Advertisement

Theoretical and Applied Genetics

, Volume 129, Issue 6, pp 1087–1097 | Cite as

Copy number variation of CBF-A14 at the Fr-A2 locus determines frost tolerance in winter durum wheat

  • Alisa-Naomi Sieber
  • C. Friedrich H. Longin
  • Willmar L. Leiser
  • Tobias WürschumEmail author
Original Article

Abstract

Key message

Frost tolerance in durum wheat is mainly controlled by copy number variation of CBF - A14 at the Fr - A2 locus.

Abstract

Frost tolerance is a key trait for successful breeding of winter durum wheat (Triticum durum) which can increase the yield performance in regions favoring autumn-sown winter cereals. The aim of this study was to investigate the genetic architecture of frost tolerance in order to provide molecular support for the breeding of winter durum wheat. To this end, a diverse panel of 170 winter and 14 spring durum wheat genotypes of worldwide origin was evaluated for frost tolerance in the field, as well as in a semi-controlled test. A total of 30,611 polymorphic genome-wide markers obtained by a genotyping-by-sequencing approach and markers for candidate loci were used to assess marker-trait associations. One major QTL was detected on chromosome 5A, likely corresponding to Frost Resistance-A2 (Fr-A2). Further analyses strongly support the conclusion that copy number variation of CBF-A14 at the Fr-A2 locus is the causal polymorphism underlying this major QTL. It explains 91.6 % of the genotypic variance and a haploblock of two strongly associated markers in the QTL region also allowed to capture the variance of this QTL. In addition to this major QTL, a much smaller contribution of 4.2 % was observed for Fr-B2. We further investigated this major QTL and found that the copy number of CBF-A14 and the frequency of the frost tolerant haplotype mirrored the climatic conditions in the genotypes’ country of origin, suggesting selection through breeding. Two functional KASP markers were developed which facilitate a high-throughput screening of the haploblock and thus a marker-based breeding of frost tolerance in winter durum wheat.

Keywords

Copy Number Variation Durum Wheat Single Nucleotide Polymorphism Marker Frost Tolerance Spring Type 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

This research was funded by the Deutsche Forschungsgemeinschaft (Grant ID: LO 1816/2-1). For conductance of field trials, we thank Dr. Julia Lafferty from Saatzucht Donau GesmbH & CoKG, Otto Kram from KWS LOCHOW GMBH, and Helmut Bimek from the University of Hohenheim. Furthermore we thank Angela Harmsen and Barbara Renz for excellent technical assistance in the laboratory and Bernd Habeck, Sabit Recaj, Bianca Yildirim, Verena Till, Sabine Frey-Tippelt, Ortwin Schildmann, Marcel Mosdorf, and Martina Schnieder for outstanding work in the field. Many thanks to Anna Tyler from Jackson Laboratory for the helpful advices in running cape.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standard

The authors declare that the experiments comply with the current laws of Germany.

Supplementary material

122_2016_2685_MOESM1_ESM.pdf (291 kb)
Supplementary material 1 (PDF 291 kb)

References

  1. Akar T, Mert Z, Yazar S, Sanal T, Avci M (2009) Sustainable use of winter durum wheat landraces under Mediterranean conditions. Afr J Biotechnol 8:4108–4116Google Scholar
  2. Aulchenko YS, Ripke S, Isaacs A, van Duijn CM (2007) GenABEL: an R library for genome-wide association analysis. Bioinformatics 23:1294–1296. doi: 10.1093/bioinformatics/btm108 CrossRefPubMedGoogle Scholar
  3. Beales J, Turner A, Griffiths S, Snape JW, Laurie DA (2007) A pseudo-response regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.). Theor Appl Genet 115:721–733. doi: 10.1007/s00122-007-0603-4 CrossRefPubMedGoogle Scholar
  4. Chen Y, Carver BF, Wang S, Zhang F, Yan L (2009) Genetic loci associated with stem elongation and winter dormancy release in wheat. Theor Appl Genet 118:881–889. doi: 10.1007/s00122-008-0946-5 CrossRefPubMedGoogle Scholar
  5. Chu C, Tan CT, Yu G, Zhong S, Xu SS, Yan L (2011) A novel retrotransposon inserted in the dominant Vrn-B1 allele confers spring growth habit in tetraploid wheat (Triticum turgidum L.). G3 (Bethesda) 1:637–645. doi:  10.1534/g3.111.001131
  6. Cochran WG, Cox GM (1957) Experimental designs. Wiley, New YorkGoogle Scholar
  7. Dhillon T, Pearce SP, Stockinger EJ, Distelfeld A, Li C, Knox AK, Vashegyi I, Vágújfalvi A, Galiba G, Dubcovsky J (2010) Regulation of freezing tolerance and flowering intemperate cereals: the VRN-1 connection. Plant Physiol 153:1846–1858. doi: 10.1104/pp.110.159079 CrossRefPubMedPubMedCentralGoogle Scholar
  8. Díaz A, Zikhali M, Turner AS, Isaac P, Laurie DA (2012) Copy number variation affecting the Photoperiod-B1 and Vernalization-A1 genes is associated with altered flowering time in wheat (Triticum aestivum). PLoS One 7:e33234. doi: 10.1371/journal.pone.0033234 CrossRefPubMedPubMedCentralGoogle Scholar
  9. Gilmour AR, Gogel BJ, Cullis BR, Thompson R (2009) ASReml user guide release 3.0. International Ltd, Hemel HempsteadGoogle Scholar
  10. Hoeser K (1954) Testing winter wheat for winter kill [Über die Prüfung von Winterweizen auf Winterfestigkeit in Auswinterungskästen]. Züchter 24:353–357Google Scholar
  11. Kling CI, Utz HF, Münzing K (2006) Autumn sowing of durum wheat-effects on quality and yield [Herbstanbau von Durumweizen–Auswirkungen auf Qualität und Ertrag]. Getreidetechnologie 60:141–147Google Scholar
  12. Knox AK, Li C, Vágújfalvi A, Galiba G, Stockinger EJ, Dubcovsky J (2008) Identification of candidate CBF genes for the frost tolerance locus Fr-Am 2 in Triticum monococcum. Plant Mol Biol 67:257–270. doi: 10.1007/s11103-008-9316-6 CrossRefPubMedGoogle Scholar
  13. Knox AK, Dhillon T, Cheng H, Tondelli A, Pecchioni N, Stockinger EJ (2010) CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals. Theor Appl Genet 121:21–35. doi: 10.1007/s00122-010-1288-7 CrossRefPubMedGoogle Scholar
  14. Lafferty J (2010) Durum-between yield and quality? In: Gesellschaft für Pflanzenzüchtung e.V. (ed), Tagung der Vereinigung der Pflanzenzüchter und Saatgutkaufleute Österreichs. Lehr- und Forschungszentrum für Landwirtschaft, Gumpenstein, pp 41–44Google Scholar
  15. Langer SM, Longin Friedrich CFH, Würschum T (2014) Flowering time control in European winter wheat. Front Plant Sci 5:537. doi: 10.3389/fpls.2014.00537 CrossRefPubMedPubMedCentralGoogle Scholar
  16. Liu W, Maurer HP, Li G, Tucker MR, Gowda M, Weissmann EA, Hahn V, Würschum T (2014) Genetic architecture of winter hardiness and frost tolerance in triticale. PLoS One 9(6):e99848. doi: 10.1371/journal.pone.0099848 CrossRefPubMedPubMedCentralGoogle Scholar
  17. Longin CFH, Sieber A-N, 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
  18. Miller A, Galiba G, Dubcovsky J (2006) A cluster of 11 CBF transcription factors is located at the frost tolerance locus Fr-Am 2 in Triticum monococcum. Mol Gen Genomics 275:193–203. doi: 10.1007/s00438-005-0076-6 CrossRefGoogle Scholar
  19. Palamarchuk A (2005) Selection strategies for traits relevant for winter and facultative durum wheat. In: Royo C, Nachit M, Di Fonzo N, Araus J (eds) Durum wheat breeding: Current approaches and future strategies, vol 2. The Haworth Press Inc, New York, pp 599–644Google Scholar
  20. Pearce S, Zhu J, Boldizsár Á, Vágújfalvi A, Burke A, Garland-Campbell K, Galiba G, Dubcovsky J (2013) Large deletions in the CBF gene cluster at the Fr-B2 locus are associated with reduced frost tolerance in wheat. Theor Appl Genet 126:2683–2697. doi: 10.1007/s00122-013-2165-y CrossRefPubMedPubMedCentralGoogle Scholar
  21. Piepho HP, Möhring J (2007) Computing heritability and selection response from unbalanced plant breeding trials. Genetics 77:1881–1888. doi: 10.1534/genetics.107.074229 CrossRefGoogle Scholar
  22. R Core Team (2013) R a language and environment for statistical computing. R foundation for statistical computing, ViennaGoogle Scholar
  23. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews T Daniel, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, Gonzalez JR, Gratacos M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME (2006) Global variation in copy number in the human genome. Nature 444:444–454. doi: 10.1038/nature05329 CrossRefPubMedPubMedCentralGoogle Scholar
  24. Sieber A-N, Würschum T, Longin CFH (2014) Evaluation of a semi-controlled test as a selection tool for frost tolerance in durum wheat (Triticum durum). Plant Breed 133:465–469. doi: 10.1111/pbr.12181 CrossRefGoogle Scholar
  25. Sieber A-N, Longin CFH, Würschum T (2015) Molecular characterization of winter durum wheat (Triticum durum) based on a genotyping-by-sequencing approach. Plant Genetic Resour. doi: 10.1017/S1479262115000349 Google Scholar
  26. Stram DO, Lee JW (1994) Variance components testing in the longitudinal mixed effects model. Biometrics 50:1171–1177. doi: 10.2307/2533455 CrossRefPubMedGoogle Scholar
  27. Sutka J, Snape JW (1989) Location of a gene for frost resistance on chromosome 5A of wheat. Euphytica 42:41–44CrossRefGoogle Scholar
  28. Szucs P, Veisz O, Vida G, Bedo Z (2003) Winter hardiness of durum wheat in Hungary. Acta Agronomica Hung 51:389–396. doi: 10.1556/AAgr.51.2003.4.3 CrossRefGoogle Scholar
  29. Tóth B, Galiba G, Fehér E, Sutka J, Snape JW (2003) Mapping genes affecting flowering time and frost resistance on chromosome 5B of wheat. Theor Appl Genet 107:509–514. doi: 10.1007/s00122-003-1275-3 CrossRefPubMedGoogle Scholar
  30. Trevaskis B, Bagnall DJ, Ellis MH, Peacock WJ, Dennis ES (2003) MADS box genes control vernalization-induced flowering in cereals. PNAS 100:13099–13104. doi: 10.1073/pnas.1635053100 CrossRefPubMedPubMedCentralGoogle Scholar
  31. Utz HF, Melchinger AE, Schön CC (2000) Bias and sampling error of the estimated proportion of genotypic variance explained by quantitative trait loci determined from experimental data in maize using cross validation and validation with independent samples. Genetics 154:1839–1849PubMedPubMedCentralGoogle Scholar
  32. Vágújfalvi A, Galiba G, Cattivelli L, Dubcovsky J (2003) The cold-regulated transcriptional activator Cbf3 is linked to the frost-tolerance locus Fr-A2 on wheat chromosome 5A. Mol Gen Genomics 269(1):60–67. doi: 10.1007/s00438-003-0806-6 Google Scholar
  33. Vágújfalvi A, Aprile A, Miller A, Dubcovsky J, Delugu G, Galiba G, Cattivelli L (2005) The expression of several Cbf genes at the Fr-A2 locus is linked to frost resistance in wheat. Mol Gen Genomics 274(5):506–514. doi: 10.1007/s00438-005-0047-y CrossRefGoogle Scholar
  34. Würschum T, Kraft T (2014) Cross-validation in association mapping and its relevance for the estimation of QTL parameters of complex traits. Heredity 112(4):463–468. doi: 10.1038/hdy.2013.126 CrossRefPubMedPubMedCentralGoogle Scholar
  35. Würschum T, Boeven PH, Langer SM, Longin CFH, Leiser WL (2015a) Multiply to conquer: copy number variations at Ppd-B1 and Vrn-A1 facilitate global adaptation in wheat. BMC Genet 16:96. doi: 10.1186/s12863-015-0258-0 CrossRefPubMedPubMedCentralGoogle Scholar
  36. Würschum T, Langer SM, Longin CFH (2015b) Genetic control of plant height in European winter wheat cultivars. Theor Appl Genet 128:865–874. doi: 10.1007/s00122-015-2476-2 CrossRefPubMedGoogle Scholar
  37. Yan L, Helguera M, Kato K, Fukuyama S, Sherman J, Dubcovsky J (2004) Allelic variation at the VRN-1 promoter region in polyploid wheat. Theor Appl Genet 109:1677–1686. doi: 10.1007/s00122-004-1796-4 CrossRefPubMedGoogle Scholar
  38. Yan L, Fu D, Li C, Blechl A, Tranquilli G, Bonafede M, Sanchez A, Valarik M, Yasuda S, Dubcovsky J (2006) The wheat and barley vernalization gene VRN3 is an orthologue of FT. PNAS 103:19581–19586. doi: 10.1073/pnas.0607142103 CrossRefPubMedPubMedCentralGoogle Scholar
  39. Yu J, Pressoir G, Briggs WH, Vroh Bi I, 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. Nature Genet 38:203–208. doi: 10.1038/ng1702 CrossRefPubMedGoogle Scholar
  40. Zhang XK, Xiao YG, Zhang Y, Xia XC, Dubcovsky J, He ZH (2008) Allelic variation at the vernalization genes, and in Chinese wheat cultivars and their association with growth habit. Crop Sci 48(2):458. doi: 10.2135/cropsci2007.06.0355 CrossRefGoogle Scholar
  41. Zhao Y, Gowda M, Würschum T, Longin C, Friedrich H, Korzun V, Kollers S, Schachschneider R, Zeng J, Fernando R, Dubcovsky J, Reif JC (2013) Dissecting the genetic architecture of frost tolerance in Central European winter wheat. J Exp Bot 64:4453–4460. doi: 10.1093/jxb/ert259 CrossRefPubMedPubMedCentralGoogle Scholar
  42. Zhu J, Pearce S, Burke A, See DR, Skinner DZ, Dubcovsky J, Garland-Campbell K (2014) 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 127:1183–1197. doi: 10.1007/s00122-014-2290-2 CrossRefPubMedGoogle Scholar
  43. Żmieńko A, Samelak A, Kozłowski P, Figlerowicz M (2014) Copy number polymorphism in plant genomes. Theor Appl Genet 127:1–18. doi: 10.1007/s00122-013-2177-7 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Alisa-Naomi Sieber
    • 1
  • C. Friedrich H. Longin
    • 1
  • Willmar L. Leiser
    • 1
  • Tobias Würschum
    • 1
    Email author
  1. 1.State Plant Breeding InstituteUniversity of HohenheimStuttgartGermany

Personalised recommendations