Skip to main content
SpringerLink
Log in

QTLs for uniform grain dimensions and germination selected during wheat domestication are co-located on chromosome 4B

  • Original Article
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Key message

A major locus on the long arm of wheat chromosome 4B controls within-spikelet variation in both grain size and seed dormancy, the latter an important survival mechanism likely eliminated from wild wheat during domestication.

Abstract

Seed dormancy can increase the probability of survival of at least some progeny under unstable environmental conditions. In wild emmer wheat, only one of the two grains in a spikelet germinates during the first rainy season following maturation; and this within-plant variation in seed dormancy is associated with both grain dimension differences and position within the spikelet. Here, in addition to characterizing these associations, we elucidate the genetic mechanism controlling differential grain dimensions and dormancy within wild tetraploid wheat spikelets using phenotypic data from a wild emmer × durum wheat population and a high-density genetic map. We show that in wild emmer, the lower grain within the spikelet is about 30 % smaller and more dormant than the larger, upper grain that germinates usually within 3 days. We identify a major locus on the long arm of chromosome 4B that explains >40 % of the observed variation in grain dimensions and seed dormancy within spikelets. This locus, designated QGD-4BL, is validated using an independent set of wild emmer × durum wheat genetic stocks. The domesticated variant of this novel locus on chromosome 4B, likely fixed during the process of wheat domestication, favors spikelets with seeds of uniform size and synchronous germination. The identification of locus QGD-4BL enhances our knowledge of the genetic basis of the domestication syndrome of one of our most important crops.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Abbo S, Lev-Yadun S, Gopher A (2012) Plant domestication and crop evolution in the near east: on events and processes. Crit Rev Plant Sci 31:241–257

    Article  Google Scholar 

  • Abbo S, Pinhasi van-Oss R, Gopher A et al (2014) Plant domestication versus crop evolution: a conceptual framework for cereals and grain legumes. Trends Plant Sci 19:351–360

    Article  CAS  PubMed  Google Scholar 

  • Avni R, Nave M, Eilam T et al (2014) Ultra-dense genetic map of durum wheat × wild emmer wheat developed using the 90 K iSelect SNP genotyping assay. Mol Breed 34:1549–1562

    Article  CAS  Google Scholar 

  • Barrero JM, Jacobsen J, Gubler F (2010) Seed dormancy: approaches for finding new genes in cereals. In: Pua EC, Davey MR (eds) Plant developmental biology-biotechnological perspectives. Springer, Berlin, Germany, pp 361–381

    Chapter  Google Scholar 

  • Barrero J, Cavanagh C, Verbyla K et al (2015) Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL. Genome Biol 16:93

    Article  PubMed  PubMed Central  Google Scholar 

  • Baskin JM, Baskin CC (2004) A classification system for seed dormancy. Seed Sci Res 14:1–16

    Google Scholar 

  • Breseghello F, Sorrells ME (2007) QTL analysis of kernel size and shape in two hexaploid wheat mapping populations. Field Crops Res 101:172–179

    Article  Google Scholar 

  • Cheplick GP (1992) Sibling competition in plants. J Ecol 80:567–575

    Article  Google Scholar 

  • Cook OF (1913) Wild wheat in Palestine. U.S Department of Agriculture, Bureau Of Plant Industry—Bulletin No. 274. BT Galloway, Washington

  • Creelman RA, Mullet JE (1995) Jasmonic acid distribution and action in plants: regulation during development and response to biotic and abiotic stress. Proc Natl Acad Sci 92:4114–4119

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Crocker WM (1916) Mechanics of dormancy in seeds. Am J Bot 3:99–120

    Article  Google Scholar 

  • Datta SC, Evenari M, Gutterman Y (1970) Heteroblasty of Aegilops ovata L. Isr J Bot 19:463–483

    Google Scholar 

  • De Vries AP (1971) Flowering biology of wheat, particularly in view of hybrid seed production—a review. Euphytica 20:152–170

    Article  Google Scholar 

  • Debeaujon I, Koornneef M (2000) Gibberellin requirement for arabidopsis seed germination is determined both by testa characteristics and embryonic abscisic acid. Plant Physiol 122:415–424

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Debeaujon I, Léon-Kloosterziel KM, Koornneef M (2000) Influence of the testa on seed dormancy, germination, and longevity in Arabidopsis. Plant Physiol 122:403–414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dyer AR (2004) Maternal and sibling factors induce dormancy in dimorphic seed pairs of Aegilops triuncialis. Plant Ecol 172:211–218

    Article  Google Scholar 

  • Evers T, Millar S (2002) Cereal grain structure and development: some implications for quality. J Cereal Sci 36:261–284

