Molecular Breeding

, Volume 21, Issue 3, pp 383–399 | Cite as

Joint analysis for heading date QTL in small interconnected barley populations

  • Alfonso Cuesta-Marcos
  • Ana M. Casas
  • Samia Yahiaoui
  • M. Pilar Gracia
  • José M. Lasa
  • Ernesto Igartua
Article

Abstract

The purpose of the present work is to validate the effect of the main QTL determining heading date in a set of 281 doubled haploid lines of barley, derived from 17 small interconnected populations, whose parents are cultivars commonly used in the Spanish barley breeding program. We used 72 molecular markers distributed across the seven chromosomes, particularly in regions known to contain flowering time genes or QTL. A combined linkage map over the 17 populations was constructed. The lines were evaluated in four field trials: two autumn sowings and two winter sowings, and in two treatments at a greenhouse trial, under controlled conditions of photoperiod and temperature. We have found that it is possible to carry out QTL detection in a complex germplasm set, representative of the materials used in an active breeding programme. In most cases two alleles per QTL were detected, though polymorphism of flanking markers was notably higher. The results revealed that there is a set of QTL that accounts for an important percentage of the phenotypic variation, suitable for marker assisted selection. Also, the role of the regions carrying the photoperiod response genes Ppd-H1 and Ppd-H2, the vernalization response genes Vrn-H1 and Vrn-H2, and the earliness per se locus Eam6, of which allele-specific or closely linked markers were available, was confirmed. These results support the use of this kind of approach for the validation of QTL found in single cross population studies, or to survey allelic diversity in plant breeding sets of materials.

Keywords

Barley Consensus map Heading date QTL validation 

Notes

Acknowledgements

This work was supported by the Spanish Ministry of Education and Research (Projects AGL2001-2289, including a scholarship granted to Mr. Alfonso Cuesta-Marcos, and AGL2004-05311) and by the European Regional Development Fund. The authors appreciate the critical reading of the manuscript by Prof. Steve Ullrich, and the valuable suggestions of two anonymous reviewers.

Supplementary material

11032_2007_9139_MOESM1_ESM.doc (37 kb)
(DOC 36.5 kb)

