Skip to main content
Log in

Exploring wheat landraces for rust resistance using a single marker scan

  • Published:
Euphytica Aims and scope Submit manuscript

Abstract

Marker-trait associations identified in diverse germplasm can be exploited in crop improvement programs. An attempt to establish such associations was made by evaluating 205 wheat landraces for stripe rust, leaf rust and stem rust responses in the field over three crop seasons. Diversity arrays technology was used to genotype the landraces and associations were identified using a single-marker scan. Sixty-eight markers were significantly associated with rust resistance. Several significantly associated loci coincided with the presence of known major genes or QTL for rust resistance. In contrast, many marker-rust response associations identified in this analysis for each of the three rust diseases uncovered new loci. Dual associations; stripe rust-leaf rust (1AL, 2BS, 2BL, 3DL, 5BS, 6BS and 7DL), leaf rust-stem rust (5BL) and stripe rust-stem rust (4BL and 6AS) resistance were also observed. These associations could enable a cost-effective targeted mapping of dual rust resistance. Some marker-trait associations identified in this study have been validated through genetic analyses and formal naming of resistance loci.

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

Access this article

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

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Abdallah O, Nazari K, Clarke E (2010) ICARDA calls for action to tackle wheat stripe rust threat to Middle East breadbasket. ICARDA media release. (http://icardablog.wordpress.com)

  • Anderson JR, Zein I, Wenzel G, Krutzfeldt B, Eder, OuZunova M, Lubberstedt T (2005) High levels of linkage disequilibrium and associations with forage quality at a Phenylalanine Ammonia-Lyase locus in European maize (Zea mays L.) inbreds. Theor Appl Genet 114:307–319

    Article  Google Scholar 

  • Aranzana MJ, Kim S, Zhao K, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang C, Toomajian C, Traw B, Zheng H, Bergelson J, Dean C, Marjoram P, Nordborg (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1:e60

    Article  PubMed  Google Scholar 

  • Arief VN (2010) Methodology development to integrate phenotypic and genotypic data from a plant breeding program through association analysis with a case study using data from the CIMMYT International Spring Wheat field trials. PhD Thesis, School of Agriculture and Food Sciences, The University of Queensland, Australia

  • Arief VN, Kroonenberg PM, DeLacy IH, Dieters MJ, Crossa J, Dreisigacker S, Braun HJ, Basford KE (2010) Construction and three-way ordination of wheat phenome atlas. J Appl Probab Stat 5:95–118

    Google Scholar 

  • Baker EP, McIntosh RA (1973) Utilization of marked telocentric chromosomes in more efficient genetic analysis. In Sears ER, Sears LMS (eds) Proceedings 4th International Wheat Genet Symposium, Agricultural Experiment Station, University of Missouri, Columbia, pp 635–636

  • Bansal UK, Bossolini E, Miah H, Keller B, Park RF, Bariana HS (2008a) Genetic mapping of seedling and adult plant stem rust resistance in two European winter wheat cultivars. Euphytica 164:821–828

    Article  Google Scholar 

  • Bansal UK, Hayden MJ, Venkata BP, Khanna R, Saini RG, Bariana HS (2008b) Genetic mapping of adult plant leaf rust resistance genes Lr48 and Lr49 in wheat. Theor Appl Genet 117:307–312

    Article  PubMed  CAS  Google Scholar 

  • Bansal UK, Hayden MJ, Gill MB, Bariana HS (2010) Chromosome location of the uncharacterized stripe rust resistance gene in wheat cultivar Rubric. Euphytica 171:121–127

    Article  Google Scholar 

  • Bansal UK, Forrest KL, Hayden MJ, Miah H, Singh H, Bariana HS (2011) Characterization of a new stripe rust resistance gene Yr47 and its genetic association with the leaf rust resistance gene Lr52. Theor Appl Genet 122:1461–1466

    Article  PubMed  CAS  Google Scholar 

  • Bariana H, Hayden M, Ahmed N, Bell J, Sharp P, McIntosh R (2001) Mapping of durable adult plant and seedling resistances to stripe rust and stem rust diseases in wheat. Aust J Agric Res 52:1247–1255

    Article  CAS  Google Scholar 

  • Bariana HS, Parry N, Barclay IR, Loughman R, McLean RJ, Shankar M, Wilson RE, Willey NJ, Francki M (2005) Identification and characterization of stripe rust resistance gene Yr34 in common wheat. Theor Appl Genet 112:1143–1148

    Article  Google Scholar 

  • Bariana H, Lehmensiek A, Bansal U, Kaur J, Willey N, Singh D, Park R (2006) New adult plant rust resistance genes in Australian wheat cultivars. ‘Breeding for Success: Diversity in Action’. In: CF Mercer (ed) Proceedings 13th Australasian plant breeding conference, Christchurch, 18–21 April 2006

  • Bariana HS, Miah H, Brown GN, Willey N, Lehmensiek A (2007) Molecular mapping of durable rust resistance in wheat and its implication in breeding. In: Wheat Production in Stressed Environments. Developments in plant breeding. Springer, 12: 723–728

  • Bariana H, Bansal U, Schmidt A, Lehmensiek A, Kaur J, Miah H, Howes N, McIntyre C (2010) Molecular mapping of adult plant stripe rust resistance in wheat and identification of pyramided QTL genotypes. Euphytica 176:251–260

    Article  CAS  Google Scholar 

  • Beavis WD (1998) QTL analyses: power, precision and accuracy. In: Paterson HA (ed) Molecular dissection of complex traits. CRC Press, Boca raton, pp 145–162

    Google Scholar 

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

    Google Scholar 

  • Bhavani S, Bansal UK, Hare R, Bariana HS (2008) Mapping of stem rust resistance genes in durum cultivar Arrivato. Int J Plant Breed 2:23–26

    Google Scholar 

  • Bhavani S, Singh RP, Argillier O, Huerto-Espino J, Singh S, Njau P (2011) Mapping of durable adult plant stem rust resistance in six CIMMYT wheats to Ug99 group of races. 2011 BGRI technical workshop, St Paul, Minnisota, USA pp 43–53

  • Boukhatem N, Baret PV, Mingeot D, Jacquemin JM (2002) Quantitative loci for resistance against yellow rust in two wheat-derived recombinant inbred line populations. Theor Appl Genet 104:111–118

    Article  PubMed  CAS  Google Scholar 

  • Breseghello F, Sorrells MS (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177

    Article  PubMed  Google Scholar 

  • Brown GN (1997) The inheritance and expression of leaf chlorosis associated with gene Sr2 for adult plant resistance to wheat stem rust. Euphytica 95:67–71

    Article  Google Scholar 

  • Carter AH, Chen XM, Garland-Campbell K, Kidwell KK (2009) Identifying QTL for high-temperature adult-plant resistance to stripe rust (Puccinia striiformis f. sp. tritici) in the spring wheat (Triticum aestivum L.) cultivar ‘Louise’. Theor Appl Genet 119:1119–1128

    Article  PubMed  Google Scholar 

  • Chhuneja P, Kaur S, Garg T, Ghai M, Kaur S, Parshar M, Bains NS, Goel RK, Keller B, Dhalliwal HS, Singh K (2007) Mapping of adult plant stripe rust resistance genes in diploid A genome species and their transfer to bread wheat. Theor Appl Genet 116:313–324

    Article  PubMed  Google Scholar 

  • Claude EE, Dyck PL, Evans LE (1986) An evaluation of 391 spring wheat introductions for resistance to stem rust and leaf rust. Can J Plant Pathol 8:132–139

    Article  Google Scholar 

  • Crossa J, Burgueno J, Dresigacker S, Vargas M, Herrera-Foessel SA, Lillemo M, Singh RP, Trethowan R, Warburton M, Franco J, Reynolds M, Crouch JH, Ortiz R (2007) Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics 177:1889–1913

    Article  PubMed  CAS  Google Scholar 

  • Devlin B, Risch N (1995) A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 29:311–322

    Article  PubMed  CAS  Google Scholar 

  • Dice LR (1945) Measures of the amount of ecological association between species. Ecology 26:297–302

