transcription in response to low temperature and water deficit. Proc Natl Acad Sci U S A. 1997;94(3):1035–40. https://doi.org/10.1073/pnas.94.3.1035.

11. Gilmour SJ, Zarka DG, Stockinger EJ, Salazar MP, Houghton JM, Thomashow MF. Low temperature regulation of the *Arabidopsis* CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J. 1998;16(4):433–42. https://doi.org/10.1046/j.1365-313x.1998.00310.x.

12. Thomashow M. Molecular basis of plant cold acclimation: insights gained from studying the CBF cold response pathway. Plant Physiol. 2010;154(2): 571–7. https://doi.org/10.1104/pp.110.161794.

13. Alonso-Blanco C, Gomez-Mena C, Llorente F, Koornneef M, Salinas J, Martinez-Zapater J. Genetic and molecular analyses of natural variation indicate *CBF2* as a candidate gene for underlying a freezing tolerance quantitative trait locus in Arabidopsis. Plant Physiol. 2005;139(3):1304–12. https://doi.org/10.1104/pp.105.068510.

14. Toth B, Galiba G, Feher E, Sutka J, Snape JW. Mapping genes affecting flowering time and frost resistance on chromosome 5B of wheat. Theor Appl Genet. 2003;107(3):509–14. https://doi.org/10.1007/s00122-003-1275-3.

15. Vagujfalvi A, Galiba G, Cattivelli L, Dubcovsky J. The cold regulated transcriptional activator *CBF3* is linked to the frost tolerance locus Fr-A2 on wheat chromosome 5A. Mol Gen Genomics. 2003;269(1):60–7. https://doi.org/10.1007/s00438-003-0806-6.

16. Knox AK, Li CX, Vagujfalvi A, Galilba G, Stockinger EJ, Dubcovsky J. Identification of candidate CBF genes for the frost tolerance locus *Fr-A(m)*2 in *Triticum monococcum*. Plant Mol Biol. 2008;67(3):257–70. https://doi.org/10.1007/s11103-008-9316-6.

17. Pasquariello M, Barabaschi D, Himmelbach A, Steuernagel B, Ariyadasa R, Stein N, et al. The barley frost resistance-H2 locus. Funct Integr Genomics. 2014;14(1):85–100. https://doi.org/10.1007/s10142-014-0360-9.

18. Sandve SR, Kosmalaa, Rudi H, Fjellheim S, Rapacz M, Yamada T, et al. Molecular mechanisms underlying frost tolerance in perennial grasses adapted to cold climates. Plant Sci. 2011;180(1):69–77. https://doi.org/10.1007/s10142-014-0360-9.

19. Tayeh N, Bahrman N, Sellier H, Bluteau A, Blassiau C, Fourment J, et al. A tandem array of *CBF/DREB1* genes is located in a major freezing tolerance QTL region on Medicago truncatula chromosome 6. BMC Genomics. 2013; 14(1):814. https://doi.org/10.1186/1471-2164-14-814.

20. Tondelli A, Francia E, Barabaschi D, Pasquariello M, Pecchioni N. Inside the *CBF* locus in Poaceae. Plant Sci. 2011;180(1):39–45. https://doi.org/10.1016/j.plantsci.2010.08.012.

21. Lejeune-Hénaut I, Hanocq B, Ébthencourt L, Fontaine V, Delbreil B, Morin J, et al. The flowering locus *Hr* colocalizes with a major QTL affecting winter frost tolerance in *Pisum sativum* L. Theor Appl Genet. 2008;116(8):1105–16. https://doi.org/10.1007/s00122-008-0739-x.

22. Dumont E, Fontaine V, Vuylsteker C, Sellier H, Bodele S, Voedts N, et al. 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. 2009;118(8):1561–71. https://doi.org/10.1007/s00122-009-1004-7.

23. Klein A, Houtin H, Rond C, Marget P, Jacquin F, Boucherot K, et al. QTL analysis of frost damage in pea suggests different mechanisms involved in frost tolerance. Theor Appl Genet. 2014;127(6):1319–30. https://doi.org/10.1007/s00122-014-2299-6.

