, Volume 143, Issue 4, pp 501–514 | Cite as

Association mapping for frost tolerance using multi-parent advanced generation inter-cross (MAGIC) population in faba bean (Vicia faba L.)

  • Ahmed Sallam
  • Regina Martsch


A multi-parent advanced generation inter-cross (MAGIC) derived from 11 founder lines in faba bean was used in this study to identify quantitative trait loci (QTL) for frost tolerance traits using the association mapping method with 156 SNP markers. This MAGIC population consists of a set of 189 genotypes from the Göttingen Winter Bean Population. The association panel was tested in two different experiments, i.e. a frost and a hardening experiment. Six morphological traits, leaf fatty acid composition, relative water content in shoots were scored in this study. The genotypes presented a large genetic variation for all traits that were highly heritable after frost and after hardening. High phenotypic significant correlations were established between traits. The principal coordinates analysis resulted in no clear structure in the current population. Association mapping was performed using a general linear model and mixed linear model with kinship. A False discovery rate of 0.20 (and 0.05) was used to test the significance of marker-trait association. As a result, many putative QTLs for 13 morphological and physiological traits were detected using both models. The results reveal that QTL mapping by association analysis is a powerful method of detecting the alleles associated with frost tolerance in the winter faba bean which can be used in accelerating breeding programs.


Vicia faba Association mapping MAGIC Frost tolerance Linkage disequilibrium Genetic analysis 



We thank apl. Prof. Dr. Wolfgang Link and PD. Dr. Wolfgang Ecke, Department of Crop Sciences, Georg-August-Univeristät Göttingen, for their valuable discussions on this work. We would like to acknowledge Prof. Dr. Donal O’sullivan, University of Reading, UK, for providing us with his consensus map (Webb et al. 2015). This work was financially supported by the Cultural Affairs & Mission Sector in Egypt and the German Academic Exchange Service (DAAD).

Conflict of interest

The authors declare that they have no competing interests and understand the conditions of ethical responsibilities that are addressed by Genetica.

Supplementary material

10709_2015_9848_MOESM1_ESM.docx (1.4 mb)
Supplementary material 1 (DOCX 1385 kb)


