Abstract
Molecular markers are employed for doubled haploid (DH) technology by researchers and applied plant breeders in many crops. In the 1990s, isozymes and RFLPs were commonly used marker technologies to characterize DHs and were later replaced by PCR- based markers (e.g., RAPDs, AFLPs, ISSRs, SSRs) and today by SNPs. Markers are used for multiple purposes in DH production, that is, for the study of genes underlying haploid induction and confirming homozygous plants of gametophytic origin. Furthermore, they are tools for investigating segregation in DH populations and for mapping simple and complex traits using DHs. The deployment of DHs and markers for developing trait-linked markers are demonstrated with examples from rapeseed, wheat, and barley. Marker development for resistance to viruses derived from genetic resources and their use in, for example, pyramiding of resistance genes, are given as an example for the combination of DH-technology and marker development in research. Today, marker systems amenable to automation are frequently used in applied plant breeding. Practical examples are given from Lantmännen (LM) (https://Lantmannen.com) using large-scale genotyping for variety development based on SSRs and SNPs.
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Tadesse W, Sanchez-Garcia M, Tawkaz S, Baum M (2019) Doubled haploid production in wheat. In: Ordon F, Friedt W (eds) Advances in breeding techniques for cereal crops. Burleigh Dodds, Cambridge, pp 93–115
Wittkop B, Cselenyi L, Friedt W, Bernhard T (2019) Doubled haploid (DH) production for barley. In: Ordon F, Friedt W (eds) Advances in breeding techniques for cereal crops. Burleigh Dodds, Cambridge, pp 117–141
Molenaar WS, Melchinger AE (2019) Production of doubled haploid lines for hybrid breeding in maize. In: Ordon F, Friedt W (eds) Advances in breeding techniques for cereal crops. Burleigh Dodds, Cambridge, pp 143–171
Werner K, Friedt W, Ordon F (2007) Localisation and combination of resistance genes against soil-borne viruses of barley (BaMMV, BaYMV) using doubled haploids and molecular markers. Euphytica 158:323–329
Perovic D, Kopahnke D, Habekuß A, Ordon F, Serfling A (2019) Marker-based harnessing of genetic diversity to improve resistance of barley to fungal and viral diseases. In: Miedaner T, Korzun V (eds) Applications of genetic and genomic research in cereals. Woodhead Publishing Series in Food Science, Technology and Nutrition, Cambridge, pp 137–164
Varshney RK, Tuberosa R (eds) (2007) Genomics-assisted crop improvement, vol 1: genomics approaches and platforms. Springer, Dordrecht
Rasheed A, Hao Y, Xia X, Khan A, Xu Y, Varshney RK, He Z (2017) Crop breeding chips and genotyping platforms: progress, challenges, and perspectives. Mol Plant 10:1047–1064
Tanksley SD, Orton TJ (1983) Isozymes in plant genetics and breeding, part A. Elsevier Science Publishers B.V., Amsterdam
Delourme R, Eber F (1992) Linkage between an isozyme marker and a restorer gene in radish cytoplasmic male sterility of rapeseed (Brassica napus L.). Theor Appl Genet 92:222–228
Koebner RMD, Martin PM (1990) Association of eyespot resistance in wheat cv. ‘Capelle-Desprez’ with endopeptidase profile. Plant Breed 104:312–317
Tuvesson S, Öhlund R, v Post L, Forster BP, Dayteg C (1998) Use of genetic markers at Svalöf Weibull AB. J Swed Seed Assoc 3:167–175
