Skip to main content
Log in

Development and evaluation of near-isogenic lines for major blast resistance gene(s) in Basmati rice

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


Key message

A set of NILs carrying major blast resistance genes in a Basmati rice variety has been developed. Also, the efficacy of pyramids over monogenic NILs against rice blast pathogen Magnaporthe oryzae has been demonstrated.


Productivity and quality of Basmati rice is severely affected by rice blast disease. Major genes and QTLs conferring resistance to blast have been reported only in non-Basmati rice germplasm. Here, we report incorporation of seven blast resistance genes from the donor lines DHMASQ164-2a (Pi54, Pi1, Pita), IRBLz5-CA (Pi2), IRBLb-B (Pib), IRBL5-M (Pi5) and IRBL9-W (Pi9) into the genetic background of an elite Basmati rice variety Pusa Basmati 1 (PB1). A total of 36 near-isogenic lines (NILs) comprising of 14 monogenic, 16 two-gene pyramids and six three-gene pyramids were developed through marker-assisted backcross breeding (MABB). Foreground, recombinant and background selection was used to identify the plants with target gene(s), minimize the linkage drag and increase the recurrent parent genome (RPG) recovery (93.5–98.6 %), respectively, in the NILs. Comparative analysis performed using 50,051 SNPs and 500 SSR markers revealed that the SNPs provided better insight into the RPG recovery. Most of the monogenic NILs showed comparable performance in yield and quality, concomitantly, Pusa1637-18-7-6-20 (Pi9), was significantly superior in yield and stable across four different environments as compared to recurrent parent (RP) PB1. Further, among the pyramids, Pusa1930-12-6 (Pi2+Pi5) showed significantly higher yield and Pusa1633-7-8-53-6-8 (Pi54+Pi1+Pita) was superior in cooking quality as compared to RP PB1. The NILs carrying gene Pi9 were found to be the most effective against the concoction of virulent races predominant in the hotspot locations for blast disease. Conversely, when analyzed under artificial inoculation, three-gene pyramids expressed enhanced resistance as compared to the two-gene and monogenic NILs.

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

Similar content being viewed by others


  • APEDA (2011) Accessed 20 Nov 2011

  • Basavaraj SH, Singh VK, Singh A, Singh A, Singh A, Anand D, Yadav S, Ellur RK, Singh D, Gopala Krishnan S, Nagarajan M, Mohapatra T, Prabhu KV, Singh AK (2010) Marker-assisted improvement of bacterial blight resistance in parental lines of Pusa RH10, a superfine grain aromatic rice hybrid. Mol Breed 26(2):293–305

    Article  CAS  Google Scholar 

  • Bonman JM, Vergel de Dios TI, Khin MM (1986) Physiologic specialization of Pyricularia oryzae in the Philippines. Plant Dis 70:767–769

    Article  Google Scholar 

  • Brunner S, Stirnweis D, Diaz Quijano C, Buesing G, Herren G, Parlange F, Barret P, Tassy C, Sautter C, Winzeler M, Keller B (2012) Transgenic Pm3 multilines of wheat show increased powdery mildew resistance in the field. Plant Biotechnol J 10:398–409

    Article  CAS  PubMed  Google Scholar 

  • Casela CR, Alexandre SF, Zeller KA, Levy M (1995) Pathotype variation in the sorghum anthracnose fungus: a phylogenetic perspective for resistance breeding. In: Leslie JF, Frederiksen RA (eds) Disease analysis through genetics and molecular biology: interdisciplinary bridges to improved sorghum and millet crops. Iowa State University Press, Ames, Iowa, pp 257–276

    Google Scholar 

  • Chen S, Xu CG, Lin XH, Zhang Q (2008) Improving bacterial blight resistance of ‘6078’, an elite restorer line of hybrid rice, by molecular marker-assisted selection. Plant Breed 120(2):133–137

    Article  Google Scholar 

  • Ellur RK, Singh AK, Gupta HS (2013) Enhancing Rice Productivity in India: Aspects and Prospects. In: Shetty PK, Ayyappan S, Swaminathan MS (eds) Climate change and sustainable food security. National Institute of Advanced Studies, IISC, Bangalore and Indian Council of Agricultural Research, New Delhi, pp 99–132

    Google Scholar 

  • Fukuoka S, Yamamoto S, Mizobuchi R, Yamanouchi U, Ono K, Kitazawa N, Yasuda N, Fujita Y, Nguyen TTT, Koizumi S, Sugimoto K, Matsumoto T, Yano M (2014) Multiple functional polymorphisms in a single disease resistance gene in rice enhance durable resistance to blast. Sci Rep 4:4550

