Theoretical and Applied Genetics

, Volume 130, Issue 11, pp 2271–2282 | Cite as

Saturation mapping of regions determining resistance to Ascochyta blight and broomrape in faba bean using transcriptome-based SNP genotyping

  • S. Ocaña-Moral
  • N. Gutiérrez
  • A. M. TorresEmail author
  • E. Madrid
Original Article


Key message

Transcriptome-based SNP markers were genotyped in a faba bean map to saturate regions bearing QTL for Ascochyta fabae and broomrape and distinguish positional and functional candidates underlying both resistances.


Faba bean is an important food crop worldwide. Marker-assisted selection for disease resistance is a top priority in current faba bean research programs, with pathogens such as Ascochyta fabae and broomrape (Orobanche crenata) being among the major constraints in global faba bean production. However, progress in genetics and genomics in this species has lagged behind that of other grain legumes. Although genetic maps are available, most markers are not in or are too distant from target genes to enable an accurate prediction of the desired phenotypes. In this study, a set of SNP markers located in gene coding regions was selected using transcriptomic data. Ninety-two new SNP markers were genotyped to obtain the most complete map reported so far in the 29H × Vf136 faba bean population. Most of the QTL regions previously described in this cross were enriched with SNP markers. Two QTLs for O. crenata resistance (Oc7 and Oc8) were confirmed. Oc7 and Oc10 located nearby a QTL for A. fabae resistance suggested that these genomic regions might encode common resistance mechanisms and could be targets for selection strategies against both pathogens. We also confirmed three regions in chromosomes II (Af2), III (Af3) and VI associated with Ascochyta blight resistance. The QTLs ratified in the present study are now flanked by or include reliable SNP markers in their intervals. This new information provides a valuable starting point in the search for relevant positional and functional candidates underlying both types of resistance.



This research was financed by the Spanish MINECO (project RTA2010-00059) co-financed by the EU through the European Regional Development Fund (ERDF) 2014–2020 “Programa Operativo de Crecimiento Inteligente” and the IFAPA project PR.AVA.AVA201601.17 co-financed by ERDF. Partial funding from the European Community’s Seventh Framework Programme (FP7/2007-2013) under the Grant agreement no. FP7-613551, LEGATO project is also acknowledged. S. Ocaña-Moral acknowledges the FPI-INIA fellowship and N. Gutiérrez the MINECO financial support through the “Juan de la Cierva” Program. The authors would like to thank Dr. CM Avila and Dr. SG Atienza for their helpful and critical comments.

Compliance with ethical standards

Conflict of interest

All authors have read and approved the final manuscript. The authors declare that they have no conflict of interest.

Supplementary material

122_2017_2958_MOESM1_ESM.xlsx (464 kb)
Additional file 1. Detailed information of the SNPs selected, annotation in the M. truncatula genome (Mtr4.0) and genotyping technique assayed (XLSX 463 kb)
122_2017_2958_MOESM2_ESM.xlsx (21 kb)
Additional file 2. List of the SNPs genotyped, annotation in the M. truncatula genome and assignment to the different faba bean LGs or chromosomes (chr.) (XLSX 21 kb)


  1. Abbes Z, Kharrat M, Delavault P, Simier P, Chaïbi W (2007) Field evaluation of the resistance of some faba bean (Vicia faba L.) genotypes to the parasitic weed Orobanche foetida Poiret. Crop Prot 26:1777–1784CrossRefGoogle Scholar
  2. Abu-Irmaileh BE (1994) Nitrogen reduces branched broomrape (Orobanche ramosa) seed germination. Weed Sci 42:57–60Google Scholar
  3. Atienza SG, Palomino C, Gutiérrez N, Alfaro CM, Rubiales D, Torres AM, Ávila CM (2016) QTLs for Ascochyta blight resistance in faba bean (Vicia faba L.): validation in field and controlled conditions. Crop Pasture Sci 67:216–224. doi: 10.1071/CP15227 Google Scholar
  4. Avila CM, Satovic Z, Sillero JC, Rubiales D, Moreno MT, Torres AM (2004) Isolate and organ-specific QTLs for Ascochyta blight resistance in faba bean. Theor Appl Genet 108:1071–1078CrossRefPubMedGoogle Scholar
  5. Bond DA, Jellis GJ, Rowland GG, Le Guen J, Robertson LD, Khalil SA, Li-Juan L (1994) Present status and future strategy in breeding faba beans (Vicia faba L) for resistance to biotic and abiotic stresses. In: Muehlbauer FJ, Kaiser WJ (eds) Expanding the production and use of cool season food legumes. Current plant science biotechnology agriculture, vol 19. Kluwer Academic Press, Dordrecht, The Netherlands, pp 592–616Google Scholar
  6. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971PubMedPubMedCentralGoogle Scholar
  7. Cubero JI, Moreno MT, Hernández L (1992) A faba bean cultivar resistant to Orobanche crenata Forsk. In: Proceedings 1st European conference on grain legumes. AEP, European Association for Grain Legume Research, Angers, France, pp 41–42Google Scholar
  8. D’Cruz AA, Babon JJ, Norton RS, Nicola NA, Nicholson SE (2013) Structure and function of the SPRY/B30.2 domain proteins involved in innate immunity. Protein Sci 22:1–10CrossRefPubMedGoogle Scholar
  9. Del Pozo O, Pedley KF, Martin GB (2004) MAPKKKα is a positive regulator of cell death associated with both plant immunity and disease. EMBO J 23:3072–3082. doi: 10.1038/sj.emboj.7600283 CrossRefPubMedPubMedCentralGoogle Scholar
  10. Díaz R, Torres AM, Satovic Z, Gutierrez MV, Cubero JI, Román B (2010) Validation of QTLs for Orobanche crenata resistance in faba bean (Vicia faba L.) across environments and generations. Theor Appl Genet 120:909–919CrossRefGoogle Scholar
  11. Díaz-Ruiz R, Satovic Z, Avila CM, Alfaro CM, Gutierrez MV, Torres AM, Román B (2009a) Confirmation of QTLs controlling Ascochyta fabae resistance in different generations of faba bean (Vicia faba L.). Crop Pasture Sci 60:353–361CrossRefGoogle Scholar
  12. Díaz-Ruiz R, Torres A, Gutierrez MV, Rubiales D, Cubero JI, Kharrat M, Satovic Z, Román B (2009b) Mapping of quantitative trait loci controlling Orobanche foetida Poir. Resistance in faba bean (Vicia faba L.). Afr J Biotechnol 8:2718–2724Google Scholar
  13. Ellwood SR, Phan HTT, Jordan M, Hane J, Torres AM, Avila CM, Cruz-Izquierdo S, Oliver RP (2008) Construction of a comparative genetic map in faba bean (Vicia faba L.); conservation of genome structure with Lens culinaris. BMC Genom 9:380CrossRefGoogle Scholar
  14. Fondevilla S, Fernández-Aparicio M, Satovic Z, Emeran AA, Torres AM, Moreno MT, Rubiales D (2010) Identification of quantitative trait loci for specific mechanisms of resistance to Orobanche crenata Forsk. in pea (Pisum sativum L.). Mol Breed 25:259–272CrossRefGoogle Scholar
  15. Fondevilla S, Almeida NF, Satovic Z, Rubiales D, Vaz Patto MC, Cubero JI, Torres AM (2011) Identification of common genomic regions controlling resistance to Mycosphaerella pinodes, earliness and architectural traits in different pea genetic backgrounds. Euphytica 182:43–52. doi: 10.1007/s10681-011-0460-8 CrossRefGoogle Scholar
