Molecular Breeding Approaches for Disease Resistance in Sugarcane

  • Mehzabin Rahman
  • Sabira Sultana
  • Deepshikha Nath
  • Surya Kalita
  • Dhiresh Chakravarty
  • Sahil Mehta
  • Shabir Hussain Wani
  • Md Aminul Islam


Currently, the cultivated sugarcane (Saccharum officinarum L.) is one of the major commercial cash crop grown in tropics and subtropics worldwide. It is cultivated nowadays for sugar, jaggery, ethanol, juices, livestock fodder, and biofuels globally. During the last few decades, multiple countries have witnessed multiple disease epidemics. The total damage during epidemics depends upon the disease severity, disease incidence, climate conditions, and cultivated variety genotype. Furthermore, vegetative reproduction in sugarcane favors the spread of diseases. In the past, the classical breeders have developed many such disease-resistant varieties; however, these varieties were ineffective due to sudden breakdown of resistance to a new virulent strain or pathovars. As a result, there are many diseases widespread including rust, wilt, red rot, pokkah boeng, and smut which seriously affect the sugarcane production, yield, and profitability. As result, multiple diseases-resistant varieties are high in demand by the sugarcane farmers as the cultivation of such elite varieties increases both direct and indirect profits. In order to enhance the disease resistance, the sugarcane breeding programs have shifted the focus toward techniques like marker-assisted breeding, genetic engineering, etc. This book chapter summarizes about the sugarcane productivity, diseases, and various approaches employed for enhancing disease resistance.


Saccharum spp. Marker-assisted breeding Transgenics Red rot QTL mapping Association mapping Linkage disequilibrium 


  1. Abdel-Halim ES (2014) Chemical modification of cellulose extracted from sugarcane bagasse: preparation of hydroxyethyl cellulose. Arab J Chem 7:362–371Google Scholar
  2. Aglawe SB, Barbadikar KM, Mangrauthia SK, Madhav MS (2018) New breeding technique “genome editing” for crop improvement: applications, potentials and challenges. 3 Biotech 8:336PubMedPubMedCentralGoogle Scholar
  3. Ahanger RA, Bhat HA, Bhat TA, Ganie S, Lone AA, Wani IA et al (2013) Impact of climate change on plant diseases. Int J Mod Plant Anim Sci 1:105–115Google Scholar
  4. Aitken KS, Jackson PA, McIntyre CL (2005) A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar. Theor Appl Genet 110:789–801PubMedGoogle Scholar
  5. Aitken K, Hermann S, Karno K, Bonnett G, McIntyre L, Jackson P (2008) Genetic control of yield related stalk traits in sugarcane. Theor Appl Genet 117:1191–1203PubMedGoogle Scholar
  6. Aitken KS, McNeil MD, Hermann S, Bundock PC, Kilian A, Heller-Uszynska K et al (2014) A comprehensive genetic map of sugarcane that provides enhanced map coverage and integrates high-throughput Diversity Array Technology (DArT) markers. BMC Genomics 15:152PubMedPubMedCentralGoogle Scholar
  7. Aljanabi SM, Parmessur Y, Kross H, Dhayan S, Saumtally S, Ramdoyal K et al (2007) Identification of a major quantitative trait locus (QTL) for yellow spot (Mycovellosiella koepkei) disease resistance in sugarcane. Mol Breed 19:1–14Google Scholar
  8. Al-Janabi SM, Honeycutt RJ, McClelland M, Sobral B (1993) A genetic linkage map of Saccharum spontaneum L.‘SES 208’. Genetics 134:1249–1260PubMedPubMedCentralGoogle Scholar
  9. Alwala S, Kimbeng CA, Veremis JC, Gravois KA (2008) Linkage mapping and genome analysis in a Saccharum interspecific cross using AFLP, SRAP and TRAP markers. Euphytica 164:37–51Google Scholar
