Development and Application of SCAR Markers for Discriminating Cytoplasmic Male Sterile Lines from Their Cognate Maintainer Lines in Indica Rice

doi:10.1016/S1672-6308(13)60122-5

Abstract

Abstract:

The DNA fragments about 1 600 bp were amplified using random amplified polymorphism DNA (RAPD) primer OPA12 with the templates of mitochondrial DNA of Zhenshan 97A and Zhenshan 97B, and were sequenced. The nucleotide sequences and lengths of the fragments from Zhenshan 97A and Zhenshan 97B showed no difference. The precise length of the fragment was 1 588 bp. Sequence characterized amplification region (SCAR) primers were then developed to discriminate the cytoplasmic male sterile (CMS) lines and their maintainer lines. A specific 1 588 bp fragment could be amplified with SCAR primers, CHI19F2/CHI19R2 and CHI20F3/CHI23R3, in the mitochondrial DNA of Zhenshan 97A, but not Zhenshan 97B. Furthermore, the specific fragment could be also amplified from the total DNA from green leaf tissues of Zhenshan 97A with SCAR primers, but not Zhenshan 97B. With the corresponding primers, the specific fragment could also be amplified from the total DNA of green leaves of other two CMS lines with wild abortive type cytoplasm (CMS-WA), namely Zhenpin A and Tianfeng A, but not in their maintainer lines. Moreover, using total DNA as template, each of the four pairs of SCAR primers could also be used to amplify the 1 588 bp fragment in CMS-ID (Indonesia paddy type) line Ⅱ-32A, but not in II-32B, and the specific fragment was amplified from the DNA of both F1 and F2 seedlings of Shanyou 63. The results of detecting the genetic purity of a man-made mixture of the seeds of Zhenshan 97A using CHI20F3/CHI23R3 were completely consistent with the phenotypes. Taken together, these results indicated that the specific 1 588 bp-fragment amplified by CHI20F3/CHI23R3 was the unique amplification products of CMS mitochondrial DNA, and could be used to distinguish CMS-WA and CMS-ID lines from their corresponding maintainer lines at the seedling stage.

Key words: Oryza sativa, cytoplasmic male sterile line, maintainer line, genetic purity, sequence characterized amplification region marker

LU Chao1, LIU Jian1, JIANG Jian-hua1, Caleb Manamik BRERIA1, TAN He-lin1, Masahiko ICHII2, HONG De-lin1. Development and Application of SCAR Markers for Discriminating Cytoplasmic Male Sterile Lines from Their Cognate Maintainer Lines in Indica Rice[J]. RICE SCIENCE, DOI: 10.1016/S1672-6308(13)60122-5 .

