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Linkage Mapping of Molecular Markers and Oligogenes

  • B. D. Singh
  • A. K. Singh

Abstract

In the year 1910, the famous “fly room” of Thomas Hunt Morgan witnessed one of the major breakthroughs in the history of genetics, i.e., the discovery of the phenomenon of genetic linkage in the fruit fly Drosophila melanogaster. Linkage is a tendency of genes being inherited together as a result of their location close to each other in the same chromosome. The strength of linkage between genes is largely dependent on the distance between them in the concerned chromosome. The closer two genes are in a chromosome, the stronger is the linkage between them and the lower is the frequency of crossing over leading to the production of new allelic combinations. Based on this expectation, Sturtevant developed the first ever linkage map in the year 1913. The maps developed by Sturtevant and the subsequent researchers were based on qualitative traits often termed as phenotypic markers. The low abundance of phenotypic markers results in large gaps in their linkage maps. Advances in molecular biology and recombinant DNA technology have supported the development of molecular markers based on DNA sequence variation. These markers are abundant and can be used to reliably classify the individuals of a population into clear-cut groups and for linkage mapping. The present chapter describes different types of linkage maps, the methodologies for the construction of linkage maps using molecular markers and oligogenic traits, and the mapping functions that are used to convert the nonadditive recombination fractions into additive genetic distances. It also provides a brief discussion about the various computer software available for linkage mapping. The readers would be able to appreciate the importance of linkage maps for localizing genes and genomic regions that are associated with various traits of economic importance and their usefulness for marker-assisted selection, map-based cloning, and comparative mapping.