  10. Alwala S, Kimbeng CA, Veremis JC, Gravois KA (2009) Identification of molecular markers associated with sugar-related traits in a Saccharum interspecific cross. Euphytica 167:127–142Google Scholar
  11. Andru S, Pan Y-B, Thongthawee S, Burner DM, Kimbeng CA (2011) Genetic analysis of the sugarcane (Saccharum spp.) cultivar ‘LCP 85-384’. I. Linkage mapping using AFLP, SSR, and TRAP markers. Theor Appl Genet 123:77–93PubMedGoogle Scholar
  12. Arencibia AD, Carmona ER, Tellez P, Chan M-T, Yu S-M, Trujillo LE et al (1998) An efficient protocol for sugarcane (Saccharum spp. L.) transformation mediated by Agrobacterium tumefaciens. Transgenic Res 7:213–222Google Scholar
  13. Arvinth S, Arun S, Selvakesavan RK, Srikanth J, Mukunthan N, Ananda Kumar P et al (2010) Genetic transformation and pyramiding of aprotinin-expressing sugarcane with cry1Ab for shoot borer (Chilo infuscatellus) resistance. Plant Cell Rep 29:383–395PubMedGoogle Scholar
  14. Aslam U, Tabassum B, Nasir IA, Khan A, Husnain T (2018) A virus-derived short hairpin RNA confers resistance against sugarcane mosaic virus in transgenic sugarcane. Transgenic Res 27:203–210PubMedGoogle Scholar
  15. Asnaghi C, Paulet F, Kaye C, Grivet L, Deu M, Glaszmann JC et al (2000) Application of synteny across Poaceae to determine the map location of a sugarcane rust resistance gene. Theor Appl Genet 101:962–969Google Scholar
  16. Asnaghi C, Roques D, Ruffel S, Kaye C, Hoarau JY, Télismart H et al (2004) Targeted mapping of a sugarcane rust resistance gene (Bru1) using bulked segregant analysis and AFLP markers. Theor Appl Genet 108:759–764PubMedGoogle Scholar
  17. Augustine SM (2017) CRISPR-Cas9 system as a genome editing tool in sugarcane. In: Mohan C (ed) Sugarcane biotechnology: challenges and prospects. Springer International Publishing, Cham, pp 155–172Google Scholar
  18. Barber CA (1996) Studies in Indian sugarcanes. No. 2. Mem Dept India Bot Ser 8:103–199Google Scholar
  19. Bortesi L, Fischer R (2015) The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnol Adv 33:41–52PubMedGoogle Scholar
  20. Bower NI, Casu RE, Maclean DJ, Reverter A, Chapman SC, Manners JM (2005) Transcriptional response of sugarcane roots to methyl jasmonate. Plant Sci 168:761–772Google Scholar
  21. Butler NM, Jiang J, Stupar MR (2018) Crop improvement using genome editing. In: Goldman I (ed) Plant breeding reviews. WILEY Blackwell, Hoboken, pp 55–102Google Scholar
  22. Butterfield MK (2007) Marker assisted breeding in sugarcane: a complex polyploid. University of Stellenbosch, StellenboschGoogle Scholar
  23. Casu RE, Dimmock CM, Chapman SC, Grof CPL, McIntyre CL, Bonnett GD et al (2004) Identification of differentially expressed transcripts from maturing stem of sugarcane by in silico analysis of stem expressed sequence tags and gene expression profiling. Plant Mol Biol 54:503–517PubMedGoogle Scholar
  24. Chakraborty S, Newton AC (2011) Climate change, plant diseases and food security: an overview. Plant Pathol 60:2–14Google Scholar
  25. Chen J-W, Lao F-Y, Chen X-W, Deng H-H, Liu R, He H-Y et al (2015) DNA marker transmission and linkage analysis in populations derived from a sugarcane (Saccharum spp.) x Erianthus arundinaceus hybrid. PLoS One 10:e0128865PubMedPubMedCentralGoogle Scholar
  26. Christy LA, Arvinth S, Saravanakumar M, Kanchana M, Mukunthan N, Srikanth J et al (2009) Engineering sugarcane cultivars with bovine pancreatic trypsin inhibitor (aprotinin) gene for protection against top borer (Scirpophaga excerptalis Walker). Plant Cell Rep 28:175–184PubMedGoogle Scholar
  27. Coakley SM, Scherm H, Chakraborty S (1999) Climate change and plant disease management. Annu Rev Phytopathol 37:399–426PubMedGoogle Scholar
