Skip to main content
SpringerLink
Log in

Population-based resequencing analysis of improved wheat germplasm at wheat leaf rust resistance locus Lr21

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

Abstract

Little is known about the genetic impacts of modern plant breeding on specific breeding target loci. Resequencing cloned genes can identify all mutations in single genes for population-based analyses of genetic changes in improved gene pools. Ninety-five wheat cultivars released in Canada from 1845 to 2004 were sequenced at the wheat leaf rust resistance locus Lr21. Characterization of the DNA fragment of length 4,071 bp, covering the Lr21 gene from −92 to +4,261, revealed 13 SNPs, four indels, 10 haplotypes, and 4 major haplotype groups. A new SCAR marker was developed to identify the resistant haplotype and haplotype groups. Non-synonymous polymorphic sites and haplotype numbers were increased over the 100 years of wheat breeding. Nucleotide diversity of the wheat cultivars was gradually reduced from 1845 to 1993 and increased after the release of the first Lr21 wheat cultivar AC Cora in 1994. Positive selection measured with Tajima’s D was observed in the cultivars released before 1935. At least two recombination events were inferred in those cultivars released before 1993. Linkage disequilibrium at the locus was decreased over time. These findings demonstrate not only the effectiveness of the wheat breeding in the improvement of leaf rust resistance, but also are useful to understand the genetic influences of a long-term artificial selection on individual loci.

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

  • Aranzana MJ, Kim S, Zhao K et al (2005) Genome-wide association mapping in Arabidopsis thaliana identifies previously known genes responsible for variation in flowering time and pathogen resistance. PLoS Genet 1:e60

    Article  PubMed  Google Scholar 

  • Borlaug N (2007) Sixty-two years of fighting hunger: personal recollections. Euphytica 157:287–297

    Article  Google Scholar 

  • Chen H, Morrell PL, de la Cruz M, Clegg MT (2008) Nucleotide diversity and linkage disequilibrium in wild avocado (Persea americana Mill.). J Hered 99:382–389

    Article  PubMed  CAS  Google Scholar 

  • Cloutier S, McCallum BD, Loutre C, Banks TW, Wicker T, Feuillet C, Keller B, Jordan MC (2007) Leaf rust resistance gene Lr1, isolated from bread wheat (Triticum aestivum L.) is a member of the large psr567 gene family. Plant Mol Biol 65:93–106

    Article  PubMed  CAS  Google Scholar 

  • DePauw RM, Boughton GR, Knott DR (1995) Hard red spring wheat. In: Slinkard AE, Knott DR (eds) Harvest of gold: the history of field crop breeding in Canada. Univ of Saskatchewan, SK, pp 5–35

    Google Scholar 

  • Donini P, Law JR, Koebner RMD, Reeves JC, Cooke RJ (2000) Temporal trends in the diversity of UK wheat. Theor Appl Genet 100:912–917

    Article  Google Scholar 

  • Dyck PL (1993) The inheritance of leaf rust resistance in the wheat cultivar Pasqua. Can J Plant Sci 73:903–906

    Article  Google Scholar 

  • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    Article  PubMed  CAS  Google Scholar 

  • Feuillet C, Travella S, Stein N, Albar L, Nubla A, Keller B (2003) Map-based isolation of the leaf rust disease resistance gene Lr10 from the hexaploid wheat (Triticum aestivum L.) genome. Proc Natl Acad Sci USA 100:15253–15258

    Article  PubMed  CAS  Google Scholar 

  • Fu YB (2006) Impact of plant breeding on genetic diversity of agricultural crops: searching for molecular evidence. Plant Genet Resour 4:71–78

    Article  CAS  Google Scholar 

  • Fu YB (2010) FPTest: a SAS routine for testing differences in allelic count. Mol Ecol Resour 10:389–392

    Article  PubMed  CAS  Google Scholar 

  • Fu YB, Somers DJ (2009) Genome-wide reduction of genetic diversity in wheat breeding. Crop Sci 49:161–168

    Article  Google Scholar 

  • Fu YB, Peterson GW, Scoles G, Rossnagel B, Schoen DJ, Richards RW (2003) Allelic diversity changes in 96 Canadian oat cultivars released from 1886 to 2001. Crop Sci 43:1989–1995

