Abstract
The use of molecular markers is gradually expanding from the field of scientific genetic analysis towards the implementation and application in breeding programs. Applications of DNA markers in breeding are based on the knowledge of the relation between genotypic and phenotypic variation. This overview of the field of molecular breeding describes current and future methods for establishing these relations through the combined use of modern DNA technologies and the laws of inheritance. The modern molecular breeder has the opportunity to control an increasing amount of traits in the breeding process through efficient application of DNA markers. Traits with different level of complexity require different approaches for discovery and molecular control. These approaches include control of genotypes and traits, at the level of linked markers, haplotypes, genes and gene alleles. In order to fully exploit the potential of molecular breeding as well as the potential of available germplasm resources, the selection methods in breeding will have to be adapted, towards the integrated use of genetic knowledge based on DNA markers.
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References
Anderson J-R, Lübberstedt T (2003) Functinal markers in plants. Trends Plant Sci 8:554–560
Aranzana M-J, Kim S, Zhao K, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang C, Toomajian C, Traw B, Zheng H, Bergelson J, Dean C, Marjoram P, Nordborg M (2005) Genome-wide Association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1:e60:0531–0539
Bentsink L, Yuan K, Koornneef M, Vreugdenhil D (2003) The genetics of phytate and phosphate accumulation in seeds and leaves of Arabidopsis thaliana, using natural variation. Theor Appl Genet 106:1234–1243
Borewitz J-O, Liang D, Ploiffe D, Chang H-S, Zhu T, Weigel D, Berry C-C, Winzler E, Chory J (2003) Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res 13:513–523
Buckler E-S, Thornsberry J-M (2002) Plant molecular diversity and applications to genomics. Curr Opin Plant Biol 5:107–111
Buntjer J-B, Sorensen A-P, Peleman J-D (2005) Haplotype diversity: The link between statistical and biological associations. Trends Plant Sci 10:466–471
Caldwell K-S, Russel J, Langridge P, Powel W (2006) Extreme population-dependent linkage disequilibrioum detected in an inbreeding plant species, hordeum vulgare. Genetics 172:557–567
Chan E-Y (2005) Advances in sequencing technology. Mutat Res 573:13–40, www.sciencedirect.com.
Chen X, Sullivan P-F (2003) Single nucleotide polymorphism genotyping: Biochemistry, protocol, cost and throughput. Pharmacogenomics J 3:77–96
Chetelata R-T, Meglicb V, Cisnerosa P (2000) A genetic map of tomato based on BC1 lycopersicon esculentum x solanum lycopersicoides reveals overall synteny but suppressed recombination between these homeologous genomes. Genetics 154:857–867
Cooper M, DeLacy I-H (1994) Relationships among analytical methods used to study genotypic variation and genotype-by-environment interaction in plant breeding multi-environment experiments. Theor Appl Genet 88:561–572
Darvasi A (1998) Experimental strategies for the genetic dissection of complex traits in animal models. Nat Genet 18:19–24
Darvasi A, Weinreb A, Minke V, Weller J-I, Soller M (1993) Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map. Genetics 134:943–951
Dekkers J-C, Hospital F (2002) The use of molecular genetics in the improvement of agricultural populations. Nat Rev Genet 3:22–32
Droc G, Ruiz M, Larmande P, Pereira A, Piffanelli P, Morel J-B, Dievart A, Courtois B, Guiderdoni E, Perin C, OryGenes DB (2006) A database for rice reverse genetics. Nucleic Acids Res 1:34
El-Din El-Assal S, Alonso-Blanco C, Peeters A-J, Raz V, Koornneef M (2001) A QTL for flowering time in Arabidopsis reveals a novel allele at CRY2. Nat Genet 29:435–440
Eshed Y, Zamir D (1995) An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141:1147–1162
Eshed Y, Zamir D (1996) Less than additive epistatic interactions of QTL in tomato. Genetics 143:1807–1817
Flint J, Valder W, Shifman S, Mott R (2005) Strategies for mapping and cloning quantitative trait genes in rodents. Nat Rev genet 6:271–285
