Abstract
Marker-assisted breeding provides a great opportunity to the present-day researchers for breeding new crop varieties by design through precise transfer of desirable gene(s). Among the molecular breeding approaches, marker-assisted backcross breeding (MABB) is an attractive proposition for breeders as it can help in improving an already popular variety for specific target traits such as resistance to disease/pest/improvement in quality. MABB has been successfully employed in transferring genes (xa13 and Xa21) governing resistance to diseases such as bacterial blight (BB), blast (Pi54, Pita, Pi1, Pi9, Pib, Piz5 and Pi5), sheath blight (qSBR 11-1), and brown plant hopper (BPH; Bph18, Bph20 and Bph21) into a number of Basmati rice varieties, namely Pusa Basmati 1, Pusa Basmati 1121, and Pusa Basmati 6 as well as long slender grain aromatic rice varieties such as Pusa Sugandh 5. Further, a major QTL for salt tolerance (Saltol) has been transferred to Pusa Basmati 1121 and Pusa Basmati 1, which are widely grown in northwestern India. Genetically enhanced donor sources in the form of near-isogenic lines (NILs) carrying major gene(s)/QTLs for resistance to biotic (BB, blast, sheath blight, and BPH) and abiotic (salt tolerance) stresses in the background Pusa Basmati 1, the first semi-dwarf, high-yielding Basmati rice variety, have been developed. QTL mapping using recombinant inbred line (RIL) population has unveiled several novel QTLs for different agronomic, grain and cooking quality traits. Besides their effective use in Basmati rice improvement, molecular markers are also utilized in basic studies as well as in maintenance breeding of Basmati rice varieties, which is discussed in the present chapter.
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References
Ahn SN, Bollich CN, Tanksley SD (1992) RFLP tagging of a gene for aroma in rice. Theor Appl Genet 84:825–828
Amarawathi Y, Singh R, Singh AK, Singh VP, Mohapatra T, Sharma TR, Singh NK (2008) Mapping of quantitative trait loci for basmati quality traits in rice (Oryza sativa L.). Mol Breed 21:49–65
Babu NN, Sharma SK, Ellur RK, Singh VK, Pal M, Pathania S, Singh VK, Singh D, Gopalakrishnan S, Bhowmick PK, Nagarajan M, Vinod KK, Singh NK, Prabhu KV, Singh AK (2012) Marker assisted improvement of Pusa Basmati 1121 for salinity tolerance. In: Abstracts of poster presentation (MB52) international conference on plant biotechnology for food security: new frontiers, National Agricultural Science Centre, New Delhi, India, 21–24 Feb 2012, pp 72–73
Babu NN, Vinod KK, Gopalakrishnan S, Bhowmick PK, Vanaja T, Krishnamurthy SL, Nagarajan M, Singh NK, Prabhu KV, Singh AK (2014) Marker based haplotype diversity of Saltol QTL in relation to seedling stage salinity tolerance in selected genotypes of rice. Indian J Genet 74(1):16–25
Bradbury LM, Fitzgerald TL, Henry RJ, Jin Q, Waters DL (2005) The gene for fragrance in rice. Plant Biotech J 3:363–370
Buttery RG, Turnbaugh JG, Ling LC (1988) Contribution of volatiles to rice aroma. J Agric Food Chem 36(5):1006–1009
Channamallikarjuna V, Sonah H, Prasad M, Rao GJN, Chand S, Upreti HC, Singh NK, Sharma TR (2010) Identification of major quantitative trait loci qSBR11-1 for sheath blight resistance in rice. Mol Breed 25:155–166
Chaudhary S, Yadav AK, Singh V, Singh BD, Ellur RK, Babu N, Bhowmick PK, Gopala Krishnan S, Nagarajan M, Vinod KK, Singh AK (2014) Development of salt tolerant “Pusa Basmati 1” through marker assisted transfer of “Saltol”, a major QTL for seedling stage salinity tolerance. In: National conference on “perspectives and trends in plant sciences and biotechnology (PTPB-2014) held at Panjab University, Chandigarh, 21–23 Feb 2014, C11
