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Plant Science Today (PST)

Review Articles

Vol. 11 No. 4 (2024)

A systematic literature review on current status and future prospects of pre-harvest sprouting management in rice

DOI
https://doi.org/10.14719/pst.3551
Submitted
15 March 2024
Published
29-08-2024 — Updated on 01-10-2024
Versions

Abstract

Pre-harvest sprouting (PHS) is a major constraint to rice in areas having high rainfall during late maturity. It poses a significant challenge to farmers, leading to yield loss and grain quality. Prolonged wet and humid conditions prevailing in North East India and incidence of cyclonic storms and heavy floods in other states cause PHS in rice. This systematic literature review (SLR) explored existing research on PHS's physiological, biochemical, molecular and environmental factors. A thorough approach that included a methodical Scopus literature search turned up 1236 papers, of which 60 research were selected for quantitative analysis following inclusion criteria. The papers dissected the genetic basis, population studies and genome analysis. Findings of seed dormancy regulation, Quantitative trait loci (QTLs) associated with PHS resistance, genes involved in improving seed dormancy, reducing abscisic acid sensitivity and breeding RILs and NILs resistant to PHS were published. Molecular and biochemical studies reported heat shock proteins (HSPs), hormone-related genes (ABA and GA) and microRNAs as potential targets for developing strategies to prevent PHS in rice. Resilience to pre-harvest sprouting was attempted through exogenous application of chemicals such as eugenol, sodium chloride, glucose, coumarin, molybdenum, maleic hydrazide and uniconazole. Despite current management practices, challenges persist due to the absence of universally resistant varieties and the variability in environmental conditions. Potential gaps identified were a lack of research papers from Indian authors on PHS, a simple and novel technology for the farming community to arrest PHS under unfavourable environmental conditions. Future research directions emphasize integrating laboratory insights into genetic and molecular mechanisms into practical field technologies.

References

  1. Sangavi S, Porpavai S. Impact of irrigation scheduling and weed management on water use efficiency and yield of direct dry seeded rice. Madras Agricultural Journal. 2018; 105(march (1-3)):1. https://doi.org/10.29321/MAJ.2018.000120
  2. Sohn SI, Pandian S, Kumar TS, Zoclanclounon YAB, Muthuramalingam P, Shilpha J, et al. Seed dormancy and pre-harvest sprouting in rice-an updated overview. International Journal of Molecular Sciences. 2021; 22(21):11804. https://doi.org/10.3390/ijms222111804
  3. Lee, Chebotarov D, McNally KL, Pede V, Setiyono TD, Raquid R, et al. Novel sources of pre-harvest sprouting resistance for japonica rice improvement. Plants. 2021; 10(8):1709. https://doi.org/10.3390/plants10081709
  4. Lu X, Zhang D, Zhang Y, Liu X, Wang S, Liu X. The molybdenum cofactor biosynthesis gene, OsCNX1, is essential for seedling development and seed germination in rice. Molecular Breeding. 2023; 43(11):77. https://doi.org/10.1007/s11032-023-01424-x
  5. Mohapatra P, Kariali E. Management of viviparous germination in rice: a strategy for development of climate resilient rice cultivation. ORYZA-An International Journal on Rice. 2016; 53(3):235-9.