    Article  Google Scholar 

  • Gnanamanickam SS, Babujee L, Priyadarisini VB, Dayakar BV, Leenakumari D, Sivaraj R, Levy M, Leong SA (2000) Lineage-exclusion resistance breeding: pyramiding of blast resistance genes for management of rice blast in India. In: Tharreau D, Lebrun MH, Talbot NJ and Notteghem JL (eds) Advances in rice blast research, developments in plant pathology, vol 15, pp 172–179

  • Gopalakrishnan S, Sharma RK, Rajkumar KA, Joseph M, Singh VP, Singh AK, Bhat KV, Singh NK, Mohapatra T (2008) Integrating marker assisted background analysis with foreground selection for identification of superior bacterial blight resistant recombinants in Basmati rice. Plant Breed 127:131–139

    Article  CAS  Google Scholar 

  • Hittalmani S, Parco A, Mew TV, Zeigler RS, Huang N (2000) Fine mapping and DNA marker-assisted pyramiding of the three major genes for blast resistance in rice. Theor Appl Genet 100(7):1121–1128

    Article  CAS  Google Scholar 

  • Imam J, Alam S, Mandal NP, Variar M, Shukla P (2014) Molecular screening for identification of blast resistance genes in north east and eastern Indian rice germplasm (Oryza sativa L.) with PCR based makers. Euphytica 196:199–211

    Article  CAS  Google Scholar 

  • Joseph M, Gopalakrishnan S, Sharma RK, Singh AK, Singh VP, Singh NK, Mohapatra T (2004) Combining bacterial blight resistance and Basmati quality characteristics by phenotypic and molecular marker assisted selection in rice. Mol Breed 13:377–387

    Article  CAS  Google Scholar 

  • Juliano BO (1971) A simplified assay for milled rice amylose. Cereal Sci Today 16:334–338

    Google Scholar 

  • Khush GS (2005) What it will take to Feed 5.0 billion rice consumers in 2030. Plant Mol Biol 59:1–6

    Article  CAS  PubMed  Google Scholar 

  • Kumar MKP, Gowda DKS, Moudgal R, Kumar NK, Gowda KTP, Vishwanath K (2013) Impact on fungicides on rice production in India. In: Nita M (ed) Fungicides-showcases of integrated plant disease management from around the world. ISBN: 978-953-51-1130-6, InTech, doi:10.5772/51009.

  • Latter BDH, McIntosh RA, Ellison FW, Brennan PS, Fisher J, Hollamby GJ, Rathjen AJ, Wilson RE (1998) Grains yields of near-isogenic lines with added genes for stem rust resistance. In: Miller TE, Koebner RMD (eds) Proceedings of the 7th international wheat genetics symposium. Institute for Plant Science Research, Cambridge, UK, pp 901–906

    Google Scholar 

  • Little RR, Hilder GB, Dawson EH (1958) Differential effect of dilute alkali on 25 varieties of milled white rice. Cereal Chem 35:111–126

    CAS  Google Scholar 

  • Luthra JK, Rao MV (1979) Multiline cultivars—How their resistance influence leaf rust disease in wheat. Euphytica 28(1):137–144

    Article  Google Scholar 

  • Lv Q, Xu X, Shang J, Jiang G, Pang Z, Zhou Z, Wang J, Liu Y, Li T, Li X, Xu J, Cheng Z, Zhao X, Li S, Zhu L (2013) Functional Analysis of Pid3-A4, an ortholog of rice blast resistance gene Pid3 revealed by allele mining in common wild rice. Phytopathology 103(6):594–599

    Article  CAS  PubMed  Google Scholar 

  • Murray HG, Thompson WF (1980) Rapid isolation of high molecular weight DNA. Nucl Acids Res 8:4321–4325

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ortelli S, Winzeler H, Winzeler M, Fried PM, Nösberger J (1996) Leaf rust resistance gene Lr9 and winter wheat yield reduction: I yield and yield components. Crop Sci 36:1590–1595

    Article  Google Scholar 

  • SES (1996) Standard evaluation system for rice. International Rice Research Institute, Manila, Philippines, p 56

    Google Scholar 

  • Singh AK, Gopala Krishnan S, Singh VP, Prabhu KV, Mohapatra T, Singh NK, Sharma TR, Nagarajan M, Vinod KK, Singh D, Singh UD, Chander S, Atwal SS, Seth R, Singh VK, Ellur RK, Singh A, Anand D, Khanna A, Yadav S, Goel N, Singh A, Shikari AB Singh A, Marathi B (2011) Marker assisted selection: a paradigm shift in Basmati breeding. Indian J Genet 71(2) special Issue: 1–9