    Article  Google Scholar 

  • Dyck PL (1994) Genetics of leaf rust resistance in 13 accessions of the Watkins wheat collection. Euphytica 80:151–155

    Article  Google Scholar 

  • Dyck PL, Jedel EE (1989) Genetics of resistance to leaf rust in two accessions of common wheat. Can J Plant Sci 69:531–534

    Article  Google Scholar 

  • Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57:461–485

    Article  PubMed  CAS  Google Scholar 

  • Herrara-Foessel S, Lagudah ES, Huerto-Espino J, Hayden MJ, Bariana HS, Singh D, Singh RP (2011) New slow-rusting leaf rust and stripe rust resistance genes Lr67 and Yr46 in wheat are pleiotropic or closely linked. Theor Appl Genet 122:239–249

    Article  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Hiebert C, Thomas J, McCallum B (2005) Locating the broad-spectrum wheat leaf rust resistance gene Lr52 (LrW) to chromosome 5B by a new cytogenetic method. Theor Appl Genet 110:1453–1457

    Article  PubMed  CAS  Google Scholar 

  • Jannink JL, Walsh JB (2002) Association mapping in plant populations. In: Kang MS (ed) Quantitative genetics genomics and plant breeding. CABI, Wallingford, pp 59–68

    Google Scholar 

  • Lagudah ES, McFadden H, Singh RP, Heurta-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

    Article  PubMed  CAS  Google Scholar 

  • Lin F, Chen XM (2007) Genetics and molecular mapping of genes for race-specific all-stage resistance and non-race specific high temperature adult-plant resistance to stripe rust in spring wheat cultivar Alpowa. Theor Appl Genet 114:1277–1287

    Article  PubMed  CAS  Google Scholar 

  • Lin F, Chen XM (2008) Molecular mapping of genes for race-specific overall resistance to stripe rust in wheat cultivar Express. Theor Appl Genet 116:797–806

    Article  PubMed  CAS  Google Scholar 

  • Lin F, Chen XM (2009) Quantitative trait loci for non-race-specific, high-temperature adult-plant resistance to stripe rust in wheat cultivar Express. Theor Appl Genet 118:631–642

    Article  PubMed  CAS  Google Scholar 

  • Lu Y, Lan C, Liang S, Zhou X, Liu D, Xhou G, Lu Q, Jing J, Wang M, Xia X, He Z (2009) QTL mapping of adult-plant resistance to stripe rust in Italian common wheat cultivars Libelulla and Strampelli. Theor Appl Genet 119:1349–1359

    Article  PubMed  CAS  Google Scholar 

  • Maccaferri M, Sanguineti MC, Mantovani P, Demontis A, Massi A, Ammar K, Kolmer JA, Czembor JH, Ezrati S, Tuberosa R (2010) Association mapping of leaf rust response in durum wheat. Mol Breed 26:189–228

    Article  CAS  Google Scholar 

  • Mackay TFC (2001) The genetic architecture of quantitative traits. Ann Rev Genet 33:303–339

    Article  Google Scholar 

  • Mago R, Simkova H, Brown-Guedira G, Dreisigacker S, Breen J, Jin Y, Singh R, Appels R, Lagudah ES, Ellis J, Dolezel J, Spielmeyer W (2011) An accurate DNA marker assay for stem rust resistance gene Sr2 in wheat. Theor Appl Genet 122:735–744

    Article  PubMed  CAS  Google Scholar 

  • Mallard S, Gaudet D, Aldeia A, Abelard C, Besnard AL, Sourdille P, Dedryver F (2005) Genetic analysis of durable resistance to yellow rust in bread wheat. Theor Appl Genet 110:1401–1409

    Article  PubMed  CAS  Google Scholar 

  • McCartney CA, Somers DJ, McCallum BD, Thomas J, Humphreys DG, Menzies JG, Brown PD (2005) Microsatellite tagging of the leaf rust resistance gene Lr16 on wheat chromosome 2BS. Mol Breed 15:329–337

    Article  CAS  Google Scholar 

  • Mcfadden ES (1930) A successful transfer of emmer characters to vulgare wheat. Agron J 22:1020–1034