24. Gupta PK, Kulwal PL, Jaiswal V. Association mapping in crop plants: opportunities and challenges. Adv Genet. 2014;85:109–47. https://doi.org/10.1016/b978-0-12-800271-1.00002-0.

25. Li YL, Bock A, Haseneyer G, Korzun V, Wilde P, Schon CC, et al. Association analysis of frost tolerance in rye using candidate genes and phenotypic data from controlled, semi-controlled, and field phenotyping platforms. BMC Plant Biol. 2011;11:146. https://doi.org/10.1186/1471-2229-11-146.

26. Zhao YS, Gowda M, Wurschum T, Longin CFH, Korzun V, Kollers S, et al. Dissecting the genetic architecture of frost tolerance in central European winter wheat. J Exp Bot. 2013;64(14):4453–60. https://doi.org/10.1093/jxb/ert259.

27. Visioni A, Tondelli A, Francia E, Pswarayi A, Malosetti M, Russell J, et al. Genome-wide association mapping of frost tolerance in barley (*Hordeum vulgare* L.). BMC Genomics. 2013;14:424. https://doi.org/10.1186/1471-2164-14-424.

28. Tondelli A, Pagani D, Ghafoori IN, Rahimi M, Ataei R, Rizza F, et al. Allelic variation at *Fr-H1/Vrn-H1* and *Fr-H2* loci is the main determinant of frost tolerance in spring barley. Environ Exp Bot. 2014;106:148–55. https://doi.org/10.1016/j.envexpbot.2014.02.014.

29. Yu XQ, Pijut PM, Byrne S, Asp T, Bai GH, Jiang YW. Candidate gene association mapping for winter survival and spring regrowth in perennial ryegrass. Plant Sci. 2015;235:37–45. https://doi.org/10.1016/j.plantsci.2015.03.003.

30. Ali MBM, Welna GC, Sallam A, Martsch R, Balko C, Gebser B, et al. Association analyses to genetically improve drought and freezing tolerance of faba bean (*Vicia faba* L.). Crop Sci. 2016;56(3):1036–48. https://doi.org/10.2135/cropsci2015.08.0503.

31. Sallam A, Arbaoui M, El-Esawi M, Abshire N, Martsch R. Identification and verification of QTL associated with frost tolerance using linkage mapping and GWAS in winter faba bean. Front Plant Sci. 2016;7:1098. https://doi.org/10.3389/fpls.2016.01098.

32. Tumino G, Voorrips RE, Rizza F, Badeck FW, Morcia C, Ghizzoni R, et al. Population structure and genome-wide association analysis for frost tolerance in oat using continuous SNP array signal intensity ratios. Theor Appl Genet. 2016;129(9):1711–24. https://doi.org/10.1007/s00122-016-2734-y.

33. Wurschum T, Longin CFH, Hahn V, Tucker MR, Leiser WL. Copy number variations of CBF genes at the *Fr-A2* locus are essential components of winter hardiness in wheat. Plant J. 2017;89(4):764–73. https://doi.org/10.1111/tpj.13424.

34. Tayeh N, Aubert G, Pilet-Nayel ML, Lejeune-Henaut I, Warkentin TD, Burstin J. Genomic tools in pea breeding programs: status and perspectives. Front Plant Sci. 2015;6:1037. https://doi.org/10.3389/fpls.2015.01037.

35. Desgroux A, L'Anthoene V, Roux-Duparque M, Riviere JP, Aubert G, Tayeh N, et al. Genome-wide association mapping of partial resistance to *Aphanomyces euteiches* in pea. BMC Genomics. 2016;17:124. https://doi.org/10.1186/s12864-016-2429-4.

36. Tayeh N, Aluome C, Falque M, Jacquin F, Klein A, Chauveau A, et al. Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high density, high resolution consensus genetic map. Plant J. 2015;84(6):1257–73. https://doi.org/10.1111/tpj.13070.