Konishi T, Ban T, Iida Y, Yoshimi R (1997) Genetic analysis of disease resistance to all strains of BaYMV in a Chinese barley landrace, Mokusekko 3. Theor Appl Genet 94:871–877
Le Gouis J, Erdogan M, Friedt W, Ordon F (1995) Potential and limitations of isozymes for chromosomal localization of resistance genes against barley mild mosaic virus (BaMMV). Euphytica 82:25–30
Helentjaris TG, King G, Slocum M, Sidenstrang C, Wegman S (1985) Restriction fragment length polymorphism as probes for plant diversity and their developments as tools for plant breeding. Plant Mol Biol 5:109–118
Dion Y, Gugel RK, Rakow GFW, Séguin-Swartz G, Landry BS (1995) RFLP mapping of resistance to the blackleg disease [causal agent, Leptosphaeria maculans (Desm.) Ces. et de Not.] in canola (Brassica napus L.). Theor Appl Genet 91:1190–1194
Graner A, Jahoor A, Schondelmaier J, Siedler H, Pillen K, Fischbeck G, Wenzel G, Hermann RG (1991) Construction of an RFLP map of barley. Theor Appl Genet 83:250–256
Pellio B, Streng S, Bauer E, Stein N, Perovic D, Schiemann A, Friedt W, Ordon F, Graner A (2005) High-resolution mapping of the Rym4/Rym5 locus conferring resistance to the barley yellow mosaic virus complex (BaMMV, BaYMV, BaYMV-2) in barley (Hordeum vulgare ssp. vulgare L.). Theor Appl Genet 110:283–293
Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218
Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18(22):6531–6535
Waugh R, Powell W (1992) Using RAPD markers for crop improvement. Trends Biotechnol V 10:186–191
Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Friters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23(21):4407–4414
Mueller UG, Wolfenbarger LL (1999) AFLP genotyping and fingerprinting. Trends Ecol Evol 14:389–394
Holton TA, Christopher JT, McClure L, Harker N, Henry RJ (2002) Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat. Mol Breed 9:63–71
Ganal MW, Röder MS (2007) Microsatellite and SNP markers in wheat breeding. In: Varshney RK, Tuberosa R (eds) Genomics-assisted crop improvement. Springer, Dordrecht, pp 1–24
Röder MS, Wendehake K, Korzun V, Bredemeijer G, Laborie D, Bertrand L, Isaac P, Rendell S, Jackson J, Cooke RJ, Vosman B, Ganal M (2002) Construction of a microsatellite-based database of European wheat varieties. Theor Appl Genet 106:67–73
Morgante M, Pfeiffer A, Jurman I, Paglia G, Olivieri AM (1998) PCR Analysis of SSR polymorphisms in plants using agarose gels. In: Karp A, Isaac PG, Ingram DS (eds) Molecular tools for screening biodiversity. Springer, Dordrecht, pp 206–207
Ramsay L, Macaulay M, degli Ivanissivich S, McLean K, Cardle L, Fuller J, Edwards K, Tuvesson S, Morgante M, Massari A, Maesti E, Marmiroli N, Sjakste T, Ganal M, Powell W, Waugh R (2000) A simple sequence repeat-based linkage map of barley. Genetics 156:1997–2005
Somers DJ, Isaac P, Edwards K (2004) A high-density microsatellite concensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet 109:1105–1114
Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics V 20(2):176–183
Reddy MP, Sarla N, Siddiq EA (2002) Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica 128:9–17
Dayteg C, Rasmussen M, Tuvesson S, Merker A, Jahoor A (2008) Development of an ISSR-derived PCR marker linked to nematode-resistance (Ha2) in spring barley. Plant Breed 127:24–27
Rafalski JA (2002) Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Sci 162:329–333
