Chin Bull Bot ›› 2019, Vol. 54 ›› Issue (4): 503-508.doi: 10.11983/CBB19087

• TECHNIQUES AND METHODS • Previous Articles     Next Articles

Protocols for Analyzing Rice Meiotic Chromosomes

Cheng Xinjie1,Yu Hengxiu1,Cheng Zhukuan2,*()   

  1. 1 Agriculture College, Yangzhou University, Yangzhou 225009, China
    2 Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
  • Received:2019-05-12 Accepted:2019-06-14 Online:2019-07-01 Published:2019-07-01
  • Contact: Cheng Zhukuan


The development of techniques to analyze pachytene chromosomes has greatly overcome most of the difficulties in cytological studies of rice chromosomes caused by their small size. Visualization of meiotic chromosomes has now become routine in cytogenetic studies of this species. This chapter provides protocols on basic meiotic chromosome preparation, FISH analysis and immunocytology in rice.

Key words: rice, meiosis, chromosome, FISH, immunostaining

Figure 1

Characterization of rice meiotic pachytene chromosomes (A) Fluorescent in situ hybridization using rice pachytene chromosomes probed with the telomeric sequence pAtT4 (red); Chromosomes stained with DAPI (blue) (Images taken with a regular fluorescence microscope); (B) Immunodetection of PAIR3 (green) and ZEP1 (red) in rice pachytene chromosomes (Images taken with a super resolution microscope). Bars=5 µm"