    Article  Google Scholar 

  • Fu YB, Peterson GW, Richards KW, Somers DJ, DePauw RM, Clarke JM (2005) Allelic reduction and genetic shift in the Canadian red hard spring wheat germplasm released from 1886 to 2004. Theor Appl Genet 110:1505–1516

    Article  PubMed  Google Scholar 

  • Fu YB, Peterson GW, Yu J-K, Gao LF, Jia JZ, Richards KW (2006) Impact of plant breeding on genetic diversity of the Canadian hard red spring wheat germplasm as revealed by EST-derived SSR markers. Theor Appl Genet 112:1239–1247

    Article  PubMed  CAS  Google Scholar 

  • Hanson WD (1959) Theoretical distribution of the initial linkage block lengths intact in the gametes of a population intermated for n generations. Genetics 44:839–846

    PubMed  CAS  Google Scholar 

  • Hill WG, Rasbash J (1986) Models of long term artificial selection in finite population. Genet Res 48:41–50

    Article  PubMed  CAS  Google Scholar 

  • Huang L, Gill BS (2001) An RGA-like marker detects all known Lr21 leaf rust resistance gene family members in Aegilops tauschii and wheat. Theor Appl Genet 103:1007–1013

    Article  CAS  Google Scholar 

  • Huang XQ, Hsam SLK, Zeller FJ, Wenzel G, Mohler V (2000) Molecular mapping of the wheat powdery mildew resistance gene Pm24 and marker validation for molecular breeding. Theor Appl Genet 101:407–414

    Article  CAS  Google Scholar 

  • Huang L, Brooks SA, Li W, Fellers J, Trick HN, Gill B (2003) Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploidy genome of breed wheat. Genetics 164:655–664

    PubMed  CAS  Google Scholar 

  • Huang L, Brooks S, Li W, Fellers J, Nelson JC, Gill B (2009) Evolution of new disease specificity at a simple resistance locus in a crop-weed complex: reconstitution of the Lr21 gene in wheat. Genetics 182:595–602

    Article  PubMed  CAS  Google Scholar 

  • Hudson RR, Kaplan NL (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111:147–164

    PubMed  CAS  Google Scholar 

  • Hyten DL, Song Q, Zhu Y, Choi I-Y, Nelson RL, Costa JM, Specht JE, Shoemaker RC, Cregan PB (2006) Impacts of genetic bottlenecks on soybean genome diversity. Proc Natl Acad Sci USA 103:16666–16671

    Article  PubMed  CAS  Google Scholar 

  • Jones H, Leigh FJ, Mackay I, Bower MA, Smith LMJ, Charles MP, Jones G, Jones MK, Brown TA, Powell W (2008) Population based re-sequencing reveals that the flowering time adaptation of cultivated barley originated east of the Fertile Crescent. Mol Biol Evol 25:2211–2219

    Article  PubMed  CAS  Google Scholar 

  • Kolmer JA (1996) Genetics of resistance to what leaf rust. Ann Rev Phytopathol 34:435–455

    Article  CAS  Google Scholar 

  • Krattinger SG, Lagudah ES, Spielmeyer W, Singh RP, Huerta-Espino J, McFadden H, Bossolini E, Selter LL, Keller B (2009) A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science 323:1360–1363

    Article  PubMed  CAS  Google Scholar 

  • Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452

    Article  PubMed  CAS  Google Scholar 

  • Liu XM, Smith CM, Gill BS, Tolmay V (2001) Microsatellite markers linked to six Russian wheat aphid resistance genes in wheat. Theor Appl Genet 102:504–510

    Article  CAS  Google Scholar 

  • Malysheva-Otta L, Ganal MW, Law JR, Reeves JC, Röder MS (2007) Temporal trends of genetic diversity in European barley cultivars (Hordeum vulgare L.). Mol Breed 20:309–322

    Article  Google Scholar 

  • Marais GF, McCallum B, Marais AS (2008) Wheat leaf rust resistance gene Lr59 derived from Aegilops peregrina. Plant Breed 127:340–345

    Article  Google Scholar 

  • McCallum BD, DePauw RM (2008) A review of wheat cultivars grown in the Canadian prairies. Can J Plant Sci 88:649–677

