Molecular Breeding

, Volume 32, Issue 2, pp 279–289 | Cite as

A high-density genetic map of the Medicago truncatula major freezing tolerance QTL on chromosome 6 reveals colinearity with a QTL related to freezing damage on Pisum sativum linkage group VI

  • Nadim Tayeh
  • Nasser Bahrman
  • Rosemonde Devaux
  • Aurélie Bluteau
  • Jean-Marie Prosperi
  • Bruno Delbreil
  • Isabelle Lejeune-Hénaut


Freezing is one of the most serious abiotic stress factors that affect cool-season legumes. It limits species geographic distribution and causes severe yield losses. Improving tolerance to freezing has long been a main concern for legume breeders. Medicago truncatula Gaertn. has been selected as a model species for legume biology. Various studies have shown significant macrosynteny between M. truncatula and agronomically important crop legumes. A major freezing tolerance quantitative trait locus (QTL), herein referred to as Mt-FTQTL6, was previously identified on M. truncatula chromosome 6. The physical location of this QTL was determined in this study and its corresponding chromosomal interval was enriched with additional markers. Markers were first developed using the draft sequence of M. truncatula euchromatin (release versions Mt3.0 and Mt3.5). Because Mt-FTQTL6 was found to coincide with an assembly gap, the Glycine max (L.) Merr. genome sequence was also used to generate markers. Five Mt-FTQTL6-linked markers were found to be common to a region on Pisum sativum L. linkage group VI harboring a QTL for freezing damage. A subset of markers was tested for transferability across 11 additional legume species. This study lays the groundwork for identifying the molecular basis of Mt-FTQTL6. Cross-legume markers will be useful in future efforts aiming to investigate the conservation of Mt-FTQTL6 in cool-season legumes and subsequently the existence of common mechanisms for response to freezing between M. truncatula and crop legumes.


Freezing tolerance Quantitative trait locus (QTL) Synteny Medicago truncatula Glycine max Pisum sativum 



The authors wish to thank Drs. Marie-Christine Quillet and Marie-Laure Pilet-Nayel for helpful discussions concerning this work, Grégoire Aubert for providing P. sativum RNA-seq data, Cécile Godé for assistance in PCR product sequencing and Frédéric Depta for plant care in the greenhouse. They acknowledge Eric Hanocq for providing the initial plant material for the construction of the large P. sativum segregating population. They would also like to thank Pascal Marget and Jean-Bernard Magnin-Robert of GRC of grain legumes, INRA, Dijon, France; Stéphane Fourtier of GRC of forage and turf species, INRA, Lusignan, France; Frederic Ottosson of NordGen, Sweden and Dave Stout of WRPIS, Pullman, Washington, USA for supplying legume seeds. They also thank the GENTYANE platform (INRA UBP, UMR 1095, Clermont-Ferrand) for genotyping. This work was partly financially supported by the Région Nord Pas-de-Calais, France (FEDER ARCIR PLANTEQ3 program). N. Tayeh was the recipient of a Ph.D. fellowship from the Ministère de l’Enseignement supérieur et de la Recherche, France.

Supplementary material

11032_2013_9869_MOESM1_ESM.xlsx (155 kb)
Supplementary material 1 (XLSX 155 kb)
11032_2013_9869_MOESM2_ESM.docx (657 kb)
Supplementary material 2 (DOCX 656 kb)