References

Akagi H, Sakamoto M, Shinjyo C, Shimada H, Fujimura T. 1994. A unique sequence located downstream from the rice mitochondrial atp6 may cause male sterility. Curr Genet, 25: 52–58.
Akagi H, Nakamura A, Sawada R, Oka M, Fujimura T. 1995. Genetic diagnosis of cytoplasmic male sterile hybrid plants of rice. Theor Appl Genet, 90: 948–951.
Akagi H, Nakamura Y, Yokozeki-Misono Y, Inagaki A, Takahashi H, Mori K, Fujimura T. 2004. Positional cloning of the rice Rf-1 gene, a restorer of BT-type cytoplasmic male sterility that encodes a mitochondrial-targeting PPR protein. Theor Appl Genet, 108: 1449–1457.
Altschul S F, Madden T L, Schaffer A A, Zhang J H, Zhang Z, Miller W, Lipman D J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucl Acids Res, 25: 3389–3402.
Andersen J R, Lübberstedt T. 2003. Functional markers in plants. Trends Plant Sci, 8(11): 554–560.
Cheng S H, Cao L Y, Zhuang J Y, Wu W M, Yang S H, Zhan X D. 2009. A breeding strategy for hybrid rice in China. In: Accelerating Hybrid Rice Development. The 5th International Symposium on Hybrid Rice, 11-15 September 2008, Changsha, Hunan, China. Los Ba?os, Manila (Philippines): International Rice Research Institute: 25–34.
Das S, Sen S, Chakraborty A, Chakraborti P, Maiti M K, Basu A, Basu D, Sen S K. 2010. An unedited 1.1 kb mitochondrial orfB gene transcript in the wild abortive cytoplasmic male sterility (WA-CMS) system of Oryza sativa L. subsp. indica. BMC Plant Biol, 10: 39.
Deng H F, He Q, Shu F, Zhang W H, Yang F, Jing Y H, Dong L, Xie H. 2006. Status and technical strategy on development of japonica hybrid rice in China. Hybrid Rice, 21(1): 1–6. (in Chinese with English abstract)
Hong D L, Ichii M. 2002. RAPD markers from mitochondrial DNA can distinguish male sterile and fertile cytoplasms in rice (Oryza sativa L.). Acta Agron Sin, 28(3): 315–320.
Ichii M, Hong D L, Ohara Y, Zhao C M, Taketa S. 2003. Characterization of CMS and maintainer lines in indica rice (Oryza sativa L.) based on RAPD marker analysis. Euphytica, 129: 249–252.
Itabashi E, Kazama T, Toriyama K. 2009. Characterization of cytoplasmic male sterility of rice with Lead Rice cytoplasm in comparison with that with Chinsurah Boro II cytoplasm. Plant Cell Rep, 28: 233–239.
Iwabuchi M, Kyozuka J, Shimamoto K. 1993. Processing followed by complete editing of an altered mitochondrial atp6 RNA restores fertility of cytoplasmic male sterile rice. EMBO J, 12(4): 1437–1446.
Jena K K, Pandey S K. 1999. DNA markers for purification of A and B lines for hybrid rice improvement. Hybrid Rice Newsl, 2: 13–14.
Kadowaki K, Ishige T, Suzuki S, Harada K, Shinjyo C. 1986. Differences in the characteristics of mitochondrial DNA between normal and male sterile cytoplasms of japonica rice. Jpn J Breed, 36: 333–339.
Kadowaki K, Osumi T, Nemoto H, Harada K, Shinjyo C. 1988. Mitochondrial DNA polymorphism in male-sterile cytoplasm of rice. Theor Appl Genet, 75: 234–236.
Kadowaki K, Harada K. 1989. Differential organization of mitochondrial gene in rice with normal and male-sterile cytoplasms. Jpn J Breed, 39: 179–186.
Kadowaki K, Suzuki T, Kazama S. 1990. A chimeric gene containing the 5′ portion of atp6 is associated with cytoplasmic male-sterility of rice. Mol Gen Genet, 224: 10–16.
Kazama T, Toriyama K. 2003. A pentatricopeptide repeat-containing gene that promotes the processing of aberrant atp6 RNA of cytoplasmic male-sterile rice. FEBS Lett, 544: 99–102.
Kazama T, Nakamura T, Watanabe M, Sugita M, Toriyama K. 2008. Suppression mechanism of mitochondrial ORF79 accumulation by Rf1 protein in BT-type cytoplasmic male sterile rice. Plant J, 55: 619–628.
Komori T, Ohta S, Murai N, Takakura Y, Kuraya Y, Suzuki S, Hiei Y, Imaseki H, Nitta N. 2004. Map-based cloning of a fertility restorer gene, Rf-1, in rice (Oryza sativa L.). Plant J, 37: 315–325.
Li J M, Yuan L P. 2000. Hybrid rice, genetics, breeding, and seed production. In: Plant Breeding Reviews. New York: John Wiley & Sons: 15–158.
Li Z B, Zhu Y G. 1988. Rice male sterile cytoplasm and fertility restoration. In: Hybrid Rice. Proceedings of the International Symposium on Hybrid Rice. 6-10 October 1986, Changsha, Hunan, China. Los Ba?os, Manila (Philippines): International Rice Research Institute: 85–102.
Lin S C, Yuan L P. 1980. Hybrid rice breeding in China. In: Innovative Approaches to Rice Breeding. Los Ba?os, Manila (Philippines): International Rice Research Institute: 35–51.
Liu Y G, Whittier R F. 1995. Thermal asymmetric interlaced PCR: Automatable amplification and sequencing of insert end fragments from PI and YAC clones for chromosome walking. Genomics, 25: 674–681.
Lu Z M, Zhao A L, Ma C Y. 1982. Studies on the degeneration of hybrid rice. Sci Agric Sin, 3: 8–15. (in Chinese with English abstract)
Lu Z M. 1983. The use of ‘three-line-seven-nursery-method’ system in the production of elites of hybrid rice. J Nanjing Agric Univ, (1): 22–26. (in Chinese with English abstract)
Lu Z M, Hong D L. 1989. Comment on self-seeding of male sterile line in Oryza sativa L. J Nanjing Agric Univ, 12(2): 6–11. (in Chinese with English abstract)