  6. Priyadarsini P, Lal MK, Pandey R, Kumar M, Malini M, Das A, et al. Variability in photosynthetic traits is associated with biomass accumulation and grain yield in basmati rice germplasm. Plant Physiology Reports. 2022; 27(4):618-24. https://doi.org/10.1007/s40502-022-00697-2
  7. Mao X, Zheng X, Sun B, Jiang L, Zhang J, Lyu S, et al. MKK3 cascade regulates seed dormancy through a negative feedback loop modulating ABA signal in rice. Rice. 2024; 17(1):2. https://doi.org/10.1186/s12284-023-00679-4
  8. Nonogaki M, Nonogaki H. Prevention of preharvest sprouting through hormone engineering and germination recovery by chemical biology. Frontiers in Plant Science. 2017; 8:90. https://doi.org/10.3389/fpls.2017.00090
  9. Liu X, Wang J, Yu Y, Kong L, Liu Y, Liu Z, et al. Identification and characterization of the rice pre-harvest sprouting mutants involved in molybdenum cofactor biosynthesis. New Phytologist. 2019; 222(1):275-85. https://doi.org/10.1111/nph.15607
  10. Liu L, Xia W, Li H, Zeng H, Wei B, Han S, et al. Salinity inhibits rice seed germination by reducing ?-amylase activity via decreased bioactive gibberellin content. Frontiers in Plant Science. 2018; 9:275. https://doi.org/10.3389/fpls.2018.00275
  11. Borges R, Miguel EC, Dias JM, da Cunha M, Bressan-Smith RE, de Oliveira JG, et al. Ultrastructural, physiological and biochemical analyses of chlorate toxicity on rice seedlings. Plant science. 2004; 166(4):1057-62. https://doi.org/10.1016/j.plantsci.2003.12.023
  12. Mengist W, Soromessa T, Legese G. Method for conducting systematic literature review and meta-analysis for environmental science research. MethodsX. 2020; 7:100777. https://doi.org/10.1016/j.mex.2019.100777
  13. Chandra A, Karthikeyan C, Mansingh P. The determinants of socio economic status of farmers-A systematic literature review. Review of applied socio-economic research. 2023; 25(1):138-50. https://doi.org/10.54609/reaser.v25i1.379
  14. Chen W, Wang W, Lyu Y, Wu Y, Huang P, Hu S, et al. OsVP1 activates Sdr4 expression to control rice seed dormancy via the ABA signaling pathway. The Crop Journal. 2021; 9(1):68-78. https://doi.org/10.1016/j.cj.2020.06.005
  15. Chen X, Tian Y, Lu X. Breeding of the dormant thermosensitive genic male-sterile lines of early rice to overcome pre-harvest sprouting of the hybrid seeds. Agronomy. 2018; 8(9):191. https://doi.org/10.3390/agronomy8090191
  16. Cheng J, Wang L, Du W, Lai Y, Huang X, Wang Z, et al. Dynamic quantitative trait locus analysis of seed dormancy at three development stages in rice. Molecular Breeding. 2014; 34:501-10. https://doi.org/10.1007/s11032-014-0053-z
  17. Cheon K-S, Jeong Y-M, Oh H, Oh J, Kang D-Y, Kim N, et al. Development of 454 new kompetitive allele-specific PCR (KASP) markers for temperate japonica rice varieties. Plants. 2020; 9(11):1531. https://doi.org/10.3390/plants9111531
  18. Cheon K-S, Won YJ, Jeong Y-M, Lee Y-Y, Kang D-Y, Oh J, et al. QTL mapping for pre-harvest sprouting resistance in japonica rice varieties utilizing genome re-sequencing. Molecular Genetics and Genomics. 2020; 295:1129-40. https://doi.org/10.1007/s00438-020-01688-4
  19. Chuxin W, Chengchao Z, Yu Z, Min X, Jindong W, Huang B, et al. OsbZIP09, a unique osbzip transcription factor of rice, promotes rather than suppresses seed germination by attenuating abscisic acid pathway. Rice Science. 2021; 28(4):358-67. https://doi.org/10.1016/j.rsci.2021.05.006
