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Rice, Marker-Assisted Breeding, and Disease Resistance

  • Sahil Mehta
  • Baljinder Singh
  • Priyanka Dhakate
  • Mehzabin Rahman
  • Md Aminul Islam
Chapter

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.

Keywords

Population Rice Yield Markers Marker-assisted selection Disease Recurrent parent Rust Xanthomonas 

References

  1. 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 23:306–316Google Scholar
  2. 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 6:886Google Scholar
  3. Atkinson NJ, Urwin PE (2012) The interaction of plant biotic and abiotic stresses: from genes to the field. J Exp Bot 63:3523–3543PubMedGoogle Scholar
  4. 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:368712Google Scholar
  5. 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 341:1–8PubMedGoogle Scholar
  6. 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 26:293–305Google Scholar
  7. Beckmann JS, Soller M (1983) Restriction fragment length polymorphisms in genetic improvement: methodologies, mapping and costs. Theor Appl Genet Theor Appl Genet:33–43Google Scholar
  8. Bellard C, Bertelsmeier C, Leadley P, Thuiller W, Courchamp F (2012) Impacts of climate change on the future of biodiversity. Ecol Lett 15:365–377PubMedPubMedCentralGoogle Scholar
  9. 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 43:1032–1043Google Scholar
  10. 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 21:101–116Google Scholar
  11. 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 51:759–770Google Scholar
  12. 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 239Google Scholar
  13. 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 120:133–137Google Scholar
  14. 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 20:708–714Google Scholar
  15. 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 1:5Google Scholar
  16. 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 161:118–127Google Scholar
  17. 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 16:538PubMedPubMedCentralGoogle Scholar
  18. 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 22:961–975PubMedGoogle Scholar
  19. 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 434:980PubMedGoogle Scholar
  20. 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 6:1785–1790Google Scholar
  21. 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 192:87–96Google Scholar
  22. Duke SO (2018) The history and current status of glyphosate. Pest Manag Sci 74:1027–1034PubMedGoogle Scholar
  23. 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 95:163–318Google Scholar
  24. 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 6:29188PubMedPubMedCentralGoogle Scholar
  25. 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 242:330–341PubMedGoogle Scholar
  26. Frisch M, Melchinger AE (2001) Marker-assisted backcrossing for simultaneous introgression of two genes. Crop Sci 41:1716–1725Google Scholar
  27. 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 11:13104–13114Google Scholar
  28. Garg P, Jaiswal P (2016) Databases and bioinformatics tools for rice research. Curr Plant Biol 7-8:39–52Google Scholar
  29. 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 48:1–32Google Scholar
  30. Gimelfarb A, Lande R (1995) Marker-assisted selection and marker-QTL associations in hybrid populations. Theor Appl Genet 91:522–528PubMedGoogle Scholar
  31. 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 296:92–100PubMedGoogle Scholar
  32. 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 127:131–139Google Scholar
  33. 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 132:61–69Google Scholar
  34. Guimarães EP (2007) Marker-assisted selection: current status and future perspectives in crops, livestock, forestry and fish. Food & Agriculture Org, RomeGoogle Scholar
  35. Gur A, Zamir D (2004) Unused natural variation can lift yield barriers in plant breeding. PLoS Biol 2:e245PubMedPubMedCentralGoogle Scholar
  36. 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 1:52–66Google Scholar
  37. 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 130:608–616Google Scholar
  38. 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 132:586–594Google Scholar
  39. Hegde SS, Prashanthi SK (2016) Identification of polymorphic markers and introgression of Pi1 and Pi2 genes for blast resistance in rice. J Farm Sci 29:327–331Google Scholar
  40. Helmy M, Tomita M, Ishihama Y (2011) OryzaPG-DB: rice proteome database based on shotgun proteogenomics. BMC Plant Biol 11:63PubMedPubMedCentralGoogle Scholar
  41. 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 100:1121–1128Google Scholar
  42. 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
  43. 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 29:448–456Google Scholar
  44. 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 95:313–320Google Scholar
  45. 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 187:449–459Google Scholar
  46. 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 49:168–178Google Scholar
