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Marker-assisted wheat breeding: present status and future possibilities

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Abstract

Wheat production and productivity in the past witnessed a remarkable growth. However, this growth rate could not be sustained during the last decade, causing concern among world wheat community. Marker-assisted selection (MAS), which is being practiced for improvement of a variety of traits in wheat around the world, may at least partly help in providing the desired solution. Marker-trait associations are now known for a number of simple, but difficult-to-score traits, so that MAS has been found useful for improvement of several of these important economic traits. Breeding strategies including marker-assisted backcrossing, forward breeding, MAS involving doubled haploid technology and F2 enrichment have been successfully utilized for this purpose. However, for improvement of complex polygenic traits, newer technologies based on high throughput genotyping associated with new marker systems (e.g., DArT and SNP), and new selection strategies such as AB-QTL, mapping-as-you-go, marker-assisted recurrent selection and genome-wide selection will have to be tried in future. The progress made in all these aspects of marker-assisted wheat breeding, and the limitations and future prospects of this emerging technology have been reviewed in this article.

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References

  • Able JA, Langridge P, Milligan AS (2007) Capturing diversity in the cereals: many options but so little promiscuity. Trends Plant Sci 12:71–79

    Article  CAS  PubMed  Google Scholar 

  • Badea A, Eudes F, Graf RJ, Laroche A, Gaudet DA, Sadasivaiah RS (2008) Phenotypic and marker-assisted evaluation of spring and winter wheat germplasm for resistance to Fusarium head blight. Euphytica 164:803–819

    Article  Google Scholar 

  • Bainotti C, Fraschina J, Salines JH, Nisi JE, Dubcovsky J, Lewis SM, Bullrich L, Vanzetti L, Cuniberti M, Campos P, Formica MB, Masiero B, Alberione E, Helguera M (2009) Registration of ‘BIOINTA 2004’ Wheat. J Plant Registr 3:165–169

    Article  Google Scholar 

  • Barloy D, Lemoine J, Abelard P, Tanguy AM, Rivoal R, Jahier J (2007) Marker-assisted pyramiding of two cereal cyst nematode resistance genes from Aegilops variabilis in wheat. Mol Breed 20:31–40

    Article  CAS  Google Scholar 

  • Bernardo R (2008) Molecular markers and selection for complex traits in plants: learning from the last 20 years. Crop Sci 48:1649–1664

    Article  Google Scholar 

  • Bernardo R, Yu J (2007) Prospects for genomewide selection for quantitative traits in maize. Crop Sci 47:1082–1090

    Article  Google Scholar 

  • Bonnett DG, Rebetzke GJ, Spielmeyer W (2005) Strategies for efficient implementation of molecular markers in wheat breeding. Mol Breed 15:75–85

    Article  CAS  Google Scholar 

  • Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177

    Article  PubMed  Google Scholar 

  • Brevis JC, Dubcovsky J (2008) Effect of the Gpc-B1 region from Triticum turgidum ssp. dicoccoides on grain yield, thousand grain weight and protein yield. p.1–3. In: Appels R, Eastwood R, Lagudah E, Langridge P, Mackay M, McIntyre L, Sharp P (eds) Proceedings of 11th International Wheat Genet Symposium, Brisbane Australia, August 24–29, 2008. Sydney University Press http://hdl.handle.net/2123/3179

  • Cakir M, Drake-Brockman F, Shankar M, Golzar H, McLean R, Bariana H, Wilson R, Barclay I, Moore C, Jones M, Loughman R (2008) Molecular mapping and marker-assisted improvement of rust resistance in the Australian wheat germplasm. p. 1–3. In: Appels R, Eastwood R, Lagudah E, Langridge P, Mackay M, McIntyre L, Sharp P (eds) Proceedings of 11th International Wheat Genet Symposium, Brisbane Australia, August 24–29, 2008. Sydney University Press. http://hdl.handle.net/2123/3317