  20. Deepika K, Lavuri K, Rathod S, Yeshala CM, Jukanti AK, Reddy SN, et al. Multivariate analysis of geographically diverse rice germplasm for genetic improvement of yield, dormancy and shattering-related traits. Plant Genetic Resources. 2021; 19(2):144-52. https://doi.org/10.1017/S1479262121000186
  21. Du L, Xu F, Fang J, Gao S, Tang J, Fang S, et al. Endosperm sugar accumulation caused by mutation of PHS 8/ISA 1 leads to pre-harvest sprouting in rice. The Plant Journal. 2018; 95(3):545-56. https://doi.org/10.1111/tpj.13970
  22. Fang J, Chai C, Qian Q, Li C, Tang J, Sun L, et al. Mutations of genes in synthesis of the carotenoid precursors of ABA lead to pre-harvest sprouting and photo?oxidation in rice. The Plant Journal. 2008;54(2):177-89. https://doi.org/10.1111/j.1365-313X.2008.03411.x
  23. Feng Y, Han Y, Han B, Zhao Y, Yang Y, Xing Y. A 4 bp InDel in the promoter of wheat gene TaAFP-B affecting seed dormancy confirmed in transgenic rice. Frontiers in Plant Science. 2022; 13:837805. https://doi.org/10.3389/fpls.2022.837805
  24. Gu X-Y, Foley ME, Horvath DP, Anderson JV, Feng J, Zhang L, et al. 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. 2011; 189(4):1515-24. https://doi.org/10.1534/genetics.111.131169
  25. Gu X-Y, Kianian SF, Hareland GA, Hoffer BL, Foley ME. Genetic analysis of adaptive syndromes interrelated with seed dormancy in weedy rice (Oryza sativa). Theoretical and Applied Genetics. 2005; 110:1108-18. https://doi.org/10.1007/s00122-005-1939-2
  26. Guo L, Zhu L, Xu Y, Zeng D, Wu P, Qian Q. QTL analysis of seed dormancy in rice (Oryza sativa L.). Euphytica. 2004; 140:155-62. https://doi.org/10.1007/s10681-004-2293-1
  27. Guo N, Tang S, Wang J, Hu S, Tang S, Wei X, et al. Transcriptome and proteome analysis revealed that hormone and reactive oxygen species synergetically regulate dormancy of introgression line in rice (Oryza sativa L.). International Journal of Molecular Sciences. 2023; 24(7):6088. https://doi.org/10.3390/ijms24076088
  28. Han C-M, Shin J-H, Kwon J-B, Kim J-S, Won J-G, Kim J-S. Comparison of morphological and physicochemical properties of a floury rice variety upon pre-harvest sprouting. Foods. 2021; 10(4):746. https://doi.org/10.3390/foods10040746
  29. Hori K, Sugimoto K, Nonoue Y, Ono N, Matsubara K, Yamanouchi U, et al. Detection of quantitative trait loci controlling pre-harvest sprouting resistance by using backcrossed populations of japonica rice cultivars. Theoretical and applied genetics. 2010; 120:1547-57. https://doi.org/10.1007/s00122-010-1275-z
  30. Hu Q, Fu Y, Guan Y, Lin C, Cao D, Hu W, et al. Inhibitory effect of chemical combinations on seed germination and pre-harvest sprouting in hybrid rice. Plant Growth Regulation. 2016; 80:281-9. https://doi.org/10.1007/s10725-016-0165-z
  31. Hu Q, Lin C, Guan Y, Sheteiwy MS, Hu W, Hu J. Inhibitory effect of eugenol on seed germination and pre-harvest sprouting of hybrid rice (Oryza sativa L.). Scientific Reports. 2017; 7(1):5295. https://doi.org/10.1038/s41598-017-04104-x
  32. Huang Y, Song J, Hao Q, Mou C, Wu H, Zhang F, et al. WEAK SEED DORMANCY 1, an aminotransferase protein, regulates seed dormancy in rice through the GA and ABA pathways. Plant Physiology and Biochemistry. 2023; 202:107923. https://doi.org/10.1016/j.plaphy.2023.107923
  33. Huh SM, Hwang Y-s, Shin YS, Nam MH, Kim DY, Yoon IS. Comparative transcriptome profiling of developing caryopses from two rice cultivars with differential dormancy. Journal of plant physiology. 2013; 170(12):1090-100. https://doi.org/10.1016/j.jplph.2013.03.003
