Skip to main content

Genome-wide association mapping of preharvest sprouting resistance in a diversity panel of European winter wheats

Journal of Applied Genetics volume 56, pages 277–285 (2015)Cite this article

Abstract

Global wheat production will benefit from cultivars showing genetic resistance to preharvest sprouting (PHS). Working on PHS resistance is still challenging due to the lack of simple protocols for the provocation of symptoms for appropriate trait differentiation under highly variable environmental conditions. Therefore, the availability of molecular markers for enhancing PHS resistance in breeding lines is of utmost importance. Genome-wide association mapping was performed to unravel the genetics of PHS resistance in a diversity panel of 124 winter wheat genotypes using both random and targeted marker locus approaches. Data for grain germination tests, spike wetting treatments, and field sprouting damage measurements of grains were collected in 11, 12, and four environments, respectively. Twenty-two quantitative trait loci (QTL) linked with 40 markers were detected for the three traits commonly used for assessing the PHS resistance of cultivars. All but five QTL on chromosomes 1B, 1D (two QTL), 3D, and 5D showed locations similar to previous studies, including prominent QTL on chromosomes 2BS, 3AS, and 4AL. The highest retrieval rate across environments was found for QTL on chromosomes 1D, 2BS, 3D, 4AL, and 7B. The study identified genomic signatures useful for marker-assisted improvement of PHS resistance not only in European breeding programs, but of global significance.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2

References

  • Akbari M, Wenzl P, Caig V, Carling J, Xia L, Yang S, Uszynski G, Mohler V, Lehmensiek A, Kuchel H, Hayden MJ, Howes N, Sharp P, Vaughan P, Rathmell B, Huttner E, Kilian A (2006) Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet 113:1409–1420

    Article  CAS  PubMed  Google Scholar 

  • Albrecht T, Wimmer V, Auinger HJ, Erbe M, Knaak C, Ouzunova M, Simianer H, Schön CC (2011) Genome-based prediction of testcross values in maize. Theor Appl Genet 123:339–350

    Article  PubMed  Google Scholar 

  • Anonymous (2010) Besondere Ernte- und Qualitätsermittlung 2010. German Federal Ministry of Food and Agriculture (BMELV). Available online at: http://www.bmelv-statistik.de/de/fachstatistiken/besondere-ernteermittlung/

  • Aulchenko YS, Ripke S, Isaacs A, van Duijn CM (2007) GenABEL: an R library for genome-wide association analysis. Bioinformatics 23:1294–1296

    Article  CAS  PubMed  Google Scholar 

  • Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B 57:289–300

    Google Scholar 

  • Bu Q, Li H, Zhao Q, Jiang H, Zhai Q, Zhang J, Wu X, Sun J, Xie Q, Wang D, Li C (2009) The Arabidopsis RING finger E3 ligase RHA2a is a novel positive regulator of abscisic acid signaling during seed germination and early seedling development. Plant Physiol 150:463–481

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  • Cabral AL, Jordan MC, McCartney CA, You FM, Humphreys DG, MacLachlan R, Pozniak CJ (2014) Identification of candidate genes, regions and markers for pre-harvest sprouting resistance in wheat (Triticum aestivum L.). BMC Plant Biol 14:340

    PubMed Central  Article  PubMed  Google Scholar 

  • Chang C, Feng JM, Si HQ, Yin B, Zhang HP, Ma CX (2010) Validating a novel allele of viviparous-1 (Vp-1Bf) associated with high seed dormancy of Chinese wheat landrace, Wanxianbaimaizi. Mol Breed 25:517–525

    Article  CAS  Google Scholar 

  • Chang C, Zhang HP, Zhao QX, Feng JM, Si HQ, Lu J, Ma CX (2011) Rich allelic variations of Viviparous-1A and their associations with seed dormancy/pre-harvest sprouting of common wheat. Euphytica 179:343–353

