H, Tahara M, Monden Y, Takasaki K, Futo S (2013) Strawberry cultivar identification by retrotransposon insertion polymorphisms. DNA Polymorph 21:64–72
Tanaka Y, Shindo A, Tahara M, Yamashita Y (2011) Species identification marker for common bean (Phaseolus vulgaris) based on a retrotransposon insertion site. DNA Polymorph 19:82–87
Yamashita H, Tahara M (2006) A LINE-type retrotransposon active in meristem stem cells causes heritable transpositions in the sweet potato genome. Plant Mol Biol 61(1–2):79–84
Tahara M, Aoki T, Suzuka S, Yamashita H, Tanaka M, Matsunaga S, Kokumai S (2004) Isolation of an active element from a high-copy-number family of retrotransposons in the sweetpotato genome. Mol Gen Genomics 272(1):116–127
Maneesha UKC (2017) Analysis of genetic diversity in pigeon pea germplasm using retrotransposon-based molecular markers. J Genet 96(4):551–561
Bonchev G, Dusinsky R, Hauptvogel P, Svec M (2017) Patterns of evolutionary trajectories and domestication history within the genus Hordeum assessed by REMAP markers. J Mol Evol 84(2–3):116–128. https://doi.org/10.1007/s00239-016-9779-z
Galindo-González L, Mhiri C, Grandbastien M-A, Deyholos MK (2016) Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions. BMC Genomics 17(1):1002
Sharma V, Nandineni MR (2014) Assessment of genetic diversity among Indian potato (Solanum tuberosum L.) collection using microsatellite and retrotransposon based marker systems. Mol Phylogenet Evol 73:10–17
Jing R, Vershinin A, Grzebyta J, Shaw P, Smýkal P, Marshall D, Ambrose MJ, Ellis TN, Flavell AJ (2010) The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis. BMC Evol Biol 10(1):44
He P, Ma Y, Zhao G, Dai H, Li H, Chang L, Zhang Z (2010) FaRE1: a transcriptionally active Ty1-copia retrotransposon in strawberry. J Plant Res 123(5):707–714
Monden Y, Takasaki K, Futo S, Niwa K, Kawase M, Akitake H, Tahara M (2014) A rapid and enhanced DNA detection method for crop cultivar discrimination. J Biotechnol 185:57–62
Ray DA (2007) SINEs of progress: mobile element applications to molecular ecology. Mol Ecol 16(1):19–33
Kavar T, Meglič V, Rozman L (2007) Diversity of Slovenian maize (Zea mays) populations by Hbr (MITE) markers and morphological traits. Russ J Genet 43(9):989–995
Zerjal T, Rousselet A, Mhiri C, Combes V, Madur D, Grandbastien M-A, Charcosset A, Tenaillon MI (2012) Maize genetic diversity and association mapping using transposable element insertion polymorphisms. Theor Appl Genet 124(8):1521–1537
Park K-C, Lee JK, Kim N-H, Shin Y-B, Lee J-H, Kim N-S (2003) Genetic variation in Oryza species detected by MITE-AFLP. Genes Genet Syst 78(3):235–243
Yaakov B, Ceylan E, Domb K, Kashkush K (2012) Marker utility of miniature inverted-repeat transposable elements for wheat biodiversity and evolution. Theor Appl Genet 124(7):1365–1373
Monden Y, Tahara M (2017) Genetic linkage analysis using DNA markers in sweetpotato. Breed Sci 67(1):41–51. https://doi.org/10.1270/jsbbs.16142
Monden Y, Hara T, Okada Y, Jahana O, Kobayashi A, Tabuchi H, Onaga S, Tahara M (2015) Construction of a linkage map based on retrotransposon insertion polymorphisms in sweet potato via high-throughput sequencing. Breed Sci 65(2):145–153
Rey-Banos R, Saenz de Miera LE, Garcia P, Perez de la Vega M (2017) Obtaining retrotransposon sequences, analysis of their genomic distribution and use of retrotransposon-derived genetic markers in lentil (Lens culinaris Medik.). PLoS One 12(4):e0176728. https://doi.org/10.1371/journal.pone.0176728
Ali SG, Darvishzadeh R, Ebrahimi A, Bihamta MR (2018) Identification of SSR and retrotransposon-based molecular markers linked to morphological characters in oily sunflower (Helianthus annuus L.) under natural and water-limited states. J Genet 97(1):189–203
Nakatsuka T, Yamada E, Saito M, Hikage T, Ushiku Y, Nishihara M (2012) Construction of the first genetic linkage map of Japanese gentian (Gentianaceae). BMC Genomics 13(1):672
