Skip to main content
SpringerLink
Log in

Dissection of QTL alleles for blast resistance based on linkage and linkage disequilibrium mapping in japonica rice seedlings

  • Original Paper
  • Published:
Australasian Plant Pathology Aims and scope Submit manuscript

Abstract

Rice blast is one of the major fungal diseases that badly reduce rice production in China and worldwide. Molecular markers tightly linked to resistant genes can be used for marker-assisted and/or genomic selection. In this study, linkage mapping and association mapping were used to identify the QTLs for the disease index of 7 and 14 days after inoculation (DI7 and DI14) conferring resistance against two highly pathogenic and locally predominant isolates (DB22 and DB77) in japonica rice at the seedling stage. The recombinant inbred line (RIL) population with 114 SSR markers derived from Dongnong 415 (resistant to rice blast) as the male parent and Lijiangxintuanheigu (LTH, susceptible to rice blast) as the female parent was used for linkage mapping. A total of 10 QTLs were identified by the inclusive composite interval mapping method (ICIM), explaining 7.89–33.75 % of the total phenotypic variance. This study was supplemented with association mapping, which was conducted using a panel of 227 japonica rice cultivars released in Northeastern China during the past 50 years with 118 selected SSR markers. A total of 13 significant marker-trait associations (P ≤ 0.01) involving 10 markers were identified using the MLM (Q + K) models in TASSEL 3.0. Among them, 8 of the SSR markers confirmed or narrowed the genomic regions for blast resistance that were reported in linkage studies, including five QTLs identified during the present study. Phenotypic effects of each allele of the 8 stable markers were compared, and 12 resistant alleles were identified. These resistant alleles could be used to design parental combinations and the expected results would be obtained by pyramiding or substituting the resistant alleles per QTL (apart from possible epistatic effects). The results should increase our understanding of the genetic basis of blast resistance and facilitate future resistant breeding in rice.

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

Similar content being viewed by others

References

  • Amante-Bordeos A, Sitch LA, Nelson R, Dalmacio RD, Oliva NP, Aswidinnoor H, Leung H (1992) Transfer of bacterial blight and blast resistance from the tetraploid wild rice Oryza minuta to cultivated rice, Oryza sativa. Theor Appl Genet 84:345–354. doi:10.1007/BF00229493

    CAS  PubMed  Google Scholar 

  • Chen XW, Li SG, Xu JC, Zhai WX, Ling ZZ, Ma BT, Wang YP, Wang WM, Cao G, Ma YQ, Shang JJ, Zhao XF, Zhou KD, Zhu LH (2004) Identification of two blast resistance genes in a rice variety, Digu. J Phytopathol 152:77–85. doi:10.1046/j.1439-0434.2003.00803.x

    Article  CAS  Google Scholar 

  • Chen S, Wang L, Que ZQ, Pan RQ, Pan QH (2005) Genetic and physical mapping of Pi37 (t), a new gene conferring resistance to rice blast in the famous cultivar st. no. 1. Theor Appl Genet 111:1563–1570. doi:10.1007/s00122-005-0086-0

    Article  CAS  PubMed  Google Scholar 

  • Chen XW, Shang JJ, Chen DX, Lei CL, Zou Y, Zhai WX, Liu GZ, Xu JC, Ling ZZ, Cao G, Ma BT, Wang YP, Zhao XF, Li SG, Zhu LH (2006) AB-lectin receptor kinase gene conferring rice blast resistance. Plant J 46:794–804. doi:10.1111/j.1365-313X.2006.02739.x

    Article  CAS  PubMed  Google Scholar 

  • Cui D, Xu CY, Tang CF, Yang CG, Yu TQ, A XX, Cao GL, Xu FR, Zhang JG, Han LZ (2013) Genetic structure and association mapping of cold tolerance in improved japonica rice germplasm at the booting stage. Euphytica 193:369–382. doi:10.1007/s10681-013-0935-x

    Article  CAS  Google Scholar 

  • Dang XJ, Thi TGT, Dong GS, Wang H, Edzesi WM, Hong DL (2014) Genetic diversity and association mapping of seed vigor in rice (Oryza sativa L.). Planta 239:1309–1319. doi:10.1007/s00425-014-2060-z

