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RGA-ILP, a new type of functional molecular markers in bread wheat

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Abstract

Markers targeting intron length polymorphism of resistance gene analogues (RGA-ILP) are not only expected to be more polymorphic than those designed from conserved exons, but also have potential resistance gene function. Based on known domains of resistance genes, more than 900 wheat RGAs were mined from public databases. Two hundred and seventy-eight intron-containing RGA candidates were predicted based on rice genomic DNA information, and 50 of them were selected for evaluation and mapping. A total of 150 RGA-ILP primer pairs, consisting of exon-primed intron-crossing primers to amplify the intronic regions of RGAs were designed. One hundred and thirty-five pairs were successfully amplified with similar or larger than expected product lengths. Three mapping populations (SOpop, NYpop and WSpop) were screened and 28 pairs of RGA-ILP primers gave reproducible polymorphic amplifications between the mapping parents. Sixteen, 14 and five loci were integrated into SOpop, NYpop and WSpop maps, respectively. The results demonstrated that this method provides an efficient approach for developing polymorphic markers.

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References

  • Aarts MGM, te Lintel Hekket B, Holub EB, Beynon JL, Stiekema WJ, Pereira A (1998) Identification of R gene homologous DNA fragments genetically linked to disease resistance loci in Arabidopsis thaliana. Mol Plant Microbe Interact 11:251–258

    Article  CAS  PubMed  Google Scholar 

  • Chen XM, Line RF, Leung H (1998) Genome scanning for resistance gene analogs in rice, barley, and wheat by high resolution electrophoresis. Theor Appl Genet 97:345–355

    Article  CAS  Google Scholar 

  • Dangl JL, Jones DG (2001) Plant pathogens and integrated defence responses to infection. Nature 411:826–833

    Article  CAS  PubMed  Google Scholar 

  • Devos KM, Atkinson MD, Chinoy CN, Liu C, Gale MD (1992) RFLP based genetic map of the homoeologous group 3 chromosomes of wheat and rye. Theor Appl Genet 83:931–939

    Article  CAS  Google Scholar 

  • Dilbirligi M, Gill KS (2003) Identification and analysis of expressed resistance gene sequences in wheat. Plant Mol Biol 53:771–787

    Article  CAS  PubMed  Google Scholar 

  • Dilbirligi M, Erayman M, Sandhu D, Sidhu D, Gill KS (2004) Identification of wheat chromosomal regions containing expressed resistance genes. Genetics 166:461–481

    Article  CAS  PubMed  Google Scholar 

  • Feuillet C, Travella S, Stein N, Albar L, Nublat 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  CAS  PubMed  Google Scholar 

  • Fu DL, Uauy C, Distelfeld A, Blechl A, Epstein L, Chen X, Sela H, Fahima T, Dubcovsky J (2009) A kinase START gene confers temperature dependent resistance to wheat stripe rust. Science 323:1357–1360

    Article  CAS  PubMed  Google Scholar 

  • Gupta PK, Balyan HS, Edwards KJ, Isaac P, Korzun V, Röder M, Gautier MF, Joudrier P, Schlatter AR, Dubcovsky J, de La Pena RC, Khairallah M, Penner G, Hayden MJ, Sharp P, Keller B, Wang RCC, Hardouin JP, Jack P, Leroy P (2002) Genetic mapping of 66 new microsatellite (SSR) loci in bread wheat. Theor Appl Genet 105:413–422

    Article  CAS  PubMed  Google Scholar 

  • Hammond-Kosack KE, Jones JD (1997) Plant disease resistance genes. Annu Rev Plant Physiol Plant Mol Biol 48:575–608

    Article  CAS  PubMed  Google Scholar 

  • He M, Haymer DS (1997) Polymorphic intron sequences detected within and between populations of the oriental fruit fly (Diptera: Tephritidae). Ann Entomol Soc Am 90:825–831

    CAS  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Hughes SS, Buckley CO, Neafsey DE (2008) Complex selection on intron size in Cryptococcus neoformans. Mol Biol Evol 25:247–253

    Article  CAS  PubMed  Google Scholar 

  • Ishikawa G, Yonemaru J, Saito M, Nakamura T (2007) PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes. BMC Genomics 8:135

    Article  PubMed  CAS  Google Scholar 

  • Kanazin V, Marck LF, Shoemarker RC (1996) Resistance gene analogs are conserved and clustered in soybean. Proc Natl Acad Sci USA 93:11746–11750

    Article  CAS  PubMed  Google Scholar 

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

    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  CAS  PubMed  Google Scholar 

  • Lagudah ES, Moullet O, Appels R (1997) Map based cloning of a gene sequence encoding a nucleotide binding domain and a leucine rich region at the Cre3 nematode resistance locus of wheat. Genome 40:659–665

