Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Prospects of breeding high-quality rice using post-genomic tools


Key message

The holistic understanding derived from integrating grain quality and sensory research outcomes in breeding high-quality rice in the light of post-genomics resources has been synthesized.


Acceptance of new rice genotypes by producers and consumers hinges not only on their potential for higher yield but recent emphasis has also been on premium-value genotypes that have the ability to satisfy consumer preferences for grain quality. This review article provides insights into how to link grain quality attributes and sensory perception to support breeding superior rice varieties. Recent advances in quality profiling and omics technologies have provided efficient approaches to identify the key genes and biochemical markers involved in rice quality traits. Emphasis has been given to the upcoming area of holistic understanding of grain quality and attributes derived from sensory evaluation to leverage integrative gene discovery strategies that enable breeding programs to efficiently tap the huge genetic diversity in rice for novel genes that enhance rice food quality.

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

Fig. 1
Fig. 2
Fig. 3


  1. Adams A, De Kimpe NG (2006) Chemistry of 2-acetyl-1-pyrroline, 6-acetyl-1,2,3,4-tetrahydropyridine, 2-acetyl-2-thiazoline, and 5-acetyl-2,3-dihydro-4H-thiazine: extraordinary Maillard flavor compounds. Chem Rev 106:2299–2319

  2. Ahn S-N, Bollich CN, Tanksley SD (1992) RFLP tagging of a gene for aroma in rice. Theor Appl Genet 84:825–828

  3. Aluko G, Martinez C, Tohme J, Castano C, Bergman CJ, Oard JH (2004) QTL mapping of grain quality traits from the interspecific cross Oryza sativa × O. glaberrima. Theor Appl Genet 109:630–639

  4. Amarawathi Y, Singh R, Singh A, Singh V, Mohapatra T, Sharma T, Singh NK (2008) Mapping of quantitative trait loci for basmati quality traits in rice (Oryza sativa L.). Mol Breed 21:49–65

  5. Ayabe S, Kasai M, Ohishi K, Hate K (2009) Textural properties and structures of starches from indica and japonica rice with similar amylose content. Food Sci Technol Res 15:299–306

  6. Bandillo N, Raghavan C, Muyco PA, Sevilla MA, Lobina IT, Dilla-Ermita CJ, Tung CW, McCouch S, Thomson M, Mauleon R, Singh RK, Gregorio G, Redona E, Leung H (2013) Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding. Rice 6:11

  7. Barton FE, Windham WR, Champagne ET, Lyon BG (1998) Optimal geometries for the development of rice quality spectroscopic chemometric models. Cereal Chem 75:315–319

  8. Beinner MA, Velasquez-Melendez G, Pessoa MC, Greiner T (2010) Iron-fortified rice is as efficacious as supplemental iron drops in infants and young children. J Nutr 140:49–53

  9. Bergman CJ, Delgado JT, Bryant RJ, Grimm CC, Cadwallader KR, Webb BD (2000) Rapid gas chromatographic technique for quantifying 2-acetyl-1-pyrroline and hexanal in rice (Oryza sativa L.). Cereal Chem 77:454–458

  10. Bett-Garber KL, Champagne ET, McClung AM, Moldenhauer KA, Linscombe S, McKenzie KS (2001) Categorizing rice cultivars based on cluster analysis of amylose content, protein content, and sensory attributes. Cereal Chem 78:551–558

  11. Bett-Garber KL, Lea J, Champagne ET, McClung AM (2012) Whole-grain rice flavor associated with assorted bran colors. J Sens Stud 27:78–86

  12. Bourgis F, Guyot R, Gherbi H, Tailliez E, Amabile I, Salse J, Lorieux M, Delseny M, Ghesquiere A (2008) Characterization of the major fragrance gene from an aromatic japonica rice and analysis of its diversity in Asian cultivated rice. Theor Appl Genet 117:353–368

  13. Bradbury LMT, Fitzgerald TL, Henry RJ, Jin Q, Waters DLE (2005) The gene for fragrance in rice. Plant Biotechnol J 3:363–370

  14. Bradbury LMT, Gillies S, Brushett D, Waters DLE, Henry RJ (2008a) Inactivation of an aminoaldehyde dehydrogenase is responsible for fragrance in rice. Plant Mol Biol 68:439–449