  34. Ishibashi Y, Sueyoshi R, Morita T, Yoshimura A, Iwaya-Inoue M. Detection of pre-harvest sprouting in rice seeds by using 1H-NMR. Environmental Control in Biology. 2005; 43(2):131-7. https://doi.org/10.2525/ecb.43.131
  35. Jang S-G, Kim B, Choi I, Lee J, Ham T-H, Kwon S-W. Fine-Mapping analysis of the genes associated with pre-harvest sprouting tolerance in rice (Oryza sativa L.). Agronomy. 2023; 13(3):818. https://doi.org/10.3390/agronomy13030818
  36. Ji H, Shin Y, Lee C, Oh H, Yoon IS, Baek J, et al. Genomic variation in Korean japonica rice varieties. Genes. 2021; 12(11):1749. https://doi.org/10.3390/genes12111749
  37. Jing S, Tian Y, Zhang H, T Hancock J, Zhu Y, Li P. The genetic and biochemical mechanisms underlying cereal seed dormancy. Phyton-International Journal of Experimental Botany. 2023; 92(4). https://doi.org/10.32604/phyton.2023.026305
  38. Kim S, Huh SM, Han HJ, Lee GS, Hwang Y-S, Cho MH, et al. A rice seed-specific glycine-rich protein OsDOR1 interacts with GID1 to repress GA signaling and regulates seed dormancy. Plant Molecular Biology. 2023; 111(6):523-39. https://doi.org/10.1007/s11103-023-01343-7
  39. Lee G-A, Jeon Y-A, Lee H-S, Hyun D-Y, Lee J-R, Lee M-C, et al. Variation in pre-harvest sprouting resistance, seed germination and changes in abscisic acid levels during grain development in diverse rice genetic resources. Plant Genetic Resources. 2018; 16(1):18-27. https://doi.org/10.1017/S1479262116000319
  40. Lee H, Choi M, Hwang W, Jeong J, Yang S, Lee C. Occurrence of rice preharvest sprouting varies greatly depending on past weather conditions during grain filling. Field Crops Research. 2021; 264:108087. https://doi.org/10.1016/j.fcr.2021.108087
  41. Li C, Ni P, Francki M, Hunter A, Zhang Y, Schibeci D, et al. Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison. Functional & integrative genomics. 2004; 4:84-93. https://doi.org/10.1007/s10142-004-0104-3
  42. Li P, Liu H, Wen H, Yang L, Chen Z, Zheng H, et al. Comprehensive genetic analysis reveals seed germination activity-related QTL and meta-QTL in rice (Oryza sativa L.). Genetic Resources and Crop Evolution. 2023; 70(3):1007-22. https://doi.org/10.1007/s10722-022-01484-6
  43. Liao Y, Bai Q, Xu P, Wu T, Guo D, Peng Y, et al. Mutation in rice Abscisic Acid2 results in cell death, enhanced disease-resistance, altered seed dormancy and development. Frontiers in Plant Science. 2018; 9:405. https://doi.org/10.3389/fpls.2018.00405
  44. Liu D, Zeng M, Wu Y, Du Y, Liu J, Luo S, et al. Comparative transcriptomic analysis provides insights into the molecular basis underlying pre-harvest sprouting in rice. BMC genomics. 2022; 23(1):771. https://doi.org/10.1186/s12864-017-4142-3
  45. Lu B, Xie K, Yang C, Wang S, Liu X, Zhang L, et al. Mapping two major effect grain dormancy QTL in rice. Molecular Breeding. 2011; 28:453-62. https://doi.org/10.1007/s11032-010-9495-0
  46. Mao X, Zhang J, Liu W, Yan S, Liu Q, Fu H, et al. The MKKK62-MKK3-MAPK7/14 module negatively regulates seed dormancy in rice. Rice. 2019; 12(1):1-14. https://doi.org/10.1186/s12284-018-0260-z
  47. Miao C, Wang Z, Zhang L, Yao J, Hua K, Liu X, et al. The grain yield modulator miR156 regulates seed dormancy through the gibberellin pathway in rice. Nature communications. 2019; 10(1):3822. https://doi.org/10.1038/s41467-019-11830-5
  48. Mizuno Y, Yamanouchi U, Hoshino T, Nonoue Y, Nagata K, Fukuoka S, et al. Genetic dissection of pre-harvest sprouting resistance in an upland rice cultivar. Breeding science. 2018; 68(2):200-9. https://doi.org/10.1270/jsbbs.17062