  • Cavanagh C, Morell M (2008) Genome resources for bread wheat. p. 1–2. In: Appels R, Eastwood R, Lagudah E, Langridge P, Mackay M, McIntyre L, Sharp P (eds) Proceedings of 11th International Wheat Genet Symposium, Brisbane Australia, August 24–29, 2008. Sydney University Press.http://hdl.handle.net/2123/3245

  • Cavanagh C, Morell M, Powell W (2008) From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Curr Opin Plant Biol 11:215–221

    Article  PubMed  CAS  Google Scholar 

  • Charmet G, Robert N, Perretant MR, Gay G, Sourdille P, Groos C, Bernard S, Bernard M (1999) Marker-assisted recurrent selection for cumulating additive and interactive QTLs in recombinant inbred lines. Theor Appl Genet 99:1143–1148

    Article  Google Scholar 

  • Charmet G, Robert N, Perretant MR, Gay G, Sourdille P, Groos C, Bernard S, Bernard M (2001) Marker assisted recurrent selection for cumulating QTLs for bread making related traits. Euphytica 119:89–93

    Article  CAS  Google Scholar 

  • Chhuneja P, Kaur S, Garg T, Ghai M, Kaur S, Prashar M, Bains NS, Goel RK, Keller B, Dhaliwal HS, Singh K (2008) Mapping of adult plant stripe rust resistance genes in diploid A genome wheat species and their transfer to bread wheat. Theor Appl Genet 116:313–324

    Article  CAS  PubMed  Google Scholar 

  • Cooper M, Podlich DW, Luo L (2007) Modeling QTL effects and MAS in plant breeding. In: Varshney R, Tuberosa R (eds) Genomic assisted crop improvement: vol 1: genomics approaches and platforms, pp. 57–95

  • Crossa J, Burgueno J, Dreisigacker S, Vargas M, Herrera-Foessel S, Lillemo M, Singh R, Trethowan R, Warburton M, Franco J, Reynolds M, Crouch J, Ortiz R (2007) Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics 177:1889–1913

    Article  CAS  PubMed  Google Scholar 

  • Davies J, Berzonsky WA, Leach GD (2006) A comparison of marker-assisted and phenotypic selection for high grain protein content in spring wheat. Euphytica 152:117–134

    Article  CAS  Google Scholar 

  • de Bustos A, Rubio P, Soler C, Garcia P, Jouve N (2001) Marker assisted selection to improve HMW-glutenins in wheat. Euphytica 119:69–73

    Article  Google Scholar 

  • Del Blanco IA, Frohberg RC, Stack RW, Berzonsky WA, Kianian SF (2003) Detection of QTL linked to Fusarium head blight resistance in’”Sumai 3’-derived North Dakota bread wheat lines. Theor Appl Genet 106:1027–1031

    CAS  PubMed  Google Scholar 

  • DePauw RM, Townley-Smith TF, Humphreys G, Knox RE, Clarke FR, Clarke JM (2005) Lillian hard red spring wheat. Can J Plant Sci 85:397–401

    Google Scholar 

  • DePauw RM, Knox RE, Thomas JB, Smith M, Clarke JM, Clarke FR, McCaig TN, Fernandez MR (2009) Goodeve hard red spring wheat. Can J Plant Sci 89:937–944

    Article  Google Scholar 

  • Dubcovsky J (2004) Marker assisted selection in public breeding programs: the wheat experience. Crop Sci 44:1895–1898

    Google Scholar 

  • Eagles HA, Bariana HS, Ogbonnaya FC, Rebetzke GJ, Hollamby GJ, Henry RJ, Henschke PH, Carter M (2001) Implementation of markers in Australian wheat breeding. Aust J Agr Res 52:1349–1356

    Article  CAS  Google Scholar 

  • Eathington SR, Crosbie TM, Edwards MD, Reiter RS, Bull JK (2007) Molecular markers in a commercial breeding program. Crop Sci 47:S154–S163