  15. Bradbury LME, Henry RJ, Waters DLE (2008b) Flavor development in Rice. In: Havkin-Frenkel D, Belanger FC (eds) Biotechnology in flavor production. Blackwell Publishing Ltd, Oxon, pp 130–142

  16. Bryant RJ, McClung AM (2011) Volatile profiles of aromatic and non-aromatic rice cultivars using SPME/GC-MS. Food Chem 124:501–513

  17. Butardo V Jr, Fitzgerald MA, Bird AR, Gidley MJ, Flanagan BM, Larroque O, Resurreccion AP, Laidlaw HK, Jobling SA, Morell MK, Rahman S (2011) Impact of down-regulation of starch branching enzyme IIb in rice by artificial microRNA- and hairpin RNA-mediated RNA silencing. J Exp Bot 62:4927–4941

  18. Buttery RG, Ling LC, Juliano BO, Turnbaugh JG (1983) Cooked rice aroma and 2-acetyl-1-pyrroline. J Agric Food Chem 31:823–826

  19. Buttery RG, Turnbaugh JG, Ling LC (1988) Contribution of volatiles to rice aroma. J Agric Food Chem 36:1006–1009

  20. Cagampang GB, Perez CM, Juliano BO (1973) A gel consistency test for eating quality in rice. J Sci Food Agric 24:1589–1594

  21. Calingacion MN, Boualaphanh C, Daygon VD, Anacleto R, Sackville-Hamilton NR, Biais B, Deborde C, Maucourt M, Moing A, Mumm R (2012) A genomics and multi-platform metabolomics approach to identify new traits of rice quality in traditional and improved varieties. Metabolomics 8:771–783

  22. Calingacion MN, Laborte A, Nelson A, Resurreccion A, Concepcion JC, Daygon VD, Mumm R, Reinke R, Dipti S, Bassinello PZ, Manful J, Sophany S, Lara KC, Bao J, Xie L, Loaiza K, El-hissewy A, Gayin J, Sharma N, Rajeswari S, Manonmani S, Rani NS, Kota S, Indrasari SD, Habibi F, Hosseini M, Tavasoli F, Suzuki K, Umemoto T, Boualaphanh C, Lee HH, Hung YP, Ramli A, Aung PP, Ahmad R, Wattoo JI, Bandonill E, Romero M, Brites CM, Hafeel R, Lur H-S, Cheaupun K, Jongdee S, Blanco P, Bryant R, Thi Lang N, Hall RD, Fitzgerald MA (2014) Diversity of global rice markets and the science required for consumer-targeted rice breeding. PLoS One 9:e85106

  23. Calpe C (2003) Status of the world rice market in 2002. 20th Session of the International Rice Commission. Food and Agriculture Organization, Bangkok

  24. Castro JV, Dumas C, Chiou H, Fitzgerald MA, Gilbert RG (2005) Mechanistic information from analysis of molecular weight distributions of starch. Biomacromolecules 6:2248–2259

  25. Champagne ET (2008) Rice aroma and flavor: a literature review. Cereal Chem 85:445–454

  26. Champagne ET, Bett KL, Vinyard BT, Webb BD, McClung AM, Barton FE, Lyon BG, Moldenhauer KA, Linscombe S, Kohlwey DE (1997) Effects of drying conditions, final moisture content, and degree of milling on rice flavor. Cereal Chem 74:566–570

  27. Champagne ET, Bett KL, Vinyard BT, McClung AM, Barton FE, Moldenhauer KA, Linscombe S, McKenzie KS (1999) Correlation between cooked rice texture and rapid visco analyser measurements. Cereal Chem 76:764–771

  28. Champagne ET, Thompson J, Bett-Garber KL, Mutters R, Miller JA, Tan E (2004a) Impact of storage of freshly harvested paddy rice on milled white rice flavor. Cereal Chem 81:444–449

  29. Champagne ET, Wood DF, Juliano BO, Bechtel DB (2004b) The rice grain and its gross composition. In: Champagne ET (ed) Rice chemistry and technology. American Association of Cereal Chemists Inc, Minneapolis, pp 77–107

  30. Champagne ET, Bett-Garber KL, Fitzgerald MA, Grimm CC, Lea J, Ki Ohtsubo, Jongdee S, Xie L, Bassinello P, Resurreccion AP, Ahmad R, Habibi F, Reinke RF (2010) Important sensory properties differentiating premium rice varieties. Rice 3:270–281