References

  1. Basten CJ, Weir BS, Zeng ZB (1995–1996). QTL Cartographer: a reference manual and tutorial for QTL mapping. Department of Statistics, North Carolina State University, Raleigh, NCGoogle Scholar
  2. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc 57:289–300Google Scholar
  3. Boyd WJR, Li CD, Grime CR et al (2003) Conventional and molecular genetic analysis of factors contributing to variation in the timing of heading among spring barley (Hordeum vulgare L) genotypes grown over a mild winter growing season. Aust J Agric Res 54:1277–1301CrossRefGoogle Scholar
  4. Breseghello F, Sorrells ME (2006) Association analysis as a strategy for improvement of quantitative traits in plants. Crop Sci 46:1323–1330CrossRefGoogle Scholar
  5. Canci PC, Nduulu LM, Muehlbauer GJ et al (2004) Validation of quantitative trait loci for Fusarium head blight and kernel discoloration in barley. Mol Breed 14:91–104CrossRefGoogle Scholar
  6. Casas AM, Igartua E, Vallés MP et al (1998) Genetic diversity of barley cultivars grown in Spain, estimated by RFLP, similarity and coancestry coefficients. Plant Breed 117:429–435CrossRefGoogle Scholar
  7. Chen X, Cho YG, McCouch SR (2002) Sequence divergence of rice microsatellites in Oryza and other plant species. Mol Genet Genomics 268:331–343PubMedCrossRefGoogle Scholar
  8. Christiansen MJ, Feenstra B, Skovgaard IM, Andersen SB (2006) Genetic analysis of resistance to yellow rust in hexaploid wheat using a mixture model for multiple crosses. Theor Appl Genet 112:581–591PubMedCrossRefGoogle Scholar
  9. Crepieux S, Lebreton C, Servin B et al (2004) Quantitative trait loci (QTL) detection in multicross inbred designs: recovering QTL identical-by-descent status information from marker data. Genetics 168:1737–1749PubMedCrossRefGoogle Scholar
  10. Crepieux S, Lebreton C, Flament P et al (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 111:1409–1419PubMedCrossRefGoogle Scholar
  11. Cuesta-Marcos A, Igartua E, Ciudad FJ, Codesal P, Russell JR, Molina-Cano JL, Moralejo M, Szűcs P, Gracia MP, Lasa JM, Casas AM. Heading date QTL in a spring × winter barley cross evaluated in Mediterranean environments. Mol Breeding (submitted)Google Scholar
  12. Dubcovsky J, Loukoianov A, Fu D et al (2006) Effect of photoperiod on the regulation of wheat vernalization genes VRN1 and VRN2. Plant Mol Biol 60:469–480PubMedCrossRefGoogle Scholar
  13. Estoup A, Jarne P, Cornuet JM (2002) Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Mol Ecol 11:1591–1604PubMedCrossRefGoogle Scholar
  14. Flint-Garcia SA, Thornsberry JM, Buckler IV ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374PubMedCrossRefGoogle Scholar
  15. Francia E, Rizza F, Cattivelli L et al (2004) Two loci on chromosome 5H determine low-temperature tolerance in a ‘Nure’ (winter) × ‘Tremois’ (spring) barley map. Theor Appl Genet 108:670–680PubMedCrossRefGoogle Scholar
  16. Franckowiak JD, Gallagher LW (1997) Early maturity locus symbol: eam7. Barley Genet Newsl 26:233Google Scholar
  17. Franckowiak JD, Konishi T (2002) Early maturity 6, Eam6. Barley Genet Newsl 32:86–87Google Scholar
  18. Horsley RD, Schmierer D, Maier C et al (2006) Identification of QTLs associated with Fusarium head blight resistance in barley accession CIho 4196. Crop Sci 46:145–156CrossRefGoogle Scholar
  19. Jannink JL, Jansen RC (2001) Mapping epistatic quantitative trait loci with one-dimensional genome searches. Genetics 157:445–454PubMedGoogle Scholar
  20. Jansen RC (1993) Interval mapping of multiple quantitative trait loci. Genetics 135:205–211PubMedGoogle Scholar
  21. Jansen RC, Stam P (1994) High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136:1447–1455PubMedGoogle Scholar
  22. Jansen RC, Jannink JL, Beavis WD (2003) Mapping quantitative trait loci in plant breeding populations: use of parental haplotype sharing. Crop Sci 43:829–834CrossRefGoogle Scholar
  23. Kane NA, Danyluk J, Tardif G, Ouellet F, Laliberte JF, Limin AE, Fowler DB, Sarhan F (2005) TaVRT-2, a member of the StMADS-11 clade of flowering repressors, is regulated by vernalization and photoperiod in wheat. Plant Physiol 138:2354–2363PubMedCrossRefGoogle Scholar
  24. Karakousis A, Gustafson JP, Chalmers KJ et al (2003) A Barley consensus map integrating SSR RFLP, and AFLP markers. Aust J Agric Res 54:1173–1185CrossRefGoogle Scholar
  25. Karsai I, Szűcs P, Mészáros K et al (2005) The Vrn-H2 locus is a major determinant of flowering time in a facultative × winter growth habit barley (Hordeum vulgare L) mapping population. Theor Appl Genet 110:1458–1466PubMedCrossRefGoogle Scholar
  26. Kjaer B, Jensen J, Giese H (1995) Quantitative trait loci for heading date and straw characters in barley. Genome 38:1098–1104PubMedGoogle Scholar
  27. Komatsuda T, Li W, Takaiwa F et al (1999) High resolution map around the vrs1 locus controlling two-rowed and sixrowed spike in barley, Hordeum vulgare. Genome 42:248–253CrossRefGoogle Scholar
  28. Kóti K, Karsai I, Szűcs P et al (2006) Validation of the two-gene epistatic model for vernalization response in a winter × spring barley cross. Euphytica 152:17–24CrossRefGoogle Scholar
  29. Laurie DA, Pratchett N, Bezant JH et al (1994) Genetic analysis of a photoperiod response gene on the short arm of chromosome 2 (2H) of Hordeum vulgare. Heredity 72:619–627Google Scholar
  30. Laurie DA, Pratchett N, Bezant JH et al (1995) RFLP mapping of five major genes and eight quantitative trait loci controlling flowering time in a winter × spring barley (Hordeum vulgare L) cross. Genome 38:575–585PubMedGoogle Scholar
