Genetic Dissection and Breeding for Grain Appearance Quality in Rice

Chapter

Abstract

Grain quality largely determines the market price of rice. Many consumers pay particular attention to high grain quality, although preferences in terms of grain size, grain shape, storage components, and fragrance are diverse. Grain chalkiness is one of the most important traits in grain appearance in both indica and japonica cultivars. Grain chalkiness critically decreases market value because of grain breakage during milling and decreased cooking and eating qualities. Recent progress in the genetic analysis of grain chalkiness has identified many quantitative trait loci (QTLs) and their underlying genes. These results provide insights into the genetic control of grain quality. To reduce grain chalkiness, breeding programs have introduced several QTLs or genes with large genetic effects into the genetic backgrounds of indica and japonica cultivars. The resultant near-isogenic lines showing high grain quality are good candidates for novel cultivars with improved grain quality.

Keywords

Rice Grain quality Grain appearance Chalkiness High temperature 

Notes

Acknowledgment

Our research was partially supported by the Science and Technology Research Promotion Program for Agriculture, Forestry, Fisheries and Food Industry (25035B and 28014B).

References

  1. Abe N, Asai H, Yago H et al (2014) Relationships between starch synthase I and branching enzyme isozymes determined using double mutant rice lines. BMC Plant Biol 14:80CrossRefPubMedPubMedCentralGoogle Scholar
  2. Arshad MS, Farooq M, Asch F et al (2017) Thermal stress impacts reproductive development and grain yield in rice. Plant Physiol Biochem 115:57–72CrossRefPubMedGoogle Scholar
  3. Bao J (2014) Genes and QTLs for rice grain quality improvement. In: Yan W, Bao J (eds) Rice – germplasm, genetics and improvement. InTech, Rijeka, pp 239–278Google Scholar
  4. Bergman CJ, Bhattacharya KR, Ohtsubo K (2004) Rice end-use quality analysis. In: Champagne ET (ed) Rice: chemistry and technology, 3rd edn. AACC Press, Louisiana, pp 415–472Google Scholar
  5. Bita CE, Gerats T (2013) Plant tolerance to high temperature in a changing environment: scientific fundamentals and production of heat stress-tolerant crops. Front Plant Sci 4:273CrossRefPubMedPubMedCentralGoogle Scholar
  6. Butardo VM, Fitzgerald MA, Bird AR et al (2011) Impact of down-regulation of starch branching enzyme IIb in rice by artificial microRNA- and hairpin RNA-mediated RNA silencing. J Exp Bot 62:4927–4941CrossRefPubMedPubMedCentralGoogle Scholar
  7. Cakir B, Shiraishi S, Tuncel A et al (2016) Analysis of the rice ADP-glucose transporter (OsBT1) indicates the presence of regulatory processes in the amyloplast stroma that control ADP-glucose flux into starch. Plant Physiol 170:1271–1283PubMedPubMedCentralGoogle Scholar
  8. Champagne ET, Bett KL, Vinyard BT et al (1999) Correlation between cooked rice texture and rapid visco analyser measurements. Cereal Chem 76:764–771CrossRefGoogle Scholar
  9. Chen L, Gao W, Chen S et al (2016) High-resolution QTL mapping for grain appearance traits and co-localization of chalkiness-associated differentially expressed candidate genes in rice. Rice 9:48CrossRefPubMedPubMedCentralGoogle Scholar
  10. Del Rosario AR, Briones VP, Vidal AJ et al (1968) Composition and endosperm structure of developing and mature rice kernel. Cereal Chem 45:225–235Google Scholar