    Article  Google Scholar 

  • Edwards M, Jonson L (1994) RFLPs for rapid recurrent selection. p. 33–40. In: Proceedings of Joint Plant Breed Symposium Series of CSSA and ASHA, Corvallis, OR. Am Soc Hort Sci, Alexandria, VA. 5–6 Aug. 1994

  • Elias EM (2005) Fusarium resistant tetraploid wheat. United States Patent Application 20050273875

  • Feuillet C, Langridge P, Waugh R (2008) Cereal breeding takes a walk on the wild side. Trends Genet 24:24–32

    Article  CAS  PubMed  Google Scholar 

  • Finkel E (2009) Richard Richards Profile: making every drop count in the buildup to a blue revolution. Science 323:1004–1005

    Article  CAS  PubMed  Google Scholar 

  • Gao AL, He HG, Chen QZ (2005) Pyramiding wheat powdery mildew resistance genes Pm2, Pm4a and Pm21 by molecular marker-assisted selection. Acta Agronomica Sinica 31:1400–1405

    CAS  Google Scholar 

  • Graybosch RA, Peterson CJ, Baenziger PS, Baltensperger DD, Nelson LA, Jin Y, Kolmer J, Seabourn B, French R, Hein G, Martin TJ, Beecher B, Schwarzacher T, Heslop-Harrison P (2009) Registration of ‘Mace’ Hard Red Winter Wheat. J Plant Registr 3:51–56

    Article  Google Scholar 

  • Gupta PK, Rustgi S, Mir RR (2008a) Array-based high-throughput DNA markers for crop improvement. Heredity 101:5–8

    Article  CAS  PubMed  Google Scholar 

  • Gupta PK, Balyan HS, Kumar J, Kulwal PK, Kumar N, Mir RR, Kumar A, Prabhu KV (2008b) QTL analysis and marker assisted selection for improvement in grain protein content and pre-harvest sprouting tolerance in bread wheat. p. 1–3. In: Appels R, Eastwood R, Lagudah E, Langridge P, Mackay M, McIntyre L, Sharp P (eds) Proceedings of 11th International Wheat Genet Symposium, Brisbane Australia, August 24–29, 2008. Sydney University Press. http://hdl.handle.net/2123/3350

  • Gupta PK, Balyan HS, Mir RR (2008c) Wheat genetics in the post-genomics era. Curr Sci 95:1660–1662

    Google Scholar 

  • Gupta PK, Mir RR, Mohan A, Kumar J (2008d) Wheat genomics: present status and future prospectus. Int J Plant Genomics 2008:896451

    CAS  PubMed  Google Scholar 

  • Gupta PK, Kumar J, Mir RR, Kumar A (2009) Marker-assisted selection as a component of conventional plant breeding. Plant Breed Rev 33:145–217

    Google Scholar 

  • Heffner EL, Sorrells ME, Jannink JL (2009) Genomic selection for crop improvement. Crop Sci 49:1–12

    Article  CAS  Google Scholar 

  • Holland JB (2004) Implementation of molecular markers for quantitative traits in breeding programs-challenges and opportunities. In: Fischer T (ed) New directions for a diverse planet. Proceedings of the 4th International Crop Science Congress, Brisbane, 26 September-1 Oct 2004. www.cropscience.org.au/icsc2004

  • Hospital F (2009) Challenges for effective marker-assisted selection in plants. Genetica 136:303–310

    Article  PubMed  Google Scholar 

  • Hospital F, Moreau L, Lacourdre F, Charcosset A, Gallais A (1997) More on the efficiency of marker-assisted selection. Theor Appl Genet 95:1181–1189

    Article  Google Scholar 

  • Howes NK, Woods SM, Townley-Smith TF (1998) Simulations and practical problems of applying multiple marker assisted selection and doubled haploids to wheat breeding programs. Euphytica 100:225–230

    Article  Google Scholar 

  • Knapp SJ (1998) Marker-assisted selection as a strategy for increasing the probability of selecting superior genotypes. Crop Sci 38:1164–1174