  28. Cordeiro GM, Pan Y-B, Henry RJ (2003) Sugarcane microsatellites for the assessment of genetic diversity in sugarcane germplasm. Plant Sci 165:181–189Google Scholar
  29. Cristofoletti PT, Kemper EL, Capella AN, Carmago SR, Cazoto JL, Ferrari F et al (2018) Development of transgenic sugarcane resistant to sugarcane borer. Trop Plant Biol 11:17–30Google Scholar
  30. D’Hont A, Lu Y, Feldmann P, Glaszmann J-C (1993) Cytoplasmic diversity in sugar cane revealed by heterologous probes. Sugar Cane (United Kingdom)Google Scholar
  31. Da Silva JA, Bressiani JA (2005) Sucrose synthase molecular marker associated with sugar content in elite sugarcane progeny. Genet Mol Biol 28:294–298Google Scholar
  32. da Silva J, Honeycutt RJ, Burnquist W, Al-Janabi SM, Sorrells ME, Tanksley SD et al (1995) Saccharum spontaneum L.‘SES 208’genetic linkage map combining RFLP-and PCR-based markers. Mol Breed 1:165–179Google Scholar
  33. Daniels J, Smith P, Paton N, Williams CA (1975) The origin of the genus Saccharum. Sugarcane Breed News 36:24–39Google Scholar
  34. Daugrois JH, Grivet L, Roques D, Hoarau JY, Lombard H, Glaszmann JC et al (1996) A putative major gene for rust resistance linked with a RFLP marker in sugarcane cultivar ‘R570’. Theor Appl Genet 92:1059–1064PubMedGoogle Scholar
  35. Dhansu P, Kumar A, Mann A, Kumar R, Meena BL, Sheoran P et al (2018) Insights into biotechnological interventions for sugarcane improvement. In: Sengar K (ed) Biotechnology to enhance sugarcane productivity and stress tolerance. CRC Press, Boca Raton, pp 131–152Google Scholar
  36. Eksomtramagel T, Pauletl F (1992) Development of a cryopreservation process for embryogenic calluses of a commercial hybrid of sugarcane (SACCHARLIM SP.) and application to different varieties. Cryo-Letters 13:239–252Google Scholar
  37. Ferreira TH, Gentile A, Vilela RD, Costa GGL, Dias LI, Endres L et al (2012) microRNAs associated with drought response in the bioenergy crop sugarcane (Saccharum spp.). PLoS One 7:e46703PubMedPubMedCentralGoogle Scholar
  38. Flint-Garcia SA, Thornsberry JM, Buckler ES IV (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374PubMedGoogle Scholar
  39. Gao S, Yang Y, Wang C, Guo J, Zhou D, Wu Q et al (2016) Transgenic sugarcane with a cry1Ac gene exhibited better phenotypic traits and enhanced resistance against sugarcane borer. PLoS One 11:e0153929PubMedPubMedCentralGoogle Scholar
  40. Gao S, Yang Y, Xu L, Guo J, Su Y, Wu Q et al (2018) Particle bombardment of the cry2A gene cassette induces stem borer resistance in sugarcane. Int J Mol Sci 19:1692PubMedCentralGoogle Scholar
  41. Garcia AAF, Kido EA, Meza AN, Souza HMB, Pinto LR, Pastina MM et al (2006) Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases. Theor Appl Genet 112:298–314PubMedGoogle Scholar
  42. Garsmeur O, Droc G, Antonise R, Grimwood J, Potier B, Aitken K et al (2018) A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nat Commun 9:2638PubMedPubMedCentralGoogle Scholar
  43. Garvin DF, Gu Y-Q, Hasterok R, Hazen SP, Jenkins G, Mockler TC et al (2008) Development of genetic and genomic research resources for Brachypodium distachyon, a new model system for grass crop research. Crop Sci 48:69–84Google Scholar
  44. Gaut BS, Long AD (2003) The lowdown on linkage disequilibrium. Plant Cell 15:1502PubMedPubMedCentralGoogle Scholar
  45. Ghini R, Hamada E, Bettiol W (2008) Climate change and plant diseases. Sci Agric 65:98–107Google Scholar
  46. Ghose AK, Kuasha M, Razzak MA, Islam MJ, Rahman MA, Hossain MA (2016) Genetic diversity analysis of sugarcane genotypes by SSR markers. Fundam Appl Agric 1:112–117Google Scholar