    Article  CAS  PubMed  Google Scholar 

  • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15

    Google Scholar 

  • Flint-Garcia SA, Thomsberry JM, Bucker ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374. doi:10.1146/annurev.arplant.54.031902.134907

    Article  CAS  PubMed  Google Scholar 

  • Fulton TM, Beck-Bunn T, Emmatty D, Eshed Y, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley SD (1997) QTL analysis of an advanced backcross of Lycopersicon peruvianum to the cultivated tomato and comparisons with QTLs found in other wild species. Theor Appl Genet 95:881–894. doi:10.1007/s001220050639

    Article  CAS  Google Scholar 

  • Guo LY, Guo W, Zhao HW, Wang JG, Liu HL, Sun J, Zheng HL, Sha HJ, Zou DT (2015) Association mapping and resistant alleles’ analysis for japonica rice blast resistance. Plant Breed 134(6):646–652. doi:10.1111/pbr.12310

    Article  CAS  Google Scholar 

  • He F, Zhang H, Liu JL, Wang ZL, Wang GL (2014) Recent advances in understanding the innate immune mechanisms and developing new disease resistance breeding strategies against the rice blast fungus Magnaporthe oryzae in rice [J]. Hereditas 36:756–765. doi:10.3724/SP.J.1005.2014.0756 (in Chinese with English abstract)

    CAS  PubMed  Google Scholar 

  • Heath MC, Valent B, Howard RJ, Chumley FG (1990a) Correlations between cytologically detected plant-fungal interactions and pathogenicity of Magnaporthe grisea toward weeping lovegrass. Phytopathology 80:1382–1386. doi:10.1094/Phyto-80-1382

    Article  Google Scholar 

  • Heath MC, Valent B, Howard RJ, Chumley FG (1990b) Interactions of two strains of Magnaporthe grisea with rice, goosegrass, and weeping lovegrass. Can J Bot 68:1627–1637. doi:10.1139/b90-209

    Article  Google Scholar 

  • Huang XH, Wei XH, Sang T, Zhao Q, Feng Q, Zhao Y, Li CY, Zhu CR, Lu TT, Zhang ZW, Li M, Fan DL, Guo YL, Wang A, Wang L, Deng LW, Li WJ, Lu YQ, Weng QJ, Liu KY, Huang T, Zhou TY, Jing YF, Li W, Lin Z, Buckler ES, Qian Q, Zhang QF, Li JY, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967. doi:10.1038/ng.695

    Article  CAS  PubMed  Google Scholar 

  • International Rice Research Institute (1996) Standard evaluation system for rice, 4th edn. International Rice Research Institute, Manila

    Google Scholar 

  • Jeung JU, Kim BR, Cho YC, Han SS, Moon HP, Lee YT, Jena KK (2007) A novel gene, Pi40 (t), linked to the DNA markers derived from NBS-LRR motifs confers broad spectrum of blast resistance in rice. Theor Appl Genet 115:1163–1177. doi:10.1007/s00122-007-0642-x

    Article  CAS  PubMed  Google Scholar 

  • Jin L, Lu Y, Xiao P, Sun M, Corke H, Bao JS (2010) Genetic diversity and population structure of a diverse set of rice germplasm for association mapping. Theor Appl Genet 121:475–487. doi:10.1007/s00122-010-1324-7

    Article  PubMed  Google Scholar 

  • Korte A, Farlow A (2013) The advantages and limitations of trait analysis with GWAS: a review. Plant Methods 9:29. doi:10.1186/1746-4811-9-29

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee S, Wamishe Y, Jia Y, Liu G, Jia MH (2009) Identification of two major resistance genes against race IE-1 k of Magnaporthe oryzae in the indica rice cultivar Zhe733. Mol Breed 24:127–134. doi:10.1007/s11032-009-9276-9

    Article  CAS  Google Scholar 

  • Li HH, Ye GY, Wang JK (2007) A modified algorithm for the improvement of composite interval mapping. Genetics 175:361–374. doi:10.1534/genetics.106.066811