  31. Chen L, Opara UL (2013) Texture measurement approaches in fresh and processed foods: a review. Food Res Int 51:823–835

  32. Chen S, Yang Y, Shi W, Ji Q, He F, Zhang Z, Cheng Z, Liu X, Xu M (2008) Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance. Plant Cell 20:1850–1861

  33. Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc B 363:557–572

  34. Cordeiro GM, Christopher MJ, Henry RJ, Reinke RF (2002) Identification of microsatellite markers for fragrance in rice by analysis of the rice genome sequence. Mol Breed 9:245–250

  35. Cuevas RP, Fitzgerald MA (2012) Genetic diversity of rice grain quality. In: Caliskan M (ed) Genetic diversity in plants. InTech, Rijeka, pp 285–310

  36. Cuevas RP, Daygon VD, Corpuz HM, Reinke RF, Waters DLE, Fitzgerald MA (2010a) Melting the secrets of gelatinisation temperature in rice. Funct Plant Biol 37:439–447

  37. Cuevas RP, Gilbert RG, Fitzgerald MA (2010b) Structural differences between hot-water-soluble and hot-water-insoluble fractions of starch in waxy rice (Oryza sativa L.). Carbohydr Polym 81:524–532

  38. Dalton T (2004) A household hedonic model of rice traits: economic values from farmers in West Africa. Agric Econ 31:149–159

  39. Edwards D, Henry RJ, Edwards KJ (2012) Advances in DNA sequencing accelerating plant biotechnology. Plant Biotechnol J 10:621–622

  40. Fitzgerald MA, Sackville-Hamilton NR, Calingacion MN, Verhoeven HA, Butardo V Jr (2008) Is there a second fragrance gene in rice? Plant Biotechnol J 6:416–423

  41. Fitzgerald MA, Bergman CJ, Resurreccion AP, Moller J, Jimenez R, Reinke RF, Martin M, Blanco P, Molina F, Chen M-H, Kuri V, Romero MV, Habibi F, Umemoto T, Jongdee S, Graterol E, Reddy KR, Bassinello PZ, Sivakami R, Rani NS, Das S, Wang Y-J, Indrasari SD, Ramli A, Ahmad R, Dipti SS, Xie L, Lang NT, Singh P, Toro DC, Tavasoli F, Mestres C (2009a) Addressing the dilemmas of measuring amylose in rice. Cereal Chem 86:492–498

  42. Fitzgerald MA, McCouch SR, Hall RD (2009b) Not just a grain of rice: the quest for quality. Trends Plant Sci 14:133–139

  43. Fitzgerald TL, Waters DLE, Brooks LO, Henry RJ (2010) Fragrance in rice (Oryza sativa) is associated with reduced yield under salt treatment. Environ Exp Bot 68:292–300

  44. Foegeding EA, Davis JP (2011) Food protein functionality: a comprehensive approach. Food Hydrocoll 25:1853–1864

  45. Fuller DQ (2011) Pathways to Asian civilizations: tracing the origins and spread of rice and rice cultures. Rice 4:78–92

  46. Gong L, Chen W, Gao Y, Liu X, Zhang H, Xu C, Yu S, Zhang Q, Luo J (2013) Genetic analysis of the metabolome exemplified using a rice population. Proc Natl Acad Sci USA 110:20320–20325

  47. Gonzalez RJ, Livore A, Pons B (2004) Physico-chemical and cooking characteristics of some rice varieties. Braz Arch Biol Technol 47:71–76

  48. Goodwin HL Jr, Koop LA, Rister ME, Miller RK, Maca JV, Chambers E, Hollingsworth M, Bett KL, Webb BD, McClung AM (1996) Developing a common language for the U.S. rice industry: Linkages among breeders, producers, processors, and consumers. TAMRC Consumer Product Market Research Report. Texas Agricultural Market Research Center, p 43

  49. Grimm CC, Bergman CJ, Delgado JT, Bryant RJ (2001) Screening for 2-acetyl-1-pyrroline in the headspace of rice using SPME/GC-MS. J Agric Food Chem 49:245–249

  50. He Y, Han Y, Jiang L, Xu C, Lu J, Xu M (2006) Functional analysis of starch-synthesis genes in determining rice eating and cooking qualities. Mol Breed 18:277–290