  11. Duan E, Wang Y, Liu L et al (2016) Pyrophosphate: fructose-6-phosphate 1-phosphotransferase (PFP) regulates carbon metabolism during grain filling in rice. Plant Cell Rep 35:1321–1331CrossRefPubMedPubMedCentralGoogle Scholar
  12. Ebata M, Tashiro T (1973) Studies on white-belly rice kernels. 1. Varietal differences in the occurrence of white-belly kernels. Proc Crop Sci Soc Japan 42:370–376CrossRefGoogle Scholar
  13. Ebitani T, Yamamoto Y, Yano M et al (2008) Identification of quantitative trait loci for grain appearance using chromosome segment substitution lines in rice. Breed Res 10:91–99CrossRefGoogle Scholar
  14. Fitzgerald MA, McCouch SR, Hall RD (2009) Not just a grain of rice: the quest for quality. Trends Plant Sci 14:133–139CrossRefPubMedGoogle Scholar
  15. Fu F-F, Xue H-W (2010) Coexpression analysis identifies rice starch regulator1, a rice AP2/EREBP family transcription factor, as a novel rice starch biosynthesis regulator. Plant Physiol 154:927–938CrossRefPubMedPubMedCentralGoogle Scholar
  16. Fujita N, Yoshida M, Kondo T et al (2007) Characterization of SSIIIa-deficient mutants of rice: the function of SSIIIa and pleiotropic effects by SSIIIa deficiency in the rice endosperm. Plant Physiol 144:2009–2023CrossRefPubMedPubMedCentralGoogle Scholar
  17. Fujita N, Satoh R, Hayashi A et al (2011) Starch biosynthesis in rice endosperm requires the presence of either starch synthase I or IIIa. J Exp Bot 62:4819–4831CrossRefPubMedPubMedCentralGoogle Scholar
  18. Fukuda M, Satoh-Cruz M, Wen L et al (2011) The small GTPase Rab5a is essential for intracellular transport of proglutelin from the Golgi apparatus to the protein storage vacuole and endosomal membrane organization in developing rice endosperm. Plant Physiol 157:632–644CrossRefPubMedPubMedCentralGoogle Scholar
  19. Fukuda M, Wen L, Satoh-Cruz M et al (2013) A guanine nucleotide exchange factor for Rab5 proteins is essential for intracellular transport of the proglutelin from the Golgi apparatus to the protein storage vacuole in rice endosperm. Plant Physiol 162:663–674CrossRefPubMedPubMedCentralGoogle Scholar
  20. Fukuda M, Kawagoe Y, Murakami T et al (2016) The dual roles of the Golgi transport 1 (GOT1B): RNA localization to the cortical endoplasmic reticulum and the export of proglutelin and α-globulin from the cortical ER to the Golgi. Plant Cell Physiol 57:2380–2391CrossRefPubMedGoogle Scholar
  21. Furukawa T, Maekawa M, Oki T et al (2007) The Rc and Rd genes are involved in proanthocyanidin synthesis in rice pericarp. Plant J 49:91–102CrossRefPubMedGoogle Scholar
  22. Gao Y, Liu C, Li Y et al (2016) QTL analysis for chalkiness of rice and fine mapping of a candidate gene for qACE9. Rice 9:41CrossRefPubMedPubMedCentralGoogle Scholar
  23. Goto K (1904) Investigations on rice quality. Rep Agric Assoc 61:7–11Google Scholar
  24. Guo T, Liu X, Wan X et al (2011) Identification of a stable quantitative trait locus for percentage grains with white chalkiness in rice (Oryza sativa). J Integr Plant Biol 53:598–607CrossRefPubMedGoogle Scholar
  25. Hakata M, Kuroda M, Miyashita T et al (2012) Suppression of α-amylase genes improves quality of rice grain ripened under high temperature. Plant Biotechnol J 10:1110–1117CrossRefPubMedGoogle Scholar
  26. He P, Li SG, Qian Q et al (1999) Genetic analysis of rice grain quality. Theor Appl Genet 98:502–508CrossRefGoogle Scholar