    Article  Google Scholar 

  • McIntosh RA, Wellings CR, Park RF (1995) Wheat rusts: an atlas of resistance genes. CSIRO Press, Melbourne

    Book  Google Scholar 

  • McIntosh RA, Dubcovsky J, Rogers J, Morris C, Appels R, Xias XC (2011) Catalogue of gene symbols for wheat 2011 Supplement. www.shigen.nig.ac.jp/wheat/komugi/genes/macgene/supplement2011.pdf

  • Mcquitty LL (1967) Expansion of similarity analysis by reciprocal pairs for discrete and continous data. Educ Psychol Meas 27:253–255

    Article  Google Scholar 

  • Miller TE, Reader SM, Ambrose MJ (2000) The Watkins collection. Ann Wheat Newsl 46:72

    Google Scholar 

  • Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Nat Acad Sci USA 76:5269–5273

    Article  PubMed  CAS  Google Scholar 

  • Neumann K, Kobiljski B, Dencic S, Varshney RK, Borner A (2010) Genome wide association mapping : a case study in bread wheat (Triticum aestivum L.). Mol Breeding. doi: 10.1007/s11032-101-9411-7

  • Pretorius ZA, Singh RP, Wagoire WW, Payne TS (2000) Detection of virulence to wheat stem rust resistance gene Sr31 in Puccinia graminis f. sp. tritici in Uganda. Plant Dis 84:203

    Article  Google Scholar 

  • Price AL, Zaitlen NA, Reich D, Patterson N (2010) New approach to population stratification in genome-wide association studies. Nat Genet 11:459–463

    Article  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000b) Association mapping in structured populations. Am J Hum Genet 67:170–181

    Article  PubMed  CAS  Google Scholar 

  • Qamar Z, Bansal UK, Bariana HS (2009) Genetics of stem rust resistance in three durum wheat cultivars. Intl J Plant Breed 3:99–102

    Google Scholar 

  • Ravel C, Praud S, Murigneux A, Linossier L, Dardevet M, Balfourier F, Dufour P, Brunel D, Charmet G (2006) Identification of Glu-B1-1 as a candidate gene for the quantity of high-molecular weight glutenin in bread wheat (Triticum aestivum L.) by means of an association study. Theor Appl Genet 112:738–743

    Article  PubMed  CAS  Google Scholar 

  • Santra DK, Chen XM, Santra M, Campbell KG, Kidwell KK (2008) Identification and mapping QTL for high-temperature adult-plant resistance to stripe rust in winter wheat (Triticum aestivum L.) cultivar ‘Stephens’. Theor Appl Genet 117:793–802

    Article  PubMed  CAS  Google Scholar 

  • Semagn K, Bjornstad A, Skinnes H, Maroy AG, Tarkegne Y, William M (2006) Distribution of DArT, AFLP and SSR markers in a genetic linkage map of a doubled-haploid hexaploid wheat population. Genome 49:545–555

    Article  PubMed  CAS  Google Scholar 

  • Shah MM, Hassan A (2005) Distribution of genes and recombination on wheat homoeologous group 6 chromosomes: a synthesis of available information. Mol Breeding 15:45–53

    Article  CAS  Google Scholar 

  • Sheen SJ, Ebeltoft DC, Smith GS (1968) Association and inheritance of ‘‘black chaff’’ and stem rust reactions in Conley wheat crosses. Crop Sci 8:477–480

    Article  Google Scholar 

  • Simons K, Adate Z, Chao S, Zhang W, Rouse M, Jin Y, Elias E, Dubcovsky J (2011) Genetic maping of stem rust resistance gene Sr13 in tetraploid wheat. Theor Appl Genet 122:649–658

    Article  PubMed  Google Scholar 

  • Sokal RR, Michener CD (1958) A statistical method for evaluating systematic relationships. Univ Kans Sci Bull 38:1409–1438

    Google Scholar 

  • Sorenson T (1948) A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons. Biologiske Skrifter 5:1–34

    Google Scholar 

  • Stich B, Melchinger AE, Piepho HP, Heckenberger M, Maurer HP, Reif JC (2006) A new tes for family-based association mapping with inbred lines from plant breeding programs. Theor Appl Genet 113:1121–1130