  16. Gabriel S, Ziaugra L, Tabbaa D (2009) SNP genotyping using the Sequenom MassARRAY iPLEX platform. Curr Protoc Hum Genet. doi: 10.1002/0471142905.hg0212s60
  17. Gao Y, Zhang Y, Zhang D, Dai X, Estelle M, Zhao Y (2015) Auxin binding protein 1 (ABP1) is not required for either auxin signaling or Arabidopsis development. Proc Nat Acad Sci USA 112:2275–2280CrossRefPubMedPubMedCentralGoogle Scholar
  18. Gressel J, Hanafi A, Head G, Marasas W, Obilana AB, Ochanda J, Souissi T, Tzotzos G (2004) Major heretofore intractable biotic constraints to African food security that may be amenable to novel biotechnological solutions. Crop Prot 23:661–689CrossRefGoogle Scholar
  19. Guo WJ, Ho TH (2008) An abscisic acid-induced protein, HVA22, inhibits gibberellin-mediated programmed cell death in cereal aleurone cells. Plant Physiol 147:1710–1722CrossRefPubMedPubMedCentralGoogle Scholar
  20. Gutiérrez N, Palomino C, Satovic Z, Ruiz-Rodríguez MD, Vitale S, Gutiérrez MV, Rubiales D, Kharrat M, Amri M, Emeran A, Cubero JI, Atienza SG, Torres AM, Avila CM (2013) QTLs for Orobanche spp. resistance in faba bean: identification and validation across different environments. Mol Breed 32:909–922CrossRefGoogle Scholar
  21. Haian Fu, Subramanian Romesh R, Masters Shane C (2000) 14-3-3 Proteins: structure, function, and regulation. Annu Rev Pharmacol 40:617–647CrossRefGoogle Scholar
  22. Jamann T, Poland J, Kolkman J, Smith L, Nelson R (2014) Unraveling genomic complexity at a quantitative resistance locus in maize. Genetics 198:333–344CrossRefPubMedPubMedCentralGoogle Scholar
  23. Kaur S, Kimber RBE, Cogan NOI, Materne M, Forster JW, Paull JG (2014) SNP discovery and high-density genetic mapping in faba bean (Vicia faba L.) permits identification of QTLs for Ascochyta blight resistance. Plant Sci 217–218:47–55CrossRefPubMedGoogle Scholar
  24. Knox MR, Ellis THN (2002) Excess heterozygosity contributes to genetic map expansion in pea recombinant inbred populations. Genetics 162:861–873PubMedPubMedCentralGoogle Scholar
  25. Kolukisaoglu U, Wein S, Blazevic D, Batistic O, Kudla J (2004) Calcium sensors and their interacting protein kinases: genomics of the Arabidopsis and rice CBL-CIPK signaling networks. Plant Physiol 134:43–58CrossRefPubMedPubMedCentralGoogle Scholar
  26. Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175CrossRefGoogle Scholar
  27. Lee J, Rudd JJ, Macioszek VK, Scheel D (2004) Dynamic changes in the localization of MAPK cascade components controlling pathogenesis-related (PR) gene expression during innate immunity in parsley. J Biol Chem 279:22440–22448. doi: 10.1074/jbc.M401099200 CrossRefPubMedGoogle Scholar
  28. Leonforte A, Sudheesh S, Cogan NO, Salisbury PA, Nicolas ME, Materne M, Forster JW, Kaur S (2013) SNP marker discovery, linkage map construction and identification of QTLs for enhanced salinity tolerance in field pea (Pisum sativum L.). BMC Plant Biol 13:161CrossRefPubMedPubMedCentralGoogle Scholar
  29. Li H (2011) A quick method to calculate QTL confidence interval. J Genet 90:355–360. doi: 10.1007/s12041-011-0077-7 CrossRefPubMedGoogle Scholar
  30. 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 142:247–258PubMedPubMedCentralGoogle Scholar
  31. Liu H, Niu Y, Gonzalez-Portilla PJ, Zhou H, Wang L, Zuo T, Qin C, Tai S, Jansen C, Shen Y, Lin H, Lee M, Ware D, Zhang Z, Lübberstedt T, Pan G (2015) An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize. BMC Genom 16:1078CrossRefGoogle Scholar
