Skip to main content
SpringerLink
Log in

Family-based mapping of quantitative trait loci in plant breeding populations with resistance to Fusarium head blight in wheat as an illustration

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Traditional quantitative trait loci (QTL) mapping approaches are typically based on early or advanced generation analysis of bi-parental populations. A limitation associated with this methodology is the fact that mapping populations rarely give rise to new cultivars. Additionally, markers linked to the QTL of interest are often not immediately available for use in breeding and they may not be useful within diverse genetic backgrounds. Use of breeding populations for simultaneous QTL mapping, marker validation, marker assisted selection (MAS), and cultivar release has recently caught the attention of plant breeders to circumvent the weaknesses of conventional QTL mapping. The first objective of this study was to test the feasibility of using family-pedigree based QTL mapping techniques generally used with humans and animals within plant breeding populations (PBPs). The second objective was to evaluate two methods (linkage and association) to detect marker-QTL associations. The techniques described in this study were applied to map the well characterized QTL, Fhb1 for Fusarium head blight resistance in wheat (Triticum aestivum L.). The experimental populations consisted of 82 families and 793 individuals. The QTL was mapped using both linkage (variance component and pedigree-wide regression) and association (using quantitative transmission disequilibrium test, QTDT) approaches developed for extended family-pedigrees. Each approach successfully identified the known QTL location with a high probability value. Markers linked to the QTL explained 40–50% of the phenotypic variation. These results show the usefulness of a human genetics approach to detect QTL in PBPs and subsequent use in MAS.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Abecasis GR, Cardon LR, Cookson WOC (2000a) A general test of association for quantitative traits in nuclear families. Am J Hum Genet 66:279–292

    Article  PubMed  CAS  Google Scholar 

  • Abecasis GR, Cookson WO, Cardon LR (2000b) Pedigree tests of transmission disequilibrium. Eur J Hum Genet 8:545–551

    Article  PubMed  CAS  Google Scholar 

  • Abecasis GR, Cherny SS, Cookson WO, Cardon LR (2002) MERLIN-rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 30:97–101

    Article  PubMed  CAS  Google Scholar 

  • Aissani B, Louis P, Lapointe G, Chagnon YC, Bouchard L, Walts B, Bouchard C (2006) A quantitative trait locus for body fat on Chromosome 1q43 in French Canadians: linkage and association studies. Obesity 14:1605–1615

    Article  PubMed  CAS  Google Scholar 

  • Almasy L, Blangero J (1998) Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet 62:1198–1211

    Article  PubMed  CAS  Google Scholar 

  • Amos CI (1994) Robust variance-components approach for assessing genetic linkage in pedigrees. Am J Hum Genet 54:535–543

    PubMed  CAS  Google Scholar 

  • Anderson JA, Waldron BL, Moreno-Sevilla B, Stack RW, Frohberg RC (1998) DNA markers for Fusarium head blight resistance QTL in two wheat populations. 1998 National FHB Forum. Michigan State University, East Lansing, MI, pp 26–27 Oct

    Google Scholar 

  • Anderson JA, Stack RW, Liu S, Waldron BL, Fjeld AD, Coyne C, Moreno-Sevilla B, Mitchell Fetch J, Song OJ, Cregan PB, Frohberg RC (2001) DNA markers for Fusarium head blight resistance QTLs in two wheat populations. Theor Appl Genet 102:1164–1168

    Article  CAS  Google Scholar 

  • Arbelbide A, Bernardo R (2006a) Mixed-model QTL mapping for kernel hardness and dough strength in bread wheat. Theor Appl Genet 112:885–890

    Article  PubMed  CAS  Google Scholar 

  • Arbelbide A, Bernardo R (2006b) Power of mixed-model QTL mapping from phenotypic, pedigree and marker data in self-pollinated crops. Theor Appl Genet 112:876–884

    Article  PubMed  CAS  Google Scholar 

  • Bai G, Shaner G (1994) Scab of wheat: prospects for control. Plant Dis 78:760–766

    Google Scholar 

  • Bai G-H, Kolb FL, Shaner GE, Domier LL (1999) Amplified fragment length polymorphism markers linked to a major quantitative trait locus controlling scab resistance in wheat. Phytopathology 89:343–348

