Skip to main content

Abstract

Molecular genetic map not only provides a powerful tool for the analysis of quantitative trait loci (QTLs) and marker-assisted selection (MAS) at the genomic level, but also lays a foundation for fine mapping and cloning important genes. In this chapter, the unique characteristics and breeding values of the six molecular genetic maps (1 DH, 3 RIL, and 2 natural populations) constructed by SSR, DarT, and SNP markers were illustrated. The parents for each genetic map have some distinguishing features, such as agronomic traits, yield, and/or quality traits. The average distances between adjacent markers in the wheat maps were appropriate (0.44–9.77 cM), thus meeting the recommended requirement for genome-wide QTL scanning. The molecular genetic maps have been used to QTL mapping for some agronomic traits, yield and quality traits, and the good results have been achieved.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Akbari M, Wenzl P, Caig V, Carling J, Xia L, Yang S, Uszynski G, Mohler V, Lehmensiek A, Kuchel H, Hayden MJ, Howes N, Sharp P, Vaughan P, Rathmell B, Huttner E, Kilian A. Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet. 2006;113:1409–20.

    Article  CAS  PubMed  Google Scholar 

  • Akhunov ED, Nicolet C, Dvorak J. Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay. Theor Appl Genet. 2009;119:507–17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Breseghello F, Sorrells ME. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics. 2006;172:1165–77.

    Article  PubMed  PubMed Central  Google Scholar 

  • Brookes AJ. The essence of SNP. Gene. 1999;234:177–86.

    Article  CAS  PubMed  Google Scholar 

  • Cadalen T, Boeuf C, Bernard S, Bernard M. An intervarietal molecular marker map in Triticum aestivum L. Em Thell. and comparison with a map from a wide cross. Theor Appl Genet. 1997;94:367–77.

    Article  CAS  Google Scholar 

  • Cavanagh CR, Chao S, Wang S, Huang BE, Stephen S, Kiani S, Forrest K, Saintenac C, Brown-Guedira GL, Akhunova A, See D, Bai G, Pumphrey M, Tomar L, Wong D, Kong S, Reynolds M, da Silva ML, Bockelman H, Talbert L, Anderson JA, Dreisigacker S, Baenziger S, Carter A, Korzun V, Morrell PL, Dubcovsky J, Morell MK, Sorrells ME, Hayden MJ, Akhunov E. Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Natl Acad Sci USA. 2013;110:8057–62.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen JF, Ren ZL, Gao LF, Jia JZ. Developing new SSR markers from EST in wheat. Acta Agro Sinica. 2005;36:154–8 (in Chinese with English abstract).

    Google Scholar 

  • Cui F. Construction of high-density wheat molecular genetic map and QTL analysis for yield-related traits. PhD Dissertation of Shandong Agricultural University, 2011 (in Chinese with English abstract).

    Google Scholar 

  • Doerge RW. Mapping and analysis of quantitative trait loci in experimental populations. Nat Rev. 2002;3:43–52.

    Article  CAS  Google Scholar 

  • Dubcovsky J, Luo MC, Zhong GY, Bransteiter R, Desai A, Kilian A, Kleinhofs A, Dvorak J. Genetic map of diploid wheat, Triticum monococcum L., and its comparison with maps of Hordeum vulgare L. Genetics. 1996;143:983–99.

    Google Scholar 

  • Ellis MH, Rebetzke GJ, Azanza F, Richards RA, Splelmayer W. Molecular mapping of gibberellin-responsive dwarfing genes in bread Wheat. Theor Appl. GeneL. 2005;111:423–30.

    Article  CAS  Google Scholar 

  • Elouafi I, Nachit MM. A genetic linkage map of the Durum × Triticum dicoccoides backcross population based on SSRs and AFLP markers, and QTL analysis for milling traits. Theor Appl Genet. 2004;108:401–13.

    Article  CAS  PubMed  Google Scholar 

  • Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecology. 2005;14:2611–20.