    Article  PubMed  PubMed Central  Google Scholar 

  • Li N, Shi JQ, Wang XF, Liu GH, Wang HZ (2014) A combined linkage and regional association mapping validation and fine mapping of two major pleiotropic QTLs for seed weight and silique length in rapeseed (Brassica napus L.). BMC Plant Biol 14:114. doi:10.1186/1471-2229-14-114

    Article  PubMed  PubMed Central  Google Scholar 

  • Lin F, Chen S, Que ZQ, Wang L, Liu XQ, Pan QH (2007) The blast resistance gene Pi37 encodes a nucleotide binding site-leucine-rich repeat protein and is a member of a resistance gene cluster on rice chromosome 1. Genetics 177:1871–1880. doi:10.1534/genetics.107.080648

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu B, Zhang SH, Zhu XY, Yang QY, Wu SZ, Mei MT, Mauleon R, Leach J, Mew T, Leung H (2004) Candidate defense genes as predictors of quantitative blast resistance in rice. Mol Plant Microbe Interact 17:1146–1152. doi:10.1094/MPMI.2004.17.10.1146

    Article  CAS  PubMed  Google Scholar 

  • Liu XQ, Yang QZ, Lin F, Hua LX, Wang CT, Wang L, Pan QH (2007) Identification and fine mapping of Pi39 (t), a major gene conferring the broad-spectrum resistance to Magnaporthe oryzae. Mol Genet Genomics 278:403–410. doi:10.1007/s00438-007-0258-5

    Article  CAS  PubMed  Google Scholar 

  • Lu YL, Zhang SH, Shah T, Xie CX, Hao ZF, Li XH, Farkhari M, Ribaut JM, Cao M, Rong TZ, Xu YB (2010) Joint linkage-linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize. Proc Natl Acad Sci 107:19585–19590. doi:10.1073/pnas.1006105107

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McCouch SR, Cho YG, Yano M, Paul E, Blinstrub M, Morishima H, Kinoshita T (1997) Report on QTL nomenclature. Rice Genet Newsl 14:11–13

    Google Scholar 

  • Mei HX, Ai N, Zhang X, Ning ZY, Zhang TZ (2014) QTLs conferring FOV 7 resistance detected by linkage and association mapping in Upland cotton. Euphytica 197:237–249. doi:10.1007/s10681-014-1063-y

    Article  Google Scholar 

  • Ordonez SA, Silva J, Oard JH (2010) Association mapping of grain quality and flowering time in elite japonica rice germplasm. J Cereal Sci 51:337–343. doi:10.1016/j.jcs.2010.02.001

    Article  Google Scholar 

  • Peng YL, Shishiyama J (1988) Temporal sequence of cytological events in rice leaves infected with Pyricularia oryzae. Can J Bot 66:730–735. doi:10.1139/b88-107

    Article  Google Scholar 

  • Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000) Association mapping in structured populations. Am J Hum Genet 67:170–181. doi:10.1086/302959

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sallaud C, Lorieux M, Roumen E, Tharreau D, Berruyer R, Svestasrani P, Garsmeur O, Ghesquiere A, Notteghem JL (2003) Identification of five new blast resistance genes in the highly blast-resistant rice variety IR64 using a QTL mapping strategy. Theor Appl Genet 106:794–803. doi:10.1007/s00122-002-1088-9

    CAS  PubMed  Google Scholar 

  • Scheuermann KK, Raimondi JV, Marschalek R, de Andrade1 A, Wickert E (2012) Magnaportheoryzae genetic diversity and its outcomes on the search for durable resistance. Mol Basis Plant Genet Divers 331–356

  • Valent B, Farrall L, Chumley FG (1991) Magnaporthe grisea genes for pathogenicity and virulence identified through a series of backcrosses. Genetics 127:87–101

    CAS  PubMed  PubMed Central  Google Scholar 

  • Van Ooijen JW, Voorrips RE (2002) JoinMap: version 3.0: software for the calculation of genetic linkage maps. University and Research Center

  • Vanniarajan C, Vinod KK, Pereira A (2012) Molecular evaluation of genetic diversity and association studies in rice (Oryza sativa L.). J Genet 91:9–19. doi:10.1007/s12041-012-0146-6

    Article  CAS  PubMed  Google Scholar 

  • Voorrips R (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78. doi:10.1093/jhered/93.1.77

