Skip to main content
SpringerLink
Log in

Quantitative trait loci for agronomic traits in an elite barley population for Mediterranean conditions

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

Advances in plant breeding through marker-assisted selection (MAS) are only possible when genes or quantitative trait loci (QTLs) can contribute to the improvement of elite germplasm. A population of recombinant inbred lines (RILs) was developed for one of the best crosses of the Spanish National Barley Breeding Program, between two six-row winter barley cultivars Orria and Plaisant. The objective of this study was to identify favourable QTLs for agronomic traits in this population, which may help to optimise breeding strategies for these and other elite materials for the Mediterranean region. A genetic linkage map was developed for 217 RILs, using 382 single nucleotide polymorphism markers, selected from the barley oligonucleotide pool assay BOPA1 and two genes. A subset of 112 RILs was evaluated for several agronomic traits over a period of 2 years at three locations, Lleida and Zaragoza (Spain) and Fiorenzuola d’Arda (Italy), for a total of five field trials. An important segregation distortion occurred during population development in the region surrounding the VrnH1 locus. A QTL for grain yield and length of growth cycle was also found at this locus, apparently linked to a differential response of the VrnH1 alleles to temperature. A total of 33 QTLs was detected, most of them for important breeding targets such as plant height and thousand-grain weight. QTL × environment interactions were prevalent for most of the QTLs detected, although most interactions were of a quantitative nature. Therefore, QTLs suitable for MAS for most traits were identified.

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

Similar content being viewed by others

References

  • Backes G, Graner A, Foroughi-Wehr B, Fischbeck G, Wenzel G, Jahoor A (1995) Localization of quantitative trait loci (QTL) for agronomic important characters by the use of a RFLP map in barley (Hordeum vulgare L). Theor Appl Genet 90:294–302

    Article  CAS  PubMed  Google Scholar 

  • Bauer AM, Hoti F, von Korff M, Pillen K, Léon J, Sillanpää MJ (2009) Advanced backcross-QTL analysis in spring barley (H. vulgare ssp. spontaneum) comparing a REML versus a Bayesian model in multi-environmental field trials. Theor Appl Genet 119:105–123

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Baum M, Grando S, Backes G, Jahoor A, Sabbagh A, Ceccarelli S (2003) QTLs for agronomic traits in the Mediterranean environment identified in recombinant inbred lines of the cross ‘Arta’ × H. spontaneum 41-1. Theor Appl Genet 107:1215–1225

    Article  CAS  PubMed  Google Scholar 

  • Borrás-Gelonch G, Denti M, Thomas WTB, Romagosa I (2012) Genetic control of pre-heading phases in the Steptoe × Morex barley population under different conditions of photoperiod and temperature. Euphytica 183:303–321

    Article  Google Scholar 

  • Burton RA, Jobling SA, Harvey AJ, Shirley NJ, Mather DE, Bacic A, Fincher GB (2008) The genetics and transcriptional profiles of the cellulose synthase-like HvCslF gene family in barley. Plant Physiol 146:1821–1833

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Casao MC, Igartua E, Karsai I, Lasa JM, Gracia MP, Casas AM (2011a) Expression analysis of vernalization and day-length response genes in barley (Hordeum vulgare L.) indicates that VRNH2 is a repressor of PPDH2 (HvFT3) under long days. J Exp Bot 62:1939–1949

    Article  CAS  PubMed  Google Scholar 

  • Casao MC, Igartua E, Karsai I, Bhat PR, Cuadrado N, Gracia MP, Lasa JM, Casas AM (2011b) Introgression of an intermediate VRNH1 allele in barley (Hordeum vulgare L.) leads to reduced vernalization requirement without affecting freezing tolerance. Mol Breed 28:475–484

    Article  CAS  Google Scholar 

  • Ceccarelli S, Grando S, Baum M (2007) Participatory plant breeding in water-limited environments. Exp Agric 43:1–25

    Article  Google Scholar 

  • Chloupek O, Forster BP, Thomas WTB (2006) The effect of semi-dwarf genes on root system size in field-grown barley. Theor Appl Genet 112:779–786

    Article  CAS  PubMed  Google Scholar 

  • Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svenson JT, Wanamaker S, Bozdog S, Roose ML, Moscou MJ, Chao S, Varshney R, Szűcs P, Sato K, Hayes PM, Mathews DE, Kleinhofs A, Muehlbauer GJ, DeYoung J, Marshall D, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:582