    Article  Google Scholar 

  • Kottearachchi NS, Uchino N, Kato K, Miura H (2006) Increased grain dormancy in white-grained wheat by introgression of pre-harvest sprouting tolerance QTL. Euphytica 152:421–428

    Article  CAS  Google Scholar 

  • Kuchel H, Guoyou Y, Fox R, Jefferies S (2005) Genetic and economic analysis of a targeted marker-assisted wheat breeding strategy. Mol Breed 16:67–78

    Article  Google Scholar 

  • Kuchel H, Fox R, Reinheimer J, Mosionek L, Willey N, Bariana H, Jefferies S (2007) The successful application of a marker-assisted wheat breeding strategy. Mol Breed 20:295–308

    Article  Google Scholar 

  • Kuchel H, Fox R, Hollamby G, Reinheimer JL, Jefferies SP (2008) The challenges of integrating new technologies into a wheat breeding programme. p. 1–5. In: Appels R, Eastwood R, Lagudah E, Langridge P, Mackay M, McIntyre L, Sharp P (eds) Proceedings of 11th International Wheat Genet Symposium. Brisbane, August 24–29, 2008. Sydney University Press. http://hdl.handle.net/2123/3400

  • Kulwal PL, Kumar N, Gaur A, Khurana P, Khurana J, Tyagi AK, Balyan HS, Gupta PK (2005) Mapping of a major QTL for pre-harvest sprouting tolerance on chromosome 3A in bread wheat. Theor Appl Genet 111:1052–1059

    Article  CAS  PubMed  Google Scholar 

  • Kumar J, Mir RR, Kumar N, Kumar A, Mohan A, Prabhu KV, Balyan HS, Gupta PK (2009) Marker assisted selection for pre-harvest sprouting tolerance and leaf rust resistance in bread wheat. Plant Breed (resubmitted after minor revision)

  • Kunert A, Naz A, Dedeck O, Pillen K, Léon J (2007) AB-QTL analysis in winter wheat: I. Detection of favorable exotic alleles for baking quality traits introgressed from synthetic hexaploid wheat (T. turgidum ssp. Dicoccoides × T. tauschii). Theor Appl Genet 115:683–695

    Article  CAS  PubMed  Google Scholar 

  • Landjeva S, Korzum V, Borner A (2007) Molecular markers: actual and potential contributions to wheat genome characterization and breeding. Euphytica 156:271–296

    Article  CAS  Google Scholar 

  • Langridge P, Lagudah E, Holton T, Appels R, Sharp P, Chalmers K (2001) Trends in genetic and genome analyses in wheat: a review. Aust J Agric Res 52:1043–1077

    Article  CAS  Google Scholar 

  • Liu J, Liu D, Tao W, Li W, Wang S, Chen P, Cheng S, Gao D (2000) Molecular marker-facilitated pyramiding of different genes for powdery mildew resistance in wheat. Plant Breed 119:21–24

    Article  CAS  Google Scholar 

  • Meuwissen T, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829

    CAS  PubMed  Google Scholar 

  • Miedaner T, Wilde F, Steiner B, Buerstmayr H, Korzun V, Ebmeyer E (2006) Stacking quantitative trait loci (QTL) for Fusarium head blight resistance from non-adapted sources in an European elite spring wheat background and assessing their effects on deoxynivalenol (DON) content and disease severity. Theor Appl Genet 112:562–569

    Article  CAS  PubMed  Google Scholar 

  • Miedaner T, Wilde F, Korzun V, Ebmeyer E, Schmolke M, Hartl L, Schön CC (2009) Marker selection for Fusarium head blight resistance based on quantitative trait loci (QTL) from two European sources compared to phenotypic selection in winter wheat. Euphytica 166:219–227

    Article  CAS  Google Scholar 

  • Moreau L, Lamarie S, Charcosset A, Gallais A (2000) Economic efficiency of one cycle of marker-assisted selection. Crop Sci 40:329–337