  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2 PubMedGoogle Scholar
  2. Arbaoui M, Link W, Satovic Z, Torres AM (2008) Quantitative trait loci of frost tolerance and physiologically related trait in faba bean (Vicia faba L.). Euphytica 164:93–104. doi: 10.1007/s10681-008-9654-0 CrossRefGoogle Scholar
  3. Aubert G, Morin J, Jacquin F, Loridon K, Quillet MC, Petit A, Rameau C, Lejeune-Hénaut I, Huguet T, Burstin J (2006) Functional mapping in pea, as an aid to the candidate gene selection and for investigating synteny with the model legume Medicago truncatula. Theor Appl Genet 112:1024–1041. doi: 10.1007/s00122-005-0205-y PubMedCrossRefGoogle Scholar
  4. Bélanger G, Castonguay Y, Bertrand A, Dhont C, Rochette P, Couture L, Drapeau R, Mongrain D, Chalifour FP, Michaud R (2006) Winter damage to perennial forage crops in eastern Canada: causes, mitigation, and prediction. Can J Plant Sci 86:33–47CrossRefGoogle Scholar
  5. Bordat A, Savois V, Nicolas M, Salse J, Chauveau A, Bourgeois M, Potier J, Houtin H, Rond C, Murat F, Marget P, Aubert G, Burstin J (2011) Translational genomics in legumes allowed placing in silico 5460 unigenes on the pea functional map and identified candidate genes in Pisum sativum L. Genes Genomes Genet 1:93–103. doi: 10.1534/g3.111.000349 Google Scholar
  6. Brouwer DJ, Duke SH, Osborn TC (2000) Mapping genetic factors associated with winter hardiness, fall growth, and freezing injury in autotetraploid alfalfa. Crop Sci 40:1387–1396CrossRefGoogle Scholar
  7. Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T, Spannagl M, Monaghan E, Nicholson C, Humphray SJ, Schoof H et al (2006) Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci USA 103(40):14959–14964. doi: 10.1073/pnas.0603228103 PubMedCrossRefGoogle Scholar
  8. Casasoli M, Derory J, Morera-Dutrey C, Brendel O, Porth I, Guehl JM, Villani F, Kremer A (2006) Comparison of quantitative trait loci for adaptive traits between oak and chestnut based on an expressed sequence tag consensus map. Genetics 172:533–546. doi: 10.1534/genetics.105.048439 PubMedCrossRefGoogle Scholar
  9. Castonguay Y, Michaud R, Nadeau P, Bertrand A (2009) An indoor screening method for improvement of freezing tolerance in alfalfa. Crop Sci 49:809–818. doi: 10.2135/cropsci2008.09.0539 CrossRefGoogle Scholar
  10. Castonguay Y, Cloutier J, Bertrand A, Michaud R, Laberge S (2010) SRAP polymorphisms associated with superior freezing tolerance in alfalfa (Medicago sativa spp. sativa). Theor Appl Genet 120:1611–1619. doi: 10.1007/s00122-010-1280-2 PubMedCrossRefGoogle Scholar
  11. Chen H, Wang S, Xing Y, Xu C, Hayes PM, Zhang Q (2003) Comparative analyses of genomic locations and race specificities of loci for quantitative resistance to Pyricularia grisea in rice and barley. Proc Natl Acad Sci USA 100(5):2544–2549. doi: 10.1073/pnas.0437898100 PubMedCrossRefGoogle Scholar
  12. Chen C, Miller P, Muehlbauer F, Neill K, Wichman D, McPhee K (2006) Winter pea and lentil response to seeding date and micro- and macro-environments. Agron J 98:1655–1663. doi: 10.2134/agronj2006.0085 CrossRefGoogle Scholar
  13. Choi HK, Mun JH, Kim DJ, Zhu H, Baek JM, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR (2004a) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA 101(43):15289–15294. doi: 10.1073/pnas.0402251101 PubMedCrossRefGoogle Scholar
  14. Choi HK, Kim D, Uhm T, Limpens E, Lim H, Mun JH, Kalo P, Penmetsa RV, Seres A, Kulikova O, Roe BA, Bisseling T, Kiss GB, Cook DR (2004b) A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa. Genetics 166:1463–1502PubMedCrossRefGoogle Scholar
  15. Cook DR (1999) Medicago truncatula—a model in the making! Curr Opin Plant Biol 2:301–304PubMedCrossRefGoogle Scholar
  16. Corpet F (1988) Multiple sequence alignment with hierarchical clustering. Nucl Acids Res 16(22):10881–10890PubMedCrossRefGoogle Scholar
  17. 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(8):1767–1782. doi: 10.1007/s00122-012-1952-1 PubMedCrossRefGoogle Scholar
  18. D’Erfurth I, Le Signor C, Aubert G, Sanchez M, Vernoud V, Darchy B, Lherminier J, Bourion V, Bouteiller N, Bendahmane A, Buitink J, Prosperi JM, Thompson R, Burstin J, Gallardo K (2012) A role for an endosperm-localized subtilase in the control of seed size in legumes. New Phytol 196:738–751. doi: 10.1111/j.1469-8137.2012.04296.x PubMedCrossRefGoogle Scholar
