Comparative karyotypic analysis of A and C genomes in the genus <italic>Oryza</italic> with <italic>C</italic><sub><italic>0</italic></sub><italic>t-1</italic> DNA and RFLP

doi:10.1007/s11703-011-1092-4

Front Agric Chin

2011, Vol. 5

Issue (2) : 173-180 https://doi.org/10.1007/s11703-011-1092-4

RESEARCH ARTICLE

Comparative karyotypic analysis of A and C genomes in the genus Oryza with C₀t-1 DNA and RFLP

Junbo ZHOU¹, Weizhen LAN²(

), Rui QIN³(

)

1. College of Life Sciences, Huzhou Teachers College, Huzhou 313000, China; 2. The Third Middle School of Wuyi, Jinhua 321200, China; 3. Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China

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Abstract

Fluorescence in situ hybridization (FISH) was applied to somatic chromosomes preparations of Oryza sativa L. (AA), O. glaberrima (AA), and O. officinalis Wall. (CC) with a labeled probe of C₀t-1 DNA. Genomic in situ hybridization to its own chromosomes (self-GISH) was conducted in a control experiment. The homologous chromosomes showed similar signal bands probed by C₀t-1 DNA, while karyotypic analysis of chromosomes between A genome in the two cultivated species and C genome in O. officinalis were conducted based on the band patterns. The ideograms with C₀t-1 DNA signal bands were also built. The nonuniform distribution of hybridization signals of C₀t-1 DNA from O. sativa and that on its own chromosome of O. officinalis were observed. However, the similarity and correspondence between C₀t-1 DNA signal patterns and genomic DNA signal patterns indicated that the self-GISH signals actually resulted from the hybridization of genomic repetitive sequences to the chromosomes. The restriction fragment length polymorphism (RFLP) marker, R2676, from the chromosome 8 of O. sativa and O. officinalis, was used as a probe to somatic hybrid on chromosomes for comparative karyotypic analysis between O. glaberrima and O. officinalis. The results showed that R2676 was located on the short arm of chromosome 7 in O. officinalis and chromosome 4 in O. glaberrima. The percentage distances from the centromere to hybridization sites were 91.56±5.62 and 86.20±3.17. Our results revealed that the relative length of O. officinalis chromosome 8 does not follow conventional chromosome length in descending order of number. C₀t-1 DNA of A genome signals were detected in the end of the short arm of O. officinalis chromosome 8, indicating that the highly and moderately repetitive DNA sequences in this region were considerably similar between C and A genomes. However, the fluorescence intensity on the chromosomes of C₀t-1 DNA of A genome was less than that of its own C genome from O. officinalis, which would be one of the causes for the fact that highly and moderately repetitive DNA sequences were amplified in O. officinalis. No homology signal of C₀t-1 DNA from O. sativa was detected in the end of the long arm of O. glaberrima, indicating that repetitive DNA sequences of A genome in two cultivated rice were lost in the evolutional history. In this paper, using comparative karyotypic analysis of RFLP combined C₀t-1 DNA signal bands, the evolutionary mechanism of genome in genus Oryza was also discussed.

Keywords C₀t-1 DNA RFLP karyotype in situ hybridization Oryza

Corresponding Author(s): LAN Weizhen,Email:lanwz@hotmail.com; QIN Rui,Email:qinrui@hotmail.com

Issue Date: 05 June 2011

Cite this article:

Junbo ZHOU,Weizhen LAN,Rui QIN. Comparative karyotypic analysis of A and C genomes in the genus Oryza with C₀t-1 DNA and RFLP[J]. Front Agric Chin, 2011, 5(2): 173-180.

URL:

https://academic.hep.com.cn/fag/EN/10.1007/s11703-011-1092-4
https://academic.hep.com.cn/fag/EN/Y2011/V5/I2/173

Fig.1 FISH images of prometaphase or metaphase chromosomes probed with C0t–1 DNA and their own total genomic DNA. Chromosomes stained with DAPI. Bars, 10 μm. FISH images A, C, and E show that the chromosomes are probed with DNA of , , and , respectively. FISH images B, D, and F show that the chromosomes are probed with their own genomic DNA of , , and , respectively. G and H show that the chromosomes are probed with its own DNA of .

Fig.2 Karyotype reconstruction base on DNA banding and idiogram of chromosomal locations of DNA in , , and . Bars, 10μm. Karyotype idiograms A–C show that the chromosomes are probed with DNA of , , and , respectively. D shows that the chromosomes are probed with its own DNA of . E, F, and G depict the distribution of the DNA of , , and , respectively. H depicts the distribution of its own DNA of . I is DNA banding corresponding to the rearranged chromosome. J is the distribution of DNA of chromosome 8 of , , and and its own DNA of chromosome 8 of , respectively.

