Abstract
Key message
“To find stable resistance using association mapping tools, QTL with major and minor effects on leaf rust reactions were identified in barley breeding lines by assessing seedlings and adult plants.”
Abstract
Three hundred and sixty (360) elite barley (Hordeum vulgare L.) breeding lines from the Northern Region Barley Breeding Program in Australia were genotyped with 3,244 polymorphic diversity arrays technology markers and the results used to map quantitative trait loci (QTL) conferring a reaction to leaf rust (Puccinia hordei Otth). The F3:5 (Stage 2) lines were derived or sourced from different geographic origins or hubs of international barley breeding ventures representing two breeding cycles (2009 and 2011 trials) and were evaluated across eight environments for infection type at both seedling and adult plant stages. Association mapping was performed using mean scores for disease reaction, accounting for family effects using the eigenvalues from a matrix of genotype correlations. In this study, 15 QTL were detected; 5 QTL co-located with catalogued leaf rust resistance genes (Rph1, Rph3/19, Rph8/14/15, Rph20, Rph21), 6 QTL aligned with previously reported genomic regions and 4 QTL (3 on chromosome 1H and 1 on 7H) were novel. The adult plant resistance gene Rph20 was identified across the majority of environments and pathotypes. The QTL detected in this study offer opportunities for breeding for more durable resistance to leaf rust through pyramiding multiple genomic regions via marker-assisted selection.
Similar content being viewed by others
References
Butler D, Cullis B, Gilmour A, Gogel B (2009) ASReml-R reference manual Release 3. QLD Department of Primary Industries and Fisheries, Brisbane
Castro AJ, Gamba F, German S, Gonzalez S, Hayes PM, Pereyra S, Perez C (2012) Quantitative trait locus analysis of spot blotch and leaf rust resistance in the BCD47 Baronesse barley mapping population. Plant Breed 131:258–266
Cone KC, McMullen MD, Bi IV, Davis GL, Yim YS, Gardiner JM, Polacco ML, Sanchez-Villeda H, Fang ZW, Schroeder SG, Havermann SA, Bowers JE, Paterson AH, Soderlund CA, Engler FW, Wing RA, Coe EH (2002) Genetic, physical, and informatics resources for maize on the road to an integrated map. Plant Physiol 130:1598–1605
Cotterill PJ, Rees RG, Platz GJ, Dillmacky R (1992) Effects of leaf rust on selected Australian barleys. Aust J Exp Agric 32:747–751
Darvasi A, Soller M (1997) A simple method to calculate resolving power and confidence interval of QTL map location. Behav Genet 27:125–132
Dill-Macky R, Rees RG, Johnston RP, Platz GJ, Mayne A (1989) Stem and leaf rusts of barley. In: Queensland Wheat Research Institute Biennial Report 1984–86. Queensland Department of Primary Industries, Toowoomba, pp 38–40
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379
Golegaonkar PG, Singh D, Park RF (2009) Evaluation of seedling and adult plant resistance to Puccinia hordei in barley. Euphytica 166:183–197
Golegaonkar PG, Park RF, Singh D (2010) Genetic analysis of adult plant resistance to Puccinia hordei in barley. Plant Breed 129:162–166
Gonzalez AM, Marcel TC, Niks RE (2012) Evidence for a minor gene-for-minor gene interaction explaining nonhypersensitive polygenic partial disease resistance. Phytopathology 102:1086–1093
Griffey CA, Das MK, Baldwin RE, Waldenmaier CM (1994) Yield losses in winter barley resulting from a new race of Puccinia hordei in North-America. Plant Dis 78:256–260
Guo B, Sleper DA, Lu P, Shannon JG, Nguyen HT, Arelli PR (2006) QTLs associated with resistance to soybean cyst nematode in soybean: meta-analysis of QTL locations. Crop Sci 46:595–602