    Article  Google Scholar 

  • Feuillet C, Langridge P, Waugh R (2008) Cereal breeding takes a walk on the wild side. Trends Genet 24:24–32

    Article  CAS  PubMed  Google Scholar 

  • Finch-Savage WE, Leubner-Metzger G (2006) Seed dormancy and the control of germination. New Phytol 171:501–523

    Article  CAS  PubMed  Google Scholar 

  • Frey A, Godin B, Bonnet M et al (2004) Maternal synthesis of abscisic acid controls seed development and yield in Nicotiana plumbaginifolia. Planta 218:958–964

    Article  CAS  PubMed  Google Scholar 

  • Fuller DQ (2007) Contrasting patterns in crop domestication and domestication rates: recent archaeobotanical insights from the old world. Ann Bot 100:903–924

    Article  PubMed  PubMed Central  Google Scholar 

  • Fuller DQ, Allaby R (2009) Seed dispersal and crop domestication: shattering, germination and seasonality in evolution under cultivation. Annu Plant Rev 38:238–295

    Google Scholar 

  • Gao F, Ayele BT (2014) Functional genomics of seed dormancy in wheat: advances and prospects. Front Plant Sci 5:458

    PubMed  PubMed Central  Google Scholar 

  • Gegas VC, Nazari A, Griffiths S et al (2010) A genetic framework for grain size and shape variation in wheat. Plant Cell 22:1046–1056

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Harel D, Holzapfel C, Sternberg M (2011) Seed mass and dormancy of annual plant populations and communities decreases with aridity and rainfall predictability. Basic Appl Ecol 12:674–684

    Article  Google Scholar 

  • Hilhorst H (1995) A critical update on seed dormancy. I. Primary dormancy. Seed Sci Res 5:61–73

    Article  CAS  Google Scholar 

  • Hilhorst HWM, Karssen CM (1992) Seed dormancy and germination: the role of abscisic acid and gibberellins and the importance of hormone mutants. Plant Growth Regul 11:225–238

    Article  CAS  Google Scholar 

  • Horovitz A, Ezrati S, Anikster Y (2013) Are soil seed banks relevant for agriculture in our day? Crop Wild Relat 27–30. http://www.pgrsecure.bham.ac.uk/sites/default/files/documents/newsletters/CWR_Issue_9.pdf

  • Jacobsen JV, Barrero JM, Hughes T et al (2013) Roles for blue light, jasmonate and nitric oxide in the regulation of dormancy and germination in wheat grain (Triticum aestivum L.). Planta 238:121–138

    Article  CAS  PubMed  Google Scholar 

  • Jansen RC (1993) Interval mapping of multiple quantitative trait loci. Genetics 135:205–211

    CAS  PubMed  PubMed Central  Google Scholar 

  • Joppa LR, Williams ND (1988) Langdon durum disomic substitution lines and aneuploid analysis in tetraploid wheat. Genome 30:222–228

    Article  Google Scholar 

  • Kao C, Zeng Z, Teasdale R (1999) Multiple interval mapping for quantitative trait loci. Genetics 152:1203–1216

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kato K, Nakamura W, Tabiki T et al (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 

  • Koornneef M, Bentsink L, Hilhorst H (2002) Seed dormancy and germination. Plant Biol 5:33–36

    CAS  Google Scholar 

  • Kulwal P, Mir R, Kumar S, Gupta P (2010) QTL analysis and molecular breeding for seed dormancy and pre-harvest sprouting tolerance in bread wheat. J Plant Biol 37:59–74

    Google Scholar 

  • Lavie D, Levy EC, Cohen A et al (1974) New germination inhibitor from Aegilops ovata L. Nature 249:388

    Article  CAS  Google Scholar 

  • Li C, Ni P, Francki M et al (2004) Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison. Funct Integr Genomics 4:84–93

    Article  CAS  PubMed  Google Scholar 

  • Liu A, Gao F, Kanno Y et al (2013a) Regulation of wheat seed dormancy by after-ripening is mediated by specific transcriptional switches that induce changes in seed hormone metabolism and signaling. PLoS ONE 8:e56570

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu S, Sehgal SK, Li J et al (2013b) Cloning and characterization of a critical regulator for preharvest sprouting in wheat. Genetics 195:263–273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Maranon T (1987) Ecology of the somatic polymorphism in seeds and the synaptospermy in Aegilops neglecta Req. ex Bertol. Anales del Jardin Botanico de Madrid (Spain) 44:97–107.‏

  • Maranon T (1989) Variations in seed size and germination in 3 aegilops species. Seed Sci Technol 17:583–588

    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 D, Mrva K, Cheong J et al (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 