37. Desgroux A, Baudais VN, Aubert V, Le Roy G, de Larambergue H, Miteul H, et al. Comparative genome-wide-association mapping identifies common loci controlling root system architecture and resistance to *Aphanomyces euteiches* in pea. Front Plant Sci. 2018;8:2195. https://doi.org/10.3389/fpls.2017.02195.

38. Liu R, Fang L, Yang T, Zhang XY, Hu JG, Zhang HY, et al. Marker-trait association analysis of frost tolerance of 672 worldwide pea (*Pisum sativum* L.) collections. Sci Rep. 2017;7:5919. https://doi.org/10.1038/s41598-017-06222-y.

39. Kreplak J, Madoui M, Cápal P, Novák P, Labadie K, Aubert G, et al. A reference genome for pea provides insight into legume genome evolution. Nat Genet. 2019;51:1411–22. https://doi.org/10.1038/s41588-019-0480-1.

40. Weller JL, Liew LC, Hecht VFG, Rajandran V, Laurie RE, Ridge S, et al. A conserved molecular basis for photoperiod adaptation in two temperate legumes. Proc Nat Acad Sci U S A. 2012;109(51):21158–63. https://doi.org/10.1073/pnas.1207943110.

41. Sun X, Yang T, Hao J, Zhang X, Ford R, Jiang J, et al. SSR genetic linkage map construction of pea (*Pisum sativum* L.) based on Chinese native varieties. Crop J. 2014;2(2):170–4. https://doi.org/10.1016/j.cj.2014.03.004.

42. Hamon C, Baranger A, Coyne CJ, McGee RJ, Le Goff I, L'Anthoëne V, et al. New consistent QTL in pea associated with partial resistance to *Aphanomyces euteiches* in multiple French and American environments. Theor Appl Genet. 2011;123(2):261–81. https://doi.org/10.1007/s00122-011-1582-z.

43. Tayeh N, Bahrman N, Devaux R, Bluteau A, Prosperi J, Delbreil B, et al. 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. Mol Breeding. 2013;32: 279–89. https://doi.org/10.1007/s11032-013-9869-1.

44. Zhu J, Pearce S, Burke A, See DR, Skinner DZ, Dubcovsky J, et al. Copy number and haplotype variation at the *VRN-A1* and central *Fr-A2* loci are associated with frost tolerance in hexaploid wheat. Theor Appl Genet. 2014; 127(5):1183–97. https://doi.org/10.1007/s00122-014-2290-2.

45. Novak A, Boldizsar A, Gierczik K, Vagujfalvi A, Adam E, Kozma-Bognar L, et al. Light and temperature signalling at the level of *CBF14* gene expression in wheat and barley. Plant Mol Biol Rep. 2017;35(4):399–408. https://doi.org/10.1007/s11105-017-1035-1.

46. Eremina M, Unterholzner SJ, Rathnayake AI, Castellanos M, Khan M, Kugler KG, et al. Brassinosteroids participate in the control of basal and acquired freezing tolerance of plants. Proc Natl Acad Sci U S A. 2016;113(40):E5982–91. https://doi.org/10.1073/pnas.1611477113.
transcription in response to low temperature and water deficit. Proc Natl Acad Sci U S A. 1997;94(3):1035–40. https://doi.org/10.1073/pnas.94.3.1035.

11. Gilmour SJ, Zarka DG, Stockinger EJ, Salazar MP, Houghton JM, Thomashow MF. Low temperature regulation of the *Arabidopsis* CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J. 1998;16(4):433–42. https://doi.org/10.1046/j.1365-313x.1998.00310.x.

12. Thomashow M. Molecular basis of plant cold acclimation: insights gained from studying the CBF cold response pathway. Plant Physiol. 2010;154(2): 571–7. https://doi.org/10.1104/pp.110.161794.

13. Alonso-Blanco C, Gomez-Mena C, Llorente F, Koornneef M, Salinas J, Martinez-Zapater J. Genetic and molecular analyses of natural variation indicate *CBF2* as a candidate gene for underlying a freezing tolerance quantitative trait locus in Arabidopsis. Plant Physiol. 2005;139(3):1304–12. https://doi.org/10.1104/pp.105.068510.