    Article  PubMed  CAS  Google Scholar 

  • Barendse W, Vaiman D, Kemp SJ, Sugimoto Y, Armitage SM, Williams JL, Sun HS, Eggen A, Agaba M, Aleyasin SA, Band M, Bishop MD, Buitkamp J, Byrne K, Collins F, Cooper L, Coppettiers W, Denys B, Drinkwater RD, Easterday K, Elduque C, Ennis S, Erhardt G, Ferretti L, Flavin N, Gao Q, Georges M, Gurung R, Harlizius B, Hawkins G, Hetzel J, Hirano T, Hulme D, Jorgensen C, Kessler M, Kirkpatrick BW, Konfortov B, Kostia S, Kuhn C, Lenstra JA, Leveziel H, Lewin HA, Leyhe B, Lil L, Martin Burriel I, McGraw RA, Miller JR, Moody DE, Moore SS, Nakane S, Nijman IJ, Olsaker I, Pomp D, Rando A, Ron M, Shalom A, Teale AJ, Thieven U, Urquhart BGD, Vage D-I, Van de Weghe A, Varvio S, Velmala R, Vilkki J, Weikard R, Woodside C, Womack JE, Zanotti M, Zaragoza P (1997) A medium-density genetic linkage map of the bovine genome. Mamm Genome 8:21–28

    Article  PubMed  CAS  Google Scholar 

  • Beavis WD (1998) QTL analyses: power, precision, and accuracy. In: Paterson AH (ed) Molecular analysis of complex traits. CRC Press, Boca Raton, pp 145–161

    Google Scholar 

  • Bink MCAM, Meuwissen THE (2004) Fine mapping of quantitative trait loci using linkage disequilibrium in inbred plant populations. Euphytica 137:95–99

    Article  CAS  Google Scholar 

  • Bink MCAM, Uimari P, Silanpaa MJ, Janss LLG, Jansen RC (2002) Multiple QTL mapping in related populations via a pedigree-analysis approach. Theor Appl Genet 104:751–762

    Article  PubMed  CAS  Google Scholar 

  • Breseghello F, Sorrells MK (2006a) Association analysis as a strategy for improvement of quantitative traits in plants. Crop Sci 46:1323–1330

    Article  Google Scholar 

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

    Google Scholar 

  • Broman KW (2001) Review of statistical methods for QTL mapping in experimental crosses. Lab Animal 30:44–52

    PubMed  CAS  Google Scholar 

  • Buerstmayr H, Steiner B, Lemmens M, Ruckenbauer P (2000) Resistance to Fusarium head blight in winter wheat: heritability and trait associations. Crop Sci 40:1012–1018

    Google Scholar 

  • Buerstmayr H, Lemmens M, Hartl L, Doldi L, Steiner B, Stierschneider M, Ruckenbauer P (2002) Molecular mapping of QTLs for Fusarium head blight resistance in spring wheat. I. Resistance to fungal spread (type II resistance). Theor Appl Genet 104:84–91

    Article  PubMed  CAS  Google Scholar 

  • Buerstmayr H, Steiner B, Hartl L, Griesser M, Angerer N, Lengauer D, Miedaner T, Schneider B, Lemmens M (2003) Molecular mapping of QTLs for Fusarium head blight resistance in spring wheat. II. Resistance to fungal penetration and spread. Theor Appl Genet 107:503–508

    Article  PubMed  CAS  Google Scholar 

  • Cherny SS, Sham PC, Cardon LR (2004) Introduction to the special issue on variance components methods for mapping quantitative trait loci. Behav Genet 34:125–126

    Article  Google Scholar 

  • Christiansen MJ, Feenstra B, Skovgaard IM, Andersen SB (2006) Genetic analysis of resistance to yellow rust in hexaploid wheat using a mixture model of multiple crosses. Theor Appl Genet 112:581–591

    Article  PubMed  CAS  Google Scholar 

  • Crawford AM, Dodds KG, Ede AJ, Pierson CA, Montgomery GW, Garmomway HG, Beattie AE, Davies K, Maddox JF, Kappes FSW, Stone RT, Yen TCN, Penty JM, Lord EA, Broom JE, Buitkamp J, Schwaiger W, Epplen JT, Matthew FP, Matthew ME, Hulme DJ, Beh KJ, McGraw RA, Beattie CW (1995) An autosomal genetic linkage map of the sheep genome. Genetics 140:703–724

    PubMed  CAS  Google Scholar 

  • Crepieux S, Lebreton C, Servin B, Charmet G (2004a) Quantitative trait loci (QTL) detection in multicross inbred designs: recovering QTL IBD status information from marker data. Genetics 168:1737–1749

    Article  PubMed  CAS  Google Scholar 

  • Crepieux S, Lebreton C, Servin B, Charmet G (2004b) IBD-based QTL detection in inbred pedigrees: a case study of cereal breeding programs. Euphytica 137:101–109