  19. Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O (2008) robust phylogenetic analysis for the non-specialist. Nucl Acids Res 36:W465–W469. doi: 10.1093/nar/gkn180 PubMedCrossRefGoogle Scholar
  20. Distelfeld A, Korol A, Dubcovsky J, Uauy C, Blake T, Fahima T (2008) Colinearity between the barley grain protein content (GPC) QTL on chromosome arm 6HS and the wheat Gpc-B1 region. Mol Breed 22:25–38. doi: 10.1007/s11032-007-9153-3 CrossRefGoogle Scholar
  21. Doyle JJ, Luckow MA (2003) The rest of the iceberg. Legume diversity and evolution in a phylogenetic context. Plant Physiol 131:900–910. doi: 10.1104/pp.102.018150 PubMedCrossRefGoogle Scholar
  22. Dumont E, Fontaine V, Vuylsteker C, Sellier H, Bodèle S, Voedts N, Devaux R, Frise M, Avia K, Hilbert JL, Bahrman N, Hanocq E, Lejeune-Hénaut I, Delbreil B (2009) Association of sugar content QTL and PQL with physiological traits relevant to frost damage resistance in pea under field and controlled conditions. Theor Appl Genet 118:1561–1571. doi: 10.1007/s00122-009-1004-7 PubMedCrossRefGoogle Scholar
  23. Fatokun CA, Menancio-Hautea DI, Danesh D, Young ND (1992) Evidence for orthologous seed weight genes in cowpea and mung bean based on RFLP mapping. Genetics 132:841–846PubMedGoogle Scholar
  24. Fırıncıoğlu HK, Erbektaş E, Doğruyol L, Mutlu Z, Ünal S, Karakurt E (2009) Phenotypic variation of autumn and spring-sown vetch (Vicia sativa ssp.) populations in central Turkey. Span. J Agric Res 7(3):596–606Google Scholar
  25. Gepts P, Beavis WD, Brummer EC, Shoemaker RC, Stalker HT, Weeden NF, Young ND (2005) Legumes as a model plant family. Genomics for food and feed report of the cross-legume advances through genomics conference. Plant Physiol 137:1228–1235. doi: 10.1104/pp.105.060871 PubMedCrossRefGoogle Scholar
  26. Gondo T, Sato S, Okumura K, Tabata S, Akashi R, Isobe S (2007) Quantitative trait locus analysis of multiple agronomic traits in the model legume Lotus japonicus. Genome 50:627–637. doi: 10.1139/G07-040 PubMedCrossRefGoogle Scholar
  27. Guy C (1990) Cold acclimation and freezing stress tolerance: role of protein metabolism. Annu Rev Plant Physiol Plant Mol Biol 41:187–223CrossRefGoogle Scholar
  28. Joseph B, Schlueter JA, Du J, Graham MA, Ma J, Shoemaker RC (2009) Retrotransposons within syntenic regions between soybean and Medicago truncatula and their contribution to local genome evolution. Plant Gen 2(3):211–223. doi: 10.3835/plantgenome2009.01.0001 CrossRefGoogle Scholar
  29. Julier B, Flajoulot S, Barre P, Cardinet G, Santoni S, Huguet T, Huyghe C (2003) Construction of two genetic linkage maps in cultivated tetraploid alfalfa (Medicago sativa) using microsatellite and AFLP markers. BMC Plant Biol 3:9PubMedCrossRefGoogle Scholar
  30. Kahraman A, Kusmenoglu I, Aydin N, Aydogan A, Erskine W, Muehlbauer FJ (2004) QTL mapping of winter hardiness genes in lentil. Crop Sci 44:13–22CrossRefGoogle Scholar
  31. Klimenko I, Razgulayeva N, Gau M, Okumura K, Nakaya A, Tabata S, Kozlov NN, Isobe S (2010) Mapping candidate QTLs related to plant persistency in red clover. Theor Appl Genet 120:1253–1263. doi: 10.1007/s00122-009-1253-5 PubMedCrossRefGoogle Scholar
  32. Komlan A, Pilet-Nayel ML, Bahrman N, Baranger A, Delbreil B, Fontaine V, Hamon C, Hanocq E, Niarquin M, Sellier H, Vuylsteker C, Prosperi JM, Lejeune-Hénaut I (2013) Genetic variability and QTL mapping of freezing tolerance and related traits in Medicago truncatula. Theor Appl Genet (submitted)Google Scholar
  33. Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175Google Scholar
  34. Kulikova O, Gualtieri G, Geurts R, Kim DJ, Cook D, Huguet T, de Jong JH, Fransz PF, Bisseling T (2001) Integration of the FISH pachytene and genetic maps of Medicago truncatula. Plant J 27:49–58PubMedCrossRefGoogle Scholar
  35. Lejeune-Hénaut I, Hanocq E, Béthencourt L, Fontaine V, Delbreil B, Morin J, Petit A, Devaux R, Boilleau M, Stempniak JJ, Thomas M, Lainé AL, Foucher F, Baranger A, Burstin J, Rameau C, Giauffret C (2008) The flowering locus Hr colocalizes with a major QTL affecting winter frost tolerance in Pisum sativum L. Theor Appl Genet 116:1105–1116. doi: 10.1007/s00122-008-0739-x PubMedCrossRefGoogle Scholar
