Skip to main content
SpringerLink
Log in

Molecular and comparative mapping of genes governing spike compactness from wild emmer wheat

  • Original Paper
  • Published:
Molecular Genetics and Genomics Aims and scope Submit manuscript

Abstract

The development and morphology of the wheat spike is important because the spike is where reproduction occurs and it holds the grains until harvest. Therefore, genes that influence spike morphology are of interest from both theoretical and practical stand points. When substituted for the native chromosome 2A in the tetraploid Langdon (LDN) durum wheat background, the Triticum turgidum ssp. dicoccoides chromosome 2A from accession IsraelA confers a short, compact spike with fewer spikelets per spike compared to LDN. Molecular mapping and quantitative trait loci (QTL) analysis of these traits in a homozygous recombinant population derived from LDN × the chromosome 2A substitution line (LDNIsA-2A) indicated that the number of spikelets per spike and spike length were controlled by linked, but different, loci on the long arm of 2A. A QTL explaining most of the variation for spike compactness coincided with the QTL for spike length. Comparative mapping indicated that the QTL for number of spikelets per spike overlapped with a previously mapped QTL for Fusarium head blight susceptibility. The genes governing spike length and compactness were not orthologous to either sog or C, genes known to confer compact spikes in diploid and hexaploid wheat, respectively. Mapping and sequence analysis indicated that the gene governing spike length and compactness derived from wild emmer could be an ortholog of the barley Cly1/Zeo gene, which research indicates is an AP2-like gene pleiotropically affecting cleistogamy, flowering time, and rachis internode length. This work provides researchers with knowledge of new genetic loci and associated markers that may be useful for manipulating spike morphology in durum wheat.

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

  • Cantrell RG, Joppa LR (1991) Genetic analysis of quantitative traits in wild emmer (Triticum turgidum L. var. dicoccoides). Crop Sci 31:645–649

    Article  Google Scholar 

  • Chen A, Baumann U, Fincher GB, Collins NC (2009a) Flt-2L, a locus in barley controlling flowering time, spike density, and plant height. Funct Integr Genomics 9:243–254

    Article  CAS  PubMed  Google Scholar 

  • Chen A, Reinheimer J, Brule-Babel A, Baumann U, Pallotta M, Fincher GB, Collins NC (2009b) Genes and traits associated with chromosome 2H and 5H regions controlling sensitivity of reproductive tissues to frost in barley. Theor Appl Genet 118:1465–1476

    Article  CAS  PubMed  Google Scholar 

  • Druka A, Franckowiak J, Lundqvist U, Bonar N, Alexander J, Houston K, Radovic S, Shahinnia F, Vendramin V, Morgante M, Stein N, Waugh R (2011) Genetic dissection of barley morphology and development. Plant Physiol 155:617–627

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Endo TR, Gill BS (1996) The deletion stocks of common wheat. J Hered 87:295–307

    Article  CAS  Google Scholar 

  • Faris JD, Friesen TL (2009) Reevaluation of a tetraploid wheat population indicates that the Tsn1-ToxA interaction is the only factor governing susceptibility to Stagonospora nodorum blotch. Phytopathology 99:906–912

    Article  CAS  PubMed  Google Scholar 

  • Faris JD, Gill BS (2002) Genomic targeting and high-resolution mapping of the domestication gene Q in wheat. Genome 45:706–718

    Article  CAS  PubMed  Google Scholar 

  • Faris JD, Haen KM, Gill BS (2000) Saturation mapping of a gene-rich recombination hot spot region in wheat. Genetics 154:823–835

    CAS  PubMed Central  PubMed  Google Scholar 

  • Faris JD, Fellers JP, Brooks SA, Gill BS (2003) A bacterial artificial chromosome contig spanning the major domestication locus Q in wheat and identification of a candidate gene. Genetics 164:311–321

    CAS  PubMed Central  PubMed  Google Scholar 

  • Garvin DF, Stack RW, Hansen JM (2009) Quantitative trait locus mapping of increased Fusarium head blight susceptibility associated with a wild emmer wheat chromosome. Phytopathology 99:447–452

    Article  CAS  PubMed  Google Scholar 

  • Gilsinger J, Kong L, Shen X, Ohm H (2005) DNA markers associated with low Fusarium head blight incidence and narrow flower opening in wheat. Theor Appl Genet 110:1218–1225