    Article  CAS  Google Scholar 

  • Chen CX, Cai SB, Bai GH (2008) A major QTL controlling seed dormancy and pre-harvest sprouting resistance on chromosome 4A in a Chinese wheat landrace. Mol Breed 21:351–358

    Article  CAS  Google Scholar 

  • Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genet Resour 4:359–361

    Article  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Flintham J, Adlam R, Bassoi M, Holdsworth M, Gale M (2002) Mapping genes for resistance to sprouting damage in wheat. Euphytica 126:39–45

    Article  CAS  Google Scholar 

  • Fulton TM, Beck-Bunn T, Emmatty D, Eshed Y, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley SD (1997) QTL analysis of an advanced backcross of Lycopersicon peruvianum to the cultivated tomato and comparisons with QTLs found in other wild species. Theor Appl Genet 95:881–894

    Article  CAS  Google Scholar 

  • Graybosch RA, Amand P, Bai G (2013) Evaluation of genetic markers for prediction of preharvest sprouting tolerance in hard white winter wheats. Plant Breed 132:359–366

    Article  CAS  Google Scholar 

  • Himi E, Maekawa M, Miura H, Noda K (2011) Development of PCR markers for Tamyb10 related to R-1, red grain color gene in wheat. Theor Appl Genet 122:1561–1576

    Article  CAS  PubMed  Google Scholar 

  • Huang BE, George AW, Forrest KL, Kilian A, Hayden MJ, Morell MK, Cavanagh CR (2012) A multiparent advanced generation inter-cross population for genetic analysis in wheat. Plant Biotechnol J 10:826–839

    Article  CAS  PubMed  Google Scholar 

  • Jaiswal V, Mir RR, Mohan A, Balyan HS, Gupta PK (2012) Association mapping for pre-harvest sprouting tolerance in common wheat (Triticum aestivum L.). Euphytica 188:89–102

    Article  CAS  Google Scholar 

  • Kato K, Nakamura W, Tabiki T, Miura H, Sawada S (2001) Detection of loci controlling seed dormancy on group 4 chromosomes of wheat and comparative mapping with rice and barley genomes. Theor Appl Genet 102:980–985

    Article  CAS  Google Scholar 

  • Knox RE, Clarke FR, Clarke JM, Fox SL, DePauw RM, Singh AK (2012) Enhancing the identification of genetic loci and transgressive segregants for preharvest sprouting resistance in a durum wheat population. Euphytica 186:193–206

    Article  CAS  Google Scholar 

  • Kottearachchi NS, Uchino N, Kato K, Miura H (2006) Increased grain dormancy in white-grained wheat by introgression of preharvest sprouting tolerance QTLs. Euphytica 152:421–428

    Article  CAS  Google Scholar 

  • Kulwal P, Ishikawa G, Benscher D, Feng Z, Yu LX, Jadhav A, Mehetre S, Sorrells ME (2012) Association mapping for pre-harvest sprouting resistance in white winter wheat. Theor Appl Genet 125:793–805

    Article  CAS  PubMed  Google Scholar 

  • Liu S, Bai G (2010) Dissection and fine mapping of a major QTL for preharvest sprouting resistance in white wheat Rio Blanco. Theor Appl Genet 121:1395–1404

    Article  PubMed  Google Scholar 

  • Liu S, Cai S, Graybosch R, Chen C, Bai G (2008) Quantitative trait loci for resistance to pre-harvest sprouting in US hard white winter wheat Rio Blanco. Theor Appl Genet 117:691–699

    Article  CAS  PubMed  Google Scholar 

  • Liu SB, Sehgal SK, Li JR, Lin M, Trick HN, Yu JM, Gill BS, Bai GH (2013) Cloning and characterization of a critical regulator for preharvest sprouting in wheat. Genetics 195:263–273

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  • Lohwasser U, Röder MS, Börner A (2005) QTL mapping of the domestication traits pre-harvest sprouting and dormancy in wheat (Triticum aestivum L.). Euphytica 143:247–249