  47. Jena KK, Mackill DJ (2008) Molecular markers and their use in marker-assisted selection in rice. Crop Sci 48:1266–1276Google Scholar
  48. 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-plantsGoogle Scholar
  49. 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 35:83Google Scholar
  50. 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 13:377–387Google Scholar
  51. 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 8:4091PubMedPubMedCentralGoogle Scholar
  52. 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 128:1243–1259PubMedGoogle Scholar
  53. Khush GS (2005) What it will take to feed 5.0 billion rice consumers in 2030. Plant Mol Biol 59:1–6PubMedGoogle Scholar
  54. 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 129:670–675Google Scholar
  55. 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 9:275–282Google Scholar
  56. Kumar S, Rao M (2018) Conventional and molecular breeding for bacterial leaf blight and blast resistance in rice. J Ecol 3:1–3Google Scholar
  57. 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 95:895–903PubMedGoogle Scholar
  58. Kurata N, Yamazaki Y (2006) Oryzabase. An integrated biological and genome information database for rice. Plant Physiol 140:12–17PubMedPubMedCentralGoogle Scholar
  59. 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 25:407–416PubMedGoogle Scholar
  60. Lande R, Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743–756PubMedPubMedCentralGoogle Scholar
  61. 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 3:1–10Google Scholar
  62. 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 126:541–547Google Scholar
  63. 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 32:709–721Google Scholar
  64. 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 30:1601–1610Google Scholar
  65. 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 7:33PubMedPubMedCentralGoogle Scholar
  66. 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 136:67–73Google Scholar
  67. 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 7:1–15Google Scholar
  68. 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 11:11PubMedPubMedCentralGoogle Scholar
  69. 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 40:2369–2388PubMedGoogle Scholar
  70. 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 97:2810–2818PubMedGoogle Scholar
  71. Miedaner T, Korzun V (2012) Marker-assisted selection for disease resistance in wheat and barley breeding. Phytopathology 102:560–566PubMedGoogle Scholar
  72. 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 3:1–10Google Scholar
  73. Mohler V, Singrün C (2004) General considerations: marker-assisted selection. Molecular marker systems in plant breeding and crop improvement. Springer, Berlin/Heidelberg, pp 305–317Google Scholar
  74. Mosa KA, Ismail A, Helmy M (2017) Omics and system biology approaches in plant stress research. Plant Stress Tolerance. Springer, Cham, pp 21–34Google Scholar
  75. Mundt CC (2014) Durable resistance: a key to sustainable management of pathogens and pests. Infect Genet Evol 27:446–455PubMedGoogle Scholar
  76. 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 8:9270PubMedPubMedCentralGoogle Scholar
  77. 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 42:2072–2079Google Scholar
  78. Nelson R, Wiesner-Hanks T, Wisser R, Balint-Kurti P (2018) Navigating complexity to breed disease-resistant crops. Nat Rev Genet 19:21PubMedGoogle Scholar
  79. 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 25:52–56Google Scholar
  80. 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 184:1–8Google Scholar
  81. Oerke EC (2005) Crop losses to pests. J Agric Sci 144:31–43Google Scholar
  82. 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 31:239–246Google Scholar
  83. 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/B9780128126899000054Google Scholar
  84. 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 146:141–154Google Scholar
  85. 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 12:4432–4438Google Scholar
  86. Population Reference Bureau (PRB) (2016) World population data sheet, Washington, DC. Retrieved 11 July 2019 from https://www.prb.org/2016-worldpopulation-data-sheet/
  87. 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:e0160027PubMedPubMedCentralGoogle Scholar
  88. 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/bat1027CrossRefPubMedPubMedCentralGoogle Scholar
  89. 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 178:111–126Google Scholar
  90. 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 127:255–260Google Scholar
  91. 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):1565–1575Google Scholar
  92. Rezbova H, Skubna O (2012) The role of transgenic crops in the future of global food and feed. AGRIS on-line. Papers Econ Informat 4:49Google Scholar
  93. Rice - Statistics & Facts (2018) Statista. Hamburg, Germany. Retrieved 11 July 2019 from https://www.statista.com/topics/1443/rice/