  47. Gilbert RA, Glynn NC, Comstock JC, Davis MJ (2009) Agronomic performance and genetic characterization of sugarcane transformed for resistance to sugarcane yellow leaf virus. Field Crop Res 111:39–46Google Scholar
  48. Glassop D, Roessner U, Bacic A, Bonnett GD (2007) Changes in the sugarcane metabolome with stem development. Are they related to sucrose accumulation? Plant Cell Physiol 48:573–584PubMedGoogle Scholar
  49. Glaszmann J-C, Lu Y, Lanaud C (1990) Variation of nuclear ribosomal DNA in sugarcane. J Genet Breed 44:191–197Google Scholar
  50. Gouy M, Rousselle Y, Thong Chane A, Anglade A, Royaert S, Nibouche S et al (2015) Genome wide association mapping of agro-morphological and disease resistance traits in sugarcane. Euphytica 202:269–284Google Scholar
  51. Guimarães CT, Honeycutt RJ, Sills GR, Sobral BW (1999) Genetic maps of Saccharum officinarum L. and Saccharum robustum Brandes & Jew. ex grassl. Genet Mol Biol 22:125–132Google Scholar
  52. Guo J, Gao S, Lin Q, Wang H, Que Y, Xu L (2015) Transgenic sugarcane resistant to Sorghum mosaic virus based on coat protein gene silencing by RNA interference. Biomed Res Int 2015:861907PubMedPubMedCentralGoogle Scholar
  53. Gupta PK, Rustgi S (2004) Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct Integr Genomics 4:139–162PubMedGoogle Scholar
  54. Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57:461–485PubMedGoogle Scholar
  55. Henry JR (2010) Basic information on the sugarcane plant. CRC Press, Boca RatonGoogle Scholar
  56. Hoarau J-Y, Grivet L, Offmann B, Raboin L-M, Diorflar J-P, Payet J et al (2002) Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). II. Detection of QTLs for yield components. Theor Appl Genet 105:1027–1037PubMedGoogle Scholar
  57. Huang Y-K, Li W-F, Zhang R-Y, Wang X-Y (2018) Diagnosis and control of sugarcane important diseases. In: Huang Y-K, Li W-F, Zhang R-Y, Wang X-Y (eds) Color illustration of diagnosis and control for modern sugarcane diseases, pests, and weeds. Springer Singapore, Singapore, pp 1–103Google Scholar
  58. Janaki-Ammal E (1941) Intergeneric hybrids of Saccharum. J Genet 41:217–253Google Scholar
  59. Jannoo N, Grivet L, Dookun A, D’Hont A, Glaszmann JC (1999) Linkage disequilibrium among modern sugarcane cultivars. Theor Appl Genet 99:1053–1060Google Scholar
  60. Jannoo N, Grivet L, David J, D’Hont A, Glaszmann J-C (2004) Differential chromosome pairing affinities at meiosis in polyploid sugarcane revealed by molecular markers. Heredity 93:460PubMedGoogle Scholar
  61. Jiang GL (2013) Molecular markers and marker-assisted breeding in plants. In: Plant breeding from laboratories to fields. IntechOpen. Available at Scholar
  62. Jung JH, Altpeter F (2016) TALEN mediated targeted mutagenesis of the caffeic acid O-methyltransferase in highly polyploid sugarcane improves cell wall composition for production of bioethanol. Plant Mol Biol 92:131–142PubMedPubMedCentralGoogle Scholar
  63. Jung C, Capistrano-Gossmann G, Braatz J, Sashidhar N, Melzer S (2018) Recent developments in genome editing and applications in plant breeding. Plant Breed 137:1–9Google Scholar
  64. Kawar PG, Pagariya MC, Dixit GB, Prasad DT (2010) Identification and isolation of SCGS phytoplasma-specific fragments by riboprofiling and development of specific diagnostic tool. J Plant Biochem Biotechnol 19:185–194Google Scholar
  65. Kopka J, Schauer N, Krueger S, Birkemeyer C, Usadel B, Bergmüller E et al (2005) GMD@CSB.DB: the Golm metabolome database. Bioinformatics 21:1635–1638PubMedGoogle Scholar