Lu Z M, Hong D L. 1999. Advances in hybrid rice seed production techniques. In: Heterosis and Hybrid Seed Production in Agronomic Crops. New York: Food Products Press, an imprint of The Haworth Press: 65–79.
Mao C X, Shi Y M, Wei S F, Song Z P, Zhou H, Wang W H, Xie L P, Liu B L. 2009. How to increase use efficiency of rice hybrids and their parental lines. In: Accelerating Hybrid Rice Development. The 5th International Symposium on Hybrid Rice, 11-15 September 2008, Changsha, Hunan, China. Los Ba?os, Manila (Philippines): International Rice Research Institute: 159–168.
Murray M G, Thompson W F. 1980. Rapid isolation of high molecular weight plant DNA. Nucl Acids Res, 8: 4321–4325.
Narayanan K K, Senthilkumar P, Venmadhi S, Thomas G, Thomas J. 1996. Molecular genetics studies on the rice mitochondrial genome. In: Rice genetics III. Proceedings of the Third International Rice Genetics Symposium. Los Ba?os, Manila (Philippines): International Rice Research Institute: 689–695.
National Standard Bureau of PRC. 1983. Crop seed test regulations GB3543-83. In: Shen Z T. 1995. Experiments of Crop Breeding. Beijing: China Agricultural Press: 154–157. (in Chinese)
Nawa S, Sano Y, Fuji T. 1985. Analysis of mitochondrial DNA in cytoplasmic male sterile rice. Rice Genet Newsl, 2: 98–99.
Ngangkham U, Parida S K, De S, Rajkumar K A, Singh A K, Singh N K, Mohapatra T. 2010. Genetic markers for wild abortive (WA) cytoplasm based male sterility and its fertility restoration in rice. Mol Breeding, 26: 275–292.
Nguyen N V. 2009. Ensuring food security in the 21st century with hybrid rice: Issues and challenges. In: Accelerating Hybrid rice development. The 5th International Symposium on Hybrid Rice, 11-15 September 2008, Changsha, Hunan, China. Los Ba?os, Manila (Philippines): International Rice Research Institute: 9–24.
Ohta H, Ogino A, Kasai M, Sano Y, Kanazawa A. 2010. Fertility restoration by Ifr1 in rice with BT-type cytoplasmic male sterility is associated with a reduced level, but not processing, of atp6-orf79 co-transcribed RNA. Plant Cell Rep, 29: 359–369.
Peng X J, Wang K, Hu C F, Zhu Y L, Wang T, Yang J, Tong J P, Li S Q, Zhu Y G. 2010. The mitochondrial gene orfH79 plays a critical role in impairing both male gametophyte development and root growth in CMS-Honglian rice. BMC Plant Biol, 10: 125.
Rajendrakumar P, Biswal A K, Balachandran S M, Ramesha M S, Viraktamath B C, Sundaram R M. 2007. A mitochondrial repeat specific marker for distinguishing wild abortive types cytoplasmic male sterile rice lines from their cognate isogenic maintainer lines. Crop Sci, 47: 207–211.
Rajendran N, Ramkumar G, Singh S, Palchamy K. 2007. Development of a DNA marker for distinguishing CMS lines from fertile lines in rice (Oryza sativa L.). Euphytica, 156: 129–139.
Rao Y S. 1988. Cytohistology of cytoplasmic male sterile lines in hybrid rice. In: Hybrid Rice. Proceedings of the International Symposium on Hybrid Rice. 6-10 October 1986, Changsha, Hunan, China. Los Ba?os, Manila (Philippines): International Rice Research Institute: 115–128.
Sane A P, Seth P, Ranade S A, Nath P, Sane P V. 1997. RAPD analysis of isolated mitochondrial DNA reveals heterogeneity in elite wild abortive (WA) cytoplasm in rice. Theor Appl Genet, 95: 1098–1103.
Shinjyo C. 1969. Cytoplasmic genetic male sterility in cultivated rice, Oryza sativa L. II: The inheritance of male sterility. Jpn J Genet, 44: 149–156.
Verma M M. 1996. Procedures for grow-out test (GOT). Seed Technol Newsl, 26: 1–4.
Virmani S S. 2003. Advances in hybrid rice research and development in the tropics. In: Hybrid Rice for Food Security, Poverty Alleviation, and Environmental Protection. Proceedings of the 4th International Symposium on Hybrid Rice. 14-17 May 2002, Hanoi, Vietnam. Los Ba?os (Philippines), International Rice Research Institute: 7–20.
Wang Z H, Zou Y J, Li X Y, Zhang Q Y, Chen L T, Wu H, Su D H, Chen Y L, Guo J X, Luo D, Long Y M, Zhong Y, Liu Y G. 2006. Cytoplasmic male sterility of rice with Boro II cytoplasm is caused by a cytotoxic peptide and is restored by two related PPR motif genes via distinct modes of mRNA silencing. Plant Cell, 18: 676–687.
Yamaguchi H, Kakiuchi H. 1983. Electrophoretic analysis of mitochondrial DNA from normal and male sterile cytoplasms in rice. Jpn J Genet, 58: 607–611.
Yashitola J, Thirumurugan T, Sundaram R M, Naseerullah M K, Ramesha M S, Sarma N P, Sonti R V. 2002. Assessment of purity of rice hybrids using microsatellite and STS markers. Crop Sci, 42: 1369–1373.
Yashitola J, Sundaram R M, Biradar S K, Thirumurugan T, Vishnupriya M R, Rajeshwari R, Viraktamath B C, Sarma N P, Sonti R V. 2004. A sequence specific PCR marker for distinguishing rice lines on the basis of wild abortive cytoplasm from their cognate maintainer lines. Crop Sci, 44: 920–924.
Yi P, Wang L, Sun Q P, Zhu Y G. 2002. Discovery of mitochondrial chimeric gene associated with male sterility of HL-rice. Chin Sci Bull, 47: 744–747.
Yuan L P. 1977. The execution and theory of developing hybrid rice. Sci Agric Sin, 1: 27–31. (in Chinese)

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