Skip to main content

Rice, Marker-Assisted Breeding, and Disease Resistance

  • Chapter
  • First Online:
Disease Resistance in Crop Plants

Abstract

In the last few decades, feeding the exponentially increasing human population has been always the biggest challenge for our plant breeders and scientists. To meet this, every plant breeder has focused on developing new and better crop varieties. Earlier, the characters selection was solely based on phenotypic observations, without the knowledge of molecular markers. However, marker-assisted breeding has emerged as the major efficient, sustainable, and accurate breeding approach employed in the last three decades. It has become breeder’s choice for introgression of genes into the recurrent parent for genetic improvement of traits including disease resistance, insect resistance, abiotic stress tolerance, taste improvement, aroma, mineral content, water use efficiency, and overall yield. This approach is highly promising as it allows pyramiding of target trait(s) in a single progeny in a very precise, stable, convenient, and fast manner. As a result, various quantitative trait loci (QTLs) and genes tightly linked to DNA markers governing resistance to rice blast disease, bacterial blight of rice, and other diseases have been identified, mapped, and transferred into susceptible lines, varieties, cultivars, and landraces of various crops including rice (Oryza sativa L.) worldwide. Overall, this book chapter reviews the use of marker-assisted breeding (MAB) for disease resistance in rice.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Arunakumari K, Durgarani C, Satturu V, Sarikonda K, Chittoor P, Vutukuri B, Laha G, Nelli A, Gattu S, Jamal M (2016) Marker-assisted pyramiding of genes conferring resistance against bacterial blight and blast diseases into Indian rice variety MTU1010. Rice Sci 23:306–316

    Article  Google Scholar 

  • Ashkani S, Rafii MY, Shabanimofrad M, Miah G, Sahebi M, Azizi P, Tanweer FA, Akhtar MS, Nasehi A (2015) Molecular breeding strategy and challenges towards improvement of blast disease resistance in rice crop. Front Plant Sci 6:886

    Google Scholar 

  • Atkinson NJ, Urwin PE (2012) The interaction of plant biotic and abiotic stresses: from genes to the field. J Exp Bot 63:3523–3543

    Article  CAS  PubMed  Google Scholar 

  • Balachiranjeevi C, Naik BS, Kumar AV, Harika G, Swamy MH, Masood HS, Kumar DT, Miriyala A, Kale R, Yugender A (2018) Marker-assisted pyramiding of two major broad-spectrum bacterial blight resistance genes, Xa21 and Xa33 into an elite maintainer line of rice, DRR17B. bioRxiv:368712

    Google Scholar 

  • Baliyan N, Malik R, Rani R, Mehta K, Vashisth U, Dhillon S, Boora KS (2018) Integrating marker-assisted background analysis with foreground selection for pyramiding bacterial blight resistance genes into Basmati rice. C R Biol 341:1–8

    Article  PubMed  Google Scholar 

  • 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 26:293–305

    Article  CAS  Google Scholar 

  • Beckmann JS, Soller M (1983) Restriction fragment length polymorphisms in genetic improvement: methodologies, mapping and costs. Theor Appl Genet Theor Appl Genet:33–43

    Google Scholar 

  • Bellard C, Bertelsmeier C, Leadley P, Thuiller W, Courchamp F (2012) Impacts of climate change on the future of biodiversity. Ecol Lett 15:365–377

    Article  PubMed  PubMed Central  Google Scholar 

  • Bharani M, Nagarajan P, Rabindran R, Saraswathi R, Balasubramanian P, Ramalingam J (2010) Bacterial leaf blight resistance genes (Xa21, xa13 and xa5) pyramiding through molecular marker assisted selection into rice cultivars. Arch Phytopathol Plant Protect 43:1032–1043

    Article  CAS  Google Scholar 

  • Bharathkumar S, Paulraj RD, Brindha P, Kavitha S, Gnanamanickam S (2008) Improvement of bacterial blight resistance in rice cultivars Jyothi and IR50 via marker-assisted backcross breeding. J Crop Improv 21:101–116

    Article  CAS  Google Scholar 

  • Bhatia D, Sharma R, Vikal Y, Mangat G, Mahajan R, Sharma N, Lore JS, Singh N, Bharaj TS, Singh K (2011) Marker-assisted development of bacterial blight resistant, dwarf, and high yielding versions of two traditional basmati rice cultivars. Crop Sci 51:759–770

    Article  Google Scholar 

  • Chen S, Lin X, Xu C, Zhang Q (2000) Improvement of bacterial blight resistance of Minghui 63, an elite restorer line of hybrid rice, by molecular marker-assisted selection, vol 40, p 239

    Google Scholar 

  • Chen S, Xu C, Lin X, Zhang Q (2001) Improving bacterial blight resistance of ‘6078′, an elite restorer line of hybrid rice, by molecular marker-assisted selection. Plant Breed 120:133–137

    Article  CAS  Google Scholar 

  • Chen X, Li S, Ma Y, Li H, Zhou K, Zhu L (2004) Marker-assisted selection and pyramiding for three blast resistance genes, Pi-d (t) 1, Pi-b, Pi-ta2, in rice. Chin J Biotechnol 20:708–714

    Google Scholar 

  • Chen H, Chen Z, Ni S, Zuo S-M, Pan X-B, Zhu X (2008) Pyramiding three genes with resistance to blast by marker assisted selection to improve rice blast resistance of Jin 23B. Chin J Rice Sci 1:5

    Google Scholar 

  • Chen Z, Zhang Y, Feng F, Feng M, Jiang W, Ma Y, Pan C, Hua H, Li G, Pan X (2014) Improvement of japonica rice resistance to sheath blight by pyramiding qSB-9TQ and qSB-7TQ. Field Crop Res 161:118–127

    Article  Google Scholar 

  • Copetti D, Zhang J, El Baidouri M, Gao D, Wang J, Barghini E, Cossu RM, Angelova A, Roffler S, Ohyanagi H (2015) RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics 16:538

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Crossa J, Pérez-Rodríguez P, Cuevas J, Montesinos-López O, Jarquín D, de los Campos G, Burgueño J, Camacho-González JM, Pérez-Elizalde S, Beyene Y (2017) Genomic selection in plant breeding: methods, models, and perspectives. Trends Plant Sci 22:961–975

    Article  CAS  PubMed  Google Scholar 

  • Dean RA, Talbot NJ, Ebbole DJ, Farman ML, Mitchell TK, Orbach MJ, Thon M, Kulkarni R, Xu J-R, Pan H (2005) The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434:980

    Article  CAS  PubMed  Google Scholar 

  • Dnyaneshwar SU, Agrawal T, Kadu T, Pradhan A, Verulkar ASKSB (2018) Improvement of Dubraj and Safri-17 varieties for conferring resistance against bacterial leaf blight through marker assisted selection approach. IJCS 6:1785–1790

    Google Scholar 

  • Dokku P, Das K, Rao G (2013) Pyramiding of four resistance genes of bacterial blight in Tapaswini, an elite rice cultivar, through marker-assisted selection. Euphytica 192:87–96

    Article  Google Scholar 

  • Duke SO (2018) The history and current status of glyphosate. Pest Manag Sci 74:1027–1034

    Article  CAS  PubMed  Google Scholar 

  • Dwivedi SL, Crouch JH, Mackill DJ, Xu Y, Blair MW, Ragot M, Upadhyaya HD, Ortiz R (2007) The molecularization of public sector crop breeding: progress, problems, and prospects. Adv Agron 95:163–318

    Article  CAS  Google Scholar 

  • Ellur RK, Khanna A, Bhowmick PK, Vinod K, Nagarajan M, Mondal KK, Singh NK, Singh K, Prabhu KV, Singh AK (2016a) Marker-aided incorporation of Xa38, a novel bacterial blight resistance gene, in PB1121 and comparison of its resistance spectrum with xa13+ Xa21. Sci Rep 6:29188

    Article  PubMed  PubMed Central  Google Scholar 

  • Ellur RK, Khanna A, Yadav A, Pathania S, Rajashekara H, Singh VK, Krishnan SG, Bhowmick PK, Nagarajan M, Vinod K (2016b) Improvement of basmati rice varieties for resistance to blast and bacterial blight diseases using marker assisted backcross breeding. Plant Sci 242:330–341

    Article  CAS  PubMed  Google Scholar 

  • Frisch M, Melchinger AE (2001) Marker-assisted backcrossing for simultaneous introgression of two genes. Crop Sci 41:1716–1725

    Article  Google Scholar 

  • Fu C, Wu T, Liu W, Wang F, Li J, Zhu X, Huang H, Liu ZR, Liao Y, Zhu M (2012) Genetic improvement of resistance to blast and bacterial blight of the elite maintainer line Rongfeng B in hybrid rice (Oryza sativa L.) by using marker-assisted selection. Afr J Biotechnol 11:13104–13114

    Article  CAS  Google Scholar 

  • Garg P, Jaiswal P (2016) Databases and bioinformatics tools for rice research. Curr Plant Biol 7-8:39–52

    Article  Google Scholar 

  • Gazal A, Dar Z, Wani S, Lone A, Shikari A, Ali G, Abidi I (2016) Molecular breeding for enhancing resilience against biotic and abiotic stress in major cereals. SABRAO J Breed Genet 48:1–32

    Google Scholar 

  • Gimelfarb A, Lande R (1995) Marker-assisted selection and marker-QTL associations in hybrid populations. Theor Appl Genet 91:522–528

    Article  CAS  PubMed  Google Scholar 

  • Goff SA, Ricke D, Lan T-H, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H (2002) A draft sequence of the rice genome (Oryza sativa L ssp japonica). Science 296:92–100

    Article  CAS  PubMed  Google Scholar 

  • Gopalakrishnan S, Sharma R, Anand Rajkumar K, Joseph M, Singh V, Singh A, Bhat K, Singh N, 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 

  • Gouda PK, Saikumar S, Varma CM, Nagesh K, Thippeswamy S, Shenoy V, Ramesha MS, Shashidhar HE (2013) Marker-assisted breeding of Pi-1 and Piz-5 genes imparting resistance to rice blast in PRR 78, restorer line of Pusa RH-10 B asmati rice hybrid. Plant Breed 132:61–69

    Article  CAS  Google Scholar 

  • Guimarães EP (2007) Marker-assisted selection: current status and future perspectives in crops, livestock, forestry and fish. Food & Agriculture Org, Rome

    Google Scholar 

  • Gur A, Zamir D (2004) Unused natural variation can lift yield barriers in plant breeding. PLoS Biol 2:e245

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Guvvala LD, Koradi P, Shenoy V, Marella LS (2013) Improvement of resistance to bacterial blight through marker assisted backcross breeding and field validation in rice (Oryza sativa). Res J Biol 1:52–66

    Google Scholar 

  • Hari Y, Srinivasarao K, Viraktamath BC, Hariprasad AS, Laha GS, Ahmed MI, Natarajkumar P, Ramesha MS, Neeraja CN, Balachandran SM (2011) Marker-assisted improvement of a stable restorer line, KMR-3R and its derived hybrid KRH2 for bacterial blight resistance and grain quality. Plant Breed 130:608–616

    Article  CAS  Google Scholar 

  • Hari Y, Srinivasarao K, Viraktamath BC, Hari Prasad AS, Laha GS, Ahmed MI, Natarajkumar P, Sujatha K, Srinivas Prasad M, Pandey M (2013) Marker-assisted introgression of bacterial blight and blast resistance into IR 58025B, an elite maintainer line of rice. Plant Breed 132:586–594

    Article  CAS  Google Scholar 

  • Hegde SS, Prashanthi SK (2016) Identification of polymorphic markers and introgression of Pi1 and Pi2 genes for blast resistance in rice. J Farm Sci 29:327–331

    Google Scholar 

  • Helmy M, Tomita M, Ishihama Y (2011) OryzaPG-DB: rice proteome database based on shotgun proteogenomics. BMC Plant Biol 11:63

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Holland JB (2004) Implementation of molecular markers for quantitative traits in breeding programs—challenges and opportunities. New Directions for a Diverse Planet: Proceedings for the 4th International Crop Science Congress Regional Institute, Gosford, Australia, www.cropscience.org.au/icsc2004

  • Hua L-X, Liang L-Q, He X-Y, Wang L, Zhang W-S, Liu W, Liu X-Q, Lin F (2015) Development of a marker specific for the rice blast resistance gene Pi39 in the Chinese cultivar Q15 and its use in genetic improvement. Biotechnol Biotechnol Equip 29:448–456

    Article  CAS  Google Scholar 

  • Huang N, Angeles E, Domingo J, Magpantay G, Singh S, Zhang G, Kumaravadivel N, Bennett J, Khush G (1997) Pyramiding of bacterial blight resistance genes in rice: marker-assisted selection using RFLP and PCR. Theor Appl Genet 95:313–320

    Article  CAS  Google Scholar 

  • Huang B, Xu J, Hou M, Ali J, Mou T (2012) Introgression of bacterial blight resistance genes Xa7, Xa21, Xa22 and Xa23 into hybrid rice restorer lines by molecular marker-assisted selection. Euphytica 187:449–459

    Article  CAS  Google Scholar 

  • Jairin J, Kotchasatit U, Saleeto S, Jearakongman S, Srivilai K, Chamarerk V, Kothcharerk J, Pattawatang P, Korinsak S, Wongsaprom C (2017) Application of marker-assisted breeding to improve biotic stress resistance for rainfed lowland rice in Northeastern Thailand. SABRAO J Breed Genet 49:168–178

    Google Scholar 

  • Jena KK, Mackill DJ (2008) Molecular markers and their use in marker-assisted selection in rice. Crop Sci 48:1266–1276

    Article  Google Scholar 

  • Jiang GL (2013) Molecular markers and marker-assisted breeding in plants. In: Plant breeding from laboratories to fields. IntechOpen. Available at https://www.intechopen.com/books/plant-breeding-from-laboratories-to-fields/molecular-markers-and-marker-assisted-breeding-in-plants

  • Jiang J, Yang D, Ali J, Mou T (2015) Molecular marker-assisted pyramiding of broad-spectrum disease resistance genes, Pi2 and Xa23, into GZ63-4S, an elite thermo-sensitive genic male-sterile line in rice. Mol Breed 35:83

    Article  CAS  Google Scholar 

  • Joseph M, Gopalakrishnan S, Sharma R, Singh V, Singh A, Singh N, 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 

  • Khan GH, Shikari AB, Vaishnavi R, Najeeb S, Padder BA, Bhat ZA, Parray GA, Bhat MA, Kumar R, Singh NK (2018) Marker-assisted introgression of three dominant blast resistance genes into an aromatic rice cultivar Mushk Budji. Sci Rep 8:4091

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Khanna A, Sharma V, Ellur RK, Shikari AB, Gopala Krishnan S, Singh UD, Prakash G, Sharma TR, Rathour R, Variar M, Prashanthi SK, Nagarajan M, Vinod KK, Bhowmick PK, Singh NK, Prabhu KV, Singh BD, Singh AK (2015) Development and evaluation of near-isogenic lines for major blast resistance gene(s) in Basmati rice. Theor Appl Genet 128:1243–1259

    Article  CAS  PubMed  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 

  • Koide Y, Kawasaki A, Telebanco-Yanoria MJ, Hairmansis A, Nguyet NTM, Bigirimana J, Fujita D, Kobayashi N, Fukuta Y (2010) Development of pyramided lines with two resistance genes, Pish and Pib, for blast disease (Magnaporthe oryzae B. Couch) in rice (Oryza sativa L.). Plant Breed 129:670–675

    Article  CAS  Google Scholar 

  • Krishnakumar R, Kumaravadivel N (2018) Marker-assisted selection for biotic stress (bacterial leaf blight and gall midge) tolerance in Bc4F4 generation of rice (Oryza sativa L.). Electron J Plant Breed 9:275–282

    Article  Google Scholar 

  • Kumar S, Rao M (2018) Conventional and molecular breeding for bacterial leaf blight and blast resistance in rice. J Ecol 3:1–3

    Google Scholar 

  • Kumar VA, Balachiranjeevi CH, Naik SB, Rambabu R, Rekha G, Harika G, Hajira SK, Pranathi K, Vijay S, Anila M (2016) Marker-assisted improvement of the elite restorer line of rice, RPHR-1005 for resistance against bacterial blight and blast diseases. J Genet 95:895–903

    Article  CAS  PubMed  Google Scholar 

  • Kurata N, Yamazaki Y (2006) Oryzabase. An integrated biological and genome information database for rice. Plant Physiol 140:12–17

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kwon S-W, Cho Y-C, Kim Y-G, Suh J-P, Jeung J-U, Roh J-H, Lee S-K, Jeon J-S, Yang S-J, Lee Y-T (2008) Development of near-isogenic Japonica rice lines with enhanced resistance to Magnaporthe grisea. Mol Cells 25:407–416

    CAS  PubMed  Google Scholar 

  • Lande R, Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743–756

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee J-H, Lee J-Y, Yoon Y-N, Kim S-Y, Hur Y-J, Yeo U-S, Sohn Y-B, Song Y-C, Park D-S, Nam M-H (2015) Enhancement of panicle blast resistance in Korean rice cultivar ‘Saeilmi’ by marker assisted backcross breeding. Plant Breed Biotechnol 3:1–10

    Article  CAS  Google Scholar 

  • Li Y, Wu C, Jiang G, Wang L, He Y (2007) Dynamic analyses of rice blast resistance for the assessment of genetic and environmental effects. Plant Breed 126:541–547

    Article  Google Scholar 

  • Luo Y, Yin Z (2013) Marker-assisted breeding of Thai fragrance rice for semi-dwarf phenotype, submergence tolerance and disease resistance to rice blast and bacterial blight. Mol Breed 32:709–721

    Article  CAS  Google Scholar 

  • Luo Y, Sangha JS, Wang S, Li Z, Yang J, Yin Z (2012) Marker-assisted breeding of Xa4, Xa21 and Xa27 in the restorer lines of hybrid rice for broad-spectrum and enhanced disease resistance to bacterial blight. Mol Breed 30:1601–1610

    Article  CAS  Google Scholar 

  • Luo Y, Zakaria S, Basyah B, Ma T, Li Z, Yang J, Yin Z (2014) Marker-assisted breeding of Indonesia local rice variety Siputeh for semi-dwarf phenotype, good grain quality and disease resistance to bacterial blight. Rice 7:33

    Article  PubMed  PubMed Central  Google Scholar 

  • Luo W, Huang M, Guo T, Xiao W, Wang J, Yang G, Liu Y, Wang H, Chen Z, Zhuang C (2017) Marker-assisted selection for rice blast resistance genes Pi2 and Pi9 through high-resolution melting of a gene-targeted amplicon. Plant Breed 136:67–73

    Article  CAS  Google Scholar 

  • Man S, Vinarao RB, Surek H, Jena KK (2016) Marker-assisted introgression of a broad-spectrum resistance gene, Pi40 improved blast resistance of two elite rice (Oryza sativa L.) cultivars of Turkey. Mol Plant Breed 7:1–15

    Google Scholar 

  • Mi J, Yang D, Chen Y, Jiang J, Mou H, Huang J, Ouyang Y, Mou T (2018) Accelerated molecular breeding of a novel P/TGMS line with broad-spectrum resistance to rice blast and bacterial blight in two-line hybrid rice. Rice 11:11

    Article  PubMed  PubMed Central  Google Scholar 

  • Miah G, Rafii MY, Ismail MR, Puteh A, Rahim HA, Asfaliza R, Latif MA (2013) Blast resistance in rice: a review of conventional breeding to molecular approaches. Mol Biol Rep 40:2369–2388

    Article  CAS  PubMed  Google Scholar 

  • Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Latif MA (2017) Marker-assisted introgression of broad-spectrum blast resistance genes into the cultivated MR219 rice variety. J Sci Food Agric 97:2810–2818

    Article  CAS  PubMed  Google Scholar 

  • Miedaner T, Korzun V (2012) Marker-assisted selection for disease resistance in wheat and barley breeding. Phytopathology 102:560–566

    Article  PubMed  Google Scholar 

  • Mohamed A, Ali R, Elhassan O, Suliman E, Mugoya C, Masiga CW, Elhusien A, Hash CT (2014) First products of DNA marker-assisted selection in sorghum released for cultivation by farmers in sub-Saharan Africa. J Plant Sci Mol Breed 3:1–10

    Article  Google Scholar 

  • Mohler V, Singrün C (2004) General considerations: marker-assisted selection. Molecular marker systems in plant breeding and crop improvement. Springer, Berlin/Heidelberg, pp 305–317

    Google Scholar 

  • Mosa KA, Ismail A, Helmy M (2017) Omics and system biology approaches in plant stress research. Plant Stress Tolerance. Springer, Cham, pp 21–34

    Google Scholar 

  • Mundt CC (2014) Durable resistance: a key to sustainable management of pathogens and pests. Infect Genet Evol 27:446–455

    Article  PubMed  Google Scholar 

  • Muthuramalingam P, Krishnan SR, Pandian S, Mareeswaran N, Aruni W, Pandian SK, Ramesh M (2018) Global analysis of threonine metabolism genes unravel key players in rice to improve the abiotic stress tolerance. Sci Rep 8:9270

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Narayanan NN, Baisakh N, Cruz V, Gnanamanickam SS, Datta K, Datta SK (2002) Molecular breeding for the development of blast and bacterial blight resistance in rice cv. IR50. Crop Sci 42:2072–2079

    Article  CAS  Google Scholar 

  • Nelson R, Wiesner-Hanks T, Wisser R, Balint-Kurti P (2018) Navigating complexity to breed disease-resistant crops. Nat Rev Genet 19:21

    Article  CAS  PubMed  Google Scholar 

  • Nguyen HT, Vu QH, Van Mai T, Nguyen TT, Vu LD, Nguyen TT, Nguyen LV, Vu HTT, Nong HT, Dinh TN (2018) Marker-assisted selection of XA21 conferring resistance to bacterial leaf blight in indica rice cultivar LT2. Rice Sci 25:52–56

    Article  CAS  Google Scholar 

  • Ni D, Song F, Ni J, Zhang A, Wang C, Zhao K, Yang Y, Wei P, Yang J, Li L (2015) Marker-assisted selection of two-line hybrid rice for disease resistance to rice blast and bacterial blight. Field Crop Res 184:1–8

    Article  Google Scholar 

  • Oerke EC (2005) Crop losses to pests. J Agric Sci 144:31–43

    Article  Google Scholar 

  • Pandey MK, Rani NS, Sundaram RM, Laha GS, Madhav MS, Rao KS, Sudharshan I, Hari Y, Varaprasad GS, Rao LVS (2013) Improvement of two traditional Basmati rice varieties for bacterial blight resistance and plant stature through morphological and marker-assisted selection. Mol Breed 31:239–246

    Article  Google Scholar 

  • Parida AK, Panda A, Rangani J (2018) Metabolomics-guided elucidation of abiotic stress tolerance mechanisms in plants. In: Plant metabolites and regulation under environmental stress. Academic Press, pp 89–131. Available at https://www.sciencedirect.com/science/article/pii/B9780128126899000054

  • Pathak MD, Khan ZR (1994) Insect pests of rice. International Rice Research Institute. Available at https://books.google.co.in/books?hl=en&lr=&id=7MuyJh0FLj4C&oi=fnd&pg=PP2&dq=Pathak+MD,+Khan+ZR+(1994)+Insect+pests+of+rice.+Int+Rice+Res+Inst&ots=WcnQJsrAU&sig=2zXw2NM8w5HAwbNG9HSHkDb1Qyk#v=onepage&q=Pathak%20MD%2C%20Khan%20ZR%20(1994)%20Insect%20pests%20of%20rice.%20Int%20Rice%20Res%20Inst&f=false

  • Peng JH, Fahima T, Röder M, Li Y, Grama A, Nevo E (2000) Microsatellite high-density mapping of the stripe rust resistance gene YrH52 region on chromosome 1B and evaluation of its marker-assisted selection in the F2 generation in wild emmer wheat. New Phytol 146:141–154

    Article  CAS  Google Scholar 

  • Pinta W, Toojinda T, Thummabenjapone P, Sanitchon J (2013) Pyramiding of blast and bacterial leaf blight resistance genes into rice cultivar RD6 using marker assisted selection. Afr J Biotechnol 12:4432–4438

    Article  Google Scholar 

  • Population Reference Bureau (PRB) (2016) World population data sheet, Washington, DC. Retrieved 11 July 2019 from https://www.prb.org/2016-worldpopulation-data-sheet/

  • Pradhan SK, Barik SR, Sahoo A, Mohapatra S, Nayak DK, Mahender A, Meher J, Anandan A, Pandit E (2016) Population structure, genetic diversity and molecular marker-trait association analysis for high temperature stress tolerance in rice. PLoS One 11:e0160027

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Priya P, Jain M (2013) RiceSRTFDB: a database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis. Database 2013:bat027. https://doi.org/10.1093/database/bat1027

    Article  PubMed  PubMed Central  Google Scholar 

  • Rajpurohit D, Kumar R, Kumar M, Paul P, Awasthi A, Basha PO, Puri A, Jhang T, Singh K, Dhaliwal HS (2011) Pyramiding of two bacterial blight resistance and a semidwarfing gene in type 3 Basmati using marker-assisted selection. Euphytica 178:111–126

    Article  Google Scholar 

  • Ramalingam J, Basharat HS, Zhang G (2002) STS and microsatellite marker-assisted selection for bacterial blight resistance and waxy genes in rice, Oryza sativa L. Euphytica 127:255–260

    Article  CAS  Google Scholar 

  • Reinke R, Kim SM, Kim BK (2018) Developing japonica rice introgression lines with multiple resistance genes for brown planthopper, bacterial blight, rice blast, and rice stripe virus using molecular breeding. Mol Gen Genomics 293(6):1565–1575

    Article  CAS  Google Scholar 

  • Rezbova H, Skubna O (2012) The role of transgenic crops in the future of global food and feed. AGRIS on-line. Papers Econ Informat 4:49

    Google Scholar 

  • Rice - Statistics & Facts (2018) Statista. Hamburg, Germany. Retrieved 11 July 2019 from https://www.statista.com/topics/1443/rice/

  • Ronald PC, Albano B, Tabien R, Abenes L, Wu K-s, McCouch S, Tanksley SD (1992) Genetic and physical analysis of the rice bacterial blight disease resistance locus, Xa21. Mol Gen Genet 236:113–120

    Article  CAS  PubMed  Google Scholar 

  • Salvi S, Tuberosa R (2005) To clone or not to clone plant QTLs: present and future challenges. Trends Plant Sci 10:297–304

    Article  CAS  PubMed  Google Scholar 

  • Sanan-Mishra N, Tripathi A, Goswami K, Shukla RN, Vasudevan M, Goswami H (2018) ARMOUR–A Rice miRNA: mRNA interaction resource. Front Plant Sci 9:602

    Article  PubMed  PubMed Central  Google Scholar 

  • Sanchez AC, Brar DS, Huang N, Li Z, Khush GS (2000) Sequence tagged site marker-assisted selection for three bacterial blight resistance genes in rice. Crop Sci 40:792–797

    Article  CAS  Google Scholar 

  • Sasaki T (2005) The map-based sequence of the rice genome. Nature 436:793

    Article  CAS  Google Scholar 

  • Savary S, Ficke A, Aubertot J-N, Hollier C (2012) Crop losses due to diseases and their implications for global food production losses and food security. Food Security 4(2):519–537

    Google Scholar 

  • Shakoor N, Lee S, Mockler TC (2017) High throughput phenotyping to accelerate crop breeding and monitoring of diseases in the field. Curr Opin Plant Biol 38:184–192

    Article  PubMed  Google Scholar 

  • Singh S, Sidhu JS, Huang N, Vikal Y, Li Z, Brar DS, Dhaliwal HS, Khush GS (2001) Pyramiding three bacterial blight resistance genes (xa5, xa13 and Xa21) using marker-assisted selection into indica rice cultivar PR106. Theor Appl Genet 102:1011–1015

    Article  CAS  Google Scholar 

  • Singh AK, Gopalakrishnan S, Singh VP, Prabhu KV, Mohapatra T, Singh NK, Sharma TR, Nagarajan M, Vinod KK, Singh D (2011) Marker assisted selection: a paradigm shift in Basmati breeding. Indian J Genet Plant Breed 71:120–128

    CAS  Google Scholar 

  • Singh A, Singh VK, Singh SP, Pandian RTP, Ellur RK, Singh D, Bhowmick PK, Gopala Krishnan S, Nagarajan M, Vinod KK, Singh UD, Prabhu KV, Sharma TR, Mohapatra T, Singh AK (2012a) Molecular breeding for the development of multiple disease resistance in Basmati rice. AoB Plants 2012:pls029

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Singh VK, Singh A, Singh S, Ellur RK, Choudhary V, Sarkel S, Singh D, Krishnan SG, Nagarajan M, Vinod K (2012b) Incorporation of blast resistance into “PRR78”, an elite Basmati rice restorer line, through marker assisted backcross breeding. Field Crop Res 128:8–16