    Article  CAS  PubMed  Google Scholar 

  • Gonzalez-Hernadez JL, Elias EM, Kianian SF (2004) Mapping genes for grain protein concentration and grain yield on chromosome 5B of Triticum turgidum (L.) var. dicoccoides. Euphytica 139:217–225

    Article  Google Scholar 

  • Gonzalez-Hernandez JL, Singh PK, Mergoum M, Adhikari TB, Kianian SF, Simsek S, Elias EM (2009) A quantitative trait locus on chromosome 5B controls resistance of Triticum turgidum (L.) var. dicoccoides to Stagonospora nodorum blotch. Euphytica 166:199–206

    Article  CAS  Google Scholar 

  • Houston K, McKim SM, Comadran J, Bonar N, Druka I, Uzrek N, Cirillo E, Guzy-Wrobelska J, Collins NC, Halpin C, Hansson M, Dockter C, Druka A, Waugh R (2013) Variation in the interaction between alleles of HvAPETALA2 and microRNA172 determines the density of grains on the barley inflorescence. Proc Natl Acad Sci USA 110:16675–16680

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Jantasuriyarat C, Vales MI, Watson CJW, Riera-Lizarazu O (2004) Identification and mapping of genetic loci affecting the free-threshing habit and spike compactness in wheat (Triticum aestivum L.). Theor Appl Genet 108:261–273

    Article  CAS  PubMed  Google Scholar 

  • Joehanes R, Nelson JC (2008) QGene 4.0, an extensive Java QTL-analysis platform. Bioinformatics 24:2788–2789

    Article  CAS  PubMed  Google Scholar 

  • Johnson EB, Nalam VJ, Zemetra RS, Riera-Lizarazu O (2008) Mapping the compactum locus in wheat (Triticum aestivum L.) and its relationship to other spike morphology genes of the Triticeae. Euphytica 163:193–201

    Article  Google Scholar 

  • Joppa LR (1993) Chromosome engineering in tetraploid wheat. Crop Sci 33:908–913

    Article  Google Scholar 

  • Joppa LR, Cantrell RG (1990) Chromosomal location of genes for grain protein content of wild tetraploid wheat. Crop Sci 30:1059–1064

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  • Joppa LR, Hareland GA, Cantrell RG (1991) Quality characteristics of the Langdon durum-dicoccoides chromosome substitution lines. Crop Sci 31:1513–1517

    Article  Google Scholar 

  • Joppa LR, Du C, Hart GE, Hareland GA (1997) Mapping gene(s) for grain protein in tetraploid wheat (Triticum turgidum L.) using a population of recombinant inbred chromosome lines. Crop Sci 37:1586–1589

    Article  CAS  Google Scholar 

  • Kato K, Miura H, Sawada S (1999) QTL mapping of genes controlling ear emergence time and plant height on chromosome 5A of wheat. Theor Appl Genet 98:472–476

    Article  CAS  Google Scholar 

  • Kato K, Sonokawa R, Miura H, Sawada S (2003) Dwarfing effect associated with the threshability gene Q on wheat chromosome 5A. Plant Breed 122:489–492

    Article  CAS  Google Scholar 

  • Klindworth DL, Hareland GA, Elias EM, Faris JD, Chao S, Xu SS (2009) Agronomic and quality characteristics of two new sets of Langdon durum-wild emmer wheat chromosome substitution lines. J Cereal Sci 50:29–35

    Article  CAS  Google Scholar 

  • Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175

    Article  Google Scholar 

  • Kumar S, Gill BS, Faris JD (2007) Identification and characterization of segregation distortion loci along chromosome 5B in tetraploid wheat. Mol Genet Genomics 278:1870196

    Article  Google Scholar 

  • Kuspira J, Unrau J (1957) Genetic analysis of certain characters in common wheat using whole chromosome substitution lines. Can J Plant Sci 37:300–326

    Article  Google Scholar 

  • Lorieux M (2012) MapDisto: fast and efficient computation of genetic linkage maps. Mol Breed 30:1231–1235

    Article  CAS  Google Scholar 

  • Mackey J (1954) Neutron and X-ray experiments in wheat and revision of the speltoid problem. Hereditas 40:65–180