Keywords

Genetic Distance Linkage Group Mapping Population Double Haploid Recurrent Parent 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Abe A, Kosugi S, Yoshida K et al (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30:174–179PubMedCrossRefGoogle Scholar
  2. Albini G, Joets FM (2003) ActionMap: a web-based software that automates loci assignments to framework maps. Nucleic Acids Res 31:3815–3818PubMedCentralPubMedCrossRefGoogle Scholar
  3. Austin RS, Vidaurre D, Stamatiou G et al (2011) Next-generation mapping of Arabidopsis genes. Plant J 67:715–725PubMedCrossRefGoogle Scholar
  4. Bennetzen JL, Ma J (2003) The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr Opin Plant Biol 6:128–133PubMedCrossRefGoogle Scholar
  5. Castiglioni P, Pozzi C, Heun M et al (1998) An AFLP-based procedure for the efficient mapping of mutations and DNA probes in barley. Genetics 149:2039–2056PubMedCentralPubMedGoogle Scholar
  6. Churchill GA, Giovannoni JJ, Tanksley SD (1993) Pooled-sampling makes high-resolution mapping practical with DNA markers. Proc Natl Acad Sci USA 90:16–20PubMedCentralPubMedCrossRefGoogle Scholar
  7. de Vienne D (ed) (2003) Molecular markers in plant genetics and biotechnology. Science Publishers, EnfieldGoogle Scholar
  8. Echt C, Knapp S, Liu B-H (1992) Genome mapping with non-inbred crosses using Gmendel 2.0. Maize Genet Coop Newsl 66:27–29Google Scholar
  9. Edwards MD, Gifford DK (2012) High-resolution genetic mapping with pooled sequencing. BMC Bioinformatics 13(Suppl 6):S8. http://www.biomedcentral.com/1471-2105/13/S6/S8
  10. Hackett CA, Milne I, Bradshaw JE et al (2007) TetraploidMap for Windows: linkage map construction and QTL mapping in autotetraploid species. J Heredity 98:727–729CrossRefGoogle Scholar
  11. Haldane JBS (1919) The combination of linkage values and the calculation of the distance between the loci of linked factors. J Genet 8:299–309CrossRefGoogle Scholar
  12. Haldane JBS, Waddington C (1931) Inbreeding and linkage. Genetics 16:357–374PubMedCentralPubMedGoogle Scholar
  13. Hass-Jacobus B, Jackson SA (2005) Physical mapping of plant chromosomes. In: Meksem K, Kahl G (eds) The handbook of plant genome mapping, genetic and physical mapping. WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim, pp 133–149Google Scholar
  14. Hill JT, Demarest BL, Bisgrove BW et al (2013a) MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq. Genome Res 23:687–697PubMedCentralPubMedCrossRefGoogle Scholar
  15. Hill TA, Ashrafi H, Reyes-Chin-Wo S et al (2013b) Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K Unigene pepper GeneChip. PLoS ONE 8:e56200. doi: 10.1371/journal.pone.0056200 PubMedCentralPubMedCrossRefGoogle Scholar
  16. Iwata H, Ninomiya S (2006) AntMap: constructing genetic linkage maps using an ant colony optimization algorithm. Breed Sci 56:371–377CrossRefGoogle Scholar
  17. Kaeppler SM, Philips RL, Kim TS (1993) Use of near-isogenic lines derived by backcrossing or selfing to map quantitative traits. Theor Appl Genet 87:233–237PubMedCrossRefGoogle Scholar
  18. Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175CrossRefGoogle Scholar
  19. Lander ES, Green P, Abrahamson J et al (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181PubMedCrossRefGoogle Scholar
  20. Liu S, Yeh C-T, Tang HM et al (2012) Gene mapping via bulked segregant RNA-Seq (BSR-Seq). PLoS ONE 7:e36406. doi: 10.1371/ journal.pone.0036406 PubMedCentralPubMedCrossRefGoogle Scholar
  21. Matise TC, Perlin M, Chakravarti A (1993) MultiMap: an expert system for automated genetic linkage mapping. Proc Int Conf Intell Syst Mol Biol 1:260–265PubMedGoogle Scholar
  22. Michelmore RW, Paran I, Kesseli RV (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 88:9829–9832CrossRefGoogle Scholar
  23. Morton NE (1955) Sequential tests for the detection of linkage. Am J Hum Genet 7:277–318PubMedCentralPubMedGoogle Scholar
  24. Qin P, Wang Y, Li Y et al (2013) Analysis of cytoplasmic effects and fine-mapping of a genic male sterile line in rice. PLoS ONE 8:e61719. doi: 10.1371/journal.pone.0061719 PubMedCentralPubMedCrossRefGoogle Scholar
  25. Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP. Plant J 3:739–744CrossRefGoogle Scholar
  26. Tan Y-D, Fu Y-X (2006) A novel method for estimating linkage maps. Genetics 173:2383–2390PubMedCentralPubMedCrossRefGoogle Scholar
  27. Van Ooijen JW (2006) JoinMap® 4, software for the calculation of genetic linkage maps in experimental populations. Kyazma B.V., WageningenGoogle Scholar
  28. Vision TJ, Brown DG, Shmoys DB et al (2000) Selective mapping: a strategy for optimizing the construction of high-density linkage maps. Genetics 155:407–420PubMedCentralPubMedGoogle Scholar
  29. Wu J, Jenkins JN, McCarty JC et al (2011a) Comparisons of four approximation algorithms for large-scale linkage map construction. Theor Appl Genet 123:649–655PubMedCentralPubMedCrossRefGoogle Scholar
  30. Wu Y, Close TJ, Lonardi S (2011b) Accurate construction of consensus genetic maps via integer linear programming. Comp Biol Bioinform 8:381–394Google Scholar
  31. Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407CrossRefGoogle Scholar

Copyright information

© Author(s) 2015

Authors and Affiliations

  • B. D. Singh
    • 1
  • A. K. Singh
    • 2
  1. 1.School of BiotechnologyBanaras Hindu UniversityVaranasiIndia
  2. 2.Division of GeneticsIndian Agricultural Research InstituteNew DelhiIndia

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