  31. Liu Y, Zeng ZB (2000) A general mixture model approach for mapping quantitative trait loci from diverse cross designs involving multiple inbred lines. Genet Res 75:345–355PubMedCrossRefGoogle Scholar
  32. Macaulay M, Ramsay L, Powell W et al (2001) A representative, highly informative ‘genotyping set’ of barley SSRs. Theor Appl Genet 102:801–809CrossRefGoogle Scholar
  33. Melchinger AE, Utz HF, Schön CC (2004) QTL analyses of complex traits with cross validation, bootstrapping and other biometric methods. Euphytica 137:1–11CrossRefGoogle Scholar
  34. Moralejo M, Swanston JS, Muñoz P et al (2004) Use of new EST markers to elucidate the genetic differences in grain protein content between European and North American two-rowed malting barleys. Theor Appl Genet 110:116–125PubMedCrossRefGoogle Scholar
  35. Muranty H (1996) Power of tests for quantitative trait loci detection using full-sib families in different schemes. Heredity 76:156–165Google Scholar
  36. van Ooijen JW, Voorrips RE (2001) JoinMap® 3.0, Software for the calculation of genetic linkage maps. Plant Research International, Wageningen, NetherlandsGoogle Scholar
  37. van Oosterom EJ, Acevedo E (1992) Adaptation of barley (Hordeum vulgareL) to harsh Mediterranean environments III. Plant ideotype and grain yield. Euphytica 62:29–38CrossRefGoogle Scholar
  38. Pan A, Hayes PM, Chen F et al (1994) Genetic analysis of the components of winterhardiness in barley (Hordeum vulgare L). Theor Appl Genet 89:900–910CrossRefGoogle Scholar
  39. Pillen K, Binder A, Kreuzkam B et al (2000) Mapping new EMBL-derived barley microsatellites and their use in differentiating German barley cultivars. Theor Appl Genet 101:652–660CrossRefGoogle Scholar
  40. Rae SJ, Keith R, Mackie A et al (2006) Small cross mapping of barley quality characters. Eucarpia meeteing, Cereals Section, Lleida, Spain, November 13–17Google Scholar
  41. Ramsay L, Macaulay M, degli Ivanissevich S et al (2000) A simple sequence repeat-based linkage map of barley. Genetics 156:1997–2005PubMedGoogle Scholar
  42. Rebaï A, Goffinet B (2000) More about quantitative trait locus mapping with diallel designs. Genet Res 75:243–247PubMedCrossRefGoogle Scholar
  43. Rostoks N, Mudie S, Cardle L et al (2005) Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol Gen Genomics 274:515–527CrossRefGoogle Scholar
  44. Sakamoto Y, Ishiguro M, Kitagawa G (1986) Akaike information criterion statistics. KTK Scientific Publishers, Tokyo, pp 83–85Google Scholar
  45. Schwarz G (1978) Estimating the dimension of a model. Ann Statistic 6:461–464CrossRefGoogle Scholar
  46. Stracke S, Börner A (1998) Molecular mapping of the photoperiod response gene ea7 in barley. Theor Appl Genet 97:797–800CrossRefGoogle Scholar
  47. Swanston JS, Russell JR, Pérez-Vendrell AM et al (2006) Efficient selection of β-glucan content enhances wider utilisation of barley grain. Eucarpia meeteing, Cereals Section, Lleida, Spain, November 13–17Google Scholar
  48. Szűcs P, Karsai I, von Zitzewitz J, Cooper L et al (2006) Positional relationships between photoperiod response QTL and photoreceptor and vernalization genes in barley. Theor Appl Genet 112:1277–1285PubMedCrossRefGoogle Scholar
  49. Szűcs P, Skinner JS, Karsai I et al (2007) Validation of the VRN-H2/VRN-H1 epistatic model in barley reveals that intron length variation in VRN-H1 may account for a continuum of vernalization sensitivity. Mol Genet Genom doi:  10.1007/s00438-006-0195-8
  50. Trevaskis B, Hemming MN, Peacock WJ et al (2006) HvVRN2 Responds to daylength, whereas HvVRN1 is regulated by vernalization and developmental status. Plant Physiol 140:1397–1405PubMedCrossRefGoogle Scholar
  51. Turner A, Beales J, Faure S et al (2005) The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley. Science 310:1031–1034PubMedCrossRefGoogle Scholar
  52. Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621–630PubMedCrossRefGoogle Scholar
  53. Verhoeven KJ, Jannink JL, McIntyre LM (2006) Using mating designs to uncover QTL and the genetic architecture of complex traits. Heredity 96:139–149PubMedCrossRefGoogle Scholar
  54. Wenzl P, Li H, Carling J et al (2006) A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genomics 7:206–215PubMedCrossRefGoogle Scholar
  55. Xu SZ (1998) Mapping quantitative trait loci using multiple families of line crosses. Genetics 148:517–524PubMedGoogle Scholar
  56. Yan L, Loukoianov A, Tranquilli G et al (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci USA 100:6263–6268PubMedCrossRefGoogle Scholar
  57. Yan L, Loukoianov A, Blechl A et al (2004) The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303:1640–1644PubMedCrossRefGoogle Scholar
  58. Yan L, Fu D, Li C et al (2006) The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proc Natl Acad Sci USA 103:19581–19586PubMedCrossRefGoogle Scholar
  59. Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468PubMedGoogle Scholar
  60. von Zitzewitz J, Szűcs P, Dubcovsky J et al (2005) Molecular and structural characterization of barley vernalization genes. Plant Mol Biol 59:449–467CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Alfonso Cuesta-Marcos
    • 1
  • Ana M. Casas
    • 1
  • Samia Yahiaoui
    • 1
  • M. Pilar Gracia
    • 1
  • José M. Lasa
    • 1
  • Ernesto Igartua
    • 1
  1. 1.Department of Genetics and Plant ProductionAula Dei Experimental Station, CSICZaragozaSpain

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