  27. Hori K, Yano M (2013) Genetic improvement of grain quality in japonica rice. In: Varshnet R, Tuberosa R (eds) Translational genomics for crop breeding: abiotic stress, yield and quality II. Wiley Blackwell, Iowa, pp 143–160CrossRefGoogle Scholar
  28. Hori K, Kataoka T, Miura K et al (2012) Variation in heading date conceals quantitative trait loci for other traits of importance in breeding selection of rice. Breed Sci 62:223–234CrossRefPubMedPubMedCentralGoogle Scholar
  29. Hori K, Yamamoto T, Yano M (2017) Genetic dissection of agronomically important traits in closely related temperate japonica rice cultivars. Breed Sci. doi: https://doi.org/10.1270/jsbbs.17053
  30. Huang R, Jiang L, Zheng J et al (2013) Genetic bases of rice grain shape: so many genes, so little known. Trends Plant Sci 18:218–226CrossRefPubMedGoogle Scholar
  31. Inagaki O (1899) On the white-belly rice. Rep Agri Assoc 47:14–15Google Scholar
  32. IPCC (2013) Climate change 2013: the physical science basis. Fifth assessment report. Cambridge University Press, CambridgeGoogle Scholar
  33. Ishimaru T, Hirabayashi H, Sasaki K et al (2016) Breeding efforts to mitigate damage by heat stress to spikelet sterility and grain quality. Plant Prod Sci 19:12–21CrossRefGoogle Scholar
  34. Jagadish SK, Murty MR, Quick WP (2015) Rice responses to rising temperatures – challenges, perspectives and future directions. Plant Cell Environ 38:1686–1698CrossRefPubMedGoogle Scholar
  35. Juliano BO, Hicks PA (1996) Rice functional properties and rice food products. Food Rev Int 12:71–103CrossRefGoogle Scholar
  36. Kamijima O, Yamamoto J, Nakanishi K (1981) Studies on rice breeding for sake brewing. II. Segregations in the frequency of white-core kernels, kernel weight and culm length in F2 populations, and relationships of these characters. Sci Rep Fac Agri Kobe Univ 14:265–272Google Scholar
  37. Kang HG, Park S, Matsuoka M et al (2005) White-core endosperm floury endosperm-4 in rice is generated by knockout mutations in the C4-type pyruvate orthophosphate dikinase gene (OsPPDKB). Plant J 42:901–911CrossRefPubMedGoogle Scholar
  38. Kobayashi A, Genliang B, Shenghai Y et al (2007) Detection of quantitative trait loci for white-back and basal-white kernels under high temperature stress in japonica rice varieties. Breed Sci 57:107–116CrossRefGoogle Scholar
  39. Kobayashi A, Sonoda J, Sugimoto K et al (2013) Detection and verification of QTLs associated with heat-induced quality decline of rice (Oryza sativa L.) using recombinant inbred lines and near-isogenic lines. Breed Sci 63:339–346CrossRefPubMedPubMedCentralGoogle Scholar
  40. Kobayashi A, Sugimoto K, Hayashi T et al (2016) Development of a near isogenic line of ‘Koshihikari’ with a seed dormancy gene and an evaluation of its resistance to heat-induced quality decline. Breed Res 18:1–10CrossRefGoogle Scholar
  41. Kusano M, Fukushima A, Fujita N et al (2012) Deciphering starch quality of rice kernels using metabolite profiling and pedigree network analysis. Mol Plant 5:442–451CrossRefPubMedGoogle Scholar
  42. Li H, Chen Z, Hu M et al (2011) Different effects of night versus day high temperature on rice quality and accumulation profiling of rice grain proteins during grain filling. Plant Cell Rep 30:1641–1659CrossRefPubMedGoogle Scholar