  49. Nguyen T, Fu K, Mou C, Yu J, Zhu X, Huang Y, et al. Fine mapping of qSdr9, a novel locus for seed dormancy (SD) in weedy rice, and development of NILs with a strong SD allele. Molecular Breeding. 2020; 40:1-11. https://doi.org/10.1007/s11032-020-01148-2
  50. Nguyen T, Zhou C, Zhang T, Yu J, Miao R, Huang Y, et al. Identification of QTL for seed dormancy from weedy rice and its application to elite rice cultivar 'Ninggeng 4'. Molecular Breeding. 2019; 39:1-12. https://doi.org/10.1007/s11032-019-1031-2
  51. Park M, Choi W, Shin S-Y, Moon H, Lee D, Gho Y-S, et al. Identification of genes and microRNAs affecting pre-harvest sprouting in rice (Oryza sativa L.) by transcriptome and small RNAome analyses. Frontiers in Plant Science. 2021; 12:1677. https://doi.org/10.3389/fpls.2021.727302
  52. Phan PDT, Van Vu B. Improving the pre-harvest sprouting resistance of rice cultivar IR36 using wild rice (Oryza rufipogon) W630. Cereal Research Communications. 2021:1-7. https://doi.org/10.1007/s42976-021-00162-0
  53. Qin M, Zhang Y, Yang Y, Miao C, Liu S. Seed-specific overexpression of SPL12 and IPA1 improves seed dormancy and grain size in rice. Frontiers in Plant Science. 2020; 11:532771. https://doi.org/10.3389/fpls.2020.532771
  54. SASAKI K, KAZAMA Y, Youn C, Tadashi S. Confirmation of novel quantitative trait loci for seed dormancy at different ripening stages in rice. Rice Science. 2013; 20(3):207-12. https://doi.org/10.1016/S1672-6308(13)60123-7
  55. Shi J, Shi J, Liang W, Zhang D. Integrating GWAS and transcriptomics to identify genes involved in seed dormancy in rice. Theoretical and Applied Genetics. 2021; 134:3553-62. https://doi.org/10.1007/s00122-021-03911-1
  56. Song S, Wang G, Wu H, Fan X, Liang L, Zhao H, et al. OsMFT2 is involved in the regulation of ABA signaling-mediated seed germination through interacting with OsbZIP23/66/72 in rice. The Plant Journal. 2020; 103(2):532-46. https://doi.org/10.1111/tpj.14748
  57. Subburaj S, Cao S, Xia X, He Z. Phylogenetic analysis, lineage-specific expansion and functional divergence of seed dormancy 4-like genes in plants. PLoS One. 2016; 11(6):e0153717. https://doi.org/10.1371/journal.pone.0153717
  58. Tao L, Wang X, Tan H, Chen H, Yang C, Zhuang J, et al. Physiological analysis on pre-harvest sprouting in recombinant inbred rice lines. Frontiers of Agriculture in China. 2007; 1:24-9. https://doi.org/10.1007/s11703-007-0004-0
  59. Tejakhod S, Ellis RH. Effect of simulated flooding during rice seed development and maturation on subsequent seed quality. Seed Science Research. 2018; 28(1):72-81. https://doi.org/10.1017/S0960258517000368
  60. Wang J, Korkmaz U, Guo M, Pipatpongpinyo W, Gu X-Y. Pyramiding seed dormancy genes to improve resistance of semi-dwarf varieties to pre-harvest sprouting in rice. Molecular Breeding. 2020; 40:1-12. https://doi.org/10.1007/s11032-020-01172-2
  61. Wang L, Cheng J, Lai Y, Du W, Huang X, Wang Z, et al. Identification of QTLs with additive, epistatic and QTL× development interaction effects for seed dormancy in rice. Planta. 2014; 239:411-20. https://doi.org/10.1007/s00425-013-1991-0
  62. Xu F, Tang J, Gao S, Cheng X, Du L, Chu C. Control of rice pre-harvest sprouting by glutaredoxin-mediated abscisic acid signaling. The Plant Journal. 2019; 100(5):1036-51. https://doi.org/10.1111/tpj.14501
  63. Zhang C, Zhou L, Lu Y, Yang Y, Feng L, Hao W, et al. Changes in the physicochemical properties and starch structures of rice grains upon pre-harvest sprouting. Carbohydrate polymers. 2020; 234:115893. https://doi.org/10.1016/j.carbpol.2020.115893