    Article  CAS  Google Scholar 

  • Maccaferri M, Zhang J, Bulli P, Abate Z, Chao S, Cantu D, Bossolini E, Chen X, Pumphrey M, Dubcovsky J (2015) A genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a worldwide collection of hexaploid spring wheat (Triticum aestivum L.). G3 (Bethesda) 5:449–465

    Article  Google Scholar 

  • Mares DJ (1983) Preservation of dormancy in freshly harvested wheat grain. Aust J Agric Res 34:33–38

    Article  Google Scholar 

  • Mares DJ (1987) Preharvest sprouting in white grained wheats. In: Mares DJ (ed) Fourth international symposium on preharvest sprouting in cereals. Westview Press, Boulder, CO, pp 64–74

    Google Scholar 

  • Mares DJ, Mrva K (2001) Mapping quantitative trait loci associated with variation in grain dormancy in Australian wheat. Aust J Agric Res 52:1257–1265

    Article  CAS  Google Scholar 

  • Mares DJ, Mrva K (2014) Wheat grain preharvest sprouting and late maturity alpha-amylase. Planta 240:1167–1178

    Article  CAS  PubMed  Google Scholar 

  • Mares DJ, Mrva K, Cheong J, Williams K, Watson B, Storlie E, Sutherland M, Zou Y (2005) A QTL located on chromosome 4A associated with dormancy in white- and red-grained wheats of diverse origin. Theor Appl Genet 111:1357–1364

    Article  CAS  PubMed  Google Scholar 

  • McCarty DR, Hattori T, Carson CB, Vasil V, Lazar M, Vasil IK (1991) The Viviparous-1 developmental gene of maize encodes a novel transcriptional activator. Cell 66:895–905

    Article  CAS  PubMed  Google Scholar 

  • Mohler V, Schmolke M, Paladey E, Seling S, Hartl L (2012) Association analysis of Puroindoline-D1 and Puroindoline b-2 loci with 13 quality traits in European winter wheat (Triticum aestivum L.). J Cereal Sci 56:623–628

    Article  CAS  Google Scholar 

  • Moncada P, Martínez CP, Borrero J, Chatel M, Gauch H Jr, Guimaraes E, Tohme J, McCouch SR (2001) Quantitative trait loci for yield and yield components in an Oryza sativa × Oryza rufipogon BC2F2 population evaluated in an upland environment. Theor Appl Genet 102:41–52

    Article  CAS  Google Scholar 

  • Mori M, Uchino N, Chono M, Kato K, Miura H (2005) Mapping QTLs for grain dormancy on wheat chromosome 3A and the group 4 chromosomes, and their combined effect. Theor Appl Genet 110:1315–1323

    Article  CAS  PubMed  Google Scholar 

  • Munkvold JD, Tanaka J, Benscher D, Sorrells ME (2009) Mapping quantitative trait loci for preharvest sprouting resistance in white wheat. Theor Appl Genet 119:1223–1235

    Article  CAS  PubMed  Google Scholar 

  • Nakamura S, Abe F, Kawahigashi H, Nakazono K, Tagiri A, Matsumoto T, Utsugi S, Ogawa T, Handa H, Ishida H, Mori M, Kawaura K, Ogihara Y, Miura H (2011) A wheat homolog of MOTHER OF FT AND TFL1 acts in the regulation of germination. Plant Cell 23:3215–3229

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  • Oberforster M, Ratzenböck A, Werteker M, Neumayer A, Zechner E, Hartl L (2012) Variabilität und Beziehungen von Samendormanz, Auswuchs und Fallzahl in einem Sortiment europäischer Winterweizen. 62. Tagung der Vereinigung der Pflanzenzüchter und Saatgutkaufleute Österreichs 22.–23. November 2011. LFZ Raumberg-Gumpenstein, pp 61–68