    Article  PubMed Central  PubMed  Google Scholar 

  • Comadran J, Russell JR, van Eeuwijk FA, Ceccarelli S, Grando S, Baum M, Stanca AM, Pecchioni N, Mastrangelo AM, Akar T, Al-Yassin A, Benbelkacem A, Choumane W, Ouabbou H, Dahan R, Bort J, Araus JL, Pswarayi A, Romagosa I, Hackett CA, Thomas WTB (2008) Mapping adaptation of barley to droughted environments. Euphytica 161:35–45

    Article  Google Scholar 

  • Comadran J, Russell JR, Booth A, Pswarayi A, Ceccarelli S, Grando S, Stanca AM, Pecchioni N, Akar T, Al-Yassin A, Benbelkacem A, Ouabbou H, Bort J, van Eeuwijk FA, Thomas WTB, Romagosa I (2011) Mixed model association scans of multi-environmental trial data reveal major loci controlling yield and yield related traits in Hordeum vulgare in Mediterranean environments. Theor Appl Genet 122:1363–1373

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Cuesta-Marcos A, Igartua E, Ciudad FJ, Codesal P, Russell JR, Molina-Cano JL, Moralejo M, Szűcs P, Gracia MP, Lasa JM, Casas AM (2008a) Heading date QTL in a spring × winter barley cross evaluated in Mediterranean environments. Mol Breed 21:455–471

    Article  Google Scholar 

  • Cuesta-Marcos A, Casas AM, Yahiaoui S, Gracia MP, Lasa JM, Igartua E (2008b) Joint analysis for heading date QTL in small interconnected barley populations. Mol Breed 21:383–399

    Article  Google Scholar 

  • Cuesta-Marcos A, Casas AM, Hayes PM, Gracia MP, Lasa JM, Ciudad F, Codesal P, Molina-Cano JL, Igartua E (2009) Yield QTL affected by heading date in Mediterranean grown barley. Plant Breed 128:46–53

    Article  CAS  Google Scholar 

  • Fisk SP, Cuesta-Marcos A, Cistué L, Russell J, Smith KP, Baenziger S, Bedo Z, Corey A, Filichkin T, Karsai I, Waugh R, Hayes PM (2013) FR-H3: a new QTL to assist in the development of fall-sown barley with superior low temperature tolerance. Theor Appl Genet 126:335–347

    Article  PubMed  Google Scholar 

  • Francia E, Rizza F, Cattivelli L, Stanca AM, Galiba G, Tóth B, Hayes PM, Skinner JS, Pecchioni N (2004) Two loci on chromosome 5H determine low-temperature tolerance in a “Nure” (winter) × “Tremois” (spring) barley map. Theor Appl Genet 108:670–680

    Article  CAS  PubMed  Google Scholar 

  • Francia E, Tondelli A, Rizza F, Badeck FW, Li Destri Nicosia O, Akar T, Grando S, Al-Yassin A, Benbelkacem A, Thomas WTB, van Eeuwijk F, Romagosa I, Stanca AM, Pecchioni N (2011) Determinants of barley grain yield in a wide range of Mediterranean environments. Field Crops Res 120:169–178

    Article  Google Scholar 

  • Hemming MN, Fieg S, Peacock WJ, Dennis ES, Trevaskis B (2009) Regions associated with repression of the barley (Hordeum vulgare) VERNALIZATION1 gene are not required for cold induction. Mol Genet Genomics 282:107–117

    Article  CAS  PubMed  Google Scholar 

  • Kjaer B, Jensen J (1996) Quantitative trait loci for grain yield and yield components in a cross between a six-rowed and a two-rowed barley. Euphytica 90:39–48

    Google Scholar 

  • Lakew B, Eglinton J, Henry RJ, Baum M, Grando S, Ceccarelli S (2011) The potential contribution of wild barley (Hordeum vulgare ssp. spontaneum) germplasm to drought tolerance of cultivated barley (H. vulgare ssp. vulgare). Field Crops Res 120:161–168

    Article  Google Scholar 

  • Laurie DA, Pratchett N, Bezant JH, Snape JW (1994) Genetic analysis of a photoperiod response gene on the short arm of chromosome 2 (2H) of Hordeum vulgare (barley). Heredity 72:619–627

    Article  CAS  Google Scholar 

  • Li JZ, Huang XQ, Heinrichs F, Ganal MW, Röder MS (2005) Analysis of QTLs for yield, yield components, and malting quality in a BC3-DH population of spring barley. Theor Appl Genet 110:356–363