    Article  Google Scholar 

  • Singh AK, Singh VK, Singh A, Ellur RK, Pandian RTP, Krishnan SG, Singh UD, Nagarajan M, Vinod KK, Prabhu KV (2015) Introgression of multiple disease resistance into a maintainer of Basmati rice CMS line by marker assisted backcross breeding. Euphytica 203:97–107

    Article  CAS  Google Scholar 

  • Singh B, Mehta S, Tiwari M, Bhatia S (2018) Legume breeding for fungal resistance: a lesson to learn. In: Islam MA, Dhakate P (eds) Molecular approaches for plant improvement, vol 1. Kalpaz Publication, New Delhi, pp 159–180

    Google Scholar 

  • Smita S, Lenka SK, Katiyar A, Jaiswal P, Preece J, Bansal KC (2011) QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice. Database 2011:bar037

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sreewongchai T, Toojinda T, Thanintorn N, Kosawang C, Vanavichit A, Tharreau D, Sirithunya P (2010) Development of elite indica rice lines with wide spectrum of resistance to Thai blast isolates by pyramiding multiple resistance QTLs. Plant Breed 129:176–180

    Article  CAS  Google Scholar 

  • Stenberg JA, Heil M, Åhman I, Björkman C (2015) Optimizing crops for biocontrol of pests and disease. Trends Plant Sci 20:698–712

    Article  CAS  PubMed  Google Scholar 

  • Sugiura N, Tsuji T, Fujii K, Kato T, Saka N, Touyama T, Hayano Saito Y, Izawa T (2004) Molecular marker-assisted selection in a recurrent backcross breeding for the incorporation of resistance to rice stripe virus and panicle blast in rice (Oryza sativa L.). Breed Res (Japan) 6:143–148

    Article  Google Scholar 

  • Sundaram RM, Vishnupriya MR, Biradar SK, Laha GS, Reddy GA, Rani NS, Sarma NP, Sonti RV (2008) Marker assisted introgression of bacterial blight resistance in Samba Mahsuri, an elite indica rice variety. Euphytica 160:411–422

    Article  Google Scholar 

  • Tanweer FA, Rafii MY, Sijam K, Rahim HA, Ahmed F, Ashkani S, Latif MA (2015) Introgression of blast resistance genes (putative Pi-b and Pi-kh) into elite rice cultivar MR219 through marker-assisted selection. Front Plant Sci 6:1002

    Article  PubMed  PubMed Central  Google Scholar 

  • Telebanco-Yanoria MJ, Koide Y, Fukuta Y, Imbe T, 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 

  • Toenniessen GH, O’Toole JC, DeVries J (2003) Advances in plant biotechnology and its adoption in developing countries. Curr Opin Plant Biol 6:191–198

    Article  PubMed  Google Scholar 

  • Usatov A, Kostylev P, Azarin K, Markin N, Makarenko M, Khachumova V, Bibov MY (2016) Introgression of the rice blast resistance genes Pi1, Pi2 and Pi33 into Russian rice varieties by marker-assisted selection. Indian J Genet Plant Breed 76:18–23

    Article  CAS  Google Scholar 

  • Wallace JS, Acreman MC, Sullivan CA (2003) The sharing of water between society and ecosystems: from conflict to catchment-based co-management. Philoso Trans R Soc Lond B Biol Sci 358:2011–2026

    Article  CAS  Google Scholar 

  • Wang J, Chapman SC, Bonnett DG, Rebetzke GJ, Crouch J (2007) Application of population genetic theory and simulation models to efficiently pyramid multiple genes via marker-assisted selection. Crop Sci 47:582–588

    Article  Google Scholar 

  • Wang Y, Pinson S, Fjellstrom R, Tabien R (2012) Phenotypic gain from introgression of two QTL, qSB9-2 and qSB12-1, for rice sheath blight resistance. Mol Breed 30:293–303

    Article  CAS  Google Scholar 

  • Wen S, Gao B (2012) Introgressing blast resistant gene Pi-9 (t) into elite rice restorer Luhui17 by marker-assisted selection. Rice Genom Genet 2:31–36

    Google Scholar 

  • Whittaker JC, Haley CS, Thompson R (1997) Optimal weighting of information in marker-assisted selection. Genet Res 69:137–144

    Article  Google Scholar 

  • Wiesner-Hanks T, Nelson R (2016) Multiple disease resistance in plants. Annu Rev Phytopathol 54:229–252

    Article  CAS  PubMed  Google Scholar 

  • Win KM, Korinsak S, Sirithunya P, Lanceras-Siangliw J, Jamboonsri W, Da T, Patarapuwadol S, Toojinda T (2013) Marker assisted introgression of multiple genes for bacterial blight resistance into aromatic Myanmar rice MK-75. Field Crop Res 154:164–171

    Article  Google Scholar 

  • Wongsaprom C, Sirithunya P, Vanavichit A, Pantuwan G, Jongdee B, Sidhiwong N, Lanceras-Siangliw J, Toojinda T (2010) Two introgressed quantitative trait loci confer a broad-spectrum resistance to blast disease in the genetic background of the cultivar RD6 a Thai glutinous jasmine rice. Field Crop Res 119:245–251