  1. Alghamdi S, Al-Faifi SA, Migdadi HM, Khan MA, EL-Harty EH, Ammar MH (2012) Molecular diversity assessment using sequence related amplified polymorphism (SRAP) markers in Vicia faba L. Int J Mol Sci 13:16457–16471. doi: 10.3390/ijms131216457 PubMedCentralPubMedCrossRefGoogle Scholar
  2. Amar S, Ecke W, Becker HC, Möllers C (2008) QTL for phytosterol and sinapate ester content in Brassica napus L. collocate with the two erucic acid genes. Theor Appl Genet 116:1051–1106. doi: 10.1007/s00122-008-0734-2 PubMedCentralPubMedCrossRefGoogle Scholar
  3. Arbaoui M (2007) Detailed genetic analysis of faba bean (Vicia faba L.) winter-hardiness and related traits. PhD thesis. University of Göttingen, GermanyGoogle Scholar
  4. Arbaoui M, Link W (2008) Effect of hardening on frost tolerance and fatty acid composition of leaves and stems of a set of faba bean (Vicia faba L.) genotypes. Euphytica 162:211–219. doi: 10.1007/s10681-007-9521-4 CrossRefGoogle Scholar
  5. Arbaoui M, Link W, Satovic Z, Torre MA (2008) Quantitative trait loci of frost tolerance and physiologically related traits in faba bean (Vicia faba L.). Euphytica 164:93–104Google Scholar
  6. Badaruddin M, Meyer DW (2001) Factors modifying frost tolerance of legume species. Crop Sci 41:1911–1916. doi: 10.2135/cropsci2001.1911 CrossRefGoogle Scholar
  7. Bandillo N, Raghavan C, Muyco PA, Sevilla MAL, Lobina IT, Dilla-Ermita CJ, Leung H (2013) Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding. Rice 6(1):11PubMedCrossRefGoogle Scholar
  8. Basunanda P, Radoev M, Ecke W, Friedt W, Becker HC, Snowdon RJ (2009) Comparative mapping of quantitative trait loci involved in heterosis for seedling and yield traits in oil seed rape (Brassica napus L.). Theor Appl Genet 120:271–281. doi: 10.1007/s00122-009-1133-z PubMedCentralCrossRefGoogle Scholar
  9. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300Google Scholar
  10. Bernardo R (2008) Molecular markers and selection for complex traits in plants: learning from the last 20 years. Crop Sci 48(5):1649–1664Google Scholar
  11. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23(19):2633–2635. doi: 10.1093/bioinformatics/btm308 PubMedCrossRefGoogle Scholar
  12. Branca A, Paape TD, Zhou P, Briskine R, Farmer AD, Mudge J, Tiffin P (2011) Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proc Natl Acad Sci 108:864–870. doi: 10.1073/pnas.1104032108 CrossRefGoogle Scholar
  13. Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172(2):1165–1177Google Scholar
  14. Cai D, Xiao Y, Yang W, Ye W, Wang B, Younas M, Jiangsheng W, Liu K (2014) Association mapping of six yield-related traits in rapeseed (Brassica napus L.). Theor Appl Genet 127(1):85–96PubMedCrossRefGoogle Scholar
  15. Cavanagh C, Morell M, Mackay I, Powell W (2008) From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Curr Opin Plant Biol 11:215–221PubMedCrossRefGoogle Scholar
  16. Cruz-Izquierdo S, Avila CM, Satovic Z, Palomino C, Gutierrez N, Ellwood SR, Phan HTT, Cubero JI, Torres AM (2012) Comparative genomics to bridge Vicia faba with model and closely-related legume species: stability of QTLs for flowering and yield-related traits. Theor Appl Genet 125:1767–1782. doi: 10.1007/s00122-012-1952-1 PubMedCrossRefGoogle Scholar
  17. Cyril J, Powell GL, Duncan RR, Baird WV (2002) Changes in membrane polar lipid fatty acids of Seashore Paspalum in response to low temperature exposure. Crop Sci 42:2031–2037. doi: 10.2135/cropsci2002.2031 CrossRefGoogle Scholar
  18. Ecke W, Clemens R, Honsdorf N, Becker HC (2010) Extent and structure of linkage disequilibrium in canola quality winter rapeseed (Brassica napus L.). Theor Appl Genet 120(5):921–931. doi: 10.1007/s00122-009-1221-0 PubMedCentralPubMedCrossRefGoogle Scholar
  19. Eujayl I, Erskine W, Baum M, Pehu E (1999) Inheritance and linkage analysis of frost injury in lentil. Crop Sci 39:639–642. doi: 10.2135/cropsci1999.0011183X003900020004x CrossRefGoogle Scholar