    Article  CAS  Google Scholar 

  • Crepieux S, Lebreton C, Flament P, Charmet G (2005) Application of a new IBD-based QTL mapping method to common wheat breeding population: analysis of kernel hardness and dough strength. Theor Appl Genet 111:1409–1419

    Article  PubMed  Google Scholar 

  • Cuthbert PA, Somers DJ, Thomas J, Cloutier S, Brule-Babel A (2006) Fine mapping Fhb1, a major gene controlling Fusarium head blight resistance in bread wheat (Triticum aestivum L.). Theor Appl Genet 112:1465–1472

    Article  PubMed  CAS  Google Scholar 

  • de Koning D, Haley CS (2005) Genetical genomics in humans and model organisms. Tren Genet 21:377–381

    Article  Google Scholar 

  • del Blanco IA, Cholick FA, Buchenau G, Rudd JC (1993) Inheritance and diallel analysis of resistance to Fusarium head blight in wheat. In: Agronomy abstracts. American Society of Agronomy, Cincinnati, 85 pp

  • Deng FY (2003) Tests of linkage and association of the COL1A2 gene with bone phenotypes variation in Chinese nuclear families. Bone 33:614–619

    Article  PubMed  CAS  Google Scholar 

  • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15

    Google Scholar 

  • Elbein SC, Hasstedt SJ (2002) Quantitative trait linkage analysis of lipid-related traits in familial type 2 diabetes. Diabetes 51:528–535

    Article  PubMed  CAS  Google Scholar 

  • Farbrother JE, Kirov G, Owen MJ, Pong-Wong R, Haley CS, Guggenheim JA (2004) Linkage analysis of the genetic loci for high myopia on 18p, 12q, and 17q in 51 U.K. Families. Invest Ophthalmol Vis Sci 45:2879–2885

    Article  PubMed  Google Scholar 

  • Flint-Garcia S, Thornsberry JM, Buckler ESIV (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374

    Article  PubMed  CAS  Google Scholar 

  • Gebhardt C, Ballvora A, Walkemeier B, Oberhagemann P, Schüler K (2004) Assessing genetic potential in germplasm collections of crop plants by marker-trait association: a case study for potatoes with quantitative variation of resistance to late blight and maturity type. Mol Breeding 13:93–102

    Article  CAS  Google Scholar 

  • Glazier AM, Nadeau JH, Aitman TJ (2002) Finding genes that underlie complex traits. Science 298:2345–2349

    Article  PubMed  CAS  Google Scholar 

  • Goffinet B, Gerber S (2000) Quantitative trait loci: a meta analysis. Genetics 155:463–473

    PubMed  CAS  Google Scholar 

  • Goswami RS, Kistler HC (2004) Heading for disaster: Fusarium graminearum on cereal crops. Molecular Plant Pathology 5:515–525

    Article  CAS  Google Scholar 

  • Green P, Fall KA, Crooks S (1990) Documentation for CRIMAP, Version 2.4. Washington University School of Medicine, St. Louis

  • Haseman JK, Elston RC (1972) The investigation of linkage between a quantitative trait and a marker locus. Behav Genet 2:3–19

    Article  PubMed  CAS  Google Scholar 

  • Jannink JL, Jansen RC (2001) Mapping epistatic quantitative trait loci with one-dimensional genome searches. Genetics 157:445–454

    PubMed  CAS  Google Scholar 

  • Jannink J, Bink MCAM, Jansen RC (2001) Using complex plant pedigrees to map valuable genes. Trends Plant Sci 6:337–342

    Article  PubMed  CAS  Google Scholar 

  • Jansen RC, Jannink J, Beavis WD (2003) Mapping quantitative trait loci in plant breeding populations: use of parental haplotype sharing. Crop Sci 43:829–834

    CAS  Google Scholar 

  • Korzun V, Borner A, Worland AJ, Law CN, Röder MS (1997) Application of microsatellite markers to distinguish inter-varietal chromosome substitution lines of wheat (Triticum aestivum L.). Euphytica 95:149–155

    Article  CAS  Google Scholar 

  • Lagudah ES, McFadden H, Singh RP, Huerta-Espino J, Bariana HS, Spielmeyer W (2006) Molecular genetic characterization of the Lr34/Yr18 slow rusting resistance gene region in wheat. Theor Appl Genet 114:21–30