Bhattramakki D, Rafalski A (2003) Discovery and application of single nucleotide polymorphism markers in plants. In: Henry RJ (ed) Plant genotyping: the DNA fingerprinting of plants. CABI Publishing, Wallingford, pp p179–p192
Olesen A, Andersen SB, Due IK (1988) Anther culture response in perennial ryegrass (Lolium perenne L.). Plant Breed 101:60–65
Andersen SB, Christiansen J, Farestveit B (1990) Carrot (Daucus carota L.): in vitro production of haploids and field trials. In: Bajaj YPS (ed) Biotechnology in agriculture and forestry, vol 12. Springer, Berlin, pp 393–402
Kiszczak W, Krzyżanowska D, Strycharczuk K, Kowalska U, Wolko B, Górecka K (2011) Determination of ploidy and homozygosity of carrot plants obtained from anther cultures. Acta Physiol Plant 33(2):401–407
Kiełkowska A, Adamus A, Baranski R (2014) An improved protocol for carrot haploid and doubled haploid plant production using induced parthenogenesis and ovule excision in vitro. In Vitro Cell Dev Biol Plant 50(3):376–383
Tuvesson S, Dayteg C, Hagberg P, Manninen O, Tanhuanpää P, Tenhola-Roininen T, Kiviharju K, Weyen J, Förster J, Schondelmaier J, Lafferty L, Marn M, Fleck A (2007) Molecular markers and doubled haploids in European plant breeding. Euphytica 158(3):278–294
Perera PIP, Hocher V, Verdeil JL, Bandupriya HDD, Yakandawala DMD, Weerakoon LK (2008) Androgenic potential in coconut (Cocos nucifera L.). Plant Cell Tissue Organ Cult 92:293–302
Perera PIP, Perera L, Hocher V, Verdeil J-L, Yakandawala DMD, Weerakoon LK (2008) Use of SSR markers to determine the anther-derived homozygous lines in coconut. Plant Cell Rep 27:1697–1703
Torp AM, Hansen AL, Andersen SB (2001) Chromosomal regions associated with green plant regeneration in wheat (Triticum aestivum L.) anther culture. Euphytica 119:377–387
Tuvesson IKD, Pedersen S, Olesen A, Andersen SB (1991) An effect of the 1BL/1RS chromosome on albino frequency in wheat (Triticum aestivum L.) anther culture. J Genet Breed 45:345–348
Hayward MD, Olesen A, Due IK, Jenkins R, Morris P (1990) Segregation of isozyme marker loci amongst androgenetic plants of Lolium perenne L. Plant Breed 104:68–71
Åhman I, Bengtsson T (2019) Introgression of resistance to Rhopalosiphum padi L. from wild barley into cultivated barley facilitated by doubled haploid and molecular marker techniques. Theor Appl Genet 132:1397–1408
Sayed H, Kayyal H, Ramsey L, Ceccarelli S, Baum M (2002) Segregation distortion in doubled haploid lines of barley (Hordeum vulgare L.) detected by simple sequence repeat (SSR) markers. Euphytica 125:265–272
Barchi L, Lanteri S, Portis E, Stàgel A, Valè G, Toppino L, Rotinoc GL (2010) Segregation distortion and linkage analysis in eggplant (Solanum melongena L.). Genome 53(10):805–815
Li C, Bai G, Chao S, Wang Z (2015) A high-density SNP and SSR consensus map reveals segregation distortion regions in wheat. BioMed Res Int 830618:1–10
Tuvesson S, Ljungberg A, Johansson N, Karlsson K-E, Suijs LW, Josset J-P (2000) Large-scale production of wheat and triticale double haploids through a single anther culture method. Plant Breed 119:455–459
Torp AM, Andersen SB (2009) Albinism in microspore culture. In: Touraev A, Forster BP, Jain SM (eds) Advances in haploid production in higher plants. Springer, New York, NY, pp 155–160