Flint-Garcia S-A, Thuillet A-C, Yu J, Pressoir G, Romero S-M, Mitchell S-E, Doebley J, Kresovich S, Goodman M-M, Buckler E-S (2005) Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J 44:1054–1064
Frary A, Clint NT, Frary A, Grandillo S, van der Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert K-B, Tanksley S-D (2000) fw2.2: A quanititative trait locus key to the evolution of tomato fruit size. Science 289:85–88
Fridman E, Pleban T, Zamir D (2000) A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene. Proc Natl Acad Sci USA 97:4718–4723
Frisch M, Bohn M, Melchinger A-E (1999) Comparison of selection strategies for marker-assisted backcrossing of a gene. Crop Sci 39:1295–1301
Gebhardt C, Bellin D, Henselewski H, Lehmann W, Schwarzfischer J, Valkonen J-P-T (2006) Marker-assisted combination of major genes for pathogen resistance in potato. Theor Appl Genet 112:1458–1464
Hagenblad J, Tang C, Molitor J, Werner J, Zhao K, Zheng H, Marjoram P, Weigel D, Nordborg M (2004) Haplotype structure and phenotypic associations in the chromosomal regions surrounding two Arabidopsis thaliana flowering time loci. Genetics 168:1627–1638
Harbison S-T, Yamamoto A-H, Fanara J-J, Norga K-K, Mackay T-F (2004) Quantitative trait loci affecting starvation resistance in Drosophila melanogaster. Genetics. 166:1807–1823 http://www.arabidopsis.org; http://www.cropdesign.com/general.php; http://www.fao.org/BIOTECH/docs/Barone.pdf; http://www.lemnatec.com/; http://www.pollenplus.de/pollenplus_62.php/
Huang N, Stebbins G-L, Rodriguez R-L (1992) Classification and evolution of A-amylase genes in plants. Proc Natl Acad Sci USA 89:7526–7530
Jansen J-P-A (1996) Aphid resistance in composites. International application published under the patent cooperation treaty (PCT) No. WO 97/46080.
Jansen J, Verbakel H, Peleman J, van Hintum Th-J-L (2006) A note on the measurement of genetic diversity within genebank accessions of lettuce (Lactuca sativa L.) using AFLP markers, Theor Appl Genet 112:554–561
Koornneef M, Stam P (2001) Changing paradigms in plant breeding. Plant Physiol 125:156–159
Kraakman A-T-W, Niks R-E, Van den Berg P-M-M-M, Stam P, Van Eeuwijk F-A (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168:435–446
Lev-Yadun S, Gopher A, Abbo S (2000) The cradle of agriculture Archeology. Science 288:1602–1603
Li Z-K, Fu B-Y, Gao Y-M, Xu J-L, Ali J, Lafitte H-R, Jiang Y-Z, Domingo Rey J, Vijayakumar C-H-M, Maghirang R, Zheng T-Q, Zhu L-H (2005) Genome-wide introgression lines and their use in genetic and molecular dissection of complex phenotypes in rice (Oryza sativa L.). Plant Mol Biol 59:33–52
Li L, Strahwald J, Hofferbert H-R, Lubeck J, Tacke E, Junghans H, Wunder J, Gebhardt C (2005) DNA variation at the invertase locus invGE/GF is associated with tuber quality traits in populations of potato breeding clones. Genetics. 170:813–821
Liu J, van Eck J, Cong B, Tanksley S-D (2002) A new class of regulatory genes underlying the cause of pear-shaped fruit. Proc Natl Acad Sci USA 99:13302–13306
Lübberstedt T, Melchinger A-E, Dussle C, Vuylsteke M, Kuiper M (2000) Relationship among early European maize inbreds: IV genetic diversity revealed with AFLP markers and comparison with RFLP, RAPD, and pedigree data. Crop Sci 40:783–791
Mackay T-F-C (2001) The genetic architecture of quantitative traits. Annu Rev Genet 35:303–339
Mackay T-F-C (2004) The genetic architecture of quantitative traits: lessons from Drosophila. Curr Opin Genet Dev 14:253–257
Margulies M, Michael M, Altman W-E, Attiya S, Bader J-S, Bemben L-A, Berka J, Braverman M-S, Chen Y-J, Chen Z, Dewell S-B, Du L, Fierro J-M, Gomes X-V, Godwin B-C, He W, Helgesen S, Ho C-H, Irzyk G-P, Jando S-C, Alenquer M-L-I, Jarvie T-P, Jirage K-B, Kim J-B,Knight J-R, Lanza J-R, Leamon J-H, Lefkowitz S-M, Lei M, Li J, Lohman K-L, Lu H, Makhijani V-B, McDade K-E, McKenna M-P, Myers E-W, Nickerson E, Nobile J-R, Plant R, Puc B-P, Ronan M-T, Roth G-T, Sarkis G-J, Simons J-F, Simpson J-W, Srinivasan M, Tartaro K-R, Tomasz A, Vogt K-A, Volkmer G-A, Wang S-H, Wang Y, Weiner M-P, Yu P, Begley R-F, Rothberg J-M (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380