Tab.1 Karyotypic comparison of , , and based on the analysis of 10 metaphases

Fig.3 FISH images of physical location of an RFLP marker (R2676, 1.8 kb) on chromosomes of and . Chromosomes are stained with PI. Bars, 10 μm. A and B show that the R2676 marker signals are detected in metaphase and interphase chromosomes of , respectively. C and G are the enlarged idiograms of the signal-tagged chromosomes for R2676 marker of and , respectively. D and H show that the signal locations are mapped on the chromosome 8 maps of and by green dots. E and F show that the metaphase and prophase chromosomes are probed with R2676 marker of , respectively.

Tab.2 Karyotype comparison of chromosome 8 of and based on 5 metaphase spreads possessing a similar degree of condensation

1	Bennetzen J L, Ma J, Devos K M (2005). Mechanisms of recent genome size variation in flowering plants. Ann Bot , 95(1): 127-132 doi: 10.1093/aob/mci008 pmid:15596462
2	Causse M A, Fulton T M, Cho Y G, Ahn S N, Chunwongse J, Wu K, Xiao J, Yu Z, Ronald P C, Harrington S E, Second G, McCouch S R, Tanksley S D (1994). Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics , 138(4): 1251-1274 pmid:7896104
3	Cheng Z K, Dong F G, Langdon T, Ouyang S, Buell C R, Gu M H, Blattner F R, Jiang J M (2002). Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell , 14(8): 1691-1704 doi: 10.1105/tpc.003079 pmid:12172016
4	Cheng Z K, Buell C R, Wing R A, Gu M H, Jiang J M (2001a). Toward a cytological characterization of the rice genome. Genome Res , 11(12): 2133-2141 doi: 10.1101/gr.194601 pmid:11731505
5	Cheng Z K, Presting G G, Buell C R, Wing R A, Jiang J M (2001b). High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice. Genetics , 157(4): 1749-1757 pmid:11290728
6	Cheng Z K, Stupar R M, Gu M H, Jiang J M (2001c). 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(1): 24-31 doi: 10.1007/s004120000126 pmid:11398973
7	Cheng Z K, Yan H H, Yu H X, Tang S C, Jiang J M, Gu M H, Zhu L H (2001d). Development and applications of a complete set of rice telotrisomics. Genetics , 157(1): 361-368 pmid:11139516
8	Doyle J J, (1990). Isolation of plant DNA from fresh tissue. Focus , 12: 13-15
9	Flavell R B (1986). Repetitive DNA and chromosome evolution in plants. Philos Trans R Soc Lond B Biol Sci , 312(1154): 227-242 doi: 10.1098/rstb.1986.0004 pmid:2870519
10	Flavell R B, Bennett M D, Smith J B, Smith D B (1974). Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem Genet , 12(4): 257-269 doi: 10.1007/BF00485947 pmid:4441361
11	Hall A E, Keith K C, Hall S E, Copenhaver G P, Preuss D (2004). The rapidly evolving field of plant centromeres. Curr Opin Plant Biol , 7(2): 108-114 doi: 10.1016/j.pbi.2004.01.008 pmid:15003208
12	Harrison G E, Heslop-Harrison J S (1995). Centromeric repetitive DNA sequences in the genus Brassica. Theor Appl Genet , 90(2): 157-165 doi: 10.1007/BF00222197
13	Harushima Y, Yano M, Shomura A, Sato M, Shimano T (1998). A high-density rice gentic linkage map with 2275 markers using a single F2 population. Genetics , 144: 1883-1891
14	Jackson S A, Cheng Z K, Wang M L, Goodman H M, Jiang J M (2000). Comparative fluorescence in situ hybridization mapping of a 431-kb Arabidopsis thaliana bacterial artificial chromosome contig reveals the role of chromosomal duplications in the expansion of the Brassica rapa genome. Genetics , 156(2): 833-838 pmid:11014828