  32. Mader E, Hopwood J (2013) Pollinator management for organic seed producers. 28 pp. Portland, Oregon: The Xerces SocietyGoogle Scholar
  33. Madrid E, Palomino C, Plötner A, Horres R, Jüngling R, Rotter B, Winter P, Kahl G, Torres AM (2013) DeepSuperSage analysis of the Vicia faba transcriptome in response to Ascochyta fabae infection. Phytopathol Mediterr 52:166–182Google Scholar
  34. Maurin N, Tivoli B (1992) Variation in the resistance of Vicia faba to Ascochyta fabae in relation to disease development in field trials. Plant Pathol 41:737–744CrossRefGoogle Scholar
  35. Meng X, Zhang S (2013) MAPK cascades in plant disease resistance signaling. Annu Rev Phytopathol 51:245–266. doi: 10.1146/annurev-phyto-082712-102314 CrossRefPubMedGoogle Scholar
  36. Millán T, Madrid E, Cubero JI, Amri M, Castro P, Rubio J (2015) Chickpea. In: De Ron A (ed) Handbook of Plant Breeding, vol 10. Springer, Grain Legumes, pp 85–109Google Scholar
  37. Ocaña S, Seoane P, Bautista R, Palomino C, Claros GM, Torres AM, Madrid E (2015) Large-scale transcriptome analysis in faba bean (Vicia faba L.) under Ascochyta fabae infection. PLoS ONE 10:e0135143. doi: 10.1371/journal.pone.0135143 CrossRefPubMedPubMedCentralGoogle Scholar
  38. Parker C (2009) Observations on the current status of Orobanche and Striga problems worldwide. Pest Manag Sci 65:453–459. doi: 10.1002/ps.1713 CrossRefPubMedGoogle Scholar
  39. Perfetto L, Gherardini PF, Davey NE, Diella F, Helmer-Citterich M, Cesareni G (2013) Exploring the diversity of SPRY/B30.2-mediated interactions. Trends Biochem Sci 38:38–46CrossRefPubMedGoogle Scholar
  40. Pitzschke A, Schikora A, Hirt H (2009) MAPK cascade signaling networks in plant defence. Curr Opin Plant Biol 12:421–426CrossRefPubMedGoogle Scholar
  41. Poland JA, Bradbury PJ, Buckler ES, Nelson RJ (2011) Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc Natl Acad Sci USA 108:6893–6898CrossRefPubMedPubMedCentralGoogle Scholar
  42. Ponting CP, Schultz J, Bork P (1997) SPRY domains in ryanodine receptors (Ca2+ release channels). Trends Biochem Sci 22:193–194CrossRefPubMedGoogle Scholar
  43. Prioul-Gervais S, Deniot G, Receveur EM, Frankewitz A, Fourmann M, Rameau C, Pilet-Nayel ML, Baranger A (2007) Candidate genes for quantitative resistance to Mycosphaerella pinodes in pea (Pisum sativum L.). Theor Appl Genet 114:971–984CrossRefPubMedGoogle Scholar
  44. Rodriguez MC, Petersen M, Mundy J (2010) Mitogenactivated protein kinase signaling in plants. Annu Rev Plant Biol 61:621–649CrossRefPubMedGoogle Scholar
  45. Rojas AM, Fuentes G, Rausell A, Valencia A (2012) The Ras protein superfamily: evolutionary tree and role of conserved amino acids. J Cell Biol 196:189–201CrossRefPubMedPubMedCentralGoogle Scholar
  46. Román B, Torres AM, Rubiales D, Cubero JI, Satovic Z (2002) Mapping of quantitative trait loci controlling broomrape (Orobanche crenata Forsk.) resistance in faba bean (Vicia faba L.). Genome 45:1057–1063CrossRefPubMedGoogle Scholar
  47. Román B, Satovic Z, Avila CM, Rubiales D, Moreno MT, Torres AM (2003) Locating genes associated with Ascochyta fabae resistance in Vicia faba. Aust J Agric Res 54:85–90CrossRefGoogle Scholar
  48. Romeis T, Ludwig A, Martin R, Jones JDG (2001) Calcium dependent protein kinases play an essential role in a plant defence response. EMBO J 20:5556–5567CrossRefPubMedPubMedCentralGoogle Scholar
  49. Rubiales D (2003) Parasitic plants, wild relatives and the nature of resistance. New Phytol 160:459–461CrossRefGoogle Scholar
  50. Satovic Z, Avila CM, Cruz-Izquierdo S, Díaz-Ruíz R, García-Ruíz GM, Palomino C, Gutiérrez N, Vitale S, Ocaña-Moral S, Gutiérrez MV, Cubero JI, Torres AM (2013) A reference consensus genetic map for molecular markers and economically important traits in faba bean (Vicia faba L.). BMC Genom 14:932CrossRefGoogle Scholar