  66. Le Cunff L, Garsmeur O, Raboin L-M, Pauquet J, Telismart H, Selvi A et al (2008) Diploid/polyploid syntenic shuttle mapping and haplotype-specific chromosome walking toward a rust resistance gene (Bru1) in highly polyploid sugarcane (2n≈ 12x≈ 115). Genetics 180:649PubMedPubMedCentralGoogle Scholar
  67. Li T, Liu B, Spalding MH, Weeks DP, Yang B (2012) High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat Biotechnol 30:390PubMedGoogle Scholar
  68. Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T et al (2008) Gramene: a growing plant comparative genomics resource. Nucleic Acids Res 36:D947–D953PubMedGoogle Scholar
  69. Lu Y, D’Hont A, Walker D, Rao P, Feldmann P, Glaszmann J-C (1994) Relationships among ancestral species of sugarcane revealed with RFLP using single copy maize nuclear probes. Euphytica 78:7–18Google Scholar
  70. Malzahn A, Lowder L, Qi Y (2017) Plant genome editing with TALEN and CRISPR. Cell Biosci 7:21–21PubMedPubMedCentralGoogle Scholar
  71. McIntyre CL, Whan VA, Croft B, Magarey R, Smith GR (2005) Identification and validation of molecular markers associated with pachymetra root rot and brown rust resistance in sugarcane using map- and association-based approaches. Mol Breed 16:151–161Google Scholar
  72. McQualter RB, Dale JL, Hardin RH, McMahon JA, Smith GR (2004) Production and evaluation of transgenic sugarcane containing a Fiji disease virus (FDV) genome segment S9- derived synthetic resistance gene. Aust J Agric Res 55:139–145Google Scholar
  73. Ming R, Liu S-C, Lin Y-R, Da Silva J, Wilson W, Braga D et al (1998) Detailed alignment of Saccharum and Sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes. Genetics 150:1663–1682PubMedPubMedCentralGoogle Scholar
  74. Mohan C (2016) Genome editing in sugarcane: challenges ahead. Front Plant Sci 7:1542–1542PubMedPubMedCentralGoogle Scholar
  75. Mohanta TK, Bashir T, Hashem A, Abd Allah EF, Bae H (2017) Genome editing tools in plants. Genes 8:399PubMedCentralGoogle Scholar
  76. Mudge J, Andersen WR, Kehrer RL, Fairbanks DJ (1996) A RAPD genetic map of Saccharum officinarum. Crop Sci 36:1362–1366Google Scholar
  77. Mustafa G, Khan MS (2012) Prospecting the utility of antibiotics as lethal selection agents for chloroplast transformation in sugarcane. Int J Agric Biol 14:307–310Google Scholar
  78. Nair NV, Nair S, Sreenivasan TV, Mohan M (1999) Analysis of genetic diversity and phylogeny in Saccharum and related genera using RAPD markers. Genet Resour Crop Evol 46:73–79Google Scholar
  79. Nayyar S, Sharma BK, Kaur A, Kalia A, Sanghera GS, Thind KS et al (2017) Red rot resistant transgenic sugarcane developed through expression of β-1,3-glucanase gene. PLoS One 12:e0179723PubMedPubMedCentralGoogle Scholar
  80. Nerkar G, Thorat A, Sheelavantmath S, Kassa HB, Devarumath R (2018) Genetic transformation of sugarcane and field performance of transgenic sugarcane. In: Gosal SS, Wani SH (eds) Biotechnologies of crop improvement, volume 2: transgenic approaches. Springer International Publishing, Cham, pp 207–226Google Scholar
  81. Nibouche S, Tibère R, Costet L (2012) The use of Erianthus arundinaceus as a trap crop for the stem borer Chilo sacchariphagus reduces yield losses in sugarcane: preliminary results. Crop Prot 42:10–15Google Scholar
  82. Nordborg M, Tavaré S (2002) Linkage disequilibrium: what history has to tell us. Trends Genet 18:83–90Google Scholar
  83. Oliveira KM, Pinto LR, Marconi TG, Margarido GRA, Pastina MM, Teixeira LHM et al (2007) Functional integrated genetic linkage map based on EST-markers for a sugarcane (Saccharum spp.) commercial cross. Mol Breed 20:189–208Google Scholar