14. Toth B, Galiba G, Feher E, Sutka J, Snape JW. Mapping genes affecting flowering time and frost resistance on chromosome 5B of wheat. Theor Appl Genet. 2003;107(3):509–14. https://doi.org/10.1007/s00122-003-1275-3.

15. Vagujfalvi A, Galiba G, Cattivelli L, Dubcovsky J. The cold regulated transcriptional activator *CBF3* is linked to the frost tolerance locus Fr-A2 on wheat chromosome 5A. Mol Gen Genomics. 2003;269(1):60–7. https://doi.org/10.1007/s00438-003-0806-6.

16. Knox AK, Li CX, Vagujfalvi A, Galilba G, Stockinger EJ, Dubcovsky J. Identification of candidate CBF genes for the frost tolerance locus Fr-A(m)2 in *Triticum monococcum*. Plant Mol Biol. 2008;67(3):257–70. https://doi.org/10.1007/s11103-008-9316-6.

17. Pasquariello M, Barabaschi D, Himmelbach A, Steuernagel B, Ariyadasa R, Stein N, et al. The barley frost resistance-H2 locus. Funct Integr Genomics. 2014;14(1):85–100. https://doi.org/10.1007/s10142-014-0360-9.

18. Sandve SR, Kosmalaa, Rudi H, Fjellheim S, Rapacz M, Yamada T, et al. Molecular mechanisms underlying frost tolerance in perennial grasses adapted to cold climates. Plant Sci. 2011;180(1):69–77. https://doi.org/10.1007/s10142-014-0360-9.

19. Tayeh N, Bahrman N, Sellier H, Bluteau A, Blassiau C, Fourment J, et al. A tandem array of *CBF/DREB1* genes is located in a major freezing tolerance QTL region on Medicago truncatula chromosome 6. BMC Genomics. 2013; 14(1):814. https://doi.org/10.1186/1471-2164-14-814.

20. Tondelli A, Francia E, Barabaschi D, Pasquariello M, Pecchioni N. Inside the *CBF* locus in Poaceae. Plant Sci. 2011;180(1):39–45. https://doi.org/10.1016/j.plantsci.2010.08.012.

21. Lejeune-Hénaut I, Hanocq B, Ébthencourt L, Fontaine V, Delbreil B, Morin J, et al. The flowering locus *Hr* colocalizes with a major QTL affecting winter frost tolerance in *Pisum sativum* L. Theor Appl Genet. 2008;116(8):1105–16. https://doi.org/10.1007/s00122-008-0739-x.

22. Dumont E, Fontaine V, Vuylsteker C, Sellier H, Bodele S, Voedts N, et al. 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. 2009;118(8):1561–71. https://doi.org/10.1007/s00122-009-1004-7.

23. Klein A, Houtin H, Rond C, Marget P, Jacquin F, Boucherot K, et al. QTL analysis of frost damage in pea suggests different mechanisms involved in frost tolerance. Theor Appl Genet. 2014;127(6):1319–30. https://doi.org/10.1007/s00122-014-2299-6.

24. Gupta PK, Kulwal PL, Jaiswal V. Association mapping in crop plants: opportunities and challenges. Adv Genet. 2014;85:109–47. https://doi.org/10.1016/b978-0-12-800271-1.00002-0.

25. Li YL, Bock A, Haseneyer G, Korzun V, Wilde P, Schon CC, et al. Association analysis of frost tolerance in rye using candidate genes and phenotypic data from controlled, semi-controlled, and field phenotyping platforms. BMC Plant Biol. 2011;11:146. https://doi.org/10.1186/1471-2229-11-146.

26. Zhao YS, Gowda M, Wurschum T, Longin CFH, Korzun V, Kollers S, et al. Dissecting the genetic architecture of frost tolerance in central European winter wheat. J Exp Bot. 2013;64(14):4453–60. https://doi.org/10.1093/jxb/ert259.