    Article  Google Scholar 

  • McCallum BD, Seto-Goh P (2008) Physiologic specialization of Puccinia triticina in Canada in 2005. Can J Plant Pathol 30:124–132

    Article  CAS  Google Scholar 

  • McCallum BD, Fetch T, Chong J (2007) Cereal rust control in Canada. Aust J Agric Res 58:639–647

    Article  Google Scholar 

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

    Google Scholar 

  • Morrison JW (1960) Marquis wheat, a triumph of scientific endeavor. Agric Hist 34:182–188

    Google Scholar 

  • National Research Council, Committee on Genetic Vulnerability of Major Crops (1972) Genetic Vulnerability of Major Crops. Natl Acad Sci, Washington, DC

    Google Scholar 

  • Neatby KW (1942) New varieties of spring wheat resistant to stem rust in the Canadian West, and their genetical background. Emp J Exp Agric 10:245–252

    Google Scholar 

  • Peterson RF, Campbell AB, Hannah AE (1948) A diagrammatic scale for estimating rust intensity on leaves and stems of cereals. Can J Res 26:496–500

    Article  Google Scholar 

  • Robertson A (1960) A theory of limits in artificial selection. Proc R Soc Lond B153:234–249

    Article  Google Scholar 

  • Rowland GG, Kerber ER (1974) Telocentric mapping in hexaploid wheat of genes for leaf rust resistance and other characters derived from Aegilops squarrosa. Can J Genet Cytol 16:137–144

    Google Scholar 

  • SAS Institute Inc. (2008) The SAS system for windows V9.2. SAS Institute Incorporated, Cary

    Google Scholar 

  • Singh S, Franks CD, Huang L, Brown-Guedira GL, Marshall DS, Gill BS, Fritz A (2004) Lr41, Lr39, and a leaf rust resistance gene from Aegilops cylindrica may be allelic and are located on wheat chromosome 2DS. Theor Appl Genet 108:586–591

    Article  PubMed  CAS  Google Scholar 

  • Slinkard AE, Knott DR (1995) Harvest of gold: the history of field crop breeding in Canada. Univ of Saskatchewan, SK

    Google Scholar 

  • Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437–460

    PubMed  CAS  Google Scholar 

  • Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595

    PubMed  CAS  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  PubMed  CAS  Google Scholar 

  • Topol EJ, Frazer KL (2007) The resequencing imperative. Nat Genet 39:439–440

    Article  PubMed  CAS  Google Scholar 

  • Tripp R (1996) Biodiversity and modern crop varieties: sharpening the debate. Agric Hum Values 13:48–63

    Article  Google Scholar 

  • Wall JD (1999) Recombination and the power of statistical tests of neutrality. Genet Res 74:65–79

    Article  Google Scholar 

  • Walsh B (2005) Population- and quantitative-genetic models of selection limits. Plant Breed Rev 24:177–225

    Google Scholar 

  • Zeng Z-B, Cockerham CC (1990) Long-term response to artificial selection with multiple alleles—study by simulation. Theor Popul Biol 37:254–272

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

Authors would like to thank Dr. Ron DePauw for his help in wheat class identification; Mr. Dallas Kessler and Mr. Eugene Timmermans for their assistance in accession identification and rust resistance data extraction from GRIN-CA; Ms. Marcie Heggie for her technical assistance in DNA sequencing; and three anonymous reviewers for their constructive comments on an early version of the manuscript.

Author information

Authors and Affiliations

  1. Plant Gene Resources of Canada, Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada

    Yong-Bi Fu & Gregory W. Peterson

  2. Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada

    Brent D. McCallum

  3. Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA

    Li Huang

Authors
  1. Yong-Bi Fu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gregory W. Peterson
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Brent D. McCallum
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Li Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yong-Bi Fu.

Additional information

Communicated by M. Sorrells.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Table S1 (DOCX 28 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Fu, YB., Peterson, G.W., McCallum, B.D. et al. Population-based resequencing analysis of improved wheat germplasm at wheat leaf rust resistance locus Lr21 . Theor Appl Genet 121, 271–281 (2010). https://doi.org/10.1007/s00122-010-1308-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-010-1308-7

Keywords

Search

Navigation