  36. Loridon K, McPhee K, Morin J, Dubreuil P, Pilet-Nayel ML, Aubert G, Rameau C, Baranger A, Coyne C, Lejeune-Hénaut L, Burstin J (2005) Microsatellite marker polymorphism and mapping in pea (Pisum sativum L.). Theor Appl Genet 111:1022–1031. doi: 10.1007/s00122-005-0014-3 PubMedCrossRefGoogle Scholar
  37. Maughan PJ, Maroof MAS, Buss GR (1996) Molecular-marker analysis of seed-weight: genomic locations, gene action, and evidence for orthologous evolution among three legume species. Theor Appl Genet 93:574–579CrossRefGoogle Scholar
  38. Mudge J, Cannon SB, Kalo P, Oldroyd GE, Roe BA, Town CD, Young ND (2005) Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana. BMC Plant Biol 5:15. doi: 10.1186/1471-2229-5-15 PubMedCrossRefGoogle Scholar
  39. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar
  40. Sadeghipour O, Aghaei P (2012) Comparison of autumn and spring sowing on performance of chickpea (Cicer arietinum L.) varieties. Int J Biosci 2(6):49–58Google Scholar
  41. Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T, Nakao M, Sasamoto S, Watanabe A, Ono A, Kawashima K, Fujishiro T, Katoh M, Kohara M, Kishida Y, Minami C et al (2008) Genome structure of the legume, Lotus japonicus. DNA Res 15:227–239. doi: 10.1093/dnares/dsn008 PubMedCrossRefGoogle Scholar
  42. Schlueter JA, Scheffler BE, Jackson S, Shoemaker RC (2008) Fractionation of synteny in a genomic region containing tandemly duplicated genes across Glycine max, Medicago truncatula, and Arabidopsis thaliana. J Hered 99(4):390–395. doi: 10.1093/jhered/esn010 PubMedCrossRefGoogle Scholar
  43. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183. doi: 10.1038/nature08670 PubMedCrossRefGoogle Scholar
  44. Shin JH, Van K, Kim DH, Kim KD, Jang YE, Choi BS, Kim MY, Lee SH (2008) The lipoxygenase gene family: a genomic fossil of shared polyploidy between Glycine max and Medicago truncatula. BMC Plant Biol 8:133. doi: 10.1186/1471-2229-8-133 PubMedCrossRefGoogle Scholar
  45. Timko MP, Rushton PJ, Laudeman TW, Bokowiec MT, Chipumuro E, Cheung F, Town CD, Chen X (2008) Sequencing and analysis of the gene-rich space of cowpea. BMC Genomics 9:103. doi: 10.1186/1471-2164-9-103 PubMedCrossRefGoogle Scholar
  46. Timmerman-Vaughan GM, McCallum JA, Frew TJ, Weeden NF, Russell AC (1996) Linkage mapping of quantitative trait loci controlling seed weight in pea (Pisum sativum L.). Theor Appl Genet 93:431–439CrossRefGoogle Scholar
  47. Van Ooijen JW (2006) Joinmap® 4, software for the calculation of genetic linkage maps in experimental populations. Kyazma B.V, WageningenGoogle Scholar
  48. Van Ooijen JW (2009) MapQTL® 6, software for the mapping of quantitative trait loci in experimental populations of diploid species. Kyazma B.V, WageningenGoogle Scholar
  49. Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MTA, Azam S, Fan G, Whaley AM, Farmer AD, Sheridan J, Iwata A, Tuteja R, Penmetsa RV et al (2012) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30(1):83–89. doi: 10.1038/nbt.2022 CrossRefGoogle Scholar
  50. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93(1):77–78PubMedCrossRefGoogle Scholar
  51. Young ND, Debellé F, Oldroyd GED, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KFX, Gouzy J, Schoof H, Van De Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M et al (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480:520–524. doi: 10.1038/nature10625 PubMedCrossRefGoogle Scholar
  52. Zhu H, Cannon SB, Young ND, Cook DR (2002) Phylogeny and genomic organization of the TIR and Non-TIR NBS-LRR resistance gene family in Medicago truncatula. Mol Plant Microbe Interact 15(6):529–539PubMedCrossRefGoogle Scholar
  53. Zorrilla-Fontanesi Y, Cabeza A, Domínguez P, Medina JJ, Valpuesta V, Denoyes-Rothan B, Sánchez-Sevilla JF, Amaya I (2011) Quantitative trait loci and underlying candidate genes controlling agronomical and fruit quality traits in octoploid strawberry (Fragaria x ananassa). Theor Appl Genet 123:755–778. doi: 10.1007/s00122-011-1624-6 PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Nadim Tayeh
    • 1
  • Nasser Bahrman
    • 1
    • 2
  • Rosemonde Devaux
    • 2
  • Aurélie Bluteau
    • 1
    • 2
  • Jean-Marie Prosperi
    • 3
  • Bruno Delbreil
    • 1
  • Isabelle Lejeune-Hénaut
    • 2
  1. 1.Université Lille 1, UMR 1281 SADVVilleneuve d’Ascq CedexFrance
  2. 2.INRA, UMR 1281 SADVPéronne CedexFrance
  3. 3.INRA, UMR AGAPMontpellier CedexFrance

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