  20. Falconer DS, Mackay TFC (1996) Introduction to quantitative genetics, 4th edn. Prentice Hall, HarlowGoogle Scholar
  21. Fedoruk M (2013) Linkage and association mapping of seed size and sharp in lentil. PhD thesis. University of Saskatchewan, CanadaGoogle Scholar
  22. Gasim S (2003) Winter-hardy faba bean: applied genetic research on the reproductive mode of the European gene pool. PhD thesis. University of Göttingen, GermanyGoogle Scholar
  23. Gasim S, Abel S, Link W (2004) Extent, variation and breeding impact of natural cross-fertilization in German winter faba beans using hilum colour as marker. Euphytica 136(2):193–200CrossRefGoogle Scholar
  24. Herzog H (1987a) Freezing resistance and development of faba beans as affected by ambient temperatures, soil moisture and variety. J Agron Crop Sci 159:90–100. doi: 10.1111/j.1439-037X.1987.tb00617.x CrossRefGoogle Scholar
  25. Herzog H (1987b) A quantitative method to assess freezing resistance in faba beans. J Agron Crop Sci 158:195–204. doi: 10.1111/j.1439-037X.1987.tb00263.x CrossRefGoogle Scholar
  26. Herzog H (1988) Winter hardiness in faba beans: varietal differences and interrelations among selection criteria. Plant Breed 101:269–276. doi: 10.1111/j.1439-0523.1988.tb00299.x CrossRefGoogle Scholar
  27. Herzog H (1989) Influence of pre-hardening duration and dehardening temperatures on varietal freezing resistance in faba beans (Vicia faba L.). Agronomie 9:55–61CrossRefGoogle Scholar
  28. Honsdorf N, Becker HC, Ecke W (2010) Association mapping for phenological, morphological, and quality traits in canola quality winter rapeseed (Brassica napus L.). Genome 53(11):899–907PubMedCrossRefGoogle Scholar
  29. Ingvarsson PK (2005) Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., salicaceae). Genetics 169:945–953. doi: 10.1534/genetics.104.034959 PubMedCentralPubMedCrossRefGoogle Scholar
  30. Link W, Balko C, Stoddard LF (2010) Winter hardiness in faba bean: physiology and breeding. Field crops res 115:287–296Google Scholar
  31. Kaur S, Cogan NO, Forster JW, Paull JG (2014) Assessment of genetic diversity in faba bean based on single nucleotide polymorphism. Diversity 6(1):88–101CrossRefGoogle Scholar
  32. Kraakman ATW, Niks RE, Van den Berg PMMM, Stam P, Van Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168(1):435–446. doi: 10.1534/genetics.104.026831 PubMedCentralPubMedCrossRefGoogle Scholar
  33. Kumar J, Pratap A, Solanki RK, Gupta DS, Goyal A, ChaturvedI SK et al (2011) Advances in genomics resources for improving food legume crops. J Agric Sci 150:289–318Google Scholar
  34. Lehninger AL (1977) Biochemistry, 2nd edn. Worth Publisher, New YorkGoogle Scholar
  35. Long NV, Dolstra O, Malosetti M, Kilian B, Graner A, Visser RG, van der Linden CG (2013) Association mapping of salt tolerance in barley (Hordeum vulgare L.). Theor Appl Genet 126(9):2335–2351. doi: 10.1007/s00122-013-2139-0 PubMedCrossRefGoogle Scholar
  36. Longin CFH, Sieber AN, Reif JC (2013) Combining frost tolerance, high grain yield and good pasta quality in durum wheat. Plant Breed 132:353–358. doi: 10.1111/pbr.12064 CrossRefGoogle Scholar
  37. Lyons JM, Wheaton TA, Pratt HK (1964) Relationship between the physical nature of mitochondrial membranes and chilling sensitivity in plants. Plant Physiol 39:262–268PubMedCentralPubMedCrossRefGoogle Scholar
  38. Mackay I, Powell W (2007) Methods for linkage disequilibrium mapping in crops. Trends Plant Sci 12:57–63PubMedCrossRefGoogle Scholar
  39. Maqbool A, Shafiq S, Lake L (2010) Radiant frost tolerance in pulse crops—a review. Euphytica 172:1–12. doi: 10.1007/s10681-009-0031-4 CrossRefGoogle Scholar
  40. Oraguzie NC, Wilcox PL (2007) Association mapping in plant. Springer, Berlin, pp 1–11CrossRefGoogle Scholar
  41. Pearson TA, Manolio TA (2008) How to interpret a genome-wide association study. Jama 299:1335–1344Google Scholar
  42. Pene S (2013) Analysis of ecological data: exploratory and euclidean methods in envrionmental sciences. R package version 1.6.2.
