International Journal of Genetics and Molecular Biology
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Article Number - C6603782570


Vol.3(1), pp. 7-24 , January 2011

ISSN: 2006-9863



Full Length Research Paper

Application of subspecies-specific marker system identified from Oryza sativa to Oryza glaberrima accessions and Oryza sativa × Oryza glaberrima F1 interspecific progenies


Isaac Kofi Bimpong1,2, Joong Hyoun Chin2*, Joie Ramos2 and Hee-Jong Koh3




 

1Africa Rice Centre, BP 96. St Louis, Senegal.

2International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.

3Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea


Email: kofibimpong@yahoo.com






 Accepted: 07 December 2010  Published: 31 January 2011

Copyright © 2011 Author(s) retain the copyright of this article.
This article is published under the terms of the Creative Commons Attribution License 4.0


 

Interspecific hybrids (F1's) between Asian rice (Oryza sativa 2n=24 AA) and African rice (Oryza glaberrima 2n=24 AA) are almost completely sterile. This hybrid sterility barrier is mainly caused by an arrest of pollen development at the microspore stage. Intersubspecific F1 hybrid sterility is mainly caused by cryptic chromosomal aberrations and allelic interaction between indica and japonica. To identify O. glaberrima specific loci, 67 subspecies-specific (SS) sequenced-tagged site (STS) marker were used to evaluate 30 O. glaberrimaaccessions, which could be classified into sub eleven groups. SPI (subspecies-prototype index) of O. glaberrima accessions ranged from 51.67 to 60.00, suggesting intermediate subspecific type based on whole-genome. Some informative markers for classifying O.glaberrima accessions, called reference markers, S01054, S01160, S02085, S02140, S03041, and S08107, showed indica allele, which might have contributed to genomic diversification of O. glaberrima. Ten (14.9%) SS markers generated glaberrima-specific allele, implying loci adjacent with these markers could be a key for interspecific hybrid sterility. Only 40 (59.7%) SS markers might be useful in O. glaberrima analysis, as other markers did not amplify heterozygous allele in Fof O. sativa × O. glaberrima.

 

Key words: Oryza glaberrima, Oryza sativa, sequenced-tagged site, subspecies-specific,interspecific progenies

 

Barry MB, Pham JL, Noyer JL, Billot C, Courtois B, Ahmadi N (2007). Genetic diversity of the two cultivated rice species (O. sativa & O. glaberrima) in Maritime Guinea. Evidence for interspecific recombination. Euphytica 154: 127-137.
http://dx.doi.org/10.1007/s10681-006-9278-1
 
Bi XZ, Xiao YH, Liu WF (1997). Studies on subspecies differentiating protein markers in Oryza sativa by two-dimensional polyacrylamide gel electrophoresis. Rice Genet. Newslett., 14: 31-33.
 
Bimpong IK, Mendoza EMT, Hernandez JE, Mendioro MS, Brar DS (2009). Identification and Mapping of QTLs for Drought Tolerance Introgressed from Oryza glaberrima Steud. into Indica Rice (Oryza. sativa L). PhD thesis submitted to the University of the Philippines. Los Banos Philippines
 
Bimpong IK, Carpena AL, Borromeo TH, Mendioro MS, Brar DS (2004). Nematode resistance of backcross derivatives of Oryza sativa L crosses with Oryza glaberrima Steud. and molecular characterization of introgression. Thesis submitted to the University of the Philippines. Los Banos Philippines
 
Causse MA, Fulto TM, Cho YG, Ahn SN, Chuncongse J (1994). Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138: 1251-1274.
PMid:7896104 PMCid:PMC1206261
 
Chin JH, Kim JH, Jiang W, Chu SH, Woo MO, Han L, Brar D, Koh HJ (2007). Identification of Subspecies-specific STS Markers and Their Association with Segregation Distortion in Rice (Oryza sativa L.) J. Crop Sci. Biotechnol. 10(3): 175-184.
 