    Article  CAS  PubMed  Google Scholar 

  • Li JZ, Huang XQ, Heinrichs F, Ganal MW, Röder MS (2006) Analysis of QTLs for yield components, agronomic traits and disease resistance in an advanced backcross population of spring barley. Genome 49:454–466

    Article  CAS  PubMed  Google Scholar 

  • Lister DL, Thaw S, Bower MA, Jones H, Charles MP, Jones G, Smith LMJ, Howe CJ, Brown TA, Jones MK (2009) Latitudinal variation in a photoperiod response gene in European barley: insight into the dynamics of agricultural spread from ‘historic’ specimens. J Archaeol Sci 36:1092–1098

    Article  Google Scholar 

  • Muñoz-Amatriaín M, Moscou MJ, Bhat PR, Svensson JT, Bartoš J, Suchánková P, Šimková H, Endo TR, Fenton RD, Lonardi S, Castillo AM, Chao S, Cistué L, Cuesta-Marcos A, Forrest KL, Hayden MJ, Hayes PM, Horsley RD, Makoto K, Moody D, Sato K, Vallés MP, Wulff BBH, Muehlbauer GJ, Doležel J, Close TJ (2011) An improved consensus linkage map of barley based on flow-sorted chromosomes and single nucleotide polymorphism markers. Plant Genome 4:238–239

    Article  Google Scholar 

  • Pasam RK, Sharma R, Malosetti M, van Eeuwijk FA, Haseneyer G, Kilian B, Graner A (2012) Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biol 12:16

    Article  PubMed Central  PubMed  Google Scholar 

  • Ponce-Molina LJ, Casas AM, Gracia MP, Silvar C, Mansour E, Thomas WBT, Schweizer G, Herz M, Igartua E (2012) Quantitative trait loci and candidate loci for heading date in a large population of a wide barley cross. Crop Sci 52:2469–2480

    Article  Google Scholar 

  • Pswarayi A, van Eeuwijk FA, Ceccarelli S, Grando S, Comadran J, Russell JR, Francia E, Pecchioni N, Li Destri O, Akar T, Al-Yassin A, Benbelkacem A, Choumane W, Karrou M, Ouabbou H, Bort J, Araus JL, Molina-Cano JL, Thomas WTB, Romagosa I (2008) Barley adaptation and improvement in the Mediterranean basin. Plant Breed 127:554–560

    Article  Google Scholar 

  • Rajasekaran P, Thomas WTB, Wilson A, Lawrence P, Young G, Ellis RP (2004) Genetic control over grain damage in a spring barley mapping population. Plant Breed 123:17–23

    Article  CAS  Google Scholar 

  • Romagosa I, Han F, Ullrich SE, Hayes PM, Wesenberg DM (1999) Verification of yield QTL through realized molecular marker-assisted selection responses in a barley cross. Mol Breed 5:143–152

    Article  Google Scholar 

  • Sameri M, Komatsuda T (2007) Localization of quantitative trait loci for yield components in a cross Oriental × Occidental barley cultivar (Hordeum vulgare L.). Jpn Agric Res Q 41:195–199

    Article  Google Scholar 

  • Szűcs P, Blake VC, Bhat PR, Chao S, Close TJ, Cuesta-Marcos A, Muehlbauer GJ, Ramsay L, Waugh R, Hayes PM (2009) An integrated resource for barley linkage map and malting quality QTL alignment. Plant Genome 2:134–140

    Article  Google Scholar 

  • Teulat B, Merah O, Souyris I, This D (2001) QTLs for agronomic traits from a Mediterranean barley progeny grown in several environments. Theor Appl Genet 103:774–787

    Article  CAS  Google Scholar 

  • Turner A, Beales J, Faure S, Dunford RP, Laurie DA (2005) The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley. Science 310:1031–1034

    Article  CAS  PubMed  Google Scholar 

  • van Eeuwijk FA, Bink MCAM, Chenu K, Chapman SC (2010) Detection and use of QTL for complex traits in multiple environments. Curr Opin Plant Biol 13:193–205

    Article  PubMed  Google Scholar 

  • van Ooijen JW (2006) JoinMap 4, software for the calculation of genetics linkage maps in experimental populations. Kyazma, BV, Wageningen