    Article  CAS  PubMed  Google Scholar 

  • Wang GL, Mackill DJ, Bonman JM, McCouch SR, Champoux MC, Nelson RJ (1994) RFLP mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar. Genetics 136:1421–1434

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang SK, Wu K, Yuan QB, Liu XY, Liu ZB, Lin XY, Zeng RZ, Zhu HT, Dong GJ, Qian Q, Zhang GQ, Fu XD (2012) Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet 44:950–954. doi:10.1038/ng.2327

    Article  CAS  PubMed  Google Scholar 

  • Wang JG, Jiang TB, Zou DT, Zhao HW, Li Q, Liu HL, Zhou CJ (2014) Genetic diversity and genetic relationships of japonica rice varieties in northeast Asia based on SSR markers. Biotechnol Biotechnol Equip 28:230–237. doi:10.1080/13102818.2014.908019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wen WW, Mei HW, Feng FJ, Yu SB, Huang ZC, Wu JH, Chen L, Xu XY, Luo LJ (2009) Population structure and association mapping on chromosome 7 using a diverse panel of Chinese germplasm of rice (Oryza sativa L. ). Theor Appl Genet 119:459–470. doi:10.1007/s00122-009-1052-z

    Article  PubMed  Google Scholar 

  • Wu JL, Fan YY, Li DB, Zheng KL, Leung H, Zhuang JY (2005) Genetic control of rice blast resistance in the durably resistant cultivar Gumei 2 against multiple isolates. Theor Appl Genet 111:50–56. doi:10.1007/s00122-005-1971-2

    Article  CAS  PubMed  Google Scholar 

  • Yu JM, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155–160. doi:10.1016/j.copbio.2006.02.003

    Article  CAS  PubMed  Google Scholar 

  • Zhang YX, Yang JY, Shan ZL, Chen S, Qiao WH, Zhu XY, Xie QJ, Zhu HT, Zhang ZM, Zeng RZ, Ding XH, Zhang GQ (2012) Substitution mapping of QTLs for blast resistance with SSSLs in rice (Oryza sativa L.). Euphytica 184:141–150. doi:10.1007/s10681-011-0601-0

    Article  Google Scholar 

  • Zhang TZ, Qian N, Zhu XF, Chen H, Wang S, Mei HX, Zhang YM (2013) Variations and transmission of QTL alleles for yield and fiber qualities in upland cotton cultivars developed in China. PLoS ONE 8:e57220. doi:10.1371/journal.pone.0057220

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zheng HL, Zhao HW, Liu HL, Wang JG, Zou DT (2015) QTL analysis of Na+ and K+ concentrations in shoots and roots under NaCl stress based on linkage and association analysis in japonica rice. Euphytica 201:109–121. doi:10.1007/s10681-014-1192-3

    Article  CAS  Google Scholar 

  • Zhou JH, Wang JL, Xu JC, Lei CL, Ling ZZ (2004) Identification and mapping of a rice blast resistance gene Pi-g (t) in the cultivar Guangchangzhan. Plant Pathol 53:191–196. doi:10.1111/j.1365-3059.2004.00986.x

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by the national science and technology support program (2013BAD20B04) and science and technology tender program of Heilongjiang province Graduate of science (GA14B102) and technology innovation project of Northeast Agricultural University (yjscx14041).

Author information

Authors and Affiliations

  1. College of Agriculture, Northeast Agricultural University, Harbin, 150030, People’s Republic of China

    Liying Guo, Hongwei Zhao, Jingguo Wang, Hualong Liu, Hongliang Zheng, Jian Sun, Luomiao Yang, Hanjing Sha & Detang Zou

Authors
  1. Liying Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hongwei Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jingguo Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hualong Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hongliang Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jian Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Luomiao Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Hanjing Sha
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Detang Zou
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Detang Zou.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(DOCX 33 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Guo, L., Zhao, H., Wang, J. et al. Dissection of QTL alleles for blast resistance based on linkage and linkage disequilibrium mapping in japonica rice seedlings. Australasian Plant Pathol. 45, 209–218 (2016). https://doi.org/10.1007/s13313-016-0405-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13313-016-0405-8

Keywords

Search

Navigation