    Article  Google Scholar 

  • Naz AA, Kunert A, Lind V, Pillen K, Léon J (2008) AB-QTL analysis in winter wheat: II. Genetic analysis of seedling and field resistance against leaf rust in a wheat advanced backcross population. Theor Appl Genet 116:1095–1104

    Article  CAS  PubMed  Google Scholar 

  • Nocente F, Gazza L, Pasquini M (2007) Evaluation of leaf rust resistance genes Lr1, Lr9, Lr24, Lr47 and their introgression into common wheat cultivars by marker-assisted selection. Euphytica 155:329–336

    Article  CAS  Google Scholar 

  • Ogbonnaya FC, Subrahmanyam NC, Moullet O, de Majnik J, Eagles HA, Brown JS, Eastwood RF, Kollmorgen J, Appels R, Lagudah ES (2001) Diagnostic DNA markers for cereal cyst nematode resistance in bread wheat. Aust J Agri Res 52:1367–1374

    Article  CAS  Google Scholar 

  • Parker GD, Chalmers KJ, Rathjen AJ, Langridge P (1998) Mapping loci associated with flour color in wheat (Triticum aestivum L.). Theor Appl Genet 97:238–245

    Article  CAS  Google Scholar 

  • Podlich DW, Winkler CR, Cooper M (2004) Mapping as you go: an effective approach for marker-assisted selection of complex traits. Crop Sci 44:1560–1571

    Article  Google Scholar 

  • Powell W, Langridge P (2004) Unfashionable crop species flourish in the 21st century. Genome Biol 5:233

    Article  PubMed  Google Scholar 

  • Pumphrey MO, Bernardo R, Anderson JA (2007) Validating the Fhb1 QTL for Fusarium head blight resistance in near-isogenic wheat lines developed from breeding populations. Crop Sci 47:200–206

    Article  CAS  Google Scholar 

  • Randhawa HS, Mutti JS, Kidwell K, Morris CF, Chen X, Gill KS (2009) Rapid and targeted introgression of genes into popular wheat cultivars using marker-assisted background selection. PLoS ONE 4:e5752

    Article  PubMed  CAS  Google Scholar 

  • Ravel C, Praud S, Murigneux A, Linossier L, Dardevet M, Balfourier F, Dufour P, Brunel D, Charmet G (2006) Identification of Glu-B1–1 as a candidate gene for the quantity of high-molecular-weight glutenin in bread wheat (Triticum aestivum L.) by means of an association study. Theor Appl Genet 112:738–743

    Article  CAS  PubMed  Google Scholar 

  • Schuster SC (2008) Next-generation sequencing transforms today’s biology. Nature Methods 5:16–18

    Article  CAS  PubMed  Google Scholar 

  • Shi JR, Xu DH, Yang HY, Lu QX, Ban T (2008) DNA marker analysis for pyramided of Fusarium head blight (FHB) resistance QTLs from different germplasm. Genetica 133:77–84

    Article  CAS  PubMed  Google Scholar 

  • Singh R, Datta D, Priyamvada, Singh S, Tiwari R (2004) Marker-assisted selection for leaf rust resistance genes Lr19 and Lr24 in wheat (Triticum aestivum L.). J Appl Genet 45:399–403

    PubMed  Google Scholar 

  • Somers DJ, Thomas J, DePauw R, Fox S, Humphreys G, Fedak G (2005) Assembling complex genotypes to resist Fusarium in wheat (Triticum aestivum L.). Theor Appl Genet 111:1623–1631

    Article  CAS  PubMed  Google Scholar 

  • Sorrells ME (2007) Application of new knowledge, technologies, and strategies to wheat improvement. Euphytica 157:299–306

    Article  Google Scholar 

  • Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203

    Article  Google Scholar 

  • Tommasini L, Schnurbusch T, Fossati D, Mascher F, Keller B (2007) Association mapping of Stagonospora nodorum blotch resistance in modern European winter wheat varieties. Theor Appl Genet 115:697–708

    Article  CAS  PubMed  Google Scholar 

  • Torada A, Koike M, Ikeguchi S, Tsutsui I (2008) Mapping of a major locus controlling seed dormancy using bachcrossed progenies in wheat (Triticum aestivum L.). Genome 51:426–432