    Article  Google Scholar 

  • Wu Y, Yu L, Pan C, Dai Z, Li Y, Xiao N, Zhang X, Ji H, Huang N, Zhao B (2016) Development of near-isogenic lines with different alleles of Piz locus and analysis of their breeding effect under Yangdao 6 background. Mol Breed 36:12

    Article  CAS  Google Scholar 

  • Xiao W-M, Luo L-X, Hui W, Tao G, Liu Y-Z, Zhou J-Y, Zhu X-Y, Yang Q-Y, Chen Z-Q (2016) Pyramiding of Pi46 and Pita to improve blast resistance and to evaluate the resistance effect of the two R genes. J Integr Agric 15:2290–2298

    Article  CAS  Google Scholar 

  • Xiao N, Wu Y, Pan C, Yu L, Chen Y, Liu G, Li Y, Zhang X, Wang Z, Dai Z (2017) Improving of rice blast resistances in japonica by pyramiding major R genes. Front Plant Sci 7:1918

    Article  PubMed  PubMed Central  Google Scholar 

  • Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407

    Article  Google Scholar 

  • Xu Q, Ni H, Chen Q, Sun F, Zhou T, Lan Y, Zhou Y (2013) Comparative proteomic analysis reveals the cross-talk between the responses induced by H2O2 and by long-term rice black-streaked dwarf virus infection in rice. PLoS One 8:e81640

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yap R, Hsu YC, Wu YP, Lin YR, Kuo CW (2016) Multiplex PCR genotyping for five bacterial blight resistance genes applied to marker-assisted selection in rice (Oryza sativa). Plant Breed 135:309–317

    Article  CAS  Google Scholar 

  • Yellareddygari SKR, Reddy MS, Kloepper JW, Lawrence KS, Fadamiro H (2014) Rice sheath blight: a review of disease and pathogen management approaches. J Plant Pathol Microbiol 5:241

    Google Scholar 

  • Yoshimura S, Yoshimura A, Iwata N, McCouch SR, Abenes ML, Baraoidan MR, Mew TW, Nelson RJ (1995) Tagging and combining bacterial blight resistance genes in rice using RAPD and RFLP markers. Mol Breed 1:375–387

    Article  CAS  Google Scholar 

  • Yu J, Hu S, Wang J, Wong GK-S, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X (2002) A draft sequence of the rice genome (Oryza sativa L ssp indica). Science 296:79–92

    Article  CAS  PubMed  Google Scholar 

  • Yugander A, Sundaram RM, Singh K, Ladhalakshmi D, Rao LVS, Madhav MS, Badri J, Prasad MS, Laha GS (2018) Incorporation of the novel bacterial blight resistance gene Xa38 into the genetic background of elite rice variety improved Samba Mahsuri. PLoS One 13:e0198260

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang W, Smith C (1993) Simulation of marker-assisted selection utilizing linkage disequilibrium: the effects of several additional factors. Theor Appl Genet 86:492–496

    Article  CAS  PubMed  Google Scholar 

  • Zhang J, Li X, Jiang G, Xu Y, He Y (2006) Pyramiding of Xa7 and Xa21 for the improvement of disease resistance to bacterial blight in hybrid rice. Plant Breed 125:600–605

    Article  CAS  Google Scholar 

  • Zhang Y, Zang Q, Xu B, Zheng W, Ban R, Zhang H, Yang Y, Hao Q, Iqbal F, Li A (2016) IsomiR Bank: a research resource for tracking IsomiRs. Bioinformatics 32:2069–2071

    Article  PubMed  CAS  Google Scholar 

  • Zhao H, Yao W, Ouyang Y, Yang W, Wang G, Lian X, Xing Y, Chen L, Xie W (2014) RiceVarMap: a comprehensive database of rice genomic variations. Nucleic Acids Res 43:D1018–D1022

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhou Y-L, Xu J-L, Zhou S-C, Yu J, Xie X-W, Xu M-R, Sun Y, Zhu L-H, Fu B-Y, Gao Y-M (2009) Pyramiding Xa23 and Rxo1 for resistance to two bacterial diseases into an elite indica rice variety using molecular approaches. Mol Breed 23:279–287

    Article  CAS  Google Scholar 

  • Zuo S, Zhang L, Wang H, Yin Y, Zhang Y, Chen Z, Ma Y, Pan X (2008) Prospect of the QTL-qSB-9 Tq utilized in molecular breeding program of japonica rice against sheath blight. J Genet Genomics 35:499–505

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Mehta, S., Singh, B., Dhakate, P., Rahman, M., Islam, M.A. (2019). Rice, Marker-Assisted Breeding, and Disease Resistance. In: Wani, S.H. (eds) Disease Resistance in Crop Plants. Springer, Cham. https://doi.org/10.1007/978-3-030-20728-1_5

Download citation

Publish with us

Policies and ethics