27. Visioni A, Tondelli A, Francia E, Pswarayi A, Malosetti M, Russell J, et al. Genome-wide association mapping of frost tolerance in barley (*Hordeum vulgare* L.). BMC Genomics. 2013;14:424. https://doi.org/10.1186/1471-2164-14-424.

28. Tondelli A, Pagani D, Ghafoori IN, Rahimi M, Ataei R, Rizza F, et al. Allelic variation at *Fr-H1/Vrn-H1* and *Fr-H2* loci is the main determinant of frost tolerance in spring barley. Environ Exp Bot. 2014;106:148–55. https://doi.org/10.1016/j.envexpbot.2014.02.014.

29. Yu XQ, Pijut PM, Byrne S, Asp T, Bai GH, Jiang YW. Candidate gene association mapping for winter survival and spring regrowth in perennial ryegrass. Plant Sci. 2015;235:37–45. https://doi.org/10.1016/j.plantsci.2015.03.003.

30. Ali MBM, Welna GC, Sallam A, Martsch R, Balko C, Gebser B, et al. Association analyses to genetically improve drought and freezing tolerance of faba bean (*Vicia faba* L.). Crop Sci. 2016;56(3):1036–48. https://doi.org/10.2135/cropsci2015.08.0503.

31. Sallam A, Arbaoui M, El-Esawi M, Abshire N, Martsch R. Identification and verification of QTL associated with frost tolerance using linkage mapping and GWAS in winter faba bean. Front Plant Sci. 2016;7:1098. https://doi.org/10.3389/fpls.2016.01098.

32. Tumino G, Voorrips RE, Rizza F, Badeck FW, Morcia C, Ghizzoni R, et al. Population structure and genome-wide association analysis for frost tolerance in oat using continuous SNP array signal intensity ratios. Theor Appl Genet. 2016;129(9):1711–24. https://doi.org/10.1007/s00122-016-2734-y.

33. Wurschum T, Longin CFH, Hahn V, Tucker MR, Leiser WL. Copy number variations of CBF genes at the *Fr-A2* locus are essential components of winter hardiness in wheat. Plant J. 2017;89(4):764–73. https://doi.org/10.1111/tpj.13424.

34. Tayeh N, Aubert G, Pilet-Nayel ML, Lejeune-Henaut I, Warkentin TD, Burstin J. Genomic tools in pea breeding programs: status and perspectives. Front Plant Sci. 2015;6:1037. https://doi.org/10.3389/fpls.2015.01037.

35. Desgroux A, L'Anthoene V, Roux-Duparque M, Riviere JP, Aubert G, Tayeh N, et al. Genome-wide association mapping of partial resistance to *Aphanomyces euteiches* in pea. BMC Genomics. 2016;17:124. https://doi.org/10.1186/s12864-016-2429-4.

36. Tayeh N, Aluome C, Falque M, Jacquin F, Klein A, Chauveau A, et al. Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high density, high resolution consensus genetic map. Plant J. 2015;84(6):1257–73. https://doi.org/10.1111/tpj.13070.

37. Desgroux A, Baudais VN, Aubert V, Le Roy G, de Larambergue H, Miteul H, et al. Comparative genome-wide-association mapping identifies common loci controlling root system architecture and resistance to *Aphanomyces euteiches* in pea. Front Plant Sci. 2018;8:2195. https://doi.org/10.3389/fpls.2017.02195.

38. Liu R, Fang L, Yang T, Zhang XY, Hu JG, Zhang HY, et al. Marker-trait association analysis of frost tolerance of 672 worldwide pea (*Pisum sativum* L.) collections. Sci Rep. 2017;7:5919. https://doi.org/10.1038/s41598-017-06222-y.

39. Kreplak J, Madoui M, Cápal P, Novák P, Labadie K, Aubert G, et al. A reference genome for pea provides insight into legume genome evolution. Nat Genet. 2019;51:1411–22. https://doi.org/10.1038/s41588-019-0480-1.

