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Genetic variability in trait-specific rice germplasm groups based on coefficient of parentage, SSR markers and fertility restoration

Published online by Cambridge University Press:  12 May 2014

Pawan Khera
Affiliation:
Barwale Foundation, Barwale Chambers, # 3-6-666, Street No. 10, Himayathnagar, Hyderabad500 029, Andhra Pradesh, India International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324, India
Akhilesh Kumar Singh*
Affiliation:