  64. Zhang H, Li M, He D, Wang K, Yang P. Mutations on ent-kaurene oxidase 1 encoding gene attenuate its enzyme activity of catalyzing the reaction from ent-kaurene to ent-kaurenoic acid and lead to delayed germination in rice. PLoS Genetics. 2020; 16(1):e1008562. https://doi.org/10.1371/journal.pgen.1008562
  65. Zhang X-Q, Li C, Panozzo J, Westcott S, Zhang G, Tay A, et al. Dissecting the telomere region of barley chromosome 5HL using rice genomic sequences as references: new markers for tracking a complex region in breeding. Molecular breeding. 2011; 27:1-9. https://doi.org/10.1007/s11032-010-9408-2
  66. Zhao B, Zhang H, Chen T, Ding L, Zhang L, Ding X, et al. Sdr4 dominates pre?harvest sprouting and facilitates adaptation to local climatic condition in Asian cultivated rice. Journal of Integrative Plant Biology. 2022; 64(6):1246-63. https://doi.org/10.1111/jipb.13266
  67. Zhou Y, Xie Y, Cai J, Liu C, Zhu H, Jiang R, et al. Substitution mapping of QTLs controlling seed dormancy using single segment substitution lines derived from multiple cultivated rice donors in seven cropping seasons. Theoretical and Applied Genetics. 2017; 130:1191-205. https://doi.org/10.1007/s00122-017-2881-9
  68. Zhu D, Qian Z, Wei H, Guo B, Xu K, Dai Q, et al. The effects of field pre-harvest sprouting on the morphological structure and physicochemical properties of rice (Oryza sativa L.) starch. Food chemistry. 2019; 278:10-6. https://doi.org/10.1016/j.foodchem.2018.11.017
  69. Zhu LW, Cao DD, Hu QJ, Guan YJ, Hu WM, Nawaz A, et al. Physiological changes and sHSPs genes relative transcription in relation to the acquisition of seed germination during maturation of hybrid rice seed. Journal of the Science of Food and Agriculture. 2016; 96(5):1764-71. https://doi.org/10.1002/jsfa.7283
  70. Gong D, He F, Liu J, Zhang C, Wang Y, Tian S, et al. Understanding of hormonal regulation in rice seed germination. Life. 2022; 12(7):1021. https://doi.org/10.3390/life12071021
  71. Zhu G, Ye N, Zhang J. Glucose-induced delay of seed germination in rice is mediated by the suppression of ABA catabolism rather than an enhancement of ABA biosynthesis. Plant and Cell Physiology. 2009; 50(3):644-51. https://doi.org/10.1093/pcp/pcp022
  72. Chen B-X, Peng Y-X, Gao J-D, Zhang Q, Liu Q-J, Fu H, et al. Coumarin-induced delay of rice seed germination is mediated by suppression of abscisic acid catabolism and reactive oxygen species production. Frontiers in Plant Science. 2019:828. https://doi.org/10.3389/fpls.2019.00828
  73. Vivitha P, Raveendran M, Vijayalakshmi D. Introgression of QTLs controlling spikelet fertility maintains membrane integrity and grain yield in improved white Ponni derived progenies exposed to heat stress. Rice Science. 2017; 24(1):32-40. https://doi.org/10.1016/j.rsci.2016.05.006
  74. Rahman H, Dakshinamurthi V, Ramasamy S, Manickam S, Kaliyaperumal AK, Raha S, et al. Introgression of submergence tolerance into CO 43, a popular rice variety of India, through marker-assisted backcross breeding. Czech Journal of Genetics and Plant Breeding. 2018; 54(3):101-8. https://doi.org/10.17221/149/2017-CJGPB
  75. Vinitha A, Vijayalakshmi D, Parthipan T. Physiology and performance of anaerobic germination tolerant rice varieties under direct seeded cultivation. Plant Physiology Reports. 2024:1-13. https://doi.org/10.1007/s40502-024-00780-w

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