    Article  PubMed  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 

  • Lange M, Andrew T, Snieder H, Ge D, Simon Futers T, Standeven K, Spector TD, Grant PJ, Ariëns RAS (2006) Factor XIII-A subunit gene point to V34L as the main functional locus joint linkage and association of six single-nucleotide polymorphisms in the factor XIII-A subunit gene point to V34L as the main functional locus. Arterioscler Thromb Vasc Biol 26:1914–1919

    Article  PubMed  Google Scholar 

  • Lee SH, Van der Werf JHJ (2005) The role of pedigree information in combined linkage disequilibrium and linkage mapping of quantitative trait loci in a general complex pedigree. Genetics 169:455–466

    Article  PubMed  CAS  Google Scholar 

  • Li W, Li D, Wang S, Zhang S, Zhao H, Arlen Pricel R (2003) Linkage and linkage disequilibrium mapping of genes influencing human obesity in chromosome region 7q22.1–7q35. Diabetes 52:1557–1561

    Article  PubMed  CAS  Google Scholar 

  • Liu S, Anderson JA (2003a) Marker assisted evaluation of Fusarium head blight resistant wheat germplasm. Crop Sci 43:760–766

    CAS  Google Scholar 

  • Liu S, Anderson JA (2003b) Targeted molecular mapping of a major wheat QTL for Fusarium head blight resistance using wheat ESTs and synteny with rice. Genome 46:817–823

    Article  PubMed  CAS  Google Scholar 

  • Maccaferri M, Sanguineti MC, Noli E, Tuberosa R (2005) Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Mol Breed 15:271–289

    Article  CAS  Google Scholar 

  • Mackay TFC (2001) The genetic architecture of quantitative traits. Ann Rev Genet 33:303–339

    Article  Google Scholar 

  • Majumder PP, Ghosh S (2005) Mapping quantitative trait loci in humans: achievements and limitations. J Clin Invest 115:1419–1424

    Article  PubMed  CAS  Google Scholar 

  • Malhotra A, Looker HC, and Hanson RL (2007) Exploration of non-hierarchical classification methods combined with linkage analysis to identify loci influencing clusters of co-regulated transcripts. BMC Proc 1(Suppl 1):S48

    Google Scholar 

  • Malosetti M, van der Linden CG, Vosman B, van Eeuwijk FA (2007) A mixed-model approach to association mapping using pedigree information with an illustration of resistance to Phytophthora infestans in Potato. Genetics 175:879–889

    Article  PubMed  CAS  Google Scholar 

  • Mars GD, Windelinckx A, Huygens W, Peeters MW, Beunen GP, Aerssens J, Vlietinck R, Thomis MAI (2008) Genome-wide linkage scan for maximum and length-dependent knee muscle strength in young men: significant evidence for linkage at chromosome 14q24.3. J Med Genet 45:275–283

    Google Scholar 

  • Mertin B, Anthony GC, Dupont S, Vionnet N, Dina C, Gallina S, Houari M, Blangero J, Froguel P (2002) A quantitative trait locus influencing type 2 diabetes susceptibility maps to a region on 5q in an extended French family. Diabetes 51:3568–3572

    Article  Google Scholar 

  • Miedaner T (1997) Review: breeding wheat and rye for resistance to Fusarium diseases. Plant Breed 116:201–220

    Article  Google Scholar 

  • Neff MW, Broman KW, Mellersh CS, Ray K, Acland GM, Aguirre GD, Ziegle JS, Ostrander EA, Rine J (1999) A Second-generation genetic linkage map of the domestic dog, Canis familiaris. Genetics 151:803–820

    PubMed  CAS  Google Scholar 

  • Park HM (2006) Univariate analysis and normality test using SAS, STATA, and SPSS. The Trustees of Indiana University. http://www.indiana.edu/~statmath

  • Pratt SC, Daly MJ, Kruglyak L (2000) Exact multipoint quantitative-trait linkage analysis in pedigrees by variance components. Am J Hum Genet 66:1153–1157

    Article  PubMed  CAS  Google Scholar 

  • Pugh EW, Jaquish CE, Sorant AJ, Doestsch JP, Bailey-Wilson JE, Wilson AF (1997) Comparison of sib-pair and variance components methods for genomic screening. Genet Epidemiol 14:867–872

    Article  PubMed  CAS  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 

  • Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ESIV (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci (USA) 98:11479–11484

    Article  CAS  Google Scholar 

  • Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier M, Leroy P, Ganal MW (1998) A Microsatellite map of wheat. Genetics 149:2007–2023

    PubMed  Google Scholar 

  • Sham PC, Purcell S, Cherny SS, Abecasis GR (2002) Powerful regression-based quantitative-trait linkage analysis of general pedigrees. Am J Hum Genet 71:238–253