[1] Arumuganathan K, Earle ED ( 1991). Estimation of nuclear DNA content of plants by flow cytometry. Plant Mol Biol Rep 9, 229-241.
[2] Che L, Tang D, Wang K, Wang M, Zhu K, Yu H, Gu M, Cheng Z ( 2011). OsAM1 is required for leptotene transition in rice. Cell Res 21, 654-665.
[3] Cheng Z, Buell CR, Wing RA, Gu M, Jiang J ( 2001 a). Toward a cytological characterization of the rice genome. Genome Res 11, 2133-2141.
[4] Cheng Z, Dong F, Langdon T, Ouyang S, Buell CR, Gu M, Blattner FR, Jiang J ( 2002). Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14, 1691-1704.
[5] Cheng Z, Stupar RM, Gu M, Jiang J ( 2001 b). A tandemly repeated DNA sequence is associated with both knob-like heterochromatin and a highly decondensed structure in the meiotic pachytene chromosomes of rice. Chromosoma 110, 24-31.
[6] Goff SA ( 1999). Rice as a model for cereal genomics. Curr Opin Plant Biol 2, 86-89.
[7] Ji JH, Tang D, Shen Y, Xue ZH, Wang HJ, Shi WQ, Zhang C, Du GJ, Li YF, Cheng ZK ( 2016). P31 comet, a member of the synaptonemal complex, participates in meiotic DSB formation in rice . Proc Natl Acad Sci USA 113, 10577-10582.
[8] Kurata N, Omura T, Iwata N ( 1981). Studies on centromere, chromomere and nucleolus in pachytene nuclei of rice, Oryza sativa, microsporocytes. Cytologia 46, 791-800.
[9] Li X, Chao D, Wu Y, Huang X, Chen K, Cui L, Su L, Ye W, Chen H, Chen H, Dong N, Guo T, Shi M, Feng Q, Zhang P, Han B, Shan J, Gao J, Lin H ( 2015). Natural alleles of a proteasome α2 subunit gene contribute to thermotolerance and adaptation of African rice. Nat Genet 47, 827-833.
[10] Li YF, Qin BX, Shen Y, Zhang FF, Liu CZ, You HL, Du GJ, Tang D, Cheng ZK ( 2018). HEIP1 regulates crossover formation during meiosis in rice. Proc Natl Acad Sci USA 115, 10810-10815.
[11] Luo Q, Li YF, Shen Y, Cheng ZK ( 2014). Ten years of gene discovery for meiotic event control in rice. J Genet Genomics 41, 125-137.
[12] Ma Y, Dai X, Xu Y, Luo W, Zheng X, Zeng D, Pan Y, Lin X, Liu H, Zhang D, Xiao J, Guo X, Xu S, Niu Y, Jin J, Zhang H, Xu X, Li L, Wang W, Qian Q, Ge S, Chong K ( 2015). COLD1 confers chilling tolerance in rice. Cell 160, 1209-1221.
[13] Miao CB, Tang D, Zhang HG, Wang M, Li YF, Tang SZ, Yu HX, Gu MH, Cheng ZK ( 2013). CENTRAL REGION COMPONENT 1, a novel synaptonemal complex component, is essential for meiotic recombination initiation in rice. Plant Cell 25, 2998-3009.
[14] Nonomura K, Morohoshi A, Nakano M, Eiguchi M, Miyao A, Hirochika H, Kurata N ( 2007). A germ cell specific gene of the ARGONAUTE family is essential for the progression of premeiotic mitosis and meiosis during sporogenesis in rice. Plant Cell 19, 2583-2594.
[15] Pawlowski WP, Golubovskaya IN, Timofejeva L, Meeley RB, Sheridan WF, Cande WZ ( 2004). Coordination of meiotic recombination, pairing, and synapsis by PHS1. Science 303, 89-92.
[16] Ren LJ, Tang D, Zhao TT, Zhang FF, Liu CZ, Xue ZH, Shi WQ, Du GJ, Shen Y, Li YF, Cheng ZK ( 2018). OsSPL regulates meiotic fate acquisition in rice. New Phytol 218, 789-803.
[17] Tang X, Bao W, Zhang W, Cheng Z ( 2007). Identification of chromosomes from multiple rice genomes using a universal molecular cytogenetic marker system. J Integr Plant Biol 49, 953-960.
[18] Wang K, Tang D, Wang M, Lu J, Yu H, Liu J, Qian B, Gong Z, Wang X, Chen J, Gu M, Cheng Z ( 2009). MER3 is required for normal meiotic crossover formation, but not for presynaptic alignment in rice. J Cell Sci 122, 2055-2063.
[19] Wang M, Wang K, Tang D, Wei C, Li M, Shen Y, Chi Z, Gu M, Cheng Z ( 2010). The central element protein ZEP1 of the synaptonemal complex regulates the number of crossovers during meiosis in rice. Plant Cell 22, 417-430.
[20] Wang Y, Xiong G, Hu J, Jiang L, Yu H, Xu J, Fang Y, Zeng L, Xu E, Xu J, Ye W, Meng X, Liu R, Chen H, Jing Y, Wang Y, Zhu X, Li J, Qian Q ( 2015). Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nat Genet 47, 944-948.
[21] Wu HK ( 1967). Note on preparing of pachytene chromosomes by double mordant. Sci Agric 15, 40-44.
[22] Yu H, Wang M, Tang D, Wang K, Chen F, Gong Z, Gu M, Cheng Z ( 2010). OsSPO11-1 is essential for both homologous chromosome pairing and crossover formation in rice. Chromosoma 119, 625-636.
[23] Zhang F, Tang D, Shen Y, Xue ZH, Shi WQ, Ren LJ, Du GJ, Li Y, Cheng ZK ( 2017). The F-box protein ZYGO1 mediates bouquet formation to promote homologous pairing, synapsis, and recombination in rice meiosis. Plant Cell 29, 2597-2609.
[24] Zhao TT, Ren LJ, Chen XJ, Yu HX, Liu CJ, Shen Y, Shi WQ, Tang D, Du GJ, Li YF, Ma BJ, Cheng ZK ( 2018). The OsRR24/LEPTO1 type-B response regulator is essential for the organization of leptotene chromosomes in rice meiosis. Plant Cell 30, 3024-3037.
[1] yuchun Rao. Research Progress on Rice Root Genetics and Breeding [J]. Chin Bull Bot, 2020, 55(3): 0-0.
[2] Han Mei-ling, Tan Ru-jiao, Chao Dai-yin. A New Progress of Green Revolution: Epigenetic Modification Dual-regulated by Gibberellin and Nitrogen Supply Contributes to Breeding of High Yield and Nitrogen Use Efficiency Rice [J]. Chin Bull Bot, 2020, 55(1): 5-8.
[3] Zhang Tong,Guo Yalu,Chen Yue,Ma Jinjiao,Lan Jinping,Yan Gaowei,Liu Yuqing,Xu Shan,Li Liyun,Liu Guozhen,Dou Shijuan. Expression Characterization of Rice OsPR10A and Its Function in Response to Drought Stress [J]. Chin Bull Bot, 2019, 54(6): 711-722.
[4] Xu Wanyue, Wang Yingxiang. Chromosome Behaviors of Male Meiocytes by Chromosome Spread in Arabidopsis thaliana [J]. Chin Bull Bot, 2019, 54(5): 620-624.
[5] Zhang Shuo, Wu Changyin. Long Noncoding RNA Ef-cd Promotes Maturity Without Yield Penalty in Rice [J]. Chin Bull Bot, 2019, 54(5): 550-553.
[6] Li Weitao, He Min, Chen Xuewei. Discovery of ZmFBL41 Chang7-2 as A Key Weapon against Banded Leaf and Sheath Blight Resistance in Maize [J]. Chin Bull Bot, 2019, 54(5): 547-549.
[7] Tian Huaidong, Li Jing, Tian Baohua, Niu Pengfei, Li Zhen, Yue Zhongxiao, Qu Yajuan, Jiang Jianfang, Wang Guangyuan, Cen Huihui, Li Nan, Yan Feng. Method for N-methyl-N-nitrosourea Mutagenesis on Hermaphroditic Germ Cells of Rice [J]. Chin Bull Bot, 2019, 54(5): 625-633.
[8] Zhou Chun, Jiao Ran, Hu Ping, Lin Han, Hu Juan, Xu Na, Wu Xianmei, Rao Yuchun, Wang Yuexing. Gene Mapping and Candidate Gene Analysis of Rice Early Senescence Mutant LS-es1 [J]. Chin Bull Bot, 2019, 54(5): 606-619.
[9] Liu Dongfeng, Tang Yongyan, Luo Shengtao, Luo Wei, Li Zhitao, Chong Kang, Xu Yunyuan. Identification of Chilling Tolerance of Rice Seedlings by Cold Water Bath [J]. Chin Bull Bot, 2019, 54(4): 509-514.
[10] Li Fan, Ruan Jiwei. High-throughput Identification of Meiotic Anti-CO Mutants by Fluorescent Reporters [J]. Chin Bull Bot, 2019, 54(4): 522-530.
[11] Liu Jin, Yao Xiaoyun, Yu Liqin, Li Hui, Zhou Huiying, Wang Jiayu, Li Maomao. Detection and Analysis of Dynamic Quantitative Trait Loci at Three Years for Seed Storability in Rice (Oryza sativa) [J]. Chin Bull Bot, 2019, 54(4): 464-473.
[12] Cheng Guangqian,Jia Keli,Li Na,Deng Chuanliang,Li Shufen,Gao Wujun. Bioinformatics Analysis and Chromosome Location of Nuclear Integrants of Plastid DNA in Asparagus officinalis [J]. Chin Bull Bot, 2019, 54(3): 328-334.
[13] Wang Xiaolin,Wang Ertao. NRT1.1B Connects Root Microbiota and Nitrogen Use in Rice [J]. Chin Bull Bot, 2019, 54(3): 285-287.
[14] Li Lulu, Yin Wenchao, Niu Mei, Meng Wenjing, Zhang Xiaoxing, Tong Hongning. Functional Analysis of Brassinosteroids in Salt Stress Responses in Rice [J]. Chin Bull Bot, 2019, 54(2): 185-193.
[15] Yang Dewei,Wang Mo,Han Libo,Tang Dingzhong,Li Shengping. Progress of Cloning and Breeding Application of Blast Resistance Genes in Rice and Avirulence Genes in Blast Fungi [J]. Chin Bull Bot, 2019, 54(2): 265-276.
Full text