  51. Heffner EL, Sorrells ME, Jannink J-L (2009) Genomic selection for crop improvement. Crop Sci 49:1–12

  52. Heuberger AL, Lewis MR, Chen M-H, Brick MA, Leach JE, Ryan EP (2010) Metabolomic and functional genomic analyses reveal varietal differences in bioactive compounds of cooked rice. PLoS One 5:e12915

  53. Huang T-C, Teng C-S, Chang J-L, Chuang H-S, Ho C-T, Wu M-L (2008) Biosynthetic mechanism of 2-acetyl-1-pyrroline and its relationship with Δ1-pyrroline-5-carboxylic acid and methylglyoxal in aromatic rice (Oryza sativa L.) callus. J Agric Food Chem 56:7399–7404

  54. Huang X, Kurata N, Wei X, Wang Z-X, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, Guo Y, Lu Y, Zhou C, Fan D, Weng Q, Zhu C, Huang T, Zhang L, Wang Y, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan X, Xu Q, Dong G, Zhan Q, Li C, Fujiyama A, Toyoda A, Lu T, Feng Q, Qian Q, Li J, Han B (2012) A map of rice genome variation reveals the origin of cultivated rice. Nature 490:497–501

  55. Huang X, Yang S, Gong J, Zhao Y, Feng Q, Gong H, Li W, Zhan Q, Cheng B, Xia J, Chen N, Hao Z, Liu K, Zhu C, Huang T, Zhao Q, Zhang L, Fan D, Zhou C, Lu Y, Weng Q, Wang ZX, Li J, Han B (2015) Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis. Nat Commun 6:6258

  56. Jannink J-L, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genomics 9:166–177

  57. Jin Q, Waters DLE, Cordeiro GM, Henry RJ, Reinke RF (2003) A single nucleotide polymorphism (SNP) marker linked to the fragrance gene in rice (Oryza sativa L.). Plant Sci 165:359–364

  58. Juliano BO (1979) The chemical basis of rice grain quality. Workshop on chemical aspects of rice grain quality. International Rice Research Institute, Los Banos

  59. Juliano BO (2001) Asian perspective on rice sensory quality. Cereal Foods World 46:531–535

  60. Juliano BO, Villareal CP (1993) Grain quality evaluation of world rices. International Rice Research Institute, Los Banos

  61. Juliano BO, Perez CM, Kaosa-Ard M (1990) Grain quality characteristics of export rices in selected markets. Cereal Chem 67:192–197

  62. Juliano BO, Perez CM, Resurreccion AP (2009) Apparent amylose content and gelatinization temperature types of Philippine rice accessions in the IRRI Gene Bank. Philippine Agric Sci 92:106–109

  63. Kam K, Murray JM, Arcot J, Ward RM (2012) Fortification of parboiled rice with folic acid: consumer acceptance and sensory evaluation. Food Res Int 49:354–363

  64. Kaminski TA, Brackmann A, da Silva LP, Nicoletti AM, Roberto BS (2013) Changes in culinary, viscoamylographic, and sensory characteristics during rice storage at different temperatures. J Stored Prod Res 53:37–42

  65. Kasem S, Waters DLE, Henry RJ (2012) Analysis of genetic diversity in starch genes in the wild relatives of rice. Trop Plant Biol 5:286–308

  66. Kaur H, Singh B (2013) Classification and grading rice using multi-class SVM. Int Sci Res Publ 3:1–5

  67. Kharabian-Masouleh A, Waters DLE, Reinke RF, Henry RJ (2011) Discovery of polymorphisms in starch related genes in rice germplasm by amplification of pooled DNA and deeply parallel sequencing. Plant Biotechnol J 9:1074–1085

  68. Kharabian-Masouleh A, Waters DLE, Reinke RF, Ward R, Henry RJ (2012) SNP in starch biosynthesis genes associated with nutritional and functional properties of rice. Sci Rep 2:557. doi:10.1038/srep00557

  69. Khush GS (2001) Green revolution: the way forward. Nat Rev Genet 2:815–822

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

  71. Kovach MJ, Calingacion MN, Fitzgerald MA, McCouch SR (2009) The origin and evolution of fragrance in rice (Oryza sativa L.). Proc Natl Acad Sci USA 106:14444–14449

  72. Kowittaya C, Lumdubwong N (2014) Molecular weight, chain profile of rice amylopectin and starch pasting properties. Carbohydr Polym 108:216–223