Muñoz-Amatriaín M, Svensson JT, Castillo AM, Close TJ, Vallés MP (2009) Microspore embryogenesis: assignment of genes to embryo formation and green vs. albino plant production. Funct Integr Genomics 9(3):311–323
Bélanger S, Marchand S, Jacques P-E, Meyers B, Belzile F (2018) Differential expression profiling of microspores during the early stages of isolated microspore culture using the responsive barley cultivar Gobernadora. G3 Genes Genomes Genet 8(5):1603–1614
Zhou WJ, Tang GX, Hagberg P (2002) Efficient production of doubled haploid plants by immediate colchicine treatment of isolated microspores in winter Brassica napus. Plant Growth Regul 37:185–192
Rygulla W, Snowdon RJ, Friedt W, Happstadius I, Cheung WY, Chen D (2008) Identification of quantitative trait loci for resistance against Verticillium longisporum in oilseed rape (Brassica napus). Phytopathology 98(2):215–221
Bertholdsson NO, Tuvesson S (2005) Possibilities to use marker assisted selection to improve allelopathic activity in cereals. In: Proceedings of the COST SUSVAR/ECO-PB workshop on ‘organic plant breeding strategies and the use of molecular markers”, 17–19 Jan 2005, Driebergen, pp 67–71
Ordon F, Friedt W (1993) Mode of inheritance and genetic diversity of BaMMV-resistance of exotic barley germplasms carrying genes different from ‘ym4’. Theor Appl Genet 86:229–233
Palloix A, Ordon F (2011) Advanced breeding for virus resistance in plants. In: Caranta C, Miguel A, Aranda MA, Tepfer M, López-Moya JJ (eds) Recent advances in plant virology. CaisterAcademic Press, Norfolk, pp 195–218
Scheurer KS, Friedt W, Huth W, Waugh R, Ordon F (2001) QTL analysis of tolerance to a German strain of BYDV-PAV in barley (Hordeum vulgare L.). Theor Appl Genet 103:1074–1083
Juergens M, Paetsch C, Krämer I, Zahn M, Rabenstein R, Schondelmaier J, Schliephake E, Snowdon R, Friedt W, Ordon F (2010) Genetic analyses of the host-pathogen system Turnip yellows virus (TuYV) – rapeseed (Brassica napus L.) and development of molecular markers for TuYV-resistance. Theor Appl Genet 120:735–744
Michelmore R (1995) Molecular approaches to manipulation of disease resistance genes. Annu Rev Phytopathol 15:393–427
Ordon F, Bauer E, Friedt W, Graner A (1995) Marker-based selection for the ym4 BaMMV-resistance gene in barley using RAPDs. Agronomie 15:481–485
Graner A, Bauer E (1993) RFLP mapping of the ym4 virus resistance gene in barley. Theor Appl Genet 86:689–693
Weyen J, Bauer E, Graner A, Friedt W, Ordon F (1996) RAPD-mapping of the distal portion of chromosome 3 of barley including the BaMMV/BaYMV resistance gene ym4. Plant Breed 115:285–287
Graner A, Streng S, Kellermann A, Proeseler G, Schiemann A, Peterka H, Ordon F (1999) Molecular mapping of genes conferring resistance to soil-borne viruses in barley – an approach to promote understanding of host-pathogen interactions. J Plant Dis Protect 106:405–410
Graner A, Bauer E, Kellermann A, Proeseler G, Wenzel G, Ordon F (1995) RFLP analysis of resistance to the barley yellow mosaic virus complex. Agronomie 15:475–479
Ping Y, Perovic D, Habekuß A, Zhou R, Graner A, Ordon F, Stein N (2013) Gene-based high-density mapping of the gene rym7 conferring resistance to Barley mild mosaic virus (BaMMV). Mol Breed 32:27–37
Nissan-Azzous F, Graner A, Friedt W, Ordon F (2005) Fine-mapping of the BaMMV, BaYMV-1 and BaYMV-2 resistance of barley (Hordeum vulgare) accession PI1963. Theor Appl Genet 110:212–218