15	Jiang J M, Nasuda S, Dong F G, Scherrer C W, Woo S S, Wing R A, Gill B S, Ward D C (1996). A conserved repetitive DNA element located in the centromeres of cereal chromosomes. Proc Natl Acad Sci U S A , 93(24): 14210-14213 doi: 10.1073/pnas.93.24.14210 pmid:8943086
16	Jiang N, Feschotte C, Zhang X Y, Wessler S R (2004). Using rice to understand the origin and amplification of miniature inverted repeat transposable elements (MITEs). Curr Opin Plant Biol , 7(2): 115-119 doi: 10.1016/j.pbi.2004.01.004 pmid:15003209
17	Jin W W, Lamb J C, Vega J M, Dawe R K, Birchler J A, Jiang J M (2005). Molecular and functional dissection of the maize B chromosome centromere. Plant Cell , 17(5): 1412-1423 doi: 10.1105/tpc.104.030643 pmid:15805482
18	Jin W W, Melo J R, Nagaki K, Talbert P B, Henikoff S, Dawe R K, Jiang J M (2004). Maize centromeres: organization and functional adaptation in the genetic background of oat. Plant Cell , 16(3): 571-581 doi: 10.1105/tpc.018937 pmid:14973167
19	Kumar A, Bennetzen J L (1999). Plant retrotransposons. Anne Rev Genet , 33(1): 479-532 doi: 10.1146/annurev.genet.33.1.479 pmid:10690416
20	Kurata N, Nagamura Y, Yamamoto K, Harushima Y, Sue N, Wu J, Antonio B A, Shomura A, Shimizu T, Lin S Y, Inoue T, Fukuda A, Shimano T, Kuboki Y, Toyama T, Miyamoto Y, Kirihara Y, Hayasaka K, Miyao A, Monna L, Zhong H S, Tamura Y, Wang Z X, Momma T, Umehara Y, Yano M, Sasaki T, Minobe Y (1994). A 300 kilobase interval genetic map of rice including 883 expressed sequences. Nat Genet , 8(4): 365-372 doi: 10.1038/ng1294-365 pmid:7894488
21	Lan W Z, He G C, Wang C Y, Wu S J, Qin R (2007). Comparative analysis of genomes in Oryza sativa, O. officinalis, and O. meyeriana with C₀t-1 DNA and genomic DNA of cultivated rice. Agric Sci China , 6(9): 1027-1034 doi: 10.1016/S1671-2927(07)60143-6
22	Lan W Z, Qin R, Li G, He G C (2006). Comparative analysis of A, B, C and D genomes in the genus Oryza with C₀t-1 DNA of C genome. Chinese Sci Bull , 51(14): 1710-1720 doi: 10.1007/s11434-006-2049-5
23	Li C B, Zhang D M, Ge S, Lu B R, Hong D Y (2001). Differentiation and inter-genomic relationships among C, E and D genomes in the Oryza officinalis complex (Poaceae) as revealed by multicolor genomic in situ hybridization. Theor Appl Genet , 103(2-3): 197-203 doi: 10.1007/s001220100562
24	Lu B R (1999). Taxonomy of the genus Oryza (Poaceae): historical perspective and current status. Int Rice Res Newslett , 243: 4-8
25	Matyásek R, Gazdová B, Fajkus J, Bezdek M (1997). NTRS, a new family of highly repetitive DNAs specific for the T1 chromosome of tobacco. Chromosoma , 106(6): 369-379 doi: 10.1007/s004120050258 pmid:9362545
26	Mishima M, Ohmido N, Fukui K, Yahara T (2002). Trends in site-number change of rDNA loci during polyploid evolution in Sanguisorba (Rosaceae). Chromosoma , 110(8): 550-558 doi: 10.1007/s00412-001-0175-z pmid:12068972
27	Ohmido N, Akiyama Y, Fukui K (1998). Physical mapping of unique nucleotide sequences on identified rice chromosomes. Plant Mol Biol , 38(6): 1043-1052 doi: 10.1023/A:1006062905742 pmid:9869410
28	Ohmido N, Kijima K, Akiyama Y, de Jong J H, Fukui K (2000). Quantification of total genomic DNA and selected repetitive sequences reveals concurrent changes in different DNA families in indica and japonica rice. Mol Gen Genet , 263(3): 388-394 doi: 10.1007/s004380051182 pmid:10821172
29	Qin R, Wei W H, Jin W W, He G C, Song Y C (2001). Physical location of rice Gm–6, Pi–5(t) genes in O. officinallis with BAC– FISH. Chinese Sci Bull , 46(8): 2427-2430 doi: 10.1007/BF03182829