  84. Osakabe Y, Watanabe T, Sugano SS, Ueta R, Ishihara R, Shinozaki K et al (2016) Optimization of CRISPR/Cas9 genome editing to modify abiotic stress responses in plants. Sci Rep 6:26685–26685PubMedPubMedCentralGoogle Scholar
  85. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K et al (2006) The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res 35:D883–D887PubMedPubMedCentralGoogle Scholar
  86. Pachauri RK, Allen MR, Barros VR, Broome J, Cramer W, Christ R et al. 2014. Climate change 2014: synthesis report. Contribution of Working Groups I, II and III to the fifth assessment report of the Intergovernmental Panel on Climate Change. IPCCGoogle Scholar
  87. Palhares AC, Rodrigues-Morais TB, Van Sluys M-A, Domingues DS, Maccheroni W Jr, Jordão H Jr et al (2012) A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers. BMC Genet 13:51–51PubMedPubMedCentralGoogle Scholar
  88. Pandiyan M, Senthil N, Packiaraj D, Jagadeesh S (2012) Greengram germplasm for constituting of core collection. Wudpecker J Agric Res 1:223–232Google Scholar
  89. Pastina M, Malosetti M, Gazaffi R, Mollinari M, Margarido G, Oliveira K et al (2012) A mixed model QTL analysis for sugarcane multiple-harvest-location trial data. Theor Appl Genet 124:835–849PubMedGoogle Scholar
  90. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551PubMedGoogle Scholar
  91. Pinto LR, Garcia AAF, Pastina MM, Teixeira LHM, Bressiani JA, Ulian EC et al (2010) Analysis of genomic and functional RFLP derived markers associated with sucrose content, fiber and yield QTLs in a sugarcane (Saccharum spp.) commercial cross. Euphytica 172:313–327Google Scholar
  92. Quétier F (2016) The CRISPR-Cas9 technology: closer to the ultimate toolkit for targeted genome editing. Plant Sci 242:65–76PubMedGoogle Scholar
  93. Raboin LM, Oliveira KM, Lecunff L, Telismart H, Roques D, Butterfield M et al (2006) Genetic mapping in sugarcane, a high polyploid, using bi-parental progeny: identification of a gene controlling stalk colour and a new rust resistance gene. Theor Appl Genet 112:1382–1391PubMedGoogle Scholar
  94. Raboin L-M, Pauquet J, Butterfield M, D’Hont A, Glaszmann J-C (2008) Analysis of genome-wide linkage disequilibrium in the highly polyploid sugarcane. Theor Appl Genet 116:701–714PubMedGoogle Scholar
  95. Reffay N, Jackson PA, Aitken KS, Hoarau J-Y, D’Hont A, Besse P et al (2005) Characterisation of genome regions incorporated from an important wild relative into Australian sugarcane. Mol Breed 15:367–381Google Scholar
  96. Régnière J (2011) Invasive species, climate change and forest health. Forests in development: a vital balance. Springer, Dordrecht, pp 27–37Google Scholar
  97. Rossi M, Araujo PG, Paulet F, Garsmeur O, Dias VM, Chen H et al (2003) Genomic distribution and characterization of EST-derived resistance gene analogs (RGAs) in sugarcane. Mol Gen Genomics 269:406–419Google Scholar
  98. Rumke C (1934) Saccharum-Erianthus bastardan. Arch Suik Ned Indie 42:211–261Google Scholar
  99. Samson F, Brunaud V, Duchêne S, De Oliveira Y, Caboche M, Lecharny A et al (2004) FLAGdb++: a database for the functional analysis of the Arabidopsis genome. Nucleic Acids Res 32:D347–D350PubMedPubMedCentralGoogle Scholar
  100. Sanghera GS, Singh RP, Tyagi V, Thind KS (2017) Recent genomic approaches for sugarcane improvement: opportunities and challenges. In: Quality and quantum improvement in field crops, pp 109–152Google Scholar
  101. Sauer NJ, Mozoruk J, Miller RB, Warburg ZJ, Walker KA, Beetham PR et al (2016) Oligonucleotide-directed mutagenesis for precision gene editing. Plant Biotechnol J 14:496–502PubMedGoogle Scholar
  102. Scindiya M, Malathi P, Kaverinathan K, Ramesh Sundar A, Viswanathan R (2018) RNA-mediated silencing of PKS1 gene in Colletotrichum falcatum causing red rot in sugarcane. Eur J Plant Pathol 153:371. Scholar