Chin JH, Lu X, Haefele SM, Gamuyao R, Ismail A, Wissuwa M, Heuer S (2010) Development and application of gene-based markers for the major rice QTL Phosphorus uptake 1. Theor Appl Genet 120(6):1073–1086
Eizenga GC, Agrama HA, Lee FN, Yan WG, Jia Y (2006) Identifying novel resistance genes in newly introduced blast resistant rice germplasm. Crop Sci 46:1870–1878
Ellur RK, Pathania S, Singh VK, Singh D, Gopala Krishnan S, Bhowmick PK, Nagarajan M, Vinod KK, Singh UD, Mondal KK, Chander S, Mohapatra T, Sharma TR, Prabhu KV, Singh AK (2012) Marker assisted breeding for incorporation of bacterial blight, blast and brown plant hopper resistance in Pusa Basmati 1121. In: Abstracts of poster presentation (MB48) international conference on plant biotechnology for food security: new frontiers, National Agricultural Science Centre, New Delhi, India, 21–24 Feb 2012, pp 70–71
Ellur RK, Pathania S, Gopala Krishnan S, Bhowmick PK, Nagarajan M, Vinod KK, Singh UD, Rathour R, Prabhu KV, Singh AK (2013a) Pyramiding of blast resistance genes in the Basmati rice variety Pusa Basmati 1121 (P0049). In: Abstract book: 7th international rice genetics symposium, Manila, Philippines, 5–8 Nov 2013, pp. 363–364
Ellur RK, Pathania S, Gopala Krishnan S, Bhowmick PK, Vinod KK, Singh UD, Mondal KK, Rathour R, Prabhu KV, Singh AK (2013b). Pyramiding of bacterial blight and blast resistance genes in the Basmati rice variety Pusa Basmati 6 through marker assisted backcross breeding (PVII-192). In: 11th international symposium on rice functional genomics—sustaining food and nutritional security, New Delhi, India, 20–23 Nov 2013, pp 146
Ellur RK, Khanna A, Yadav A, Pathania S, Rajashekara H, Singh VK, Gopala Krishnan S, Bhowmick PK, Nagarajan M, Vinod KK, Prakash G, Mondal KK, Singh NK, Singh AK (2016) Improvement of Basmati rice varieties for resistance to blast and bacterial blight diseases using marker assisted backcross breeding. Plant Sci 242:330–341
Fjellstrom R, Conaway-Bormans CA, McClung AM, Marchetti MA, Shank AR, Park WD (2004) Development of DNA markers suitable for marker-assisted selection of three Pi genes conferring resistance to multiple Pyricularia grisea pathotypes. Crop Sci 44:1790–1798
Fjellstrom R, McClung AM, Shank AR (2006) SSR markers closely linked to the Pi-z locus are useful for selection of blast resistance in a broad array of rice germplasm. Mol Breed 17:149–157
Fuentes JL, Correa-Victoria FJ, Escobar F, Prado G, Aricapa G, Duque MC, Tohme J (2008) Identification of microsatellite markers linked to the blast resistance gene Pi-1(t) in rice. Euphytica 160:295–304
Gamuyao R, Chin JH, Tanaka JP, Pesaresi P, Catausan S, Dalid C, Slamet-Loedin IS, Mendoza EMT, Wissuwa M, Heuer S (2012) The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature 488:535–539
Gopala Krishnan S, Waters DLE, Katiyar SK, Sadananda AR, Satyadev V, Henry R (2012) Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing. Plant Biotech J 10(6):623–634
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
Gregorio GB (1997) Tagging salinity tolerance genes in rice using amplified fragment length polymorphism (AFLP). Ph.D. thesis, University of the Philippines, Los Baños, p 118
Jena KK, Kim S (2010) Current status of brown planthopper (BPH) resistance and genetics. Rice 3:161–171