30	Ren N, Song Y C, Bi X Z, Ding Y, Liu L H, (1997). The physical location of genes cdc2 and prh1 in maize (Zea mays L.). Hereditas , 126(3): 211-217 doi: 10.1111/j.1601-5223.1997.00211.x pmid:9350135
31	Riera-Lizarazu O, Vales M I, Ananiev E V, Rines H W, Phillips R L (2000). Production and characterization of maize chromosome 9 radiation hybrids derived from an oat-maize addition line. Genetics , 156(1): 327-339 pmid:10978296
32	Shishido R, Ohmido N, Fukui K (2001). Chromosome painting as a tool for rice genetics and breeding. Methods Cell Sci , 23(1-3): 125-133 doi: 10.1023/A:1013130707341 pmid:11741149
33	Song Y C, Gustafson J P (1995). The physical location of fourteen RFLP markers in rice (Oryza sativa L.). Theor Appl Genet , 90(1): 113-119 doi: 10.1007/BF00221003
34	Tan G X, Jin H J, Li G, He R F, Zhu L L, He G C (2005). Production and characterization of a complete set of individual chromosome additions from Oryza officinalis to Oryza sativa using RFLP and GISH analyses. Theor Appl Genet , 111(8): 1585-1595 doi: 10.1007/ s00122 –005– 0090– 4
35	Uozu S, Ikehashi H, Ohmido N, Ohtsubo H, Ohtsubo E, Fukui K (1997). Repetitive sequences: cause for variation in genome size and chromosome morphology in the genus Oryza. Plant Mol Biol , 35(6): 791-799 doi: 10.1023/A:1005823124989 pmid:9426599
36	Vaughan D A (1994). The Wild Relatives of Rice. A Genetic Resources Hand book . Manila: IRRI
37	Vaughan D A, Morishima H, Kadowaki K (2003). Diversity in the Oryza genus. Curr Opin Plant Biol , 6(2): 139-146 doi: 10.1016/S1369-5266(03)00009-8 pmid:12667870
38	Wang Z X, Kurata N, Saji S, Katayose Y, Minobe Y (1995). A chromosome 5-specific repetitive DNA sequence in rice (Oryza sativa L.). Theor Appl Genet , 90(7-8): 907-913 doi: 10.1007/BF00222902
39	Werner J E, Endo T R, Gill B S (1992). Toward a cytogenetically based physical map of the wheat genome. Proc Natl Acad Sci U S A , 89(23): 11307-11311 doi: 10.1073/pnas.89.23.11307 pmid:1360666
40	Yan H H, Jin W W, Nagaki K, Tian S L, Ouyang S, Buell C R, Talbert P B, Henikoff S, Jiang J M (2005). Transcription and histone modifications in the recombination-free region spanning a rice centromere. Plant Cell , 17(12): 3227-3238 doi: 10.1105/tpc.105.037945 pmid:16272428
41	Yan H H, Liu G Q, Cheng Z K, Li X B, Liu G Z, Min S K, Zhu L H (2002). A genome-specific repetitive DNA sequence from Oryza eichingeri: characterization, localization, and introgression to O. sativa.Theor Appl Genet , 104(2-3): 177-183 doi: 10.1007/s001220100766 pmid:12582684
42	Zhao Q, Zhang Y, Cheng Z K, Chen M S, Wang S Y, Feng Q, Huang Y C, Li Y, Tang Y S, Zhou B, Chen Z, Yu S, Zhu J, Hu X, Mu J, Ying K, Hao P, Zhang L, Lu Y, Zhang L S, Liu Y, Yu Z, Fan D, Weng Q, Chen L, Lu T, Liu X, Jia P, Sun T, Wu Y, Zhang Y, Lu Y, Li C, Wang R, Lei H, Li T, Hu H, Wu M, Zhang R, Guan J, Zhu J, Fu G, Gu M, Hong G, Xue Y, Wing R, Jiang J, Han B (2002). A fine physical map of the rice chromosome 4. Genome Res , 12(5): 817-823 doi: 10.1101/gr.48902 pmid:11997348
43	Zwick M S, Hanson R E, Islam-Faridi M N, Stelly D M, Wing R A, Price H J, McKnight T D (1997). A rapid procedure for the isolation of C₀t-1 DNA from plants. Genome , 40(1): 138-142 doi: 10.1139/g97-020 pmid:18464813
44	Zwick M S, Islam-Faridi M N, Zhang H B, Hodnett G L, Gomez M I, Kim J S, Price H J, Stelly D M (2000). Distribution and sequence analysis of the centromere-associated repetitive element CEN38 of sorghum bicolor (Poaceae). Am J Bot , 87(12): 1757-1764 doi: 10.2307/2656825 pmid:11118410

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