  43. Li Y, Fan C, Xing Y et al (2014) Chalk5 encodes a vacuolar H+-translocating pyrophosphatase influencing grain chalkiness in rice. Nat Genet 46:398–404CrossRefPubMedGoogle Scholar
  44. Li S, Wei X, Ren Y et al (2017) OsBT1 encodes an ADP-glucose transporter involved in starch synthesis and compound granule formation in rice endosperm. Sci Rep 7:40124CrossRefPubMedPubMedCentralGoogle Scholar
  45. Lin Z, Zhang X, Wang Z et al (2017) Metabolomic analysis of pathways related to rice grain chalkiness by a notched-belly mutant with high occurrence of white-belly grains. BMC Plant Biol 17:39CrossRefPubMedPubMedCentralGoogle Scholar
  46. Liu F, Ren Y, Wang Y et al (2013) OsVPS9A functions cooperatively with OsRAB5A to regulate post-Golgi dense vesicle-mediated storage protein trafficking to the protein storage vacuole in rice endosperm cells. Mol Plant 6:1918–1932CrossRefPubMedGoogle Scholar
  47. Lo PC, Hu L, Kitano H et al (2016) Starch metabolism and grain chalkiness under high temperature stress. Natl Sci Rev 3:280–282CrossRefGoogle Scholar
  48. Maeda H, Yamaguchi T, Omoteno M et al (2014) Genetic dissection of black grain rice by the development of a near isogenic line. Breed Sci 64:134–141CrossRefPubMedPubMedCentralGoogle Scholar
  49. Matsushima R, Maekawa M, Kusano M et al (2014) Amyloplast-localized SUBSTANDARD STARCH GRAIN4 protein influences the size of starch grains in rice endosperm. Plant Physiol 164:623–636CrossRefPubMedGoogle Scholar
  50. Matsushima R, Maekawa M, Kusano M et al (2016) Amyloplast membrane protein SUBSTANDARD STARCH GRAIN6 controls starch grain size in rice endosperm. Plant Physiol 170:1445–1459PubMedPubMedCentralGoogle Scholar
  51. Meuwissen TE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819PubMedPubMedCentralGoogle Scholar
  52. Mitsui T, Shiraya T, Kaneko K et al (2013) Proteomics of rice grain under high temperature stress. Front Plant Sci 4:36CrossRefPubMedPubMedCentralGoogle Scholar
  53. Monaco MK, Stein J, Naithani S et al (2014) Gramene 2013: comparative plant genomics resources. Nucleic Acids Res 42:D1193–D1199CrossRefPubMedGoogle Scholar
  54. Murata K, Iyama Y, Yamaguchi T et al (2014) Identification of a novel gene (Apq1) from the indica rice cultivar ‘Habataki’ that improves the quality of grains produced under high temperature stress. Breed Sci 64:273–281CrossRefPubMedPubMedCentralGoogle Scholar
  55. Peng C, Wang Y, Liu F et al (2014) FLOURY ENDOSPERM6 encodes a CBM48 domain-containing protein involved in compound granule formation and starch synthesis in rice endosperm. Plant J 77:917–930CrossRefPubMedGoogle Scholar
  56. Qiu X, Pang Y, Yuan Z et al (2016) Genome-wide association study of grain appearance and milling quality in a worldwide collection of indica rice germplasm. PLoS One 10:e0145577CrossRefGoogle Scholar
  57. Ren Y, Wang Y, Liu F et al (2014) GLUTELIN PRECURSOR ACCUMULATION3 encodes a regulator of post-Golgi vesicular traffic essential for vacuolar protein sorting in rice endosperm. Plant Cell 26:410–425CrossRefPubMedPubMedCentralGoogle Scholar
  58. Ryoo N, Yu C, Park CS et al (2007) Knockout of a starch synthase gene OsSSIIIa/Flo5 causes white-core floury endosperm in rice (Oryza sativa L.) Plant Cell Rep 26:1083–1095CrossRefPubMedGoogle Scholar
  59. Schaeffer LR (2006) Strategy for applying genome-wide selection in dairy cattle. J Anim Breed Genet 123:218–223CrossRefPubMedGoogle Scholar
  60. She KC, Kusano H, Koizumi K et al (2010) A novel factor FLOURY ENDOSPERM2 is involved in regulation of rice grain size and starch quality. Plant Cell 22:3280–3294CrossRefPubMedPubMedCentralGoogle Scholar
  61. Shirasawa K, Sekii T, Ogihara Y et al (2013) Identification of the chromosomal region responsible for high-temperature stress tolerance during the grain-filling period in rice. Mol Breed 32:223–232CrossRefGoogle Scholar
  62. Shumiya A, Tanabe K, Haga T et al (1972) Effects of ripening conditions on the grain quality of rice cultivars. 1. Differences in the grain quality of cultivars with the same heading date. Res Bull Aichi Pref Agri Expt Sta 4:24–38Google Scholar
  63. Sreenivasulu N, Butardo JM, Misra G et al (2015) Designing climate-resilient rice with ideal grain quality suited for high-temperature stress. J Exp Bot 66:1737–1748CrossRefPubMedPubMedCentralGoogle Scholar
  64. Takeda K, Saito K (1983) Heritability of kernel weight and white belly frequency in rice and genetic correlation. Jpn J Breed 33:468–469CrossRefGoogle Scholar
  65. Takemoto Y, Coughlan SJ, Okita TW et al (2002) The rice mutant esp2 greatly accumulates the glutelin precursor and deletes the protein disulfide isomerase. Plant Physiol 128:1212–1222CrossRefPubMedPubMedCentralGoogle Scholar
  66. Tan YF, Xing YZ, Li JX et al (2000) Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid. Theor Appl Genet 101:823–829CrossRefGoogle Scholar
  67. Tanaka K, Miyazaki M, Uchikawa O et al (2010) Effects of the nitrogen nutrient condition and nitrogen application on kernel quality of rice. Jpn J Crop Sci 79:450–459CrossRefGoogle Scholar
  68. Tang XJ, Peng C, Zhang J et al (2016) ADP-glucose pyrophosphorylase large subunit 2 is essential for storage substance accumulation and subunit interactions in rice endosperm. Plant Sci 249:70–83CrossRefPubMedGoogle Scholar
  69. Toyosawa Y, Kawagoe Y, Matsushima R et al (2016) Deficiency of starch synthase IIIa and IVb alters starch granule morphology from polyhedral to spherical in rice endosperm. Plant Physiol 170:1255–1270PubMedPubMedCentralGoogle Scholar
  70. Wada T, Miyahara K, Sonoda J et al (2015) Detection of QTLs for white-back and basal-white grains caused by high temperature during ripening period in japonica rice. Breed Sci 65:216–225CrossRefPubMedPubMedCentralGoogle Scholar
  71. Wakamatsu K, Sasaki O, Tanaka A (2009) Effects of the amount of insolation and humidity during the ripening period on the grain quality of brown rice in warm regions of Japan. Jpn J Crop Sci 78:476–482CrossRefGoogle Scholar
  72. Wan XY, Wan JM, Weng JF et al (2005) Stability of QTLs for rice grain dimension and endosperm chalkiness characteristics across eight environments. Theor Appl Genet 110:1334–1346CrossRefPubMedGoogle Scholar
  73. Wang C, Shu Q (2007) Fine mapping and candidate gene analysis of purple pericarp gene Pb in rice (Oryza sativa L.) Chin Sci Bull 52:3097–3104CrossRefGoogle Scholar
  74. Wang E, Wang J, Zhu X et al (2008) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet 40:1370–1374CrossRefPubMedGoogle Scholar
  75. Wang C, Xu H, Zhu Y et al (2013) OsbZIP58, a basic leucine zipper transcription factor, regulates starch biosynthesis in rice endosperm. J Exp Bot 64:3453–3466CrossRefPubMedPubMedCentralGoogle Scholar
  76. Wang X, Pang Y, Wang C et al (2016a) New candidate genes affecting rice grain appearance and milling quality detected by genome-wide and gene-based association analyses. Front Plant Sci 7:1998–1998PubMedGoogle Scholar
  77. Wang Y, Liu F, Ren Y et al (2016b) GOLGI TRANSPORT 1B regulates protein export from the endoplasmic reticulum in rice endosperm cells. Plant Cell 28:2850–2865CrossRefPubMedPubMedCentralGoogle Scholar
  78. Wei X, Jiao G, Lin H et al (2017) GRAIN INCOMPLETE FILLING 2 regulates grain filling and starch synthesis during rice caryopsis development. J Integr Plant Biol 59:134–153CrossRefPubMedGoogle Scholar
  79. Woo MO, Ham TH, Ji HS et al (2008) Inactivation of the UGPase1 gene causes genic male sterility and endosperm chalkiness in rice (Oryza sativa L.) Plant J 54:190–204CrossRefPubMedPubMedCentralGoogle Scholar
  80. Xu JJ, Zhang XF, Xue HW (2016) Rice aleurone layer specific OsNF-YB1 regulates grain filling and endosperm development by interacting with an ERF transcription factor. J Exp Bot 67:6399–6411CrossRefPubMedPubMedCentralGoogle Scholar
  81. Yamakawa H, Hakata M (2010) Atlas of rice grain filling-related metabolism under high temperature: joint analysis of metabolome and transcriptome demonstrated inhibition of starch accumulation and induction of amino acid accumulation. Plant Cell Physiol 51:795–809CrossRefPubMedPubMedCentralGoogle Scholar
  82. Yamakawa H, Hirose T, Kuroda M et al (2007) Comprehensive expression profiling of rice grain filling-related genes under high temperature using DNA microarray. Plant Physiol 144:258–277CrossRefPubMedPubMedCentralGoogle Scholar
  83. Yamakawa H, Ebitani T, Terao T (2008) Comparison between locations of QTLs for grain chalkiness and genes responsive to high temperature during grain filling on the rice chromosome map. Breed Sci 58:337–343CrossRefGoogle Scholar
  84. Yang R, Sun C, Bai J et al (2012) A putative gene sbe3-rs for resistant starch mutated from SBE3 for starch branching enzyme in rice (Oryza sativa L.) PLoS One 7:e43026CrossRefPubMedPubMedCentralGoogle Scholar
  85. Yang J, Kim SR, Lee SK et al (2015) Alanine aminotransferase 1 (OsAlaAT1) plays an essential role in the regulation of starch storage in rice endosperm. Plant Sci 240:79–89CrossRefPubMedGoogle Scholar
  86. Yano K, Yamamoto E, Aya K et al (2016) Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice. Nat Genet 48:927–934CrossRefPubMedGoogle Scholar
  87. Zhang G, Cheng Z, Zhang X et al (2011) Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch. Genome 54:448–459CrossRefPubMedGoogle Scholar
  88. Zhang L, Ren Y, Lu B et al (2016) FLOURY ENDOSPERM7 encodes a regulator of starch synthesis and amyloplast development essential for peripheral endosperm development in rice. J Exp Bot 67:633–647CrossRefPubMedGoogle Scholar
  89. Zhao K, Tung CW, Eizenga GC et al (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2:467CrossRefPubMedPubMedCentralGoogle Scholar
  90. Zheng TQ, Xu JL, Li ZK et al (2007) Genomic regions associated with milling quality and grain shape identified in a set of random introgression lines of rice (Oryza sativa L.) Plant Breed 126:158–163CrossRefGoogle Scholar
  91. Zhou L, Chen L, Jiang L et al (2009) Fine mapping of the grain chalkiness QTL qPGWC-7 in rice (Oryza sativa L.) Theor Appl Genet 118:581–590CrossRefPubMedGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  1. 1.National Agriculture and Food Research Organization (NARO), Institute of Crop ScienceTsukubaJapan

Personalised recommendations