    Article  CAS  PubMed  Google Scholar 

  • Laroche A, Frick MM, Huel R, Nykiforuk C, Conner B, Kuzyk A (2000) Molecular identification of the wheat stripe rust resistance gene Yr10, the first full length leucine zipper nucleotide binding site leucine rich repeat resistance gene in cereals. http://www.ncbi.nlm.nih.gov/nuccore/11990499?report=genbank

  • Lu YQ, Wang XS, Huang WS, Xiao TX, Zheng Y, Wu WR (2006) Development of amplified consensus genetic markers in Gramineae based on rice intron length polymorphisms. Sci Agric Sin 39:433–439

    CAS  Google Scholar 

  • Maleki L, Faris JD, Bowden RL, Gill BS, Fellers JP (2003) Physical and genetic mapping of wheat kinase analogs and NBS-LRR resistance gene analogs. Crop Sci 43:660–670

    Article  CAS  Google Scholar 

  • McFadden HG, Lehmensiek A, Lagudah ES (2006) Resistance gene analogues of wheat: molecular genetic analysis of ESTs. Theor Appl Genet 113:987–1002

    Article  CAS  PubMed  Google Scholar 

  • McIntosh RA, Yamazaki Y, Dubcovsky J, Rogers J, Morris C, Somers DJ, Appels R, Devos KM (2008) In: Proceedings of the 11th international wheat genetics symposium, Brisbane, Australia

  • Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW, Young ND (1999) Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide binding superfamily. Plant J 20:317–332

    Article  CAS  PubMed  Google Scholar 

  • Mondragon-Palomino M, Meyers BC, Michelmore RW, Gaut BS (2002) Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res 12:1305–1315

    Article  CAS  PubMed  Google Scholar 

  • Nori S, Combes MC, Anthomy F, Lashermes P (2001) Origin, diversity and evolution of NBS type disease resistance gene homologues in coffee tree (coffea. L). Mol Genet Genomics 265:654–662

    Article  Google Scholar 

  • Salse J, Bolot S, Throude M, Jouffe V, Piegub B, Quraishi UM, Calcagno T, Cookeb R, Delsenyb M, Feuillet C (2008) Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell 20:11–24

    Article  CAS  PubMed  Google Scholar 

  • Seah S, Spielmeyer W, Jahier J, Sivasithamparam K, Lagudah ES (2000) Resistance gene analogs within an introgressed chromosomal segment derived from Triticum ventricosum that confers resistance to nematode and rust pathogens in wheat. Mol Plant Microbe Interact 13:334–341

    Article  CAS  PubMed  Google Scholar 

  • Spielmeyer W, Huang L, Bariana H, Laroche A, Gill BS, Lagudah ES (2000) NBS-LRR sequence family is associated with leaf and stripe rust resistance on the end of homoeologous chromosome group 1S of wheat. Theor Appl Genet 101:1139–1144

    Article  CAS  Google Scholar 

  • Tamura K, Yonemaru J, Hisano H, Kanamori H, King J, King I, Tase K, Sanada Y, Komatsu T, Yamada T (2009) Development of intron-flanking EST markers for the Lolium/Festuca complex using rice genomic information. Theor Appl Genet. doi: 10.1007/s00122-009-1003-8

  • Wei H, Fu Y, Arora R (2005) Intron-flanking EST-PCR markers: from genetic marker development to gene structure analysis in Rhododendron. Theor Appl Genet 111:1347–1356

    Article  CAS  PubMed  Google Scholar 

  • Yahiaoui N, Srichumpa P, Dudler R, Keller B (2004) Genome analysis at different ploidy levels allows cloning of the powdery mildew resistance gene Pm3b from hexaploid wheat. Plant J 37:528–538

    Article  CAS  PubMed  Google Scholar 

  • Yu YG, Buss GR, Saghai-Maroof MA (1996) Isolation of a superfamily of candidate disease resistance genes in soybean based on a conserved nucleotide binding site. Proc Natl Acad Sci USA 93:11751–11756

    Article  CAS  PubMed  Google Scholar 

  • Zhao XQ, Wu WR (2008) Construction of a genetic map based on ILP markers in rice. Hereditas 30:225–230

    CAS  PubMed  Google Scholar 

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Acknowledgments

The authors thank Prof. Robert McIntosh and another three anonymous reviewers for helpful comments on the manuscript. The study was supported by National 863 Program of China (No. 2006AA10A104).

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Authors and Affiliations

  1. Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China

    World Shang, Ronghua Zhou, Jizeng Jia & Lifeng Gao

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  1. World Shang
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  2. Ronghua Zhou
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  3. Jizeng Jia
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  4. Lifeng Gao
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Correspondence to Jizeng Jia or Lifeng Gao.

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Shang, W., Zhou, R., Jia, J. et al. RGA-ILP, a new type of functional molecular markers in bread wheat. Euphytica 172, 263–273 (2010). https://doi.org/10.1007/s10681-009-0063-9

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  • DOI: https://doi.org/10.1007/s10681-009-0063-9

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