Werner K, Rönnicke S, Le Gouis J, Friedt W, Ordon F (2003) Mapping of a new BaMMV-resistance gene derived from the variety ‘Taihoku A’. J Plant Dis Protect 110:304–311
Humbroich K, Jaiser H, Schiemann A, Devaux P, Jacobi A, Cselenyi L, Habekuß A, Friedt W, Ordon F (2010) Mapping of resistance against BaMMV-Teik – an rym5 resistance breaking strain of BaMMV – in the Taiwanese barley cultivar ‘Taihoku A’. Plant Breed 129:346–348
Le Gouis J, Devaux P, Werner K, Hariri D, Bahrman N, Beghin D, Ordon F (2004) rym15 from the Japanese cultivar ‘Chikurin Ibaraki 1’ is a new Barley Mild Mosaic Virus (BaMMV) resistance gene mapped on chromosome 6H. Theor Appl Genet 108:1521–1525
Kai H, Takata K, Tsukazaki M, Furusho M, Baba T (2012) Molecular mapping of Rym17, a dominant and rym18 a recessive Barley yellow mosaic virus (BaYMV) resistance genes derived from Hordeum vulgare L. Theor Appl Genet 124:577–583
Werner K, Friedt W, Laubach W, Waugh R, Ordon F (2003) Dissection of resistance to soil-borne yellow mosaic inducing viruses of barley (BaMMV, BaYMV, BaYMV-2) in a complex breeder’s cross by SSRs and simultaneous mapping of BaYMV/BaYMV-2 resistance of ‘Chikurin Ibaraki 1’. Theor Appl Genet 106:1425–1432
Perovic D, Krämer I, Habekuß A, Perner K, Pickering R, Proeseler G, Kanyuka K, Ordon F (2014) Genetic analyses of BaMMV/BaYMV resistance in barley accession HOR4224 result in the identification of an allele of the translation initiation factor 4e (Hv-eIF4E) exclusively effective against barley mild mosaic virus (BaMMV). Theor Appl Genet 127:1061–1071
Perovic D, Förster J, Devaux P, Hariri D, Guilleroux M, Kanyuka K, Lyons R, Weyen J, Feuerhelm D, Kastirr U, Sourdille P, Röder M, Ordon F (2009) Mapping and diagnostic marker development for soil-borne cereal mosaic virus resistance in bread wheat. Mol Breed 23:641–653
Ordon F, Schiemann A, Pellio B, Dauck V, Bauer E, Streng S, Friedt W, Graner A (1999) Application of molecular markers in breeding for resistance to the barley yellow mosaic virus complex. J Plant Dis Protect 106:256–264
Habekuß A, Kühne T, Krämer I, Rabenstein F, Ehrig F, Ruge-Wehling B, Huth W, Ordon F (2008) Identification of a rym5 resistance breaking BaMMV-isolate in Germany. J Phytopathol 156:36–41
Werner K, Friedt W, Ordon F (2005) Strategies for pyramiding resistance genes against the barley yellow mosaic virus complex (BaMMV, BaYMV, BaYMV-2). Mol Breed 16:45–55
Riedel C, Habekuß A, Schliephake E, Niks R, Broer I, Ordon F (2011) Pyramiding of Ryd2 and Ryd3 conferring tolerance to a German isolate of Barley yellow dwarf virus (BYDV-PAV-ASL-1) leads to quantitative resistance against this isolate. Theor Appl Genet 123:69–76
Wilkinson PA, Winfield MO, Barker GLA, Allen AM, Burridge A, Coghill JA, Burridge A, Edwards KJ (2012) CerealsDB 2.0: an integrated resource for plant breeders and scientists. BMC Bioinformatics 13:219
Simón MR, Ayala FM, Cordo CA, Röder MS, Börner A (2007) The use of wheat/goatgrass introgression lines for the detection of gene(s) determining resistance to Septoria tritici blotch (Mycosphaerella graminicola). Euphytica 154:249–254
Brading PA, Verstappen ECP, Kema GHJ, Brown JKM (2002) A gene-for-gene relationship between wheat and Mycosphaerella graminicola, the Septoria tritici blotch pathogen. Phytopathology 92:439–445