  • Singh VK, Singh A, Singh SP, Ellur RK, Choudhary V, Sarkel S, Singh D, Gopala Krishnan S, Nagarajan M, Vinod KK, Singh UD, Rathore R, Prashanthi SK, Agrawal PK, Bhatt JC, Mohapatra T, Prabhu KV, Singh AK (2012) Incorporation of blast resistance into “PRR78”, an elite Basmati rice restorer line through marker assisted backcross breeding. Field Crops Res 128:8–16

    Article  Google Scholar 

  • Singh VK, Singh A, Singh SP, Ellur RK, Singh D, Gopala Krishnan S, Bhowmick PK, Nagarajan M, Vinod KK, Singh UD, Mohapatra T, Prabhu KV, Singh AK (2013) Marker-assisted simultaneous but stepwise backcross breeding for pyramiding blast resistance genes Pi2 and Pi54 into an elite Basmati rice restorer line PRR78. Plant Breed 132(5):486–495

    CAS  Google Scholar 

  • Sood BC, Siddiq EA (1978) A rapid technique for scent determinations in rice. Indian J Genet 38:2268–2271

    Google Scholar 

  • Tsunematsu H, Yanoria MJT, Ebron LA, Hayashi N, Ando I, Kato H, Imbe T, Khush GS (2000) Development of monogenic lines of rice for blast resistance. Breed Sci 50:229–234

    Article  Google Scholar 

  • Variar M, Vera Cruz CM, Carrillo MG, Bhatt JC, Sangar RBS (2009) Rice blast in India and strategies to develop durably resistant cultivars. In: Xiaofan W, Valent B (eds) Advances in genetics, genomics and control of rice blast disease. Springer, New York, pp 359–374

    Chapter  Google Scholar 

  • Yanoria T, Koide Y, Fukuta Y, Imbe I, Kato H, Tsunematsu H, Kobayashi N (2010) Development of near-isogenic lines of Japonica-type rice variety Lijiangxintuanheigu as differentials for blast resistance. Breed Sci 60:629–638

    Article  Google Scholar 

Download references


The research work was funded by National Agricultural Innovation project (NAIP), ICAR, India. The study is part of the Ph.D. research of the first author.

Conflict of interest

None of the authors have any conflict of interest associated with this study.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Ashok K. Singh.

Additional information

Communicated by L. Xiong.

Electronic supplementary material

Below is the link to the electronic supplementary material.


Foreground selection for the blast resistance genes using respective gene-linked molecular markers. Legend- M- 50 bp ladder, R- Pusa Basmati-1, D1- DHMAS70Q164-2a, D2: IRBLz5-CA, D3: IRBLb-B, D4 IRBL5-M, D5: IRBL9-W, 1-5: PB1 Nils carrying respective blast resistance genes (DOC 118 kb)


Scatter diagram of GGE biplot analysis depicting the mega environments and the performance of monogenic NILs across 4 locations. G1 -Pusa 1633-1-8-6-8-12, G2-Pusa 1633-1-8-6-23-7, G3-Pusa 1633-2-8-12-9-10, G4-Pusa 1633-2-8-1-4-18. G5-Pusa 1633-3-8-8-16-1, G6-Pusa 1633-3-8-20-6-12, G7-Pusa 1634-8-1-12-15, G8-Pusa 1634-4-9-6-23, G9-Pusa 1635-10-6-8-10, G10-Pusa 1635-10-5-6-18, G11-Pusa 1636-12-9-8-17, G12-Pusa 1636-12-9-12-4, G13-Pusa 1637-18-7-6-20, G14-Pusa 1637-12-8-20-5, G15- PB1(JPEG 2363 kb)


Gel consistency length (mm) of RP PB1, DP- DHMASQ164-2a and the NILs (1-11) carrying blast resistance genes(JPEG 2082 kb)


Graphical representation of RPG recovery using SNP and SSR markers in Pi9 carrying NILs. In each of the chromosomes first bar represents the NIL Pusa 1637-18-7-6-20 and second bar represents the NIL Pusa 1637-12-8-20-5(TIFF 3838 kb)

Supplementary material 5 (JPEG 6303 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Khanna, A., Sharma, V., Ellur, R.K. et al. Development and evaluation of near-isogenic lines for major blast resistance gene(s) in Basmati rice. Theor Appl Genet 128, 1243–1259 (2015).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: