Skip to main content

Variation in pre-harvest sprouting resistance, seed germination and changes in abscisic acid levels during grain development in diverse rice genetic resources

  • Gi-An Lee (a1) (a2), Young-Ah Jeon (a1), Ho-Sun Lee (a3), Do-Yun Hyun (a1), Jung-Ro Lee (a1), Myung-Chul Lee (a1), Sok-young Lee (a1), Kyung-Ho Ma (a1) and Hee-Jong Koh (a2)...

Among domesticated traits, pre-harvest sprouting (PHS) caused by the early breakage of dormancy leads to severe economic losses. Therefore, regulating PHS is important for cereal crop improvement against changes in climate. In this study, we surveyed naturally occurring variations in seed germination in diverse rice germplasm for the available resources of this trait, and investigated the changes of abscisic acid (ABA) levels during grain development by the distinguished PHS-resistant groups. We discovered wide variations in germination among the 205 rice accessions examined and found that 90 accessions are resistant (germination <20%) to PHS. Tropical and subtropical accessions, which are subjected to long wet periods, are more resistant to PHS than the other accessions. We detected an increase in germination of detached seeds from the panicle compared with intact seeds in panicle at harvesting time. This might be attributed to a weakening of the mechanical barrier that prevents water imbibition and radical emergence. ABA levels were maximal at 10 d after flowering and decreased thereafter. Interestingly, PHS-susceptible accessions maintained higher or similar ABA levels compared with PHS-resistant accessions, suggesting that the key factors for seed dormancy and its breakage are ABA perception and signal transduction rather than total ABA content. The diversity of germination ability detected in this study could be sustainably used for crop improvement and to help unveil the genetic and physiological basis of this quantitative trait.

Corresponding author
*Corresponding author. E-mail:
Hide All
Basra, S, Farooq, M, Tabassam, R and Ahmad, N (2005) Physiological and biochemical aspects of pre-sowing seed treatments in fine rice (Oryza sativa L.). Seed Science and Technology 33: 623628.
Bewley, JD and Black, M (1982) Physiology and biochemistry of seeds in relation to germination. Vol. 2. Viability, dormancy and environmental control, Springer-Verlag, New York.
Bollmark, M, Kubát, B and Eliasson, L (1988) Variation in endogenous cytokinin content during adventitious root formation in pea cuttings. Journal of Plant Physiology 132: 262265.
Challam, C, Kharshing, GA, Yumnam, JS, Rai, M and Tyagi, W (2013) Association of qLTG3–1 with germination stage cold tolerance in diverse rice germplasm from the Indian subcontinent. Plant Genetic Resources 11: 206211.
Cheng, C, Motohashi, R, Tsuchimoto, S, Fukuta, Y, Ohtsubo, H and Ohtsubo, E (2003) Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Molecular Biology and Evolution 20: 6775.
Cutler, SR, Rodriguez, PL, Finkelstein, RR and Abrams, SR (2010) Abscisic acid: emergence of a core signaling network. Annual Reviews Plant Biology 61, 651679.
De Laethauwer, S, Reheul, D, De Riek, J and Haesaert, G (2012) Vp1 expression profiles during kernel development in six genotypes of wheat, triticale and rye. Euphytica 188: 6170.
Dong, Y, Tsuzuki, E, Kamiunten, H, Terao, H, Lin, D, Matsuo, M and Zheng, Y (2003) Identification of quantitative trait loci associated with pre-harvest sprouting resistance in rice (Oryza sativa L.). Field Crops Research 81: 133139.
Finch-Savage, WE and Leubner-Metzger, G (2006) Seed dormancy and the control of germination. New Phytologist 171: 501523.
Finkelstein, R, Reeves, W, Ariizumi, T, Steber, C (2008) Molecular aspects of seed dormancy. Plant Biology 59: 387.
Gianinetti, A, Vernieri, P (2007) On the role of abscisic acid in seed dormancy of red rice. Journal of Experimental Botany 58: 34493462.
Gu, X-Y, Kianian, SF and Foley, ME (2005a) Seed dormancy imposed by covering tissues interrelates to shattering and seed morphological characteristics in weedy rice. Crop Science 45: 948955.
Gu, X-Y, Kianian, SF and Foley, ME (2005b) Phenotypic selection for dormancy introduced a set of adaptive haplotypes from weedy into cultivated rice. Genetics 171: 695704.
Gu, X-Y, Liu, T, Feng, J, Suttle, JC and Gibbons, J (2010) The qSD12 underlying gene promotes abscisic acid accumulation in early developing seeds to induce primary dormancy in rice. Plant Molecular Biology 73: 97104.
Gu, X-Y, Foley, ME, Horvath, DP, Anderson, JV, Feng, J, Zhang, L, Mowry, CR, Ye, H, Suttle, JC and Kadowaki, K-i (2011) Association between seed dormancy and pericarp color is controlled by a pleiotropic gene that regulates abscisic acid and flavonoid synthesis in weedy red rice. Genetics 189: 15151524.
Guo, L, Zhu, L, Xu, Y, Zeng, D, Wu, P and Qian, Q (2004) QTL analysis of seed dormancy in rice (Oryza sativa L.). Euphytica 140: 155162.
Hattori, T, Terada, T and Hamasuna, ST (1994) Sequence and functional analyses of the rice gene homologous to the maize Vp1. Plant Molecular Biology 24: 805810.
Haussmann, BIG, Parzies, HK, Presterl, T, Susic, Z and Miedaner, T (2003) Plant genetic resources in crop improvement. Plant Genetic Resources 2, 321.
He, X, He, Z, Zhang, L, Sun, D, Morris, C, Fuerst, E and Xia, X (2007) Allelic variation of polyphenol oxidase (PPO) genes located on chromosomes 2A and 2D and development of functional markers for the PPO genes in common wheat. Theoretical and Applied Genetics 115: 4758.
Himi, E, Mares, DJ, Yanagisawa, A and Noda, K (2002) Effect of grain colour gene (R) on grain dormancy and sensitivity of the embryo to abscisic acid (ABA) in wheat. Journal of Experimental Botany 53: 15691574.
Hori, K, Sugimoto, K, Nonoue, Y, Ono, N, Matsubara, K, Yamanouchi, U, Abe, A, Takeuchi, Y and Yano, M (2010) Detection of quantitative trait loci controlling pre-harvest sprouting resistance by using backcrossed populations of japonica rice cultivars. Theoretical and Applied Genetics 120: 15471557.
Huang, X, Kurata, N, Wei, X, Wang, Z-X, Wang, A, Zhao, Q, Zhao, Y, Liu, K, Lu, H and Li, W (2012) A map of rice genome variation reveals the origin of cultivated rice. Nature 490: 497501.
Iuchi, S, Kobayashi, M, Taji, T, Naramoto, M, Seki, M, Kato, T, Tabata, S, Kakubari, Y, Yamaguchi-Shinozaki, K and Shinozaki, K (2001) Regulation of drought tolerance by gene manipulation of 9-cis-epoxycarotenoid dioxygenase, a key enzyme in abscisic acid biosynthesis in Arabidopsis . The Plant Journal 27: 325333.
Kanno, Y, Jikumaru, Y, Hanada, A, Nambara, E, Abrams, SR, Kamiya, Y and Seo, M (2010) Comprehensive hormone profiling in developing Arabidopsis seeds: examination of the site of ABA biosynthesis, ABA transport and hormone interactions. Plant and Cell Physiology 51: 19882001.
Kermode, AR and Bewley, JD (1989) Developing seeds of Ricinus communis L., when detached and maintained in an atmosphere of high relative humidity, switch to a germinative mode without the requirement for complete desiccation. Plant Physiology 90(2): 702707.