    Google Scholar 

  • van Oosterom EJ, Kleijn D, Ceccarelli S, Nachit MM (1993) Genotype-by-environment interactions of barley in the Mediterranean region. Crop Sci 33:669–674

    Article  Google Scholar 

  • Varshney RK, Marcel TC, Ramsay L, Russell J, Röder MS, Stein N, Waugh R, Langridge P, Niks RE, Graner A (2007) A high density barley microsatellite consensus map with 775 SSR loci. Theor Appl Genet 114:1091–1103

    Article  CAS  PubMed  Google Scholar 

  • Varshney RK, Paulo MJ, Grando S, van Eeuwijk FA, Keizer LCP, Guo P, Ceccarelli S, Kilian A, Baum M, Graner A (2012) Genome wide association analyses for drought tolerance related traits in barley (Hordeum vulgare L.). Field Crops Res 126:171–180

    Article  Google Scholar 

  • von Korff M, Wang H, Léon J, Pillen K (2006) AB-QTL analysis in spring barley: II. Detection of favourable exotic alleles for agronomic traits introgressed from wild barley (H. vulgare ssp. spontaneum). Theor Appl Genet 112:1221–1231

    Article  Google Scholar 

  • von Korff M, Grando S, Del Greco A, This D, Baum M, Ceccarelli S (2008) Quantitative trait loci associated with adaptation to Mediterranean dryland conditions in barley. Theor Appl Genet 117:653–669

    Article  Google Scholar 

  • von Zitzewitz J, Szűcs P, Dubcovsky J, Yan L, Francia E, Pecchioni N, Casas A, Chen THH, Hayes PM, Skinner JS (2005) Molecular and structural characterization of barley vernalization genes. Plant Mol Biol 59:449–467

    Article  CAS  Google Scholar 

  • VSN International (2011) GenStat for Windows 14th Edition. VSN International, Hemel Hempstead

    Google Scholar 

  • Wang G, Schmalenbach I, von Korff M, Léon J, Kilian B, Rode J, Pillen K (2010) Association of barley photoperiod and vernalization genes with QTLs for flowering time and agronomic traits in a BC2DH population and a set of wild barley introgression lines. Theor Appl Genet 120:1559–1574

    Article  PubMed Central  PubMed  Google Scholar 

  • Wang H, Smith KP, Combs E, Blake T, Horsley RD, Muehlbauer GJ (2012) Effect of population size and unbalanced data sets on QTL detection using genome-wide association mapping in barley breeding germplasm. Theor Appl Genet 124:111–124

    Article  CAS  PubMed  Google Scholar 

  • Xu S (2008) Quantitative trait locus mapping can benefit from segregation distortion. Genetics 180:2201–2208

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by the Spanish Ministry of Science and Innovation (MICINN), who funded this work with the scholarship BES-2008-009623 (EM), and the projects AGL2010-21929, GEN2006-28560-E and RTA2009-00006-C04. We thank Malcolm Macaulay and Richard Keith for their assistance with genotyping software and Marvin analysis respectively. The James Hutton Institute receives grant in aid from the Scottish Government’s Rural and Environment Science and Analytical Services Division.

Author information

Authors and Affiliations

  1. Estación Experimental de Aula Dei, EEAD-CSIC, Avda. Montañana, 1005, 50059, Zaragoza, Spain

    Elsayed Mansour, Ana M. Casas, M. Pilar Gracia & Ernesto Igartua

  2. Centro Universitat de Lleida-Institut de Recerca i Tecnología Agroalimentàries (UdL-IRTA), Avda Rovira Roure 191, 25198, Lleida, Spain

    José Luis Molina-Cano & Marian Moralejo

  3. Consiglio Per la Ricerca e la Sperimentazione in Agricoltura, Genomics Research Centre, Via S. Protaso, 302, 29017, Fiorenzuola d’Arda, PC, Italy

    Luigi Cattivelli

  4. The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK

    William T. B. Thomas

Authors
  1. Elsayed Mansour
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ana M. Casas
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. Pilar Gracia
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. José Luis Molina-Cano
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Marian Moralejo
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Luigi Cattivelli
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. William T. B. Thomas
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Ernesto Igartua
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ana M. Casas.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 773 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Mansour, E., Casas, A.M., Gracia, M.P. et al. Quantitative trait loci for agronomic traits in an elite barley population for Mediterranean conditions. Mol Breeding 33, 249–265 (2014). https://doi.org/10.1007/s11032-013-9946-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11032-013-9946-5

Keywords

Search

Navigation