    Article  CAS  PubMed  Google Scholar 

  • Tucker DM, Griffey CA, Liu S, Saghai-Maroof MA (2006) Potential for effective marker-assisted selection of three quantitative trait loci conferring adult plant resistance to powdery mildew in elite wheat breeding populations. Plant Breed 125:430–436

    Article  CAS  Google Scholar 

  • Wang XY, Chen PD, Zhang SZ (2001) Pyramiding and marker-assisted selection for powdery mildew resistance genes in common wheat. Acta Genetic Sinica 28:640–646

    CAS  Google Scholar 

  • Wang J, Chapman SC, Bonnett DG, Rebetzke GJ, Crouch J (2007) Application of population genetic theory and simulation models to efficiently pyramid multiple genes via marker-assisted selection. Crop Sci 47:582–588

    Article  Google Scholar 

  • Wilde F, Korzun V, Ebmeyer E, Geiger HH, Miedaner T (2007) Comparison of phenotypic and marker-based selection for Fusarium head blight resistance and DON content in spring wheat. Mol Breed 19:357–370

    Article  CAS  Google Scholar 

  • Wilde F, Schön C, Korzun V, Ebmeyer E, Schmolke M, Hartl L, Miedaner T (2008) Marker-based introduction of three quantitative-trait loci conferring resistance to Fusarium head blight into an independent elite winter wheat breeding population. Theor Appl Genet 117:29–35

    Article  CAS  PubMed  Google Scholar 

  • William HM, Trethowan R, Crosby-Galvan EM (2007) Wheat breeding assisted by markers: CIMMYT’s experience. Euphytica 157:307–319

    Article  Google Scholar 

  • Xie C, Xu S (1998) Strategies of marker-aided recurrent selection. Crop Sci 38:626–1535

    Article  Google Scholar 

  • Yu L-X, Abate Z, Anderson JA, Bansal UK, Bariana HS, Bhavani S, Dubcovsky J, Lagudah ES, Liu S, Sambasivam PK, Singh RP, Sorrells ME (2009) Developing and optimizing markers for stem rust resistance in wheat. The Borlaug Global Rust Initiative 2009 Technical Workshop. March 17–20, 2009, Fiesta Inn, Ciudad Obregón, Sonora

  • Zhang Z, Friesen TL, Simons KJ, Xu SS, Faris JD (2009) Development, identification, and validation of markers for marker-assisted selection against the Stagonospora nodorum toxin sensitivity genes Tsn1 and Snn2 in wheat. Mol Breed 23:35–49

    Article  CAS  Google Scholar 

  • Zhou PH, Tan YF, He YQ, Xu CG, Zhang Q (2003) Simultaneous improvement for four quality traits of Zhenshan 97, an elite parent of hybrid rice, by molecular marker-assisted selection. Theor Appl Genet 106:326–331

    CAS  PubMed  Google Scholar 

  • Zhou RH, Zhu ZD, Kong XY, Huo NX, Tian QZ, Li P, Jin CY, Dong YC, Jia JZ (2005) Development of wheat near-isogenic lines for powdery mildew resistance. Theor Appl Genet 110:640–648

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The Indian National Science Academy (INSA) awarded the position of INSA Honorary Scientist to P. K. G.; Council of Scientific & Industrial Research (CSIR) awarded Senior Research Fellowship (SRF) to RRM; the Head of the Department, Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India provided the facilities.

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  1. Molecular Biology Laboratory, Department of Genetics & Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India

    P. K. Gupta & R. R. Mir

  2. Australian Centre for Plant Functional Genomics, University of Adelaide, Adelaide, SA, Australia

    Peter Langridge

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Gupta, P.K., Langridge, P. & Mir, R.R. Marker-assisted wheat breeding: present status and future possibilities. Mol Breeding 26, 145–161 (2010). https://doi.org/10.1007/s11032-009-9359-7

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