    Google Scholar 

  • Muramatsu M (1963) Dosage effect of the spelta gene q of hexaploid wheat. Genetics 48:469–482

    CAS  PubMed Central  PubMed  Google Scholar 

  • Muramatsu M (1979) Presence of the vulgare gene, Q, in a dense-spike variety of Triticum dicoccum Schübl. Report of the Plant Germ-Plasm Institute, Kyoto University, No. 4 pp 39–41

  • Muramatsu M (1985) Spike type in two cultivars of Triticum dicoccum with the spelta gene q compared with the Q-bearing variety liguliforme. Jpn J Breed 35:255–267

    Article  Google Scholar 

  • Muramatsu M (1986) The vulgare super gene, Q: its universality in durum wheat and its phenotypic effects in tetraploid and hexaploid wheats. Can J Genet Cytol 28:30–41

    Google Scholar 

  • Nair SK, Wang N, Turuspekov Y, Pourkheirandish M, Sinsuwongwat S, Chen G, Sameri M, Tagiri A, Honda I, Watanabe Y, Kanamori H, Wicker T, Stein N, Nagamura Y, Matsumoto T, Komatsuda T (2010) Cleistogamous flowering in barley arises from the suppression of microRNA-guided HvAP2 mRNA cleavage. Proc Natl Acad Sci USA 107:490–495

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Nalam VJ, Vales MI, Watson CJW, Kianian SF, Riera-Lizarazu O (2006) Map-based analysis of genes affecting the brittle rachis character in tetraploid wheat (Triticum turgidum L.). Theor Appl Genet 112:373–381

    Article  CAS  PubMed  Google Scholar 

  • Ning S, Wang N, Sakuma S, Pourkheirandish M, Wu J, Matsumoto T, Koba T, Komatsuda T (2013) Structure, transcription and post-translational regulation of the bread wheat orthologs of the barley cleistogamy gene Cly1. Theor Appl Genet 126:1273–1283

    Article  CAS  PubMed  Google Scholar 

  • Otto CD, Kianian SF, Elias EM, Stack RW, Joppa LR (2002) Genetic dissection of a major Fusarium head blight QTL in tetraploid wheat. Plant Mol Biol 48:625–632

    Article  CAS  PubMed  Google Scholar 

  • Peng J, Ronin Y, Fahima T, Roder MS, Li Y, Nevo E, Korol A (2003) Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat. Proc Natl Acad Sci USA 100:2489–2494

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier M-H, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023

    PubMed Central  PubMed  Google Scholar 

  • SAS Institute (2011) SAS/STAT 9.3 User’s Guide. SAS Institute Inc, Cary

    Google Scholar 

  • Sears ER (1947) The sphaerococcum gene in wheat. Genetics 32:102–103

    Google Scholar 

  • Sears ER (1952) Misdivision of univalents in common wheat. Chromosoma 4:535–550

    Article  CAS  PubMed  Google Scholar 

  • Sears ER (1954) The aneuploids of common wheat. Missouri Agric Exp Stn Res Bull 572:59

    Google Scholar 

  • Sears ER, Loegering WQ, Rodenhiser HA (1957) Identification of chromosomes carrying genes for stem rust resistance in four varieties of wheat. Agron J 49:208–212

    Article  Google Scholar 

  • Simons KJ, Fellers JP, Trick HN, Zhang Z, Tai Y-S, Gill BS, Faris JD (2006) Molecular characterization of the major wheat domestication gene Q. Genetics 172:547–555

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Singh PK, Mergoum M, Adhikari TB, Kianian SF, Elias EM (2007) Chromosomal location of genes for seeding resistance to tan spot and Stagonospora nodorum blotch in tetraploid wheat. Euphytica 155:27–34

    Article  Google Scholar 

  • Somers DJ, Isaac P, Edwards K (2004) A high-density microsatellite consensus map for bread wheat (Trticum aestivum L.). Theor Appl Genet 109:1105–1114

    Article  CAS  PubMed  Google Scholar 

  • Song QJ, Shi JR, Singh S, Fickus EW, Costa JM, Lewis J, Gill BS, Ward R, Cregan PB (2005) Development and mapping of microsatellite (SSR) markers in wheat. Theor Appl Genet 110:550–560