    Article  CAS  Google Scholar 

  • Falush D, Stephens M, Pritchard JK. Inference of population structure using multi locus genotype data: linked loci and correlated allele frequencies. Genetics. 2003;164:1567–87.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fayyaz E., Shanejat-Bushehri A., Tabatabel B. E. S., Adel J. Constructing a preliminary wheat genetic map using RGA and AFLP Markers. Inter J Agri Bio. 2007;9:863–7.

    Google Scholar 

  • Francki MG, Walker E, Crawford AC, Broughton S, Ohm HW, Barclay I, Wilson RE, McLean R. Comparison of genetic and cytogenetic maps of hexaploid wheat (Triticum aestivum L.) using SSR and DArT markers. Mol Genet Genomics. 2009;281:181–91.

    Article  CAS  PubMed  Google Scholar 

  • Gale MD, Atkinson MD, Chinoy CN, Harcourt RL, Liu J, Li QY. Genetic maps of hexaploid wheat. In: Li ZS, Xin ZY, editors. Proceedings of the 8th International Wheat Genetic Symposium. Agric Scientech Press, Beijing; 1995. pp. 29–40.

    Google Scholar 

  • Ganal MW, Durstewitz G, Polley A, Bérard A, Buckler ES, Charcosset A, Clarke JD, Graner EM, Hansen M, Joets J, Le Paslier MC, McMullen MD, Montalent P, Rose M, Schön CC, Sun Q, Walter H, Martin OC, Falque M. A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS ONE, 2011; 6: e28334.

    Google Scholar 

  • Guo CQ, Bai ZA, Liao PA, Jin WK. New high quality and yield wheat variety Yumai 57. China Seed Indus. 2004;4:54 (in Chinese with English abstract).

    Google Scholar 

  • Gupta M, Chyi YS, Romero SJ, Owen JL. Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple sequence repeats. Theor Appl Genet. 1994;89:998–1006.

    CAS  PubMed  Google Scholar 

  • Hai Y, Kang MH. Breeding of new wheat variety with high yield and early maturing. Henan Agr Sci. 2007;5:36–7.

    Google Scholar 

  • Jaccoud D, Peng K, Feinstein D, Kilian A. Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res. 2001;29:25–31.

    Article  Google Scholar 

  • Karakousis A, Gustafson JP, Chalmers KJ, Barr AR, Langridge P. A consensus map of barley integrating SSR, RFLP, and AFLP markers. Aust J Agric Res. 2003;54:1173–85.

    Article  CAS  Google Scholar 

  • Kerfal S, Giraldo P, Rodriguez-Quijano M, Vazquez JF, Adams K, Lukow OM, Röder MS, Somers DJ, Carrillo JM. Mapping quantitative trait loci (QTLs) associated with dough quality in a soft x hard bread wheat progeny. J Cereal Sci. 2010;52:46–52.

    Google Scholar 

  • Li SS, Jia JZ, Wei XY, et al. A intervarietal genetic map and QTL analysis for yield traits in wheat. Mol Breeding. 2007;20:167–178.

    Google Scholar 

  • Li YQ, Su ZF, Wang LX, Ji W, Yao J, Zhao CP. Increasing density of wheat genetic linkage map with molecular markers. Acta Agron Sinica. 2009;35:861–6.

    Google Scholar 

  • Lillemo M, Joshi AK, Prasad R, Chand R, Singh RP. QTL for spot blotch resistance in bread wheat line Saar co-locate to the biotrophic disease resistance loci Lr34 and Lr46. Theor Appl Genet. 2008;126:711–9.

    Article  Google Scholar 

  • Lincoln SE, Daly MJ, Lander ES. Mapping genes controlling quantitative traits using MAPMAKER/QTL version 1.1: a tutorial and reference manual. Whitehead Institute for Biometrical Research, Cambridge, Mass; 1993.