Tenhola-Roininen T, Kalendar R, Schulman AH, Tanhuanpää P (2011) A doubled haploid rye linkage map with a QTL affecting α-amylase activity. J Appl Genet 52(3):299–304
Shirasawa K, Bertioli DJ, Varshney RK, Moretzsohn MC, Leal-Bertioli SC, Thudi M, Pandey MK, Rami JF, Fonceka D, Gowda MV, Qin H, Guo B, Hong Y, Liang X, Hirakawa H, Tabata S, Isobe S (2013) Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Res 20(2):173–184. https://doi.org/10.1093/dnares/dss042
Hake AA, Shirasawa K, Yadawad A, Sukruth M, Patil M, Nayak SN, Lingaraju S, Patil PV, Nadaf HL, Gowda MVC, Bhat RS (2017) Mapping of important taxonomic and productivity traits using genic and non-genic transposable element markers in peanut (Arachis hypogaea L.). PLoS One 12(10):e0186113. https://doi.org/10.1371/journal.pone.0186113. eCollection 2017
Kolekar RM, Sukruth M, Shirasawa K, Nadaf HL, Motagi BN, Lingaraju S, Patil PV, Bhat RS (2017) Marker-assisted backcrossing to develop foliar disease resistant genotypes in TMV 2 variety of peanut (Arachis hypogaea L.). Plant Breed 136(6):948–953. https://doi.org/10.1111/pbr.12549
Kwon S, Hong S, Son J, Lee J, Cha Y, Eun M, Kim N (2006) CACTA and MITE transposon distributions on a genetic map of rice using F15 RILs derived from Milyang 23 and Gihobyeo hybrids. Mol Cells 21(3):360
Kwon S, Yu J, Park Y, Son J, Kim N, Lee J (2015) Genetic analysis of seed-shattering genes in rice using an F. Genet Mol Res 14(1):1347–1361
Monden Y, Naito K, Okumoto Y, Saito H, Oki N, Tsukiyama T, Ideta O, Nakazaki T, Wessler SR, Tanisaka T (2009) High potential of a transposon mPing as a marker system in japonica × japonica cross in rice. DNA Res 16(2):131–140
Schwarz-Sommer Z, Gübitz T, Weiss J, Gómez-di-Marco P, Delgado-Benarroch L, Hudson A, Egea-Cortines M (2010) A molecular recombination map of Antirrhinum majus. BMC Plant Biol 10(1):275
Chang RY, O’Donoughue LS, Bureau TE (2001) Inter-MITE polymorphisms (IMP): a high throughput transposon-based genome mapping and fingerprinting approach. Theor Appl Genet 102(5):773–781
Roy NS, Park K-C, Lee S-I, Im M-J, Ramekar RV, Kim N-S (2018) Development of CACTA transposon derived SCAR markers and their use in population structure analysis in Zea mays. Genetica 146(1):1–12
Smýkal P, Hýbl M, Corander J, Jarkovský J, Flavell AJ, Griga M (2008) Genetic diversity and population structure of pea (Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis. Theor Appl Genet 117(3):413–424
Im S, Kwon S, Ryu J, Jeong S, Kim J, Ahn J, Kim S, Jo Y, Choi H, Kang S (2016) Development of a transposon-based marker system for mutation breeding in sorghum (Sorghum bicolor L.). Genet Mol Res 15(3):PMID:27706735
Roncal J, Guyot R, Hamon P, Crouzillat D, Rigoreau M, Konan ONG, Rakotomalala J-J, Nowak MD, Davis AP, de Kochko A (2016) Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species. Mol Gen Genomics 291(1):155–168
Carrier G, Le Cunff L, Dereeper A, Legrand D, Sabot F, Bouchez O, Audeguin L, Boursiquot J-M, This P (2012) Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. PLoS One 7(3):e32973
Abdel-Ghani AH, Parzies HK, Omary A, Geiger HH (2004) Estimating the outcrossing rate of barley landraces and wild barley populations collected from ecologically different regions of Jordan. Theor Appl Genet 109(3):588–595
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Bhat, R.S., Shirasawa, K., Monden, Y., Yamashita, H., Tahara, M. (2020). Developing Transposable Element Marker System for Molecular Breeding. In: Jain, M., Garg, R. (eds) Legume Genomics. Methods in Molecular Biology, vol 2107. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0235-5_11
Download citation
DOI: https://doi.org/10.1007/978-1-0716-0235-5_11
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-0234-8
Online ISBN: 978-1-0716-0235-5
eBook Packages: Springer Protocols