Jena KK, Jeung JU, Lee JH, Choi HC, Brar DS (2006) High-resolution mapping of a new brown plant hopper (BPH) resistance gene, Bph18(t), and marker-assisted selection for BPH resistance in rice (Oryza sativa L.). Theor Appl Genet 112:288–297
Jeon JS, Chen D, Yi GH, Wang GL, Ronald PC (2003) Genetic and physical mapping of Pi5(t), a locus associated with broad-spectrum resistance to rice blast. Mol Gen Genomics 269:280–289
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
Khanna A, Sharma V, Shikari AB, Gopala Krishnan S, Sharma TR, Nagarajan M, Vinod KK, Singh D, Singh UD, Ellur RK, Pathania S, Prabhu KV, Singh AK (2012) Development of monogenic lines for blast resistant genes in Basmati rice. In: Abstracts of poster presentation (MB50) international conference on plant biotechnology for food security: new frontiers, National Agricultural Science Centre, New Delhi, India, Feb 21–24 2012, pp 71–72
Khanna A, Shikari AB, Gopala Krishnan S, Singh UD, Sharma TR, Rathour R, Variar M, Prashanthi SK, Nagarajan M, Singh AK (2013) Development of near isogenic lines for functional genomics of blast resistance in Basmati rice (PVII-197). In: 11th International symposium on rice functional genomics—sustaining food and nutritional security, New Delhi, India, 20–23 Nov 2013, pp 149
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 (2015a) Development and evaluation of near isogenic lines for major blast resistance gene(s) in Basmati rice. Theor Appl Genet 128:1243–1259
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, Rajashekhara H, Singh NK, Prabhu KV, Singh AK (2015b) Marker assisted pyramiding of major blast resistance genes Pi9 and Pita in the genetic background of an elite Basmati rice variety, Pusa Basmati 1. Indian J Genet 75(4):417–425
Lee SK, Song MY, Seo YS, Kim HK, Ko S, Cao PJ, Suh JP, Yi G, Roh JH, Lee S, An G, Hahn TR, Wang GL, Ronald P, Jeon JS (2009) Rice Pi5-mediated resistance to Magnaporthe oryzae requires the presence of two coiled-coil–nucleotide-binding–leucine-rich repeat genes. Genetics 181(4):1627–1638
Pathak MD, Cheng CH, Fortuno ME (1969) Resistance to Nephotettix impictiveps and Nilaparvata lugens in varieties of rice. Nature 223:502–504
Pinson SRM, Capdevielle FM, Oard JH (2005) Confirming QTLs and finding additional loci conditioning sheath blight resistance in rice (Oryza sativa L.) using recombinant inbred lines. Crop Sci 45:503–510
Qu S, Liu G, Zhou B, Bellizzi M, Zeng L, Dai L, Han B, Wang GL (2006) The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site-leucine-rich repeat protein and is a member of a multigene family in rice. Genetics 172:1901–1914
Rahman ML, Jiang W, Chu SH, Qiao Y, Ham TH, Woo MO, Lee J, Khanam MS, Chin JH, Jeung JU, Brar DS, Jena KK, Koh HJ (2009) High-resolution mapping of two rice brown planthopper resistance genes, Bph20(t) and Bph21(t), originating from Oryza minuta. Theor Appl Genet 119:1237–1246
Ronald PC, Albano B, Tabien R, Abenes L, Wu KS, McCouch SR, Tanksley SD (1992) Genetic and physical analysis of the rice bacterial blight disease resistance locus, Xa21. Mol Gen Genet 236:113–120
Sharma TR, Shanker P, Singh BK, Jana TK, Madhav MS, Gaikwad K, Singh NK, Plaha P, Rathour R (2005) Molecular mapping of rice blast resistance gene Pi-kh in the rice variety, tetep. J Plant Biochem Biotechnol 14:127–133
Sharma TR, Rai AK, Gupta GK, Singh NK (2010) Broad-spectrum blast resistance gene Pikh cloned from the rice line tetep designated as Pi54. J Plant Biochem Biotechnol 19:87–89