40. Weller JL, Liew LC, Hecht VFG, Rajandran V, Laurie RE, Ridge S, et al. A conserved molecular basis for photoperiod adaptation in two temperate legumes. Proc Nat Acad Sci U S A. 2012;109(51):21158–63. https://doi.org/10.1073/pnas.1207943110.

41. Sun X, Yang T, Hao J, Zhang X, Ford R, Jiang J, et al. SSR genetic linkage map construction of pea (*Pisum sativum* L.) based on Chinese native varieties. Crop J. 2014;2(2):170–4. https://doi.org/10.1016/j.cj.2014.03.004.

42. Hamon C, Baranger A, Coyne CJ, McGee RJ, Le Goff I, L'Anthoëne V, et al. New consistent QTL in pea associated with partial resistance to *Aphanomyces euteiches* in multiple French and American environments. Theor Appl Genet. 2011;123(2):261–81. https://doi.org/10.1007/s00122-011-1582-z.

43. Tayeh N, Bahrman N, Devaux R, Bluteau A, Prosperi J, Delbreil B, et al. 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. Mol Breeding. 2013;32: 279–89. https://doi.org/10.1007/s11032-013-9869-1.

44. Zhu J, Pearce S, Burke A, See DR, Skinner DZ, Dubcovsky J, et al. Copy number and haplotype variation at the *VRN-A1* and central *Fr-A2* loci are associated with frost tolerance in hexaploid wheat. Theor Appl Genet. 2014; 127(5):1183–97. https://doi.org/10.1007/s00122-014-2290-2.

45. Novak A, Boldizsar A, Gierczik K, Vagujfalvi A, Adam E, Kozma-Bognar L, et al. Light and temperature signalling at the level of *CBF14* gene expression in wheat and barley. Plant Mol Biol Rep. 2017;35(4):399–408. https://doi.org/10.1007/s11105-017-1035-1.

46. Eremina M, Unterholzner SJ, Rathnayake AI, Castellanos M, Khan M, Kugler KG, et al. Brassinosteroids participate in the control of basal and acquired freezing tolerance of plants. Proc Natl Acad Sci U S A. 2016;113(40):E5982–91. https://doi.org/10.1073/pnas.1611477113.
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71. Jombart T, Ahmed I. Adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. 2011;27(21):3070–1. https://doi.org/10.1093/ bioinformatics/btr521.

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73. Nei M. Genetic distance between populations. Am Nat. 1972;106(949):283–92 https://www.jstor.org/stable/2459777.

74. Pembleton LW, Cogan NOI, Forster JW. STAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations. Mol Ecol Resour. 2013;13(5):946–52 https://cran.r-project.org/ web/packages/StAMPP/index.html. Accessed 05 Dec 2019.

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76. Courtois B, Audebert A, Dardou A, Roques S, Ghneim-Herrera T, Droc G, et al. Genome-wide association mapping of root traits in a japonica rice panel. PLoS One. 2013;8(11):e78037. https://doi.org/10.1371/journal.pone. 0078037.

77. Turner S. qqman: Q-Q and manhattan plots for GWAS data. R package version 0.1.4. 2017. https://CRAN.R-project.org/package=qqman. Accessed 20 Aug 2018.

78. de Mendiburu F. agricolae: Statistical procedures for agricultural research. R package version 1.2.8. 2017. https://cran.r-project.org/web/packages/ agricolae/index.html. Accessed 07 Jun 2018.

79. Yenne SP, Thill DC, Letourneau DJ, Auld DL, Haderlie LC. Techniques for selection of glyphosate-tolerant field pea, *Pisum Sativum*, Cultivars. Weed Technol. 1988;2(3):286–90. https://doi.org/10.1017/s0890037x00030608.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Ready to submit your research? Choose BMC and benefit from:

• fast, convenient online submission

• thorough peer review by experienced researchers in your field

• rapid publication on acceptance

• support for research data, including large and complex data types

• gold Open Access which fosters wider collaboration and increased citations

• maximum visibility for your research: over 100M website views per year

At BMC, research is always in progress.

Learn more biomedcentral.com/submissions

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