    Article  PubMed  CAS  Google Scholar 

  • Shen X, Zhou M, Lu W, Ohm H (2003) Detection of Fusarium head blight resistance QTL in a wheat breeding population using bulk segregant analysis. Theor Appl Genet 106:1041–1047

    PubMed  CAS  Google Scholar 

  • Singh RP, Ma H, Rajaram S (1995) Genetic analysis of resistance to scab in spring wheat cultivar Frontana. Plant Dis 79:238–240

    Google Scholar 

  • Skøt L, Humphreys MO, Armstead I, Heywood S, Skøt KP, Sanderson R, Thomas ID, Chorlton KH, Hamilton SNR (2005) An association mapping approach to identify flowering time genes in natural populations of Lolium perenne (L.). Mol Breed 15:233–245

    Article  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Spielman R, McGinnis S, Ewens WJ (1993) Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet 52:506–516

    PubMed  CAS  Google Scholar 

  • Stack RW, Frohberg RC (1991) Inheritance of head blight resistance in a spring wheat cross (Abstr). Can J Plant Pathol 13:286

    Google Scholar 

  • Vaiman D, Schibler L, Bourgeois F, Oustry A, Amiguest Y, Cribiu EP (1996) A genetic linkage map of the male goat genome. Genetics 144:279–305

    PubMed  CAS  Google Scholar 

  • van Ooijen JW (1992) Accuracy of mapping quantitative trait loci in autogamous species. Theor Appl Genet 84:803–811

    Article  Google Scholar 

  • Verhoeven KJF, Jannink JL, McIntyre LM (2006) Using mating designs to uncover QTL and the genetic architecture of complex traits. Heredity 96:139–149

    Article  PubMed  CAS  Google Scholar 

  • Wigginton JE, Abecasis GR (2005) PEDSTATS: descriptive statistics, graphics and quality assessment for gene mapping data. Bioinformatics 21:3445–3447

    Article  PubMed  CAS  Google Scholar 

  • Wilson LM, Whitt SR, Ibanez AM, Rocheford TR, Goodman MM, Buckler ES (2004) Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16:2719–2733

    Article  PubMed  CAS  Google Scholar 

  • Xie C, Gessler DDG, Xu S (1998) Combining different line crosses for mapping quantitative trait loci using the identical by descent-based variance component method. Genetics 149:1139–1146

    PubMed  CAS  Google Scholar 

  • Xu S (1998) Mapping quantitative trait loci using multiple families of line crosses. Genetics 148:517–524

    PubMed  CAS  Google Scholar 

  • Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155–160

    PubMed  CAS  Google Scholar 

  • Zhang Y, Xu S (2004) Mapping Quantitative trait loci in F2 incorporating phenotypes of F3 progeny. Genetics 166:1981–1993

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The study was supported by the South Dakota Wheat Commission, the South Dakota Agri. Exp. Station and USDA-ARS agreement 59-0790-8-066 thru the US Wheat and Barley Scab Initiative. JLGH acknowledges support from USDA CSREES grants SD00055G, and SD00076G. We acknowledge use of the SDSU-Functional Genomics Core Facility supported in part by NSF/EPSCoR Grant No. 0091948, the Center of Excellence in Drought Tolerance through the South Dakota 2010 Initiative and the South Dakota Agri. Exp. Station. We want to thank Dr. Goncalo Abecasis for his useful comments regarding the software to analyze the data from this study. Also we would like to thank Kim Maxson-Stein, Loralie Peterson, Brandon Monier, and Jon Kleinjan for their technical assistance.

Author information

Authors and Affiliations

  1. Department of Plant Sciences, South Dakota State University, Brookings, SD, USA

    U. R. Rosyara, J. L. Gonzalez-Hernandez, K. D. Glover, K. R. Gedye & J. M. Stein

Authors
  1. U. R. Rosyara
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. J. L. Gonzalez-Hernandez
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. K. D. Glover
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. K. R. Gedye
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. J. M. Stein
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to J. L. Gonzalez-Hernandez.

Additional information

Communicated by J. Yu.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Rosyara, U.R., Gonzalez-Hernandez, J.L., Glover, K.D. et al. Family-based mapping of quantitative trait loci in plant breeding populations with resistance to Fusarium head blight in wheat as an illustration. Theor Appl Genet 118, 1617–1631 (2009). https://doi.org/10.1007/s00122-009-1010-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-009-1010-9

Keywords

Search

Navigation