  103. Sengar KE (2018) Biotechnology to enhance sugarcane productivity and stress tolerance. CRC Press, Boca Raton. Scholar
  104. Shah T, Andleeb T, Lateef S, Noor MA (2018) Genome editing in plants: advancing crop transformation and overview of tools. Plant Physiol Biochem 131:12–21PubMedGoogle Scholar
  105. Shanthy RT (2010) Participatory varietal selection in sugarcane. Sugar Tech 12:1–4Google Scholar
  106. Shukla VK, Doyon Y, Miller JC, DeKelver RC, Moehle EA, Worden SE et al (2009) Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 459:437PubMedGoogle Scholar
  107. Silva JAGD, Sorrells ME, Burnquist WL, Tanksley SD (1993) RFLP linkage map and genome analysis of Saccharum spontaneum. Genome 36:782–791PubMedGoogle Scholar
  108. Solomon S (2011) Sugarcane by-products based Industries in India. Sugar Tech 13:408–416Google Scholar
  109. Solomon S (2014) Sugarcane agriculture and sugar industry in India: at a glance. Sugar Tech 16:113–124Google Scholar
  110. Solomon S, Li Y-R (2016) Editorial-the sugar industry of asian region. Sugar Tech 18:557–558Google Scholar
  111. Souza AJ, Mendes BMJ, Mourão Filho FDAA (2007) Gene silencing: concepts, applications, and perspectives in woody plants. Sci Agric 64:645–656Google Scholar
  112. Srivastava S, Gupta PS (2008) Inter simple sequence repeat profile as a genetic marker system in sugarcane. Sugar Tech 10:48–52Google Scholar
  113. Steinhauser D, Usadel B, Luedemann A, Thimm O, Kopka J (2004) CSB.DB: a comprehensive systems-biology database. Bioinformatics 20:3647–3651PubMedGoogle Scholar
  114. Swapna M, Kumar S (2017) microRNAs and their regulatory role in sugarcane. Front Plant Sci 8:997–997PubMedPubMedCentralGoogle Scholar
  115. Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H et al (2008) The Arabidopsis information resource (TAIR): gene structure and function annotation. Nucleic Acids Res 36:D1009–D1014PubMedGoogle Scholar
  116. Tariq M, Khan A, Tabassum B, Toufiq N, Bhatti MU, Riaz S et al (2018) Antifungal activity of chitinase II against Colletotrichum falcatum Went. causing red rot disease in transgenic sugarcane. Turk J Biol 42:45PubMedPubMedCentralGoogle Scholar
  117. Telles GP, Braga MDV, Dias Z, Tzy-Li L, Quitzau JAA, Silva FRD et al (2001) Bioinformatics of the sugarcane EST project. Genet Mol Biol 24:9–15Google Scholar
  118. Thirugnanasambandam PP, Hoang NV, Henry RJ (2018) The challenge of analyzing the sugarcane genome. Front Plant Sci 9:616PubMedPubMedCentralGoogle Scholar
  119. Virupakshi S, Naik G (2008) ISSR analysis of chloroplast and mitochondrial genome can indicate the diversity in sugarcane genotypes for red rot resistance. Sugar Tech 10:65–70Google Scholar
  120. Viswanathan R, Rao GP (2011) Disease scenario and management of major sugarcane diseases in India. Sugar Tech 13:336–353Google Scholar
  121. Viswanathan C, Anburaj J, Prabu G (2014) Identification and validation of sugarcane streak mosaic virus-encoded microRNAs and their targets in sugarcane. Plant Cell Rep 33(2):265–276PubMedGoogle Scholar
  122. Wang F, Wang C, Liu P, Lei C, Hao W, Gao Y et al (2016) Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922. PLoS One 11:e0154027PubMedPubMedCentralGoogle Scholar
  123. Wang WZ, Yang BP, Feng XY, Cao ZY, Feng CL, Wang JG et al (2017) Development and characterization of transgenic sugarcane with insect resistance and herbicide tolerance. Front Plant Sci 8:1535–1535PubMedPubMedCentralGoogle Scholar