Khan, M, Cavers, PB, Kane, M and Thompson, K (1997) Role of the pigmented seed coat of proso millet (Panicum miliaceum L.) in imbibition, germination and seed persistence. Seed Science Research 7: 2126.
Khush, GS (1997) Origin, dispersal, cultivation and variation of rice. Plant Molecular Biology 35: 2534.
Kim, H, Hwang, H, Hong, J-W, Lee, Y-N, Ahn, IP, Yoon, IS, Yoo, S-D, Lee, S, Lee, SC and Kim, B-G (2011) A rice orthologue of the ABA receptor, OsPYL/RCAR5, is a positive regulator of the ABA signal transduction pathway in seed germination and early seedling growth. Journal of Experimental Botany 63: 10131024.
Kim, B, Kim, D-G, Lee, G, Seo, J, Choi, I-Y, Choi, B-S, Yang, T-J, Kim, KS, Lee, J and Chin, JH (2014) Defining the genome structure of ‘Tongil’ rice, an important cultivar in the Korean “Green Revolution”. Rice 7: 22.
Kushiro, T, Okamoto, M, Nakabayashi, K, Yamagishi, K, Kitamura, S, Asami, T, Hirai, N, Koshiba, T, Kamiya, Y and Nambara, E (2004) The Arabidopsis cytochrome P450 CYP707A encodes ABA 8′-hydroxylases: key enzymes in ABA catabolism. EMBO Journal 23: 16471656.
Li, C, Ni, P, Francki, M, Hunter, A, Zhang, Y, Schibeci, D, Li, H, Tarr, A, Wang, J and Cakir, M (2004) Genes controlling seed dormancy and pre-harvest sprouting in a rice–wheat–barley comparison. Functional & Integrative Genomics 4: 8493.
Lin, S, Sasaki, T and Yano, M (1998) Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L., using backcross inbred lines. Theoretical and Applied Genetics 96: 9971003.
Liu, Y, He, Z, Appels, R and Xia, X (2012) Functional markers in wheat: current status and future prospects. Theoretical and Applied Genetics 125: 110.
Lu, B, Xie, K, Yang, C, Wang, S, Liu, X, Zhang, L, Jiang, L and Wan, J (2011) Mapping two major effect grain dormancy QTL in rice. Molecular Breeding 28: 453462.
Marzougui, S, Sugimoto, K, Yamanouchi, U, Shimono, M, Hoshino, T, Hori, K, Kobayashi, M, Ishiyama, K and Yano, M (2012) Mapping and characterization of seed dormancy QTLs using chromosome segment substitution lines in rice. Theoretical and Applied Genetics 124: 893902.
Nakamura, S and Toyama, T (2001) Isolation of a VP1 homologue from wheat and analysis of its expression in embryos of dormant and non-dormant cultivars. Journal of Experimental Botany 52: 875876.
Qi, Y, Zhang, H, Zhang, D, Wang, M, Sun, J, Ding, L, Wang, F and Li, Z (2009) Assessing indica- japonica differentiation of improved rice varieties using microsatellite markers. Journal of Genetics and Genomics 36: 305312.
Raghavendra, AS, Gonugunta, VK, Christmann, A and Grill, E (2010) ABA perception and signalling. Trends in Plant Science 15: 395401.
Seo, M and Koshiba, T (2011) Transport of ABA from the site of biosynthesis to the site of action. Journal of Plant Research 124: 501507.
Sugimoto, K, Takeuchi, Y, Ebana, K, Miyao, A, Hirochika, H, Hara, N, Ishiyama, K, Kobayashi, M, Ban, Y and Hattori, T (2010) Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proceedings of the National Academy of Sciences of the United States of America 107: 57925797.
Sweeney, MT, Thomson, MJ, Pfeil, BE and McCouch, S (2006) Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell 18: 283294.
Umezawa, T, Okamoto, M, Kushiro, T, Nambara, E, Oono, Y, Seki, M, Kobayashi, M, Koshiba, T, Kamiya, Y and Shinozaki, K (2006) CYP707A3, a major ABA 8′-hydroxylase involved in dehydration and rehydration response in Arabidopsis thaliana . Plant Journal 46: 171182.
Urano, K, Maruyama, K, Ogata, Y, Morishita, Y, Takeda, M, Sakurai, N, Suzuki, H, Saito, K, Shibata, D and Kobayashi, M (2009) Characterization of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics. Plant Journal 57: 10651078.
Vitte, C, Ishii, T, Lamy, F, Brar, D and Panaud, O (2004) Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.). Molecular Genetics and Genomics 272: 504511.
Wan, J, Jiang, L, Tang, J, Wang, C, Hou, M, Jing, W and Zhang, L (2006) Genetic dissection of the seed dormancy trait in cultivated rice (Oryza sativa L.). Plant Science 170: 786792.
Werker, E (1980) Seed dormancy as explained by the anatomy of embryo envelopes. Israel Journal of Botany 29: 2244.
Ye, N, Jia, L and Zhang, J (2012) ABA signal in rice under stress conditions. Rice 5: 1.
Zhang, Y, Miao, X, Xia, X and He, Z (2014) Cloning of seed dormancy genes (TaSdr) associated with tolerance to pre-harvest sprouting in common wheat and development of a functional marker. Theoretical and Applied Genetics 127: 855866.
Zhu, Q and Ge, S (2005) Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytologist 167: 249265.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Plant Genetic Resources
  • ISSN: 1479-2621
  • EISSN: 1479-263X
  • URL: /core/journals/plant-genetic-resources
Please enter your name
Please enter a valid email address
Who would you like to send this to? *


Type Description Title
Supplementary materials

Lee supplementary material
Supplementary Table

 Unknown (31 KB)
31 KB