Thomas J, Fineberg N, Penner G, McCartney C, Auny T, Wise I, McCallum B (2005) Chromosome location and markers of Sm1: a gene of wheat that conditions antibiotic resistance to orange wheat blossom midge. Mol Breed 15:183–192
Miranda LM, Murphy JP, Marshall D, Leath S (2006) Pm34: a new powdery mildew resistance gene transferred from Aegilops tauschii Coss. to common wheat (Triticum aestivum L.). Theor Appl Genet 113:1497–1504
Miranda LM, Murphy JP, Marshall D, Cowger C, Leath S (2007) Chromosomal location of Pm35, a novel Aegilops tauschii derived powdery mildew resistance gene introgressed into common wheat (Triticum aestivum L.). Theor Appl Genet 114:1451–1456
Liu S, Andersson JA (2003) Marker assisted evaluation of Fusarium head blight resistant wheat germplasm. Crop Sci 43:760–766
Andersson JA, Chao S, Liu S (2007) Molecular breeding using a major QTL for Fusarium head blight resistance in wheat. Crop Sci 47:112–119
Odilbekov F, He X, Armoniené R, Saripella GV, Henriksson T, Singh PK, Chawade A (2019) QTL mapping and transcriptome analysis to identify differentially expressed genes induced by Septoria tritici blotch disease of wheat. Agronomy 9:510. https://doi.org/10.3390/agronomy9090510
Shorinola O, Bird N, Simmonds J, Berry S, Henriksson T, Jack P, Werner P, Gerjets T, Scholefield D, Balcárková B, Valárik M, Holdsworth MJ, Flintham J, Uauy C (2016) The wheat Phs-A1 pre-harvest sprouting resistance locus delays the rate of seed dormancy loss and maps 0.3 cM distal to the PM19 genes in UK germplasm. J Exp Bot 67(14):4169–4178
Dayteg C, Tuvesson S, Merker A, Jahoor A, Kolodinska Brantestam A (2007) Automation of DNA-marker analysis for molecular breeding in crops: practical experience of a plant breeding company. Plant Breed 126(4):410–415
Dayteg C (2008) Automation of molecular markers in practical breeding of spring barley (Hordeum vulgare L.). Swedish University of Agricultural Sciences, Uppsala. ISSN: 1652-6880. ISBN: 978-91-85913-31-2
Tuvesson S, v Post L, Öhlund R, Hagberg P, Graner A, Svitashev S, Schehr M, Elovsson R (1998) Molecular breeding for the BaMMV/BaYMV resistance gene ym4 in winter barley. Plant Breed 117:19–22
Dayteg C, von Post L, Öhlund R, Tuvesson S (1998) Quick DNA extraction method for practical plant breeding programmes. Plant and Animal Genome VI, San Diego, CA, p 39
v Post R, v Post L, Dayteg C, Nilsson M, Forster BP, Tuvesson S (2003) A high-throughput DNA extraction method for barley seed. Euphytica 130(2):255–260
Korzun V (2003) Molecular markers and their applications in cereals breeding. In Marker assisted selection: A fast track to increase genetic gain in plant and animal breeding?. Session I: MAS in plants. Proceedings of an international workshop organised by the Fondazione per le Biotecnologie, the University of Turin and FAO. Turin, Italy, pp 18–22
Svitashev S, v Post L, Öhlund R, Dayteg C, Hagberg P, Jönsson R, Löhde J, Elovsson R, Tuvesson S (1998) DNA mapping of the Yd2 gene in a winter barley DH population ‘Vixen’ x ‘Igri’. Plant and Animal. Genome VII, San Diego, CA, p 402
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Tuvesson, S.D., Larsson, CT., Ordon, F. (2021). Use of Molecular Markers for Doubled Haploid Technology: From Academia to Plant Breeding Companies. In: Segui-Simarro, J.M. (eds) Doubled Haploid Technology. Methods in Molecular Biology, vol 2288. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1335-1_3
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