  73. Krishnan SG, Waters DLE, Henry RJ (2014) Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome. PLoS One 9:e98843

  74. Kwak HS, Ahn BH, Lee Y, Kreger J, Lee S-Y (2013) Correlation of liking and disliking measurements in consumer acceptance tests. Food Qual Prefer 30:86–92

  75. Kwon S-W, Cho Y-C, Lee J-H, Suh J-P, Kim J-J, Kim M-K, Choi I-S, Hwang H-G, Koh H-J, Kim Y-G (2011) Identification of quantitative trait loci associated with rice eating quality traits using a population of recombinant inbred lines derived from a cross between two temperate japonica cultivars. Mol Cells 31:437–445

  76. Lanceras JC, Huang Z-L, Naivikul O, Vanavichit A, Ruanjaichon V, Tragoonrung S (2000) Mapping of genes for cooking and eating qualities in Thai jasmine rice (KDML105). DNA Res 7:93–101

  77. Lapcharoensuk R, Sirisomboon P (2014) Eating quality of cooked rice determination using Fourier transform near infrared spectroscopy. J Innov Opt Health Sci 7(6):1450003. doi:10.1142/S1793545814500035

  78. Leung H, Hettel GP, Cantrell RP (2002) International Rice Research Institute: roles and challenges as we enter the genomics era. Trends Plant Sci 7:139–142

  79. Li JY, Wang J, Zeigler RS (2014) The 3000 rice genomes project: new opportunities and challenges for future rice research. Gigascience 3:8

  80. Limpawattana M, Shewfelt RL (2010) Flavor lexicon for sensory descriptive profiling of different rice types. J Food Sci 75:S199–S205

  81. Lisle AJ, Martin M, Fitzgerald MA (2000) Chalky and translucent rice grains differ in starch composition and structure and cooking properties. Cereal Chem 77:627–632

  82. Liu G (2011) Detection of chalk degree of rice based on image processing. In: Proceedings of the 2011 International Conference on Intelligence Science and Information Engineering. IEEE Computer Society, pp 515–518

  83. Liu X, Wan X, Ma X, Wan J (2011) Dissecting the genetic basis for the effect of rice chalkiness, amylose content, protein content, and rapid viscosity analyzer profile characteristics on the eating quality of cooked rice using the chromosome segment substitution line population across eight environments. Genome 54:64–80

  84. Liu L, Waters DLE, Rose TJ, Bao J, King GJ (2013) Phospholipids in rice: significance in grain quality and health benefits: a review. Food Chem 139:1133–1145

  85. Lorieux M, Petrov M, Huang N, Guiderdoni E, Ghesquiere A (1996) Aroma in rice: genetic analysis of a quantitative trait. Theor Appl Genet 93:1145–1151

  86. Luo W, Guo T, Yang Q, Wang H, Liu Y, Zhu X, Chen Z (2014) Stacking of five favorable alleles for amylase content, fragrance and disease resistance into elite lines in rice (Oryza sativa) by using four HRM-based markers and a linked gel-based marker. Mol Breed 34:805–815

  87. Mahattanatawee K, Rouseff RL (2014) Comparison of aroma active and sulfur volatiles in three fragrant rice cultivars using GC-Olfactometry and GC-PFPD. Food Chem 154:1–6

  88. Manzanilla DO, Paris TR, Tatlonghari GT, Tobias AM, Chi TTN, Phuong NT, Siliphouthone I, Chamarerk V, Bhekasut P, Gandasoemita R (2013) Social and gender perspectives in rice breeding for submergence tolerance in Southeast Asia. Exp Agric 50:191–215

  89. Maraval I, Mestres C, Pernin K, Ribeyre F, Boulanger R, Guichard E, Gunata Z (2008) Odor-active compounds in cooked rice cultivars from Camargue (France) analyzed by GC-O and GC-MS. J Agric Food Chem 56:5291–5298

  90. Mariotti M, Fongaro L, Catenacci F (2010) Alkali spreading value and image analysis. J Cereal Sci 52:227–235

  91. Mathure SV, Jawali N, Thengane RJ, Nadaf AB (2014) Comparative quantitative analysis of headspace volatiles and their association with BADH2 marker in non-basmati scented, basmati, and non-scented rice (Oryza sativa L.) cultivars of India. Food Chem 142:383–391

  92. Matsuda F, Okazaki Y, Oikawa A, Kusano M, Nakabayashi R, Kikuchi J, J-i Yonemaru, Ebana K, Yano M, Saito K (2012) Dissection of genotype–phenotype associations in rice grains using metabolome quantitative trait loci analysis. Plant J 70:624–636

