Theoretical and Applied Genetics

, Volume 123, Issue 6, pp 897–906 | Cite as

Linkage analysis in unconventional mating designs in line crosses

Original Paper
First Online:
Received:
Accepted:

Abstract

Linkage estimation and genetic map construction with genotyped DNA markers in plants preferentially employ a few maximally informative early-generation or recombinant-inbred mating designs. Fitting their recombination models to unconventional designs adapted to cultivar development (series of backcrossing, selfing, haploid-doubling, random-intercrossing, and sib-mating steps) distorts single- and multipoint linkage estimates even with dense marker coverage. Two methods are provided for correct linkage estimation in unconventional designs: fitting a correct multigeneration model, or correcting the estimates produced by fitting a one-generation model with any conventional software. These methods also support calculation of multilocus genotype frequencies and QTL-genotype distributions and are available in software.

Keywords

Multilocus Genotype Mating Design Genotype Probability Recombination Model Advanced Intercross Line 
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.
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Notes

Acknowledgments

Hermann Buerstmayr posed a motivating question and provided sample data. Thomas Schiex and colleagues compiled contributed code into CarthaGene. Prof. Eberhard Weber pointed out errors and an alternative calculation for crossover expectation. The editor is thanked for bringing additional references to my attention. This is contribution 11-117-J from the Kansas Agricultural Experiment Station.