Chin JH, Kim JH, Kwon SW, Cho YI, Piao ZZ, Han LZ, Koh HJ (2003). Identification of subspecies-specific RAPD markers in rice. Korean J. Breed. 35(2): 102-108.
 
Cho YC, Shin YS, Ahn SN, Gregorio GB, Kang KH, Brar D, Moon HP (1999). DNA fingerprinting of rice cultivars using AFLP and RAPD markers. Korean J. Crop Sci. 44(1): 26-31.
 
Enriquez EC, Rosario TL, Brar DS, Mendioro MS, Hernandez JE, Barrion AA (2001). Production of doubled haploids from Oryza sativa L. x O. glaberrima Steud. and their characterization using microsatellite markers. PhD thesis submitted to the University of the Philippines. Los Banos Philippines
 
Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH (2004). An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res. 14: 1812-1819.
http://dx.doi.org/10.1101/gr.2479404
PMid:15342564 PMCid:PMC515328
 
Glaszmann JC (1987). Isozymes and classification of Asian rice varieties. Theor. Appl. Genet. 74: 21-30.
http://dx.doi.org/10.1007/BF00290078
PMid:24241451
 
Heuer SM, Meizan KM (2003). Assessing hybrid sterility in O. glaberrima x O. sativa hybrid progenies by PCR marker analysis and crossing with wide compatibility varieties. Theor. Appl. Genet. 107: 902-909.
http://dx.doi.org/10.1007/s00122-003-1325-x
PMid:12851767
 
Kitampura E (1962). Studies on cytoplasmic sterility of hybrids in distantly related varieties of rice O. sativa L. In Fertility of F1 hybrids between strains derived from certain Philippine and Japanese variety crosses and Japanese varieties. Jpn. J. Breed., 12: 81-84.
 
Koide Y, Onishi K, Kanazawa A, Sano Y (2008). Genetics of speciation in rice. In Rice Biology in the Genomics Era. Edited by Hirano, H.,Sano, Y., Hirai, A., Sasaki, T. Biotechnology in Agriculture and Forestry. Springer-Verlag; pp: 247-259.
 
Kubo T, Yoshimura A (2005). Epistasis underlying female sterility detected in hybrid breakdown in a japonica-indica cross of rice (Oryza sativa L.). Theor. Appl. Genet. 110: 346-355.
http://dx.doi.org/10.1007/s00122-004-1846-y
PMid:15549230
 
Li J, Xu P, Deng X, Zhou J, Hu F, Wan J, Tao D (2008). Identifcation of four genes for stable hybrid sterility and an epistatic QTL from a cross between Oryza sativa and Oryza glaberrima. Euphytica 164: 699-708
http://dx.doi.org/10.1007/s10681-008-9684-7
 
Lorieux M, Ndjionjop, N, Ghesquire A (2000). A first interspecific Oryza sativa × Oryza glaberrima microsatellite-based genetic linkage map. Theor. Appl. Genet. 100: 593-601.
http://dx.doi.org/10.1007/s001229900061
http://dx.doi.org/10.1007/s001220050078
 
McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002). Dvelopment and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 9: 199-207.
http://dx.doi.org/10.1093/dnares/9.6.199
http://dx.doi.org/10.1093/dnares/9.6.257
PMid:12597276
 
McNally K, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Ratsch G, Buell CR, Leung H, Leach JE (2009). Genomewide SNP reveals relationships among landraces and modern varieties of rice. PNAS. 106(30): 12273-12278.
http://dx.doi.org/10.1073/pnas.0900992106
PMid:19597147 PMCid:PMC2718348
 
Ohmido N, Fukui K (1995). Cytological studies of African cultivated rice. Oryza glaberrima. Theor. Appl. Genet. 91: 212-217.
http://dx.doi.org/10.1007/BF00220880
PMid:24169766
 
Park KC, Kim, NH, Cho YS, Kang, KH, Lee, JK, Kim NS (2003). Genetic variations of AA genome Oryza species measured by MITE–AFLP. Theor. Appl. Genet. 107: 203-209
http://dx.doi.org/10.1007/s00122-003-1252-x
PMid:12845436
 