  43. Pozarkova D, Koblizkova A, Roman B, Torres AM, Lucretti S, Lysak M, Dolezel J, Macas J (2002) Development and characterization of microsatellite markers from chromosome1-specific DNA libraries of Vicia faba. Biol Plant 45:337–345. doi: 10.1023/A:1016253214182 CrossRefGoogle Scholar
  44. Pritchard JK, Przeworski M (2001) Linkage disequilibrium in humans: models and data. Am J Hum Genet 69:1–14. doi: 10.1086/321275 PubMedCentralPubMedCrossRefGoogle Scholar
  45. R Core Team (2013) R: a language and environment for statistical computing. R foundation for statistical computing, Vienna.
  46. Reich DE, Cargill M, Bolk S (2001) Linkage disequilibrium in the human genome. Nature 411:199–204. doi: 10.1038/35075590 PubMedCrossRefGoogle Scholar
  47. Roth F, Link W (2010) Selection on freezing-tolerance of faba bean (Vicia faba L.): improvement of methods and results. In 60. Jahrestagung der Vereinigung der Pflanzenzüchter und Saatgutkaufleute Österreichs, 24–26 November 2009, Raumberg-Gumpenstein. Vereinigung der Pflanzenzüchter und Saatgutkaufleute Österreichs, pp 31–37Google Scholar
  48. Sallam A (2014) Detailed genetic approach to improve frost tolerance in German winter faba bean. PhD thesis. University of Göttingen, GermanyGoogle Scholar
  49. Sallam A, Link W (2012) The Göttingen frost tolerance test for winter faba beans. Biennial conference of the plant genome research working group of the GPZGoogle Scholar
  50. Sallam A, Marsch R, Moursi YS (2015) Genetic variation in morpho-physiological traits associated with frost tolerance in faba bean. Euphytica (in press). doi: 10.1007/s10681-015-1395-2
  51. Sherry RW, Buckler ES (2003) Plant functional genomics. In: Crotewold E (ed) Using natural allelic diversity to evaluate gene function. Springer, Berlin, pp 123–141Google Scholar
  52. Soto-Cerda BJ, Cloutier S (2012) Association mapping in plant genomes. INTECH Open Access PublisherGoogle Scholar
  53. Suresh S, Park JH, Cho GT, Lee HS, Baek HJ, Lee SY, Chung JW (2013) Development and molecular characterization of 55 novel polymorphic cDNA-SSR markers in faba bean (Vicia faba L.) using 454 pyrosequencing. Molecules 18(2):1844–1856PubMedCrossRefGoogle Scholar
  54. Torres MA, Weeden NF, Martin A (1993) Linkage among isozyme, RFLP and RAPD markers in Vicia faba. Theor Appl Genet 85:937–945. doi: 10.1007/BF00215032 PubMedCrossRefGoogle Scholar
  55. Utz HF (1997) A computer program for statistical analysis of plant breeding experiments. Version 2N. Institute of plant breeding, seed science AND population genetics. University of HohenheimGoogle Scholar
  56. Vigh L, Maresca B, Harwood JL (1998) Does the membrane’s physical state control the expression of heat shock and other genes? Trends Biochem Sci 2:69–374. doi: 10.1016/S0968-0004(98)01279-1 Google Scholar
  57. Webb A, Cottage A., Wood T, Khamassi K, Hobbs D, Gostkiewicz K, White M, Khazaei H, Ali M, Street D, Duc G, Stoddard F, Maalouf F, Ogbannaya F, Link W, Thomas J, O’Sullivan DM (2015) A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.). Plant Biotechnol. doi: 10.1111/pbi.12371
  58. Welna Gregor (2014) Genetische Analysen für eine markergestützte Verbesserung der Trockenstresstoleranz von Winterackerbohnen. Universität Göttingen, GöttingenGoogle Scholar
  59. Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208Google Scholar
  60. Zhao J, Dimov Z, Becker HC, Ecke W, Möllers C (2008) Mapping QTL controlling fatty acid composition in a doubled haploid rapeseed population segregating for oil content. Mol Breed 21:115–125. doi: 10.1007/s11032-007-9113-y CrossRefGoogle Scholar
  61. Zhu C, Gore M, Buckler E, Yu J (2008) Status and prospects of association mapping in plants. Plant Genome 1:5–20Google Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.Department of Crop SciencesGeorg-August-Univeristät GöttingenGöttingenGermany
  2. 2.Department of Genetics, Faculty of AgricultureAssiut UniversityAssiutEgypt

Personalised recommendations