  93. Matthews JP, Gemme S, Huebschmann HJ, Llorente C, Jimenez R, Sreenivasulu N (2014) Thermo Sci Appl 10419:1–9

  94. Meilgaard MC, Civille GV, Carr BT (2007) Sensory evaluation techniques, 4th edn. CRC Press, Boca Raton

  95. Mestres C, Ribeyre F, Pons B, Fallet V, Matencio F (2011) Sensory texture of cooked rice is rather linked to chemical than to physical characteristics of raw grain. J Cereal Sci 53:81–89

  96. Meullenet J-FC, Marks BP, Hankins J-A, Griffin VK, Daniels MJ (2000) Sensory quality of cooked long-grain rice as affected by rough rice moisture content, storage temperature, and storage duration. Cereal Chem 77:259–263

  97. Mingyin Y, Muhua L, Huadong Z (2010) Exterior quality inspection of rice based on computer vision. In: World Automation Congress (WAC), pp 369–374

  98. Moretti D, Zimmermann MB, Muthayya S, Thankachan P, Lee T-C, Kurpad AV, Hurrell RF (2006) Extruded rice fortified with micronized ground ferric pyrophosphate reduces iron deficiency in Indian schoolchildren: a double-blind randomized controlled trial. Am J Clin Nutr 84:822–829

  99. Myint KM, Courtois B, Risterucci A-M, Frouin J, Soe K, Thet KM, Vanavichit A, Glaszmann JC (2012) Specific patterns of genetic diversity among aromatic rice varieties in Myanmar. Rice 5:20

  100. Nakamura Y, Francisco PB, Hosaka Y, Sato A, Sawada T, Kubo A, Fujita N (2005) Essential amino acids of starch synthase IIa differentiate amylopectin structure and starch quality between japonica and indica rice varieties. Plant Mol Biol 58:213–227

  101. Niu X, Tang W, Huang W, Ren G, Wang Q, Luo D, Xiao Y, Yang S, Wang F, Lu B-R, Gao FY, Lu T, Liu Y (2008) RNAi-directed downregulation of OsBADH2 results in aroma (2-acetyl-1-pyrroline) production in rice (Oryza sativa L.). BMC Plant Biol 8:100

  102. Pandey MK, Rani NS, Madhav MS, Sundaram R, Varaprasad GS, Sivaranjani AKP, Bohra A, Kumar GR, Kumar A (2012) Different isoforms of starch-synthesizing enzymes controlling amylose and amylopectin content in rice (Oryza sativa L.). Biotechnol Adv 30:1697–1706

  103. Peng SB, Khush GS, Virk P, Tang QY, Zou YB (2008) Progress in ideotype breeding to increase rice yield potential. Field Crop Res 108:32–38

  104. Perez CM, Pascual CG, Juliano BO (1979) Eating quality indicators for waxy rices. Food Chem 4:179–184

  105. Perez CM, Juliano BO, Bourne MC, Anzaldua-Morales A (1993) Hardness of cooked milled rice by instrumental and sensory methods. J Texture Stud 24:81–94

  106. Ramesh M, Ali SZ, Bhattacharya KR (1999) Structure of rice starch and its relation to cooked-rice texture. Carbohydr Polym 38:337–347

  107. Rao Y, Li Y, Qian Q (2014) Recent progress on molecular breeding of rice in China. Plant Cell Rep 33:551–564

  108. Redestig H, Kusano M, Ebana K, Kobayashi M, Oikawa A, Okazaki Y, Matsuda F, Arita M, Fujita N, Saito K (2011) Exploring molecular backgrounds of quality traits in rice by predictive models based on high-coverage metabolomics. BMC Syst Biol 5:176

  109. Ridout MJ, Parker ML, Hedley CL, Bogracheva TY, Morris VJ (2006) Atomic force microscopy of pea starch: granule architecture of the rug3-a, rug4-b, rug5-a and lam-c mutants. Carbohydr Polym 65:64–74

  110. Sabouri A, Rabiei B, Toorchi M, Aharizad S, Moumeni A (2012) Mapping quantitative trait loci (QTL) associated with cooking quality in rice (Oryza sativa L.). Aust J Crop Sci 6:808–814