    Article  CAS  PubMed  Google Scholar 

  • Sood S, Kuraparthy V, Bai GH, Gill BS (2009) The major threshability genes soft glume (sog) and tenacious glume (Tg), of diploid and polyploid wheat, trace their origin to independent mutations at non-orthologous loci. Theor Appl Genet 119:341–351

    Article  PubMed  Google Scholar 

  • Sourdille P, Tixier MH, Charmet G, Gay G, Cadalen T, Bernard S, Bernard M (2000) Location of genes involved in ear compactness in wheat (Triticum aestivum) by means of molecular markers. Mol Breed 6:247–255

    Article  CAS  Google Scholar 

  • Sourdille P, Singh S, Cadalen T, Brown-Guedira GL, Gay G, Qi L, Gill BS, Dufour P, Murigneux A, Bernard M (2004) Microsatellite-based deletion bin system for the establishment of genetic-physical map relationships in wheat (Triticum aestivum L.). Funct Integr Genomics 4:12–25

    Article  CAS  PubMed  Google Scholar 

  • Stack RW, Elias EM, Mitchell Fetch J, Miller JD, Joppa LR (2002) Fusarium head blight reaction of Langdon durum-Triticum dicoccoides chromosome substitution lines. Crop Sci 42:637–642

    Article  Google Scholar 

  • Torada A, Koike M, Mochida K, Ogihara Y (2006) SSR-based linkage map with new markers using an intraspecific population of common wheat. Theor Appl Genet 112:1042–1051

    Article  CAS  PubMed  Google Scholar 

  • Tsunewaki K (1966) Comparative gene analysis of common wheat and its ancestral species. II. Waxiness, growth habit and awnedness. Jpn J Bot 19:175–254

    Google Scholar 

  • Tsunewaki K, Ebona K (1999) Production of near-isogenic lines of common wheat for glaucousness and genetic basis of this trait clarified by their use. Genes Genet Syst 74:33–41

    Article  Google Scholar 

  • Unrau J, Smith WE, McGinnis RC (1950) Spike density, speltoidy and compactoidy in hexaploid wheat. Can J Res Com 28:273–276

    Article  Google Scholar 

  • Yu J-K, Dake TM, Singh S, Benscher D, Li W, Gill BS, Sorrells ME (2004) Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat. Genome 47:805–818

    Article  CAS  PubMed  Google Scholar 

  • Zhang ZC, Friesen TL, Simons KJ, Xu SS, Faris JD (2009) Development, identification, and validation of markers for marker-assisted selection against Stagonospora nodorum toxin sensitivity genes Tsn1 and Snn2 in wheat. Mol Breed 23:35–49

    Article  Google Scholar 

  • Zhang ZC, Belcram H, Gornicki P, Charles M, Just J, Huneau C, Magdelenat G, Couloux A, Samain S, Gill BS, Rasmussen JB, Barbe V, Faris JD, Chalhoub B (2011) Duplication and partitioning in evolution and function of homoeologous Q loci governing domestication characters in polyploid wheat. Proc Natl Acad Sci USA 108:18737–18742

    Article  CAS  PubMed Central  PubMed  Google Scholar 

Download references

Acknowledgments

The authors thank Breanna Oldenburg and Megan Stoley for technical assistance and Dr. Steven S. Xu for assistance with statistical analyses. This research was supported by USDA-ARS CRIS project 5442-22000-037-00D.

Author information

Authors and Affiliations

  1. USDA-Agricultural Research Service NPA NCSL, Cereal Crops Research Unit, Red River Valley Agricultural Research Center, 1605 Albrecht BLVD, Fargo, ND, 58102-2765, USA

    Justin D. Faris, Zengcui Zhang & Steven S. Xu

  2. USDA-Agricultural Research Service, Plant Science Research Unit and Department of Agronomy and Plant Genetics, 411 Borlaug Hall, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA

    David F. Garvin

Authors
  1. Justin D. Faris
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zengcui Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. David F. Garvin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Steven S. Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Justin D. Faris.

Additional information

Communicated by S. Hohmann.

Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. USDA is an equal opportunity provider and employer.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Faris, J.D., Zhang, Z., Garvin, D.F. et al. Molecular and comparative mapping of genes governing spike compactness from wild emmer wheat. Mol Genet Genomics 289, 641–651 (2014). https://doi.org/10.1007/s00438-014-0836-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00438-014-0836-2

Keywords

Search

Navigation