  124. Weeks DP (2017) Gene editing in polyploid crops: wheat, camelina, canola, potato, cotton, peanut, sugar cane, and citrus. In: Progress in molecular biology and translational science, vol 149. Academic Press, pp 65–80. Available at Scholar
  125. Wei X, Jackson PA, McIntyre CL, Aitken KS, Croft B (2006) Associations between DNA markers and resistance to diseases in sugarcane and effects of population substructure. Theor Appl Genet 114:155–164PubMedGoogle Scholar
  126. Weng L-X, Deng H-H, Xu J-L, Li Q, Zhang Y-Q, Jiang Z-D et al (2011) Transgenic sugarcane plants expressing high levels of modified cry1Ac provide effective control against stem borers in field trials. Transgenic Res 20:759–772PubMedGoogle Scholar
  127. Wu L, Zu X, Wang S, Chen Y (2012) Sugarcane mosaic virus – Long history but still a threat to industry. Crop Prot 42:74–78Google Scholar
  128. Xu Y (2010) Molecular plant breeding. CabiGoogle Scholar
  129. Yadav RL, Solomon S (2006) Potential of developing sugarcane by-product based industries in India. Sugar Tech 8:104–111Google Scholar
  130. Yang X, Song J, Todd J, Peng Z, Paudel D, Luo Z et al (2019) Target enrichment sequencing of 307 germplasm accessions identified ancestry of ancient and modern hybrids and signatures of adaptation and selection in sugarcane (Saccharum spp.), a ‘sweet’ crop with ‘bitter’ genomes. Plant Biotechnol J 17:488–498PubMedGoogle Scholar
  131. Yao W, Ruan M, Qin L, Yang C, Chen R, Chen B et al (2017) Field performance of transgenic sugarcane lines resistant to sugarcane mosaic virus. Front Plant Sci 8:104–104PubMedPubMedCentralGoogle Scholar
  132. Yin K, Gao C, Qiu J-L (2017) Progress and prospects in plant genome editing. Nat Plants 3:17107PubMedGoogle Scholar
  133. You Q, Xu L, Zheng Y, Que Y (2013) Genetic diversity analysis of sugarcane parents in Chinese breeding programmes using gSSR markers. Sci World J 2013:1–11Google Scholar
  134. Zaman QU, Li C, Cheng H, Hu Q (2018) Genome editing opens a new era of genetic improvement in polyploid crops. Crop J 7(2, April 2019):141–150Google Scholar
  135. Zanca AS, Vicentini R, Ortiz-Morea FA, Del Bem LEV, da Silva MJ, Vincentz M et al (2010) Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane. BMC Plant Biol 10:260PubMedPubMedCentralGoogle Scholar
  136. Zhang L, Xu J, Birch RG (1999) Engineered detoxification confers resistance against a pathogenic bacterium. Nat Biotechnol 17:1021PubMedGoogle Scholar
  137. Zhangsun D, Luo S, Chen R, Tang K (2007) Improved agrobacterium-mediated genetic transformation of GNA transgenic sugarcane. Biologia 62:386Google Scholar
  138. Zhao W, Wang J, He X, Huang X, Jiao Y, Dai M et al (2004) BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res 32:D377–D382PubMedPubMedCentralGoogle Scholar
  139. Zhou D, Liu X, Gao S, Guo J, Su Y, Ling H et al (2018) Foreign cry1Ac gene integration and endogenous borer stress-related genes synergistically improve insect resistance in sugarcane. BMC Plant Biol 18:342–342PubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Mehzabin Rahman
    • 1
    • 2
  • Sabira Sultana
    • 2
  • Deepshikha Nath
    • 3
  • Surya Kalita
    • 1
  • Dhiresh Chakravarty
    • 1
  • Sahil Mehta
    • 4
  • Shabir Hussain Wani
    • 5
  • Md Aminul Islam
    • 1
    • 6
  1. 1.Bimala Prasad Chaliha CollegeNagarberaIndia
  2. 2.Department of BiotechnologyGauhati UniversityJalukbariIndia
  3. 3.Independent ResearcherSilcharIndia
  4. 4.International Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
  5. 5.Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural sciences and Technology of KashmirJammu and KashmirIndia
  6. 6.National Institute of Plant Genome ResearchNew DelhiIndia

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