  111. Septiningsih EM, Trijatmiko KR, Moeljopawiro S, McCouch SR (2003) Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107:1433–1441

  112. Septiningsih EM, Pamplona AM, Sanchez DL, Neeraja CN, Vergara GV, Heuer S, Ismail AM, Mackill DJ (2009) Development of submergence-tolerant rice cultivars: the Sub1 locus and beyond. Ann Bot 103:151–160

  113. Shao G, Tang A, Tang S, Luo J, Jiao G, Wu J, Hu P (2011) A new deletion mutation of fragrant gene and the development of three molecular markers for fragrance in rice. Plant Breed 130:172–176

  114. Shi W, Yang Y, Chen S, Xu M (2008) Discovery of a new fragrance allele and the development of functional markers for the breeding of fragrant rice varieties. Mol Breed 22:185–192

  115. Shimada H, Tada Y, Kawasaki T, Fujimura T (1993) Antisense regulation of the rice waxy gene expression using a PCR-amplified fragment of therice genome reduces the amylose content in grain starch. Theor Appl Genet 86:665–672

  116. Shrestha AK, Arcot J, Paterson JL (2003) Edible coating materials: their properties and use in the fortification of rice with folic acid. Food Res Int 36:921–928

  117. Siebenmorgen TJ, Grigg BC, Lanning SB (2013) Impacts of preharvest factors during kernel development on rice quality and functionality. Annu Rev Food Sci Technol 4:101–115

  118. Singh N, Kaur L, Sodhi NS, Sekhon KS (2005) Physicochemical, cooking and textural properties of milled rice from different Indian rice cultivars. Food Chem 89:253–259

  119. Singh A, Singh P, Singh R, Pandit A, Mahato A, Gupta D, Tyagi K, Singh A, Singh NK, Sharma T (2010) SNP haplotypes of the BADH1 gene and their association with aroma in rice (Oryza sativa L.). Mol Breed 26:325–338

  120. Son J-S, Do VB, Kim K-O, Cho MS, Suwonsichon T, Valentin D (2014) Understanding the effect of culture on food representations using word associations: the case of “rice” and “good rice”. Food Qual Prefer 31:38–48

  121. Sowbhagya CM, Ramesh BS, Bhattacharya KR (1987) The relationship between cooked-rice texture and the physicochemical characteristics of rice. J Cereal Sci 5:287–297

  122. Spindel J, Begum H, Akdemir D, Virk P, Collard B, Redoña E, Atlin G, Jannink JL, McCouch SR (2015) Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite tropical rice breeding lines. PLoS Genet 11:e1004982

  123. Sreenivasulu N, Butardo VM Jr, Misra G, Cuevas RP, Anacleto R, Kavi Kishor PB (2015) Designing climate-resilient rice with ideal grain quality suited for high-temperature stress. J Exp Bot 66:1737–1748

  124. Stone H, Bleibaum RN, Thomas HA (2012) Sensory evaluation practices, 4th edn. Academic Press, San Diego

  125. Su Y, Rao Y, Hu S, Yang Y, Gao Z, Zhang G, Liu J, Hu J, Yan M, Dong G, Li Z, Guo L, Qian Q, Zeng D (2011) Map-based cloning proves qGC-6, a major QTL for gel consistency of japonica/indica cross, responds by Waxy in rice (Oryza sativa L.). Theor Appl Genet 123:859–867

  126. Subbaiyan GK, 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 Biotechnol J 10:623–634

  127. Suwannaporn P, Linnemann A (2008) Rice-eating quality among consumers in different rice grain preference countries. J Sens Stud 23:1–13

  128. Sun S-Y, Hao W, Lin H-X (2006) Identification of QTLs for cooking and eating quality of rice grain. Rice Sci 13:161–169

  129. Tan YF, Li JX, Yu SB, Xing YZ, Xu CG, Zhang Q (1999) The three important traits for cooking and eating quality of rice grains are controlled by a single locus in an elite rice hybrid, Shanyou 63. Theor Appl Genet 99:642–648

  130. Tang H, Mitsunaga T, Kawamura Y (2006) Molecular arrangement in blocklets and starch granule architecture. Carbohydr Polym 63:555–560

  131. Thompson JL, Drake MA, Lopetcharat K, Yates MD (2004) Preference mapping of commercial chocolate milks. J Food Sci 69:S406–S413