Perry DJ, Isabela N, Bousquet J (1999). Sequence-tagged-site (STS) markers of arbitrary genes: the amount and nature of variation revealed in Norway spruce. Heredity 83: 239-248
http://dx.doi.org/10.1038/sj.hdy.6885740
PMid:10504420
 
Morishima H, Hinata K, Oka HI (1963). Comparison of modes of evolution of cultivated forms from two wild rice species, Oryza breviligulata and O. perennis. Evolution 17: 170-181.
http://dx.doi.org/10.2307/2406462
 
Ni J, Colowit PM, Mackill DJ (2002). Evaluation of genetic diversity in rice subspecies using microsatellite markers. Crop Sci. 42: 601-607.
http://dx.doi.org/10.2135/cropsci2002.0601
 
Neiman M, Linksvayer TA (2006). The conversion of variance and the evolutionary potential of restricted recombination. Heredity, 96: 111-121.
http://dx.doi.org/10.1038/sj.hdy.6800772
PMid:16333302
 
Porteres R (1956). Taxonomie agrobotanique des riz cultives O. sativa L. et O. glaberrima. S. J. Agric. Trop. Bot. Appl., 3: 341-384; 541-580; 627-700; 821-856.
 
Panaud O, Chen X, MCcouch SR (1996). Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol. Gen. Genet. 252: 597-607.
http://dx.doi.org/10.1007/s004380050267
http://dx.doi.org/10.1007/BF02172406
PMid:8914521
 
Pham J, Bougerol B (1993). Abnormal segregation in crosses between two cultivated rice species. Heredity, 70: 447-466.
http://dx.doi.org/10.1038/hdy.1993.68
 
Qian HR, Zhuang JY, Lin HX, Lu J, Zheng KL (1995). Identification of a set of RFLP probes for subspecies differentiation in Oryza sativa L. Theor. Appl. Genet. 90: 878-884.
http://dx.doi.org/10.1007/BF00222026
PMid:24172933
 
Ren F, Lu BR, Li S, Huang J, Yingguozhu (2003). A Comparative study of genetic relationships among the AA genome Oryza species using RAPD and SSR markers. Theor. Appl. Genet. 108: 113-120.
http://dx.doi.org/10.1007/s00122-003-1414-x
PMid:14504744
 
Robeniol JA, Constantino SV, Resurreccion AP, Villareal CP, Ghareyazie B, Lu BR, Katiyar SK, Menguito CA, Angeles ER, Fu H, Reddy YS, Park W, McCouch SR, Khush GS, Bennett J (1996). Sequence-tagged sites and low-cost DNA markers for rice. : [IRRI] International Rice Research Institute. 1996. Rice genetics III. Proc. 3rd International Rice Genetics Symposium, 16-20 Oct 1995. Manila (Philippines).

 


APA (2011). Application of subspecies-specific marker system identified from Oryza sativa to Oryza glaberrima accessions and Oryza sativa × Oryza glaberrima F1 interspecific progenies. International Journal of Genetics and Molecular Biology, 3(1), 7-24.
Chicago Isaac Kofi Bimpong, Joong Hyoun Chin, Joie Ramos and Hee-Jong Koh. "Application of subspecies-specific marker system identified from Oryza sativa to Oryza glaberrima accessions and Oryza sativa × Oryza glaberrima F1 interspecific progenies." International Journal of Genetics and Molecular Biology 3, no. 1 (2011): 7-24.
MLA Isaac Kofi Bimpong, et al. "Application of subspecies-specific marker system identified from Oryza sativa to Oryza glaberrima accessions and Oryza sativa × Oryza glaberrima F1 interspecific progenies." International Journal of Genetics and Molecular Biology 3.1 (2011): 7-24.
   
DOI
URL http://academicjournals.org/journal/IJGMB/article-abstract/C6603782570

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