    Google Scholar 

  • Liu ZH, Anderson JA, Hu J, Friesen TL, Rasmussen JB, Faris JD. A wheat intervarietal genetic linkage map based on microsatellite and target region amplified polymorphism markers and its utility for detecting quantitative trait loci. Theor Appl Genet. 2005;111:782–94.

    Article  CAS  PubMed  Google Scholar 

  • Liu YG, Tsunewaki K. Restriction fragment length polymorphism (RFLP) analysis in wheat. ll. Linkage maps of the RFLP sites in common wheat. Jpn J Genet. 1991;66:617–633.

    Google Scholar 

  • Lu YL, Yan JB, Guimarâes CT, Taba S, Hao ZF, Gao SB, Chen SJ, Li JS, Zhang SH, Vivek BS, Magorokosho C, Mugo S, Makumbi D, Parentoni SN, Shah T, Rong TZ, Crouch ZH, Xu YB. Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms. Theor Appl Genet. 2009;120:93–115.

    Article  CAS  PubMed  Google Scholar 

  • Mantovani P, Maccaferri M, Sanguineti MC, Tuberosa R, Catizone I, Wenzl P, Thomson B, Carling J, Huttner E, Ambrogio ED, Kilian A. An integrated DArT-SSR linkage map of durum wheat. Mol Breeding. 2008;22:629–48.

    Article  CAS  Google Scholar 

  • Marino CL, Nelson JC, Lu YH, Sorrells ME, Leroy P, Lu YH. Molecular genetic maps of the group 6 chromosomes of hexaploid wheat (Triticum aestivum L. em. Thell). Genome. 1996;39:359–366.

    Google Scholar 

  • Messmer MM, Keller M, Zanetti S, Keller B. Genetic linkage map of a wheat-spelt cross. Theor Appl Genet. 1999;98:1163–70.

    Article  CAS  Google Scholar 

  • Nachit MM, et al. Molecular linkage map for an intraspecific recombinant inbred population of durum wheat (Triticum turgidum L. var. durum). Theor Appl Genet. 2001;102:177–186.

    Google Scholar 

  • Penner. An AFLP based genome map of wheat (Triticum Agriculture. Plant and Animal Genome VI Conference aestivum) [A]. US Department of [C]. San Diego CA January, 1998, 163.

    Google Scholar 

  • Paux E, Sourdille P, Salse J, et al. A physical map of the 1-gigabase bread wheat chromosome 3B. science; 2008, 322:101–104.

    Google Scholar 

  • Peleg Z, Saranga Y, Suprunova T, Ronin YW, Röder MS, Kilian A, Korol AB, Fahima T. High-density genetic map of durum wheat × wild emmer wheat based on SSR and DArT markers. Theor Appl Genet. 2008;117:103–15.

    Article  CAS  PubMed  Google Scholar 

  • Peng JH, Zadeh H, Lazo GR, Gustafson JP, Chao S, Anderson OD, Qi LL, Echalier B, Gill BS, Dilbirligi M, Sandhu D, Gill KS, Greene RA, Sorrells ME, Akhunov ED, Dvorák J, Linkiewicz AM, Dubcovsky J, Hossain KG, Kalavacharla V, Kianian SF, Mahmoud AA, Miftahudin, Conley EJ, Anderson JA, Pathan MS, Nguyen HT, McGuire PE, Qualset CO, Lapitan NL. Chromosome bin map of expressed sequence tags in homoeologous group 1 of hexaploid wheat and homoeology with rice and Arabidopsis. Genetics. 2004;168:609–23.

    Google Scholar 

  • Pestsova E, Ganal MW, Röder MS. Isolation and mapping of microsatellite markers specific for the D genome of bread wheat. Genome. 2000;43:689–97.

    Article  CAS  PubMed  Google Scholar 

  • Pritchard JK, Wen W, Falush D. Documentation for STRUCTURE software: version 2; 2003.