McCarty D-R, Settles A-M, Suzuki M, Tan B-C, Latshaw S, Porch T, Robin K, Baier J, Avigne W, Lai J, Messing J, Koch K-E, Hannah L-C (2005) Steady-state transposon mutagenesis in inbred maize. Plant J 44:52–61
McKay B, Slaney J-K (2002) Advances in artificial intelligence, 15th Australian joint conference on artificial intelligence, Canberra, Australia, December 2–6, 2002, Proceedings Springer 2002
McKay R-I, Abbass H-A (2003) Artificial life: an introduction. Intern J Computat Intellig and Appl 3:143–144
Michelmore R-W, Paran I, Kesseli R-V (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832
Morgante M, Salamini F (2003) From plant genomics to breeding practice. Curr Opin Biotech 14:214–219
Mott R, Talbot C-J, Turri M-G, Collins A-C, Flint J (2000) A method for fine mapping quantitative trait loci in outbred animal stocks. Proc Natl Acad Sci USA 97:12649–12654
Niu T (2004) Algorithms for inferring haplotypes. Genet Epidemiol 27:334–347
Norga K-K, Gurganus M-C, Dilda C-L, Yamamoto A, Lyman R-F, Patel P-H, Rubin G-M, Hoskins R-A, Mackay T-F, Bellen H-J (2003) Quantitative analysis of bristle number in Drosophila mutants identifies genes involved in neural development. Curr Biol 19;13:1388–1396
Olsen K-M, Halldorsdottir S-S, Stinchcombe J-R, Weinig C, Schmitt J, Purugganan M-D (2004) Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles. Genetics 167:1361–1369
Paran I, Zamir D (2003) Quantitative traits in plants: Beyond the QTL. Trends Genet 19:303–306
Paterson A-H, Lander E-S, Hewitt J-D, Peterson S, Lincoln S-E et al (1988) Resolution of quantitative traits into Mendelian factors using a complete linkage map of restriction fragment length polymorphisms. Nature 335:721–726
Peleman J-D, Rouppe van der Voort J (2003) Breeding by design. Trends Plant Sci 8:330–334
Peleman J-D, Wye C.L, Zethof J, Sorensen A-P, Verbakel H, van Oeveren J, Gerats T, Rouppe van der Voort J (2005) Quantitative trait locus (QTL) Isogenic recombinant analysis: a method for High-resolution mapping of QTL within a single population. Genetics 171:1341–1352
Pillen K, Zacharias A, Léon J (2004) Comparative AB-QTL analysis in barley using a single exotic donor of Hordeum vulgare ssp. spontaneum. Theor Appl Genet 108:1591–1601
Pritchard J-K, Stephens M, Rosenberg N-A, Donnelly P (2000) Association mapping in structured populations. Am J Hum Genet 67:1070–181
Rafalski A, Morgante M (2004) Corn and humans: Recombination and linkage disequilibrium in two genomes of similar size. Trends Genet 20:103–111
Rannala B, Slatkin M (2000) Methods for multipoint disease mapping using linkage disequilibrium. Genet Epidemiol 9:S71–77
Reif J-C, Melchinger A-E, Frisch M (2005) Genetical and mathematical properties of similarity and dissimilarity coefficients applied in plant breeding and seed bank management. Crop Sci 45:1–7
Reyes-Valdes M-H (2000) A model for Marker-based selection in gene introgression breeding programs. Crop Sci 40:91–98
Roldán-Ruiz I, Calsyn E, Gilliland T-J, Coll R, van Eijk M-J-T, De Loose M (2000) Estimating genetic conformity between related ryegrass (Lolium) varieties. 2. AFLP characterization. Mol Breed 6:593–602
Rouppe van der Voort J, van der Vossen E, Bakker E, Overmars H, van Zandvoort P, Hutten R, Klein Lankhorst R, Bakker J (2000) Two additive QTLs conferring broad-spectrum resistance in potato to Globodera pallida are localized on resistance gene clusters. Theor Appl Genet 101:1122–1130
Salvi S, Tuberosa R (2005) To clone or not to clone plant QTLs: present and future challenges. Trends Plant Sci 10:297–304
Salvi S, Tuberosa R, Chiapparino E, Maccaferri M, Veillet S et al (2002) Toward positional cloning of Vgt1, a QTL controlling the transition from the vegetative to the reproductive phase in maize. Plant Mol Biol 48:601–613
Schauer N, Semel Y, Roessner U, Gur A, Balbo I, Carrari F, Pleban T, Perez-Melis A, Bruedigam C, Kopka J, Willmitzer L, Zamir D, Fernie A-R (2006) Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat Biotechnol 24:447–454
Septiningish E-M, Trijatmiko K-R, Moeljoparwiro S, McCouch.S-R (2003) Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O rufipogon Theor Appl Genet 107:1433–1441
Servin B, Martin O-C, Mézard M, Hospital, F (2004) Toward a theory of marker-assisted gene pyramiding. Genetics 168:513–523