  132. Tomlins K, Manful JT, Gayin J, Kudjawu B, Tamakloe I (2007) Study of sensory evaluation, consumer acceptability, affordability and market price of rice. J Sci Food Agric 87:1564–1575

  133. Tran N, Daygon VD, Resurreccion AP, Cuevas RP, Corpuz HM, Fitzgerald MA (2011) A single nucleotide polymorphism on the Waxy gene explains a significant component of gel consistency. Theor Appl Genet 123:519–525

  134. Tsugawa H, Tsujimoto Y, Sugitate K, Sakui N, Nishiumi S, Bamba T, Fukusaki E (2014) Highly sensitive and selective analysis of widely targeted metabolomics using gas chromatography/triple-quadrupole mass spectrometry. J Biosci Bioeng 117:122–128

  135. Tsugita T (1985) Aroma of cooked rice. Food Rev Int 1:497–520

  136. Umemoto T, Aoki N, Lin H, Nakamura Y, Inouchi N, Sato Y, Yano M, Hirabayashi H, Maruyama S (2004) Natural variation in rice starch synthase IIa affects enzyme and starch properties. Funct Plant Biol 31:671–684

  137. Varshney RK, Terauchi R, McCouch SR (2014) Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. PLoS Biol 12:e1001883

  138. Verma B (2010) Image processing techniques for grading and classification of rice. In: International conference on computer and communication technology (ICCCT), pp 220–223

  139. Vilaplana F, Hasjim J, Gilbert RG (2012) Amylose content in starches: toward optimal definition and validating experimental methods. Carbohydr Polym 88:103–111

  140. Wang K, Hasjim J, Wu AC, Henry RJ, Gilbert RG (2014) Variation in amylose fine structure of starches from different botanical sources. J Agric Food Chem 62:4443–4453

  141. Waters DLE, Henry RJ, Reinke RF, Fitzgerald MA (2006) Gelatinization temperature of rice explained by polymorphisms in starch synthase. Plant Biotechnol J 4:115–122

  142. Widjaja R, Craske JD, Wootton M (1996) Comparative studies on volatile components of non-fragrant and fragrant rices. J Sci Food Agric 70:151–161

  143. Windham WR, Lyon BG, Champagne ET, Barton FE, Webb BD, McClung AM, Moldenhauer KA, Linscombe S, McKenzie KS (1997) Prediction of cooked rice texture quality using near-infrared reflectance analysis of whole-grain milled samples. Cereal Chem 74:626–632

  144. Yang DS, Lee KS, Jeong OY, Kim KJ, Kays SJ (2008a) Characterization of volatile aroma compounds in cooked black rice. J Agric Food Chem 56:235–240

  145. Yang DS, Shewfelt RL, Lee K-S, Kays SJ (2008b) Comparison of odor-active compounds from six distinctly different rice flavor types. J Agric Food Chem 56:2780–2787

  146. Yau NJN, Huang JJ (1996) Sensory analysis of cooked rice. Food Qual Prefer 7:263–270

  147. Zader A (2011) Understanding quality food through cultural economy: the “politics of quality” in China’s northeast japonica rice. Agric Hum Values 29:53–63

  148. Zheng X-Z, Lan Y-B, Zhu J-M, Westbrook J, Hoffmann WC, Lacey RE (2009) Rapid identification of rice samples using an electronic nose. J Bionic Eng 6:290–297

Download references


The authors thank Prof. A. Dobermann, Rothamsted Research Institute, UK for insightful comments and helpful discussions. We also thank all IRRI breeders who actively contributed in developing lines with distinct quality profiles. We thank colleagues of Schimatzu Pvt. Ltd. and Thermo Scientific Ltd. for technical runs of aroma profiling using Gc–MS platforms. This work has been supported under the CGIAR thematic area Global Rice Science Partnership (GRISP) funding and Japan Breeding project.

Conflict of interest

All authors have no conflict of interest.

Author information

Correspondence to Nese Sreenivasulu.

Additional information

Roslen Anacleto and Rosa Paula Cuevas have contributed equally to this work.

Communicated by R. K. Varshney.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Anacleto, R., Cuevas, R.P., Jimenez, R. et al. Prospects of breeding high-quality rice using post-genomic tools. Theor Appl Genet 128, 1449–1466 (2015). https://doi.org/10.1007/s00122-015-2537-6

Download citation


  • Amylose
  • Quality Trait
  • Genomic Selection
  • Amylose Content
  • International Rice Research Institute