Hastie T, Tibshirani R, Narasimhan B, Chu G (2013) Impute: imputation for microarray data. R package version 1320
Hickey LT, Lawson W, Platz GJ, Dieters M, Arief VN, German S, Fletcher S, Park RF, Singh D, Pereyra S, Franckowiak J (2011) Mapping Rph20: a gene conferring adult plant resistance to Puccinia hordei in barley. Theor Appl Genet 123:55–68
Hickey LT, Lawson W, Platz GJ, Dieters M, Franckowiak J (2012) Origin of leaf rust adult plant resistance gene Rph20 in barley. Genome 55:396–399
Hong M, Singh RP (1996) Contribution of adult plant resistance gene Yr18 in protecting wheat from yellow rust. Plant Dis 80:66–69
Kicherer S, Backes G, Walther U, Jahoor A (2000) Localising QTLs for leaf rust resistance and agronomic traits in barley (Hordeum vulgare L.). Theor Appl Genet 100:881–888
Lagudah ES, McFadden H, Singh RP, Huerta-Espino J, Bariana HS, Spielmeyer W (2006) Molecular genetic characterization of the Lr34/Yr18 slow rusting resistance gene region in wheat. Theor Appl Genet 114:21–30
Lande R, Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743–756
Liu F, Gupta S, Zhang X-Q, Jones M, Loughman R, Lance R, Li C (2011) PCR markers for selection of adult plant leaf rust resistance in barley (Hordeum vulgare L.). Mol Breed 28:657–666
Long NV, Dolstra O, Malosetti M, Kilian B, Graner A, Visser RGF, van der Linden CG (2013) Association mapping of salt tolerance in barley (Hordeum vulgare L.). Theor Appl Genet 126:2335–2351
Mace ES, Jordan DR (2011) Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement. Theor Appl Genet 123:169–191
Mace ES, Rami JF, Bouchet S, Klein PE, Klein RR, Kilian A, Wenzl P, Xia L, Halloran K, Jordan DR (2009) A consensus genetic map of sorghum that integrates multiple component maps and high-throughput diversity array technology (DArT) markers. BMC Plant Biol 9:13
Marcel TC, Varshney RK, Barbieri M, Jafary H, de Kock MJD, Graner A, Niks RE (2007) A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues. Theor Appl Genet 114:487–500
McIntosh RA (1992) Close genetic-linkage of genes conferring adult-plant resistance to leaf rust and stripe rust in wheat. Plant Pathol 41:523–527
McNeal FH, Konzak CF, Smith EP, Täte WS, Russell TS (1971) A uniform system for recording and processing cereal research data. In: Agricultural Research Service bulletin. United States Department of Agriculture, Washington, DC, pp 34–121
Park RF (2009) New barley leaf rust pathotype virulent for Rph3. Plant Breeding Institute Cereal Rust Report, vol 7. http://sydney.edu.au/agriculture/documents/pbi/cereal_rust_report_2009_vol_7_5.pdf. Accessed 20 Oct 2013
Park RF, Karakousis A (2002) Characterization and mapping of gene Rph19 conferring resistance to Puccinia hordei in the cultivar ‘Reka 1’ and several Australian barleys. Plant Breed 121:232–236
Park RF, Williams M (2011) Barley leaf rust (caused by Puccinia hordei). Plant Breeding Institute Cereal Rust Survey Annual Report, vol 7, pp 7–8. http://sydney.edu.au/agriculture/documents/pbi/cereal_rust_survey_2010_11.pdf. Accessed 19 Oct 2013
Parlevliet JE, van Ommeren A (1975) Partial resistance of barley to leaf rust, Puccinia hordei. 2. Relationship between field trials, micro plot tests and latent period. Euphytica 24:293–303
Perrier X, Jacquemoud-Collet J (2006) DARwin software. http://darwin.cirad.fr
Pretorius ZA, Pienaar L, Prins R (2007) Greenhouse and field assessment of adult plant resistance in wheat to Puccinia striiformis f. sp tritici. Australas Plant Pathol 36:552–559