References

  1. Blair MW, Iriarte G, Beebe S (2006) QTL analysis of yield traits in an advanced backcross population derived from a cultivated Andean x wild common bean (Phaseolus vulgaris L.) cross. Theor Appl Genet 112:1149–1163PubMedCrossRefGoogle Scholar
  2. Darvasi A, Soller M (1995) Advanced intercross lines, an experimental population for fine genetic mapping. Genetics 141:1199–1207PubMedGoogle Scholar
  3. de Givry S, Bouchez M, Chabrier P, Milan D, Schiex T (2005) CarthaGene: multipopulation integrated genetic and radiation hybrid mapping. Bioinformatics 21:1703–1704PubMedCrossRefGoogle Scholar
  4. Falque M (2005) IRILmap: linkage map distance correction for intermated recombinant inbred lines/advanced recombinant inbred strains. Bioinformatics 21:3441–3442PubMedCrossRefGoogle Scholar
  5. Fisch RD, Ragot M, Gay G (1996) A generalization of the mixture model in the mapping of quantitative trait loci for progeny from a biparental cross of inbred lines. Genetics 143:571–577PubMedGoogle Scholar
  6. Gyenis L, Yun SJ, Smith KP, Steffenson BJ, Bossolini E, Sanguineti MC, Muehlbauer GJ (2007) Genetic architecture of quantitative trait loci associated with morphological and agronomic trait differences in a wild by cultivated barley cross. Genome 50:714–723PubMedCrossRefGoogle Scholar
  7. Haldane JBS, Waddington CH (1931) Inbreeding and linkage. Genetics 16:357–374PubMedGoogle Scholar
  8. Hospital F, Dillmann C, Melchinger AE (1996) A general algorithm to compute multilocus genotype frequencies under various mating systems. Comput Appl Biosci 12:455–462PubMedGoogle Scholar
  9. Huang XQ, Kempf H, Ganal MW, Röder MS (2004) Advanced backcross QTL analysis in progenies derived from a cross between a German elite winter wheat variety and a synthetic wheat (Triticum aestivum L.). Theor Appl Genet 109:933–943PubMedCrossRefGoogle Scholar
  10. Jiang C, Zeng Z-B (1997) Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica 101:47–58PubMedCrossRefGoogle Scholar
  11. Joehanes R, Nelson JC (2008) QGene 4.0, an extensible Java QTL-analysis platform. Bioinformatics 24:2788–2789PubMedCrossRefGoogle Scholar
  12. Kao CH, Zeng MH (2009) A study on the mapping of quantitative trait loci in advanced populations derived from two inbred lines. Genet Res 91:85–99CrossRefGoogle Scholar
  13. Lander ES, Green P (1987) Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci USA 84:2363–2367PubMedCrossRefGoogle Scholar
  14. Li J, Huang XQ, Heinrichs F, Ganal MW, Röder MS (2005) Analysis of QTLs for yield, yield components, and malting quality in a BC3-DH population of spring barley. Theor Appl Genet 110:356–363PubMedCrossRefGoogle Scholar
  15. Liu BH (1997) Statistical genomics: linkage mapping and QTL analysis. CRC Press, New YorkGoogle Scholar
  16. Liu S-C, Kowalski SP, Lan T-H, Feldmann KA, Paterson AH (1996) Genome-wide high-resolution mapping by recurrent intermating using Arabidopsis thaliana as a model. Genetics 142:247–258PubMedGoogle Scholar
  17. Martin OC, Hospital F (2006) Two- and three-locus tests for linkage analysis using recombinant inbred lines. Genetics 173:451–459PubMedCrossRefGoogle Scholar
  18. Naz A, 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 116:1095–1104PubMedCrossRefGoogle Scholar
  19. Ramchiary N, Bisht NC, Gupta V, Mukhopadhyay A, Arumugam N, Sodhi YS, Pental D, Pradhan AK (2007) QTL analysis reveals context-dependent loci for seed glucosinolate trait in the oilseed Brassica juncea: importance of recurrent selection backcross scheme for the identification of ‘true’ QTL. Theor Appl Genet 116:77–85PubMedCrossRefGoogle Scholar
  20. Rockman M, Kruglyak L (2008) Breeding designs for recombinant inbred advanced intercross lines. Genetics 179:1069–1078PubMedCrossRefGoogle Scholar
  21. Septiningsih EM, Prasetiyono J, Lubis E, Tai TH, Tjubaryat T, Moeljopawiro S, McCouch SR (2003a) Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107:1419–1432PubMedCrossRefGoogle Scholar
  22. Septiningsih EM, Trijatmiko KR, Moeljopawiro S, McCouch SR (2003b) 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 107:1433–1441PubMedCrossRefGoogle Scholar
  23. Stevens R, Buret M, Duffe P, Garchery C, Baldet P, Rothan C, Causse M (2007) Candidate genes and quantitative trait loci affecting fruit ascorbic acid content in three tomato populations. Plant Physiol 143:1943–1953PubMedCrossRefGoogle Scholar
  24. Tanksley SD, Nelson JC (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 92:191–203CrossRefGoogle Scholar
  25. Teuscher F, Broman KW (2007) Haplotype probabilities for multiple-strain recombinant inbred lines. Genetics 175:1267–1274PubMedCrossRefGoogle Scholar
  26. Thomson MJ, Tai TH, McClung AM, Lai XH, Hinga ME, Lobos KB, Xu Y, Martinez CP, McCouch SR (2003) Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet 107:479–493PubMedCrossRefGoogle Scholar
  27. Van Os H, Stam P, Visser RGF, Van Eck H (2005) RECORD: a novel method for ordering loci on a genetic linkage map. Theor Appl Genet 112:30–40PubMedCrossRefGoogle Scholar
  28. Wehrhahn C, Allard RW (1965) The detection and measurement of the effects of individual genes involved in the inheritance of a quantitative character in wheat. Genetics 51:109–119PubMedGoogle Scholar
  29. Winkler CR, Jensen NM, Cooper M, Podlich DW, Smith OS (2003) On the determination of recombination rates in intermated recombinant inbred populations. Genetics 164:741–745PubMedGoogle Scholar
  30. Wu R, Ma C-X, Casella G (2007) Statistical genetics of quantitative traits: linkage maps and QTL. Springer, New YorkGoogle Scholar
  31. Wu Y, Bhat PR, Close TJ, Lonardi S (2008) Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genet 4:e1000212PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  1. 1.Department of Plant Pathology, 4024 Throckmorton Plant Sciences CenterKansas State UniversityManhattanUSA

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