  94. 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 236:113–120PubMedGoogle Scholar
  95. Salvi S, Tuberosa R (2005) To clone or not to clone plant QTLs: present and future challenges. Trends Plant Sci 10:297–304PubMedGoogle Scholar
  96. Sanan-Mishra N, Tripathi A, Goswami K, Shukla RN, Vasudevan M, Goswami H (2018) ARMOUR–A Rice miRNA: mRNA interaction resource. Front Plant Sci 9:602PubMedPubMedCentralGoogle Scholar
  97. 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 40:792–797Google Scholar
  98. Sasaki T (2005) The map-based sequence of the rice genome. Nature 436:793Google Scholar
  99. 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):519–537Google Scholar
  100. 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 38:184–192PubMedGoogle Scholar
  101. 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 102:1011–1015Google Scholar
  102. 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 71:120–128Google Scholar
  103. 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:pls029PubMedPubMedCentralGoogle Scholar
  104. 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 128:8–16Google Scholar
  105. 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 203:97–107Google Scholar
  106. 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 159–180Google Scholar
  107. 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:bar037PubMedPubMedCentralGoogle Scholar
  108. 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 129:176–180Google Scholar
  109. Stenberg JA, Heil M, Åhman I, Björkman C (2015) Optimizing crops for biocontrol of pests and disease. Trends Plant Sci 20:698–712PubMedGoogle Scholar
  110. 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) 6:143–148Google Scholar
  111. 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 160:411–422Google Scholar
  112. 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 6:1002PubMedPubMedCentralGoogle Scholar
  113. 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 60:629–638Google Scholar
  114. Toenniessen GH, O’Toole JC, DeVries J (2003) Advances in plant biotechnology and its adoption in developing countries. Curr Opin Plant Biol 6:191–198PubMedGoogle Scholar
  115. 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 76:18–23Google Scholar
  116. 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 358:2011–2026Google Scholar
  117. 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 47:582–588Google Scholar
  118. 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 30:293–303Google Scholar
  119. Wen S, Gao B (2012) Introgressing blast resistant gene Pi-9 (t) into elite rice restorer Luhui17 by marker-assisted selection. Rice Genom Genet 2:31–36Google Scholar
  120. Whittaker JC, Haley CS, Thompson R (1997) Optimal weighting of information in marker-assisted selection. Genet Res 69:137–144Google Scholar
  121. Wiesner-Hanks T, Nelson R (2016) Multiple disease resistance in plants. Annu Rev Phytopathol 54:229–252PubMedGoogle Scholar
  122. 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 154:164–171Google Scholar
  123. 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 119:245–251Google Scholar
  124. 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 36:12Google Scholar
  125. 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 15:2290–2298Google Scholar
  126. 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 7:1918PubMedPubMedCentralGoogle Scholar
  127. Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407Google Scholar
  128. 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:e81640PubMedPubMedCentralGoogle Scholar
  129. 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 135:309–317Google Scholar
  130. 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 5:241Google Scholar
  131. 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 1:375–387Google Scholar
  132. 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 296:79–92PubMedGoogle Scholar
  133. 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:e0198260PubMedPubMedCentralGoogle Scholar
  134. Zhang W, Smith C (1993) Simulation of marker-assisted selection utilizing linkage disequilibrium: the effects of several additional factors. Theor Appl Genet 86:492–496PubMedGoogle Scholar
  135. 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 125:600–605Google Scholar
  136. 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 32:2069–2071PubMedGoogle Scholar
  137. 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–D1022PubMedPubMedCentralGoogle Scholar
  138. 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 23:279–287Google Scholar
  139. 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 35:499–505PubMedGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Sahil Mehta
    • 1
  • Baljinder Singh
    • 2
  • Priyanka Dhakate
    • 2
  • Mehzabin Rahman
    • 3
  • Md Aminul Islam
    • 2
  1. 1.International Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
  2. 2.National Institute of Plant Genome ResearchNew DelhiIndia
  3. 3.Bimala Prasad Chaliha CollegeNagarberaIndia

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