  51. Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 33:1–14CrossRefGoogle Scholar
  52. Sillero JC, Avila CM, Moreno MT, Rubiales D (2001) Identification of resistance to Ascochyta fabae in Vicia faba germplasm. Plant Breed 120:529–531CrossRefGoogle Scholar
  53. Sillero JC, Villegas-Fernández AM, Thomas J, Rojas-Molina MM, Emeran AA, Fernández-Aparicio M, Rubiales D (2010) Faba bean breeding for disease resistance. Field Crops Res 115:297–307. doi: 10.1016/j.fcr.2009.09.012 CrossRefGoogle Scholar
  54. Tai F, Yuan Z, Li S, Wang Q, Liu F, Wang W (2016) ZmCIPK8, a CBL-interacting protein kinase, regulates maize response to drought stress. Plant Cell Tissue Organ Cult 124:459–469. doi: 10.1007/s11240-015-0906-0 CrossRefGoogle Scholar
  55. Tang H, Krishnakumar V, Bidwell S, Rosen B, Chan A, Zhou S, Gentzbittel L, Childs K, Yandell M, Gundlach H, Mayer K, Schwartz D, Town C (2014) An improved genome release (version Mt4.0) for the model legume Medicago truncatula. BMC Genomics 15:312. doi: 10.1186/1471-2164-15-312 CrossRefPubMedPubMedCentralGoogle Scholar
  56. Tena G, Boudsocq M, Sheen J (2011) Protein kinase signaling networks in plant innate immunity. Curr Opin Plant Biol 14:519–529CrossRefPubMedPubMedCentralGoogle Scholar
  57. Timmerman-Vaughan GM, Frew TJ, Weeden NF (2000) Characterization and linkage mapping of R-gene analogous DNA sequences in pea (Pisum sativum L.). Theor Appl Genet 101:241–247CrossRefGoogle Scholar
  58. Tivoli B, Reynauld B, Maurin N, Berthelem P, Le Guen J (1987) Comparison of some methods for evaluation of reaction of different faba bean genotypes to Ascochyta fabae. FABIS Newsletter 17:35–38Google Scholar
  59. Torii KU (2004) Leucine-rich repeat receptor kinases in plants: structure, function, and signal transduction pathways. Int Rev Cytol 234:1–46CrossRefPubMedGoogle Scholar
  60. Van Ooijen JW (2006) JoinMap 4. Software for the calculation of genetic linkage maps in experimental populations. Kyazma B. V. Wageningen, NetherlandsGoogle Scholar
  61. Webb A, Cottage A, Wood T, Khamassi K, Hobbs D, Gostkiewicz K, White M, Khazaei H, Ali M, Street D, Duc G, Stoddard FL, Maalouf F, Ogbonnaya FC, Link W, Thomas J, O’Sullivan DM (2016) A SNP based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.). Plant Biotechnol J 14:177–185. doi: 10.1111/pbi.12371 CrossRefPubMedGoogle Scholar
  62. Wisser RJ, Sun Q, Hulbert SH, Kresovich S, Nelson RJ (2005) Identification and characterization of regions of the rice genome associated with broad-spectrum, quantitative disease resistance. Genetics 169:2277–2293CrossRefPubMedPubMedCentralGoogle Scholar
  63. Yap MW, Nisole S, Stoye JP (2005) A single amino acid change in the SPRY domain of human Trim5alpha leads to HIV-1 restriction. Curr Biol 15:73–78CrossRefPubMedGoogle Scholar
  64. Zeid M, Mitchell S, Link W, Carter M, Nawar A, Fulton T, Kresovich S (2009) Simple sequence repeats (SSRs) in faba bean: new loci from Orobanche-resistant cultivar ‘Giza 402’. Plant Breed 128:149–155CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  • S. Ocaña-Moral
    • 1
  • N. Gutiérrez
    • 1
    • 2
  • A. M. Torres
    • 1
    Email author
  • E. Madrid
    • 3
  1. 1.Área de Genómica y Biotecnología, IFAPA Centro Alameda del ObispoCórdobaSpain
  2. 2.ZAYINTEC, edificio PITA, Universidad de AlmeríaAlmeríaSpain
  3. 3.Department of Plant Developmental BiologyMax Planck Institute for Plant Breeding ResearchCologneGermany

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