Shendure J, Mitra R-D, Varma C, Church G-M (2004) Advanced sequencing technologies: methods and goals. Nat Rev Genet 5:335–344
Sicard D, Woo S-S, Arroyo-Garcia R, Ochoa O, Nguyen D, Korol A, Nevo E, Michelmore R (1999) Molecular diversity at the major cluster of disease resistance genes in cultivated and wild Lactuca spp. Theor Appl Genet 99:405–418
Smid K-J, Tórjék O, Meyer R, Schmuths H, Hoffman M-H, Altmann T (2006) Evidence for large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphis markers. Theor Appl Genet 112:1104–1114
Stuurman J, Kuhlemeier C (2005) Stable two-element control of dTph1 transposition in mutator strains of Petunia by an inactive ACT1 introgression from a wild species. Plant J 41:945–55
Syed N-H, Chen Z-J (2004) Molecular marker genotypes, heterozygosity and genetic interaction explain heterosis in Arabidopsis thaliana. Heredity 94:295–304
Syvanen A-C (2001) Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet 2:930–942
Syvanen A-C (2005) Toward genome-wide SNP genotyping. Nat Genet 37:10
Szalma S-J, Buckler E-S, Snook M-E, McMullen M-D (2005) Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks. Theor Appl Genet 110:1324–1333
Takahashi Y, Shomura A, Sasaki T, Yano M (2001) Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2. Proc Natl Acad Sci USA 98:7922–7927
Tanksley S-D, Grandillo S, Fulton T-M, Zamir, D, Eshed Y, Petiard V, Lopez J, Beck-Bunn T (1996) Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium. Theor Appl Genet 92:213–224
Tanksley S-D, McCouch S-R (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066
Tanksley S-D, Nelson J-C (1996) Advanced backcross QTL analysis: A method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203
Tanksley S-D, Young N-D, Paterson A-H, Bonierbale M-W (1989) RFLP mapping in plant breeding: new tools for an old science. Biotechnology 7:257–264
The Complex Trait Consortium (2004) The collaborative cross, a community resource for the genetic analysis of complex traits. Nat Genet 36:1133–1137
The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437:27
Thornsberry J-M, Goodman M-M, Doebley J, Kresovich S, Nielsen D, Buckler E-S (2001) IV, Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289
Thumma B-R, Nolan M-F, Evans R, Moran G-F (2005) Polymorphisms in cinnamoyl CoA reductase (CCR) are associated with variation in microfibril angle in Eucalyptus. Genet 171:1257–1265
van Eeuwijk F-A, Malosetti M, Yin X, Struik P-C, Stam P (2005) Statistical models for genotype by environment data: from conventional ANOVA models to eco-physiological QTL models. Aust J Agric Res 56:883–894
Vos P, Hogers R, Bleeker M , Reijans M, van der Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acid Res 23:4407–4414
Vuylsteke M, Kuiper M, Stam P (2000) Chromosomal regions involved in hybrid performance and heterosis: thir AFLP ®-based identification and practical use in prediction models. Heredity 85:208–218
Watson & Crick (1953) Molecular structure of nucelic acids. Nature 4356:737–738
Williams J, Kubelik A, Livak K, Rafalski J, Tingey S (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535
Wilson L-M, Whitt S-R, Ibanez-Carranza A-M, Goodman M-M, Rocheford T-R, Buckler E-S (2004) Dissection of maize kernel composition and starch production by candidate gene association, Plant Cell 16:2719–2733
Witcombe J-R, Hash C-T (2000) Resistance gene deployment strategies in cereal hybrids using maker-assisted selection: gene pyramiding, three-way hybrids and synthetic parent populations. Euphytica 112:175–186
Young N-D (1999) A cautiously optimistic vision for marker-assisted breeding. Mol breed 5:505–510
Zamir D (2001) Improving plant breeding with exotic genetic libraries. Nat Rev Genet 2:993–989
Zöllner S, Pritchard J-K (2005) Coalescent-based association mapping and fine mapping of complex trait loci. Genetics 169:1071–1092
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Sørensen, A.P., Stuurman, J., Voort, J.R.v.d., Peleman, J. (2007). Molecular Breeding: Maximizing the Exploitation of Genetic Diversity. In: Varshney, R.K., Tuberosa, R. (eds) Genomics-Assisted Crop Improvement. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-6295-7_3
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