    Google Scholar 

  • Quarrie SA, Steed A, Calestani C, Semikhodskii A, Lebreton C, Chinoy C, Steele N, Pljevljakusic D, Waterman E, Weyen J, Schondelmaier J, Habash DZ, Farmer P, Saker L, Clarkson DT, Abugalieva A, Yessimbekova M, Turuspekov Y, Abugalieva S, Tuberosa R, Sanguineti MC, Hollington PA, Aragues R, Royo A, Dodig D. A high-density genetic map of hexaploid wheat (Triticum aestivum L.) from the cross Chinese Spring × SQ1 and its use to compare QTLs for grain yield across a range of environments. Theor Appl Genet. 2005;110:865–80.

    Google Scholar 

  • Rafalski JA. Application of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol. 2002;5:94–100.

    Article  CAS  PubMed  Google Scholar 

  • Röder MS, Huang XQ, Ganal MW. Wheat microsatellites in plant breeding-Potential and Implications. In: Lörz H. & Wenzel G. (Eds.). Molecular Markers in Plant Breeding and Crop Improvement. Springer-Verlag. Heidelberg. 2004.

    Google Scholar 

  • Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier MH, Leroy P, Ganal MW. A microsatellite map of wheat. Genetics. 1998;149:2007–23.

    PubMed  PubMed Central  Google Scholar 

  • Semagn K, Bjornstad A. SkimesH, Maroy AG, Tarkegne Y, W illiam M. Distribution of DArT, AFLP, and SSR markers in a genetic linkage map of a doubled-haploid hexaploid wheat population. Genome. 2006;49:545–55.

    Article  CAS  PubMed  Google Scholar 

  • Shi PC, Wang GL, Zhang Wei, Cao LP. Construction of wheat SSR molecular linkage map and its polymorphism. Xinjiang Agri Sci. 2007;44:71–76.

    Google Scholar 

  • Somers DJ, Isaac P, Edwards K. A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet; 2004;109:1105–1114.

    Google Scholar 

  • Song Q, Hyten DL, Jia G, Quigley CV, Fickus EW, Nelson RL, Cregan PB. Development and evaluation of SoySNP50 K, a high-density genotyping array for soybean. PLoS ONE. 2013;8:e54985.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Song YX, Jing RL, Huo NX, Ren ZL, Jia JZ. Detection of QTLs for heading in common wheat (T.aestivum L.) using different populations. Sci Agri Sinica. 2006;39:2186–93.

    Google Scholar 

  • Sourdille P, Cadalen T, Guyomarc’h H, Snape JW, Perretant MR, Charmet G, Boeuf C, Bernard S, Bernard M. An update of the Courtot × Chinese Spring intervarietal molecular marker linkage map for the QTL detection of agronomic traits in wheat. Theor Appl Genet. 2003;106:530–538.

    Google Scholar 

  • Stephenson P, Bryan G, Kirby J, Collins A, Devos K, Busso C, Gale M. Fifty new microsatellite loci for the wheat genetic map. Theor Appl Genet. 1998;97:946–9

    Google Scholar 

  • Su ZQ, Hao CY, Wang LF, Dong YC, Zhang XY. Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.). Theor Appl Genet; 2011, 122: 211–223.

    Google Scholar 

  • Suenaga K, Khairallah M, William HM, Hoisington DA. A new intervarietal linkage map and its application for quantitative trait locus analysis of “gigas” features in bread wheat. Genome. 2005;48:65–75.

    Google Scholar 

  • Torada A, Koike M, Mochida K, Ogihara Y. SSR-based linkage map with new markers using an intraspecific population of common wheat. Theor Appl Genet. 2006;112:1042–51.

    Article  CAS  PubMed  Google Scholar 

  • Voorrips RE. MapChart: software for the graphical presentation of linkage maps and QTLs. J Heredity. 2002;93:77–8.

    Article  CAS  Google Scholar 

  • Wang YY, Sun XY, Zhao Y, Kong FM, Guo Y, Zhang GZ, Pu YY, Wu K, Li SS. Enrichment of a common wheat genetic map and QTL mapping for fatty acid content in grain. Plant Sci. 2011;181:65–75.