Shikari AB, Khanna A, Gopala Krishnan S, Sharma TR, Nagarajan M, Vinod KK, Singh D, Singh UD, Ellur RK, Pathania S, Prabhu KV, Singh AK (2012) Marker assisted development of near isogenic lines for major blast resistance genes (Pi54, Pi1 and Pita) in Pusa Basmati 1. In: Abstracts of poster presentation (MB51) international conference on plant biotechnology for food security: new frontiers, National Agricultural Science Centre, New Delhi, India, 21–24 Feb 2012, pp 72
Shikari AB, Khanna A, Gopala Krishnan S, Singh UD, Sharma TR, Rathour R, Variar M, Prashanthi SK, Prabhu KV, Singh AK (2013) Marker assisted pyramiding of major blast resistance genes in Basmati rice variety ‘Pusa Basmati 1’ (P0048). In: Abstract book: 7th international rice genetics symposium, Manila, Philippines, 5–8 Nov 2013, pp 362–363
Singh VP, Singh AK, Mohapatra T, Joseph M, Gopala Krishnan S, Atwal SS, Nagarajan M, Pandey KR, Gopalakrishnan J, Sinha SN, Chopra NK, Singh VK, Singh R, Tyagi JP, Singh D, Singh J, Singh J, Ravindran G (2007) Notification of Basmati rice variety Pusa 1460 (improved Pusa Basmati 1). Indian J Genet 67(3):304
Singh AK, Gopala Krishnan S, Singh VP, Mohapatra T, Prabhu KV, 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):1–9
Singh AK, Gopala Krishnan S, Bhowmick PK, Prabhu KV, VP Singh (2013) Pusa Basmati 1509–a new dawn in climate-smart cultivation. Rice India 2:6–11
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 (2012) Molecular breeding for the development of multiple disease resistant Basmati rice. AoB Plants pls029. doi:10.1093/aobpla/pls029
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, Aggrawal PK, Bhatt JC, Mohapatra T, Prabhu KV, Singh AK (2012b) Incorporation of blast resistance into “PRR78”, an elite Basmati rice restorer line, through marker assisted backcross breeding. Field Crops Res 128:8–16
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 Piz5 and Pi54 into an elite Basmati rice restorer line ‘PRR78’. Plant Breed 132(5):489–495
Srinivasachary Willocquet L, Savary S (2011) Resistance to rice sheath blight (Rhizoctonia solani Kuhn) [(teleomorph: Thanatephorus cucumeris (A.B. Frank) Donk.] disease: current status and perspectives. Euphytica 178:1–22
Thomson MJ, Ocampo MD, Egdane J, Rahman MA, Sajise AG, Adorada DL, Raiz ET, Blumwald E, Seraj ZI, Singh RK, Gregorio GB, Ismail AM (2010) Characterizing the Saltol quantitative trait locus for salinity tolerance in rice. Rice 3:148–160
Vinod KK, Gopala Krishnan S, Naresh BN, Nagarajan M, Singh AK (2013) Improving salt tolerance in rice: looking beyond the conventional. In: Ahmad P, Azooz MM, Prasad MNV (eds) Salt stress in plants: signalling, omics and adaptations. Springer, New York, pp 219–260
Wissuwa M, Yano M, Ae N (1998) Mapping of QTLs for phosphorus-deficiency tolerance in rice (Oryza sativa L.). Theor Appl Genet 97:777–783
Acknowledgement
The research work on Basmati rice improvement is funded by Indian Council of Agricultural Research, New Delhi; ICAR National Agricultural Innovation Project (ICAR-NAIP) and by the “Accelerated Crop Improvement Programme” of Department of Biotechnology, India.
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Singh, A.K., Gopala Krishnan, S. (2016). Genetic Improvement of Basmati Rice—The Journey from Conventional to Molecular Breeding. In: Rajpal, V., Rao, S., Raina, S. (eds) Molecular Breeding for Sustainable Crop Improvement. Sustainable Development and Biodiversity, vol 11. Springer, Cham. https://doi.org/10.1007/978-3-319-27090-6_10
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DOI: https://doi.org/10.1007/978-3-319-27090-6_10
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