    Article  PubMed  Google Scholar 

  • Stodart BJ, Mackey MC, Raman H (2007) Assessment of molecular diversity in landraces of bread wheat (Triticum aestivum L.) held in an ex situ collection with Diversity Arrays Technology (DArT™). Aust J Agric Res 58:1174–1182

    Article  CAS  Google Scholar 

  • Suenaga K, Singh RP, Huerto-Espino J, William HM (2003) Microsatellite markers for Lr34/Yr18 and other quantitative trait loci for leaf rust and stripe rust in bread wheat. Phytopathology 93:881–890

    Article  PubMed  CAS  Google Scholar 

  • Tar M, Purnhauser L, Csosz M (2008) Identification and localisation of molecular markers linked to the Lr52 leaf rust resistance gene of wheat. Cereal Res Commun 36:409–415

    Article  CAS  Google Scholar 

  • Tommasini L, Schnurbusch T, Fossati D, Mascher F, Keller B (2007) Association mapping of Stagonospora nodorum blotch resistance in modern European winter wheat varieties. Theor Appl Genet 115:697–708

    Article  PubMed  CAS  Google Scholar 

  • Uauy C, Brevis JC, Chen X, Khan I, Jackson L, Chicaiza O, Distelfeld A, Fahima T, Dubcovsky J (2005) High-temperature adult-plant (HTAP) stripe rust resistance gene Yr36 from Triticum turgidum ssp. dicoccoides is closely linked to the grain protein content locus Gpc-B1. Theor Appl Genet 112:97–105

    Article  PubMed  CAS  Google Scholar 

  • Vavilov NI (1926) Centres of origin of cultivated plants. Bull Appl Botany Plant Breed (Leningrad) 16:139–248

    Google Scholar 

  • Wellings CR (2011) Global status of stripe rust: a review of historical and current threats. Euphytica 179:129–141

    Article  Google Scholar 

  • William HM, Singh RP, Huerta-Espino J, Ortiz Islas S, Hoisington D (2003) Molecular marker mapping of leaf rust resistance Lr46 and its association with stripe rust resistance Yr29 in wheat. Phytopathology 93:153–159

    Article  PubMed  CAS  Google Scholar 

  • Williams WT (1976) Pattern Analysis in Agricultural Science. Elsevier, Amsterdam

    Google Scholar 

  • Wilson LM, Whitt SR, Ibanez AM, Rocheford TR, Goodman MM, Buckler ES IV (2004) Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16:2719–2733

    Article  PubMed  CAS  Google Scholar 

  • Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Current Opinion Biotech 17:155–160

    Article  CAS  Google Scholar 

  • Yu JM, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178:539–551

    Article  PubMed  Google Scholar 

  • Zhang XJ, Singh RP, Kolmer JA, Huerto-Espino J, Jin Y, Anderson JA (2008) Inheritance of leaf rust resistance in the CIMMYT wheat Weebill 1. Crop Sci 48:1037–1047

    Article  Google Scholar 

  • Zhao K, Aranzana MJ, Kim S, Lister C, Shindo C, Tang C, Toomajian C, Zheng H, Dean C, Marjoram P, Nordborg M (2007) An Arabidopsis example of association mapping in structured samples. PLoS Genet 3:e4

    Article  PubMed  Google Scholar 

  • Zöllner S, Pritchard JK (2005) Coalescent-based association mapping and fine mapping of complex trait loci. Genetics 169:1071–1092

    Article  PubMed  Google Scholar 

  • Zondervan KT, Gardon LR (2004) The complex interplay among factors that influence allelic association. Nature Rev Genet 5:89–100

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We thank Dr H. Raman for DArT data. We acknowledge financial support from Grains Research Development Corporation, Australia. Technical assistance by Dr Hanif Miah is gratefully acknowledged.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Urmil K. Bansal.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Bansal, U.K., Arief, V.N., DeLacy, I.H. et al. Exploring wheat landraces for rust resistance using a single marker scan. Euphytica 194, 219–233 (2013). https://doi.org/10.1007/s10681-013-0940-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10681-013-0940-0

Keywords

Navigation