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Linkage analysis in unconventional mating designs in line crosses

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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.

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References

  • 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 112:1149–1163

    Article  PubMed  CAS  Google Scholar 

  • Darvasi A, Soller M (1995) Advanced intercross lines, an experimental population for fine genetic mapping. Genetics 141:1199–1207

    PubMed  CAS  Google Scholar 

  • de Givry S, Bouchez M, Chabrier P, Milan D, Schiex T (2005) CarthaGene: multipopulation integrated genetic and radiation hybrid mapping. Bioinformatics 21:1703–1704

    Article  PubMed  Google Scholar 

  • Falque M (2005) IRILmap: linkage map distance correction for intermated recombinant inbred lines/advanced recombinant inbred strains. Bioinformatics 21:3441–3442

    Article  PubMed  CAS  Google Scholar 

  • 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 143:571–577

    PubMed  CAS  Google Scholar 

  • 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 50:714–723

    Article  PubMed  CAS  Google Scholar 

  • Haldane JBS, Waddington CH (1931) Inbreeding and linkage. Genetics 16:357–374

    PubMed  CAS  Google Scholar 

  • Hospital F, Dillmann C, Melchinger AE (1996) A general algorithm to compute multilocus genotype frequencies under various mating systems. Comput Appl Biosci 12:455–462

    PubMed  CAS  Google Scholar 

  • 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 109:933–943

    Article  PubMed  CAS  Google Scholar 

  • Jiang C, Zeng Z-B (1997) Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica 101:47–58

    Article  PubMed  CAS  Google Scholar 

  • Joehanes R, Nelson JC (2008) QGene 4.0, an extensible Java QTL-analysis platform. Bioinformatics 24:2788–2789

    Article  PubMed  CAS  Google Scholar 

  • Kao CH, Zeng MH (2009) A study on the mapping of quantitative trait loci in advanced populations derived from two inbred lines. Genet Res 91:85–99

    Article  CAS  Google Scholar 

  • Lander ES, Green P (1987) Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci USA 84:2363–2367

    Article  PubMed  CAS  Google Scholar 

  • 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 110:356–363

    Article  PubMed  CAS  Google Scholar 

  • Liu BH (1997) Statistical genomics: linkage mapping and QTL analysis. CRC Press, New York

    Google Scholar 

  • 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 142:247–258

    PubMed  CAS  Google Scholar 

  • Martin OC, Hospital F (2006) Two- and three-locus tests for linkage analysis using recombinant inbred lines. Genetics 173:451–459

    Article  PubMed  CAS  Google Scholar 

  • 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 116:1095–1104

    Article  PubMed  CAS  Google Scholar 

  • 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 116:77–85

    Article  PubMed  CAS  Google Scholar 

  • Rockman M, Kruglyak L (2008) Breeding designs for recombinant inbred advanced intercross lines. Genetics 179:1069–1078

    Article  PubMed  Google Scholar 

  • 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 107:1419–1432

    Article  PubMed  CAS  Google Scholar 

  • 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 107:1433–1441

    Article  PubMed  CAS  Google Scholar 

  • 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 143:1943–1953

    Article  PubMed  CAS  Google Scholar 

  • 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 92:191–203

    Article  Google Scholar 

  • Teuscher F, Broman KW (2007) Haplotype probabilities for multiple-strain recombinant inbred lines. Genetics 175:1267–1274

    Article  PubMed  Google Scholar 

  • 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 107:479–493

    Article  PubMed  CAS  Google Scholar 

  • 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 112:30–40

    Article  PubMed  CAS  Google Scholar 

  • 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 51:109–119

    PubMed  CAS  Google Scholar 

  • Winkler CR, Jensen NM, Cooper M, Podlich DW, Smith OS (2003) On the determination of recombination rates in intermated recombinant inbred populations. Genetics 164:741–745

    PubMed  Google Scholar 

  • Wu R, Ma C-X, Casella G (2007) Statistical genetics of quantitative traits: linkage maps and QTL. Springer, New York

    Google Scholar 

  • 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:e1000212

    Article  PubMed  Google Scholar 

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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.

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Authors and Affiliations

  1. Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506, USA

    James C. Nelson

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  1. James C. Nelson
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Correspondence to James C. Nelson.

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Communicated by M. Sillanpaa.

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Nelson, J.C. Linkage analysis in unconventional mating designs in line crosses. Theor Appl Genet 123, 897–906 (2011). https://doi.org/10.1007/s00122-011-1635-3

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  • DOI: https://doi.org/10.1007/s00122-011-1635-3

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