[1] Zhang Zhen-jue. Some Principles Governing Shedding of Flowers and Fruits in Vanilla fragrans[J]. Chin Bull Bot, 1985, 3(05): 36 -37 .
[2] Qian Gao;Yuying Liu;Yinan Fei;Dapeng Li;Xianglin Liu* . Research Advances into the Root Radial Patterning Gene SHORT-ROOT[J]. Chin Bull Bot, 2008, 25(03): 363 -372 .
[3] Wang Bao-shan;Zou Qi and Zhao Ke-fu. Advances in Mechanism of Crop Salt Tolerance and Strategies for Raising Crop Salt Tolerance[J]. Chin Bull Bot, 1997, 14(增刊): 25 -30 .
[4] HE Feng WU Zhen-Bin. Application of Aquatic Plants in Sewage Treatment and Water Quality Improvement[J]. Chin Bull Bot, 2003, 20(06): 641 -647 .
[5] TIAN Bao-Lin WANG Shi-Jun LI Cheng-Sen CHEN Gui-Ren. An Approach on the Origin Center, Evolution Center and the Mechanics of Evolution and Extinction of the Late Palaeozoic Cathaysian Flora[J]. Chin Bull Bot, 2000, 17(专辑): 21 -33 .
[6] ZHANG Yan FANG Li LI Tian-Fei YAO Zhao-BingJIANG Jin-Hui. Effect of Calcium on the Heat Tolerance and Active Oxygen Metabolism of Tobacco Leaves[J]. Chin Bull Bot, 2002, 19(06): 721 -726 .
[7] JIA Hu-Sen LI De-QuanHAN Ya-Qin. Cytochrome b-559 in Chloroplasts[J]. Chin Bull Bot, 2001, 18(02): 158 -162 .
[8] Wei Sun;Chonghui Li;Liangsheng Wang;Silan Dai*. Analysis of Anthocyanins and Flavones in Different-colored Flowers of Chrysanthemum[J]. Chin Bull Bot, 2010, 45(03): 327 -336 .
[9] . Phosphate_Stress Protein and Iron_Stress Protein in Plants[J]. Chin Bull Bot, 2001, 18(05): 571 -576 .
[10] ZHANG Da-Yong, JIANG Xin-Hua. An Ecological Perspective on Crop Prduction[J]. Chin J Plan Ecolo, 2000, 24(3): 383 -384 .