  • Nakamura S, Fumitaka A, Kawahigashi H et al (2011) A wheat homolog of MOTHER OF FT AND TFL1 acts in the regulation of germination. Plant Cell 23:3215–3229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ozkan H, Brandolini A, Pozzi C et al (2005) A reconsideration of the domestication geography of tetraploid wheats. Theor Appl Genet 110:1052–1060

    Article  CAS  PubMed  Google Scholar 

  • Pourkheirandish M, Hensel G, Kilian B et al (2015) Evolution of the grain dispersal system in barley. Cell 162:527–539

    Article  CAS  PubMed  Google Scholar 

  • Ramya P, Chaubal A, Kulkarni K et al (2010) QTL mapping of 1000-kernel weight, kernel length, and kernel width in bread wheat (Triticum aestivum L.). J Appl Gene 51:421–429

    Article  CAS  Google Scholar 

  • Russo MA, Ficco DBM, Laidò G et al (2014) A dense durum wheat × T. dicoccum linkage map based on SNP markers for the study of seed morphology. Mol Breed 34:1579–1597

    Article  Google Scholar 

  • Simons KJ, Fellers JP, Trick HN et al (2006) Molecular characterization of the major wheat domestication gene Q. Genetics 172:547–555

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Simpson GM (1990) Seed dormancy in grasses. Cambridge University Press, Cambridge, New York, Melbourne

  • Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066

    Article  CAS  PubMed  Google Scholar 

  • Tanno K, Willcox G (2006) How fast was wild wheat domesticated? Science 311:1886

    Article  CAS  PubMed  Google Scholar 

  • Wu QH, Chen YX, Zhou SH et al (2015) High-density genetic linkage map construction and QTL mapping of grain shape and size in the wheat population Yanda1817 × Beinong6. PloS one 10.2:e0118144.‏

  • Wurzburger J, Koller D (1973) Onset of seed dormancy in Aegilops Kotschyi Boiss. and its experimental modification. New Phytol 5:1057–1061

    Article  Google Scholar 

  • Wurzburger J, Leshem Y (1967) Gibberellin and hull controlled inhibition of germination in Aegilops kotschyi Boiss‏. Isr J Bot 16:181–186

    CAS  Google Scholar 

  • Zhukovsky PM (1928) A critical-systematical survey of the species of the genus Aegilops L. Bull Plant Breed 18:417–609

    Google Scholar 

Download references

Acknowledgments

A. Distelfeld acknowledges support from the Marie Curie International Reintegration Grant Number PIRG08-GA-2010-277036 and from the ISRAEL SCIENCE FOUNDATION (Grants No. 999/12 and 1824/12). A. Distelfeld and I. Hale acknowledge support from the United States–Israel Binational Science Foundation (BSF) Grant Number 2013396. M. Nave acknowledges support from the Manna center for food security in Tel Aviv University. The authors would like to thank Prof. Avraham Korol from the University of Haifa for assistance with the QTL analysis.

Author information

Authors and Affiliations

  1. Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, The Institute for Cereal Crop Improvement, Tel Aviv University, 69978, Tel Aviv, Israel

    Moran Nave, Raz Avni, Batsheva Ben-Zvi & Assaf Distelfeld

  2. Department of Biological Sciences, College of Life Sciences and Agriculture, University of New Hampshire, Durham, NH, 03824, USA

    Iago Hale

Authors
  1. Moran Nave
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Raz Avni
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Batsheva Ben-Zvi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Iago Hale
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Assaf Distelfeld
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Assaf Distelfeld.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Communicated by T. Komatsuda.

Electronic supplementary material

Below is the link to the electronic supplementary material.

122_2016_2704_MOESM1_ESM.pdf

Supplementary material 1 (PDF 281 kb) Supplementary table S1. Reduced-markers map used for the QTL analysis. Supplementary table S2. Grain dimensions and germination characterization of lower and upper grains within the spikelets of the chromosomal substitution lines LDN(PI481521) and 51 T. turgidum ssp. dicoccum accessions. Supplementary table S3. Summary of ΔG values and germination percentages of the RILs. Supplementary table S4. Summary of QTLs detected in the Svevo × Zavitan RIL population for dimension ratios and differential dormancy between lower (1st) and upper (2nd) grains within the spikelets of tetraploid wheat. Data is based on the 2013 and 2014 experiments. PEV = proportion of explained variance of the trait. d = the adaptive effect of an allele, calculated as half the mean difference between homozygotes with and without the allele

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Nave, M., Avni, R., Ben-Zvi, B. et al. QTLs for uniform grain dimensions and germination selected during wheat domestication are co-located on chromosome 4B. Theor Appl Genet 129, 1303–1315 (2016). https://doi.org/10.1007/s00122-016-2704-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-016-2704-4

Keywords

Search

Navigation