Qi X, Niks RE, Stam P, Lindhout P (1998) Identification of QTLs for partial resistance to leaf rust (Puccinia hordei) in barley. Theor Appl Genet 98:178
Roane CW (1972) Barley leaf rust around the world: a review. Barley Genet Newsl 15:23–27
Roy JK, Smith KP, Muehlbauer GJ, Chao S, Close TJ, Steffenson BJ (2010) Association mapping of spot blotch resistance in wild barley. Mol Breed 26:243–256
Singh S, Bowden RL (2011) Molecular mapping of adult-plant race-specific leaf rust resistance gene Lr12 in bread wheat. Mol Breed 28:137–142
Singh D, Macaigne N, Park RF (2013) Rph20: adult plant resistance gene to barley leaf rust can be detected at early growth stages. Eur J Plant Pathol 137:719–725
Smith (2011) A whole genome approach for qtl detection using a linear mixed model with correlated marker effects. In: Australasian Applied Statistics Conference 2011, Palm Cove, 12–15 July 2011
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
Verbyla AP, Cullis BR, Thompson R (2007) The analysis of QTLs by simultaneous use of the full linkage map. Theor Appl Genet 116:95–111
Visioni A, Tondelli A, Francia E, Pswarayi A, Malosetti M, Russell J, Thomas W, Waugh R, Pecchioni N, Romagosa I, Comadran J (2013) Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.). BMC Genomics 14:424
von Korff M, Wang H, Leon J, Pillen K (2005) AB-QTL analysis in spring barley. I. Detection of resistance genes against powdery mildew, leaf rust and scald introgressed from wild barley. Theor Appl Genet 111:583–590
Wang G-X, Chen Y, Zhao J-R, Li L, Korban SS, Wang F-G, Li J-S, Dai J-R, Xu M-L (2007) Mapping of defense response gene homologs and their association with resistance loci in maize. J Integr Plant Biol 49:1580–1598
Wenzl P, Li H, Carling J, Zhou M, Raman H, Paul E, Hearnden P, Maier C, Xia L, Caig V, Ovesná J, Cakir M, Poulsen D, Wang J, Raman R, Smith KP, Muehlbauer GJ, Chalmers KJ, Kleinhofs A, Huttner E, Kilian A (2006) A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genomics 7:206
Zhou H, Steffenson B (2013a) Genome-wide association mapping reveals genetic architecture of durable spot blotch resistance in US barley breeding germplasm. Mol Breed 32:139–154
Zhou H, Steffenson BJ (2013b) Association mapping of septoria speckled leaf blotch resistance in US barley breeding germplasm. Phytopathology 103:600–609
Acknowledgments
This research was supported by the Grains Research and Development Corporation of Australia (UQ00056). The authors thank Ms Julie McKavanagh (DAFFQ), Mr Ryan Fowler (DAFFQ and QAAFI) and Ms Janet Barsby (DAFFQ) for technical assistance in the laboratory and field. We also wish to acknowledge the staff at the University of Sydney for providing seedling and adult plant data on leaf rust responses for the breeding populations assessed at Cobbitty.
Conflict of interest
The authors declare that they have no conflict of interest.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by X. Qi.
Electronic supplementary material
Below is the link to the electronic supplementary material.
122_2014_2291_MOESM1_ESM.xls
Supplementary material 1 The integrated map used as the reference map for QTL projection including Wenzl et al. (2006), RWA (ND19119-5/PI 642914) and ND24260/Flagship maps, including a total of 3,476 markers positions (XLS 385 kb)
Rights and permissions
About this article
Cite this article
Ziems, L.A., Hickey, L.T., Hunt, C.H. et al. Association mapping of resistance to Puccinia hordei in Australian barley breeding germplasm. Theor Appl Genet 127, 1199–1212 (2014). https://doi.org/10.1007/s00122-014-2291-1
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-014-2291-1