    Google Scholar 

  • Wang SC, Wong DB, Forrest K, Allen A, Chao SM, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, International Wheat Genome Sequencing Consortium, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E. Characterization of polyploid wheat genomic diversity using a high-density 90000 single nucleotide polymorphism array. Plant Biotechnol J; 2014, 12:787–796.

    Google Scholar 

  • Wenzl P, Li H, Carling J, Zhou M, Raman H, Paul E, Hearnden P, Maier C, Xia L, Caig V, Ovesná J, Cakir M, Poulsen D, Wang J, Raman R, Smith KP, Muehlbauer GJ, Chalmers KJ, Kleinhofs A, Huttner Eric, Kilian A. A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genomics; 2006, 7:206.

    Google Scholar 

  • Wiedmann RT, Smith TPL, Nonneman DJ. SNP discovery in swine by reduced representation and high throughput pyrosequencing. BMC Genet. 2008;9:81.

    Article  PubMed  PubMed Central  Google Scholar 

  • Würschum T, Langer SM, Longin CFH, Korzun V, Akhunov E, Ebmeyer E, Schachschneider R, Schacht J, Kazman E, Reif JC. Population structure, genetic diversity and linkage disequilibrium in elite winter wheat assessed with SNP and SSR markers. Theor Appl Genet. 2013;126:1477–86.

    Article  PubMed  Google Scholar 

  • Xu SB. Construction of genetic map by SSR marker and location QTL for plant height and heading time in wheat. MD Dissertation of Xinjiang Agricultural University, 2005 (in Chinese with English abstract).

    Google Scholar 

  • Xue SL, Zhang ZZ, Lin F, Kong ZX, Cao Y, Li CJ, Yi HY, Mei MF, Zhao DM, Zhu HL, Xu HB, Wu JZ, Tian DG, Zhang CQ, Ma ZQ. A high-density intervarietal map of the wheat genome enriched with markers derived from expressed sequence tags. Theor Appl Genet. 2008;117:181–9.

    Google Scholar 

  • Yao Q, Zhou RH, Pan YM, Fu TH, Jia JZ. Construction of genetic linkage map and QTL analysis of agronomic important traits based on RIL population derived from common wheat variety Yanzhan 1 and Zaosui 30. Sci Agri Sinica. 2010;43:4130–9.

    Google Scholar 

  • Yu JK, Dake TM, Singh S, Benscher D, Li W, Gill B, Sorrells ME. Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat. Genome. 2004;47:805–818.

    Google Scholar 

  • Zhai HM, Tian JC. Development of wheat mutants carrying different null Wx alleles and their starch properties. Acta Agro Sinica. 2007;33(7):1359–1066 (in Chinese with English abstract).

    Google Scholar 

  • Zhang KP, Wang JJ, Zhang LY, Rong CW, Zhao FW, Peng T, Li HM, Cheng DM, Liu X, Qin HJ, Zhang AM, Tong YP, Wang DW. Association analysis of genomic loci important for grain weight control in elite common wheat varieties cultivated with variable water and fertiliser supply. PLoS ONE. 2013;8:e57853.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang KP, Zhao L, Tian JC, Chen GF, Jiang XL, Liu B. A genetic map constructed using a doubled haploid population derived from two elite Chinese common wheat varieties. J Integrat Plant Bio. 2008;50:941–50.

    Article  CAS  Google Scholar 

  • Zhou MP, Zhang X, Ren LJ, Schol TO, Bai GH, Ma HX, Lu WZ. Construction of wheat genetic linkage map by JoinMap 3.0. J Jiangsu Agri. 2003;19:133–8.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jichun Tian .

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Science Press, Beijing and Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Tian, J., Deng, Z., Zhang, K., Yu, H., Jiang, X., Li, C. (2015). Construction of Molecular Genetic Map of Wheat . In: Genetic Analyses of Wheat and Molecular Marker-Assisted Breeding, Volume 1. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-7390-4_3

Download citation

Publish with us

Policies and ethics