  • Ogbonnaya FC, Imtiaz M, Ye G, Hearnden PR, Hernandez E, Eastwood RF, Van Ginkel M, Shorter SC, Winchester JM (2008) Genetic and QTL analyses of seed dormancy and preharvest sprouting resistance in the wheat germplasm CN10955. Theor Appl Genet 116:891–902

    Article  CAS  PubMed  Google Scholar 

  • Osa M, Kato K, Mori M, Shindo C, Torada A, Miura H (2003) Mapping QTLs for seed dormancy and the Vp1 homologue on chromosome 3A in wheat. Theor Appl Genet 106:1491–1496

    CAS  PubMed  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed Central  CAS  PubMed  Google Scholar 

  • R Core Team (2014) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Home page at: http://www.R-project.org/

  • Rasul G, Humphreys DG, Brûlé-Babel A, McCartney CA, Knox RE, DePauw RM, Somers DJ (2009) Mapping QTLs for pre-harvest sprouting traits in the spring wheat cross ‘RL4452/AC Domain’. Euphytica 168:363–378

    Article  CAS  Google Scholar 

  • Rehman Arif MA, Neumann K, Nagel M, Kobiljski B, Lohwasser U, Börner A (2012) An association mapping analysis of dormancy and pre-harvest sprouting in wheat. Euphytica 188:409–417

    Article  CAS  Google Scholar 

  • Singh R, Matus-Cádiz M, Båga M, Hucl P, Chibbar RN (2010) Identification of genomic regions associated with seed dormancy in white-grained wheat. Euphytica 174:391–408

    Article  CAS  Google Scholar 

  • Somyong S, Munkvold JD, Tanaka J, Benscher D, Sorrells ME (2011) Comparative genetic analysis of a wheat seed dormancy QTL with rice and Brachypodium identifies candidate genes for ABA perception and calcium signaling. Funct Integr Genomics 11:479–490

    Article  CAS  PubMed  Google Scholar 

  • Somyong S, Ishikawa G, Munkvold JD, Tanaka J, Benscher D, Cho YG, Sorrells ME (2014) Fine mapping of a preharvest sprouting QTL interval on chromosome 2B in white wheat. Theor Appl Genet 127:1843–1855

    Article  PubMed  Google Scholar 

  • Sun YW, Jones HD, Yang Y, Dreisigacker S, Li SM, Chen XM, Shewry PR, Xia LQ (2012) Haplotype analysis of Viviparous-1 gene in CIMMYT elite bread wheat germplasm. Euphytica 186:25–43

    Article  CAS  Google Scholar 

  • Tan MK, Sharp PJ, Lu MQ, Howes N (2006) Genetics of grain dormancy in a white wheat. Aust J Agric Res 57:1157–1165

    Article  CAS  Google Scholar 

  • Torada A, Ikeguchi S, Koike M (2005) Mapping and validation of PCR-based markers associated with a major QTL for seed dormancy in wheat. Euphytica 143:251–255

    Article  CAS  Google Scholar 

  • Torada A, Koike M, Ikeguchi S, Tsutsui I (2008) Mapping of a major locus controlling seed dormancy using backcrossed progenies in wheat (Triticum aestivum L.). Genome 51:426–432

    Article  CAS  PubMed  Google Scholar 

  • Walker-Simmons M (1987) ABA levels and sensitivity in developing wheat embryos of sprouting resistant and susceptible cultivars. Plant Physiol 84:61–66

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  • Xiao SH, Zhang HP, You GX, Zhang XY, Yan CS, Chen X (2012) Integration of marker-assisted selection for resistance to pre-harvest sprouting with selection for grain-filling rate in breeding of white-kernelled wheat for the Chinese environment. Euphytica 188:85–88

    Article  Google Scholar 

  • Yang Y, Zhao XL, Xia LQ, Chen XM, Xia XC, Yu Z, He ZH, Röder M (2007) Development and validation of a Viviparous-1 STS marker for pre-harvest sprouting tolerance in Chinese wheats. Theor Appl Genet 115:971–980

    Article  CAS  PubMed  Google Scholar 

  • Zhang HP, Feng JM, Yin B, Chang C, Si HQ, Ma CX (2009) Detection and validation of molecular marker associated with pre-harvest sprouting resistance in Chinese wheat. Mol Plant Breed 7:45–50

    Google Scholar 

  • Zhang Y, Miao X, Xia X, He Z (2014) Cloning of seed dormancy genes (TaSdr) associated with tolerance to pre-harvest sprouting in common wheat and development of a functional marker. Theor Appl Genet 127:855–866

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

Excellent technical assistance from Petra Greim and Josef Schuhbauer from LfL and Manuela Dinterer and Thomas Miksch from AGES is highly appreciated. We also thank all people at LfL, AGES, and breeding companies who assisted in fulfilling the research aims. The international ERANET-CORNET research project named “Efficient phenotypic and molecular selection methods for enhancing preharvest sprouting tolerance of European wheat germplasm”—Robust Wheat (CORNET 825860) was funded by the FFG (Austrian Research Promotion Agency), the Austrian Seed Association, and the Börse für landwirtschaftliche Produkte in Wien. German Funding: “Das IGF-Vorhaben 39 EN/1 der Forschungsvereinigung Gemeinschaft zur Förderung der privaten deutschen Pflanzenzüchtung e.V.—GFP, Kaufmannstraße 71, 53115 Bonn wurde über die AiF im Rahmen des Programms zur Förderung der Industriellen Gemeinschaftsforschung und -entwicklung (IGF) vom Bundesministerium für Wirtschaft und Technologie aufgrund eines Beschlusses des Deutschen Bundestages gefördert”.

Conflict of interest

The authors declare that they have no conflict of interest.

Compliance with ethical standards

All experiments included in this study comply with the current laws of the country in which they were performed.

Author information

Affiliations

  1. Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture (LfL), Am Gereuth 8, 85354, Freising, Germany

    Theresa Albrecht, Lorenz Hartl & Volker Mohler

  2. Austrian Agency for Health and Food Safety (AGES), Spargelfeldstraße 191, 1220, Vienna, Austria

    Michael Oberforster

  3. Secobra Saatzucht GmbH, Feldkirchen 3, 85368, Moosburg, Germany

    Hubert Kempf

  4. Saatzucht Josef Breun GmbH & Co. KG, Amselweg 1, 91074, Herzogenaurach, Germany

    Ludwig Ramgraber

  5. Limagrain GmbH, Salder Straße 4, 31226, Peine-Rosenthal, Germany

    Johannes Schacht

  6. Lantmännen SW Seed Hadmersleben GmbH, Kroppenstedter Straße 4, 39398, Hadmersleben, Germany

    Ebrahim Kazman

  7. Saatzucht LFS Edelhof, Edelhof 1, 3910, Zwettl, Austria

    Elisabeth Zechner

  8. Saatzucht Donau GesmbH & CoKG, Reichersberg 86, 4981, Reichersberg am Inn, Austria

    Anton Neumayer

Authors
  1. Theresa Albrecht
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Michael Oberforster
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hubert Kempf
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ludwig Ramgraber
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Johannes Schacht
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ebrahim Kazman
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Elisabeth Zechner
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Anton Neumayer
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Lorenz Hartl
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Volker Mohler
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Volker Mohler.

Additional information

Communicated by: Andrzej Górny

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(PDF 985 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Albrecht, T., Oberforster, M., Kempf, H. et al. Genome-wide association mapping of preharvest sprouting resistance in a diversity panel of European winter wheats. J Appl Genetics 56, 277–285 (2015). https://doi.org/10.1007/s13353-015-0286-5

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13353-015-0286-5

Keywords

  • Ear sprouting
  • Seed dormancy
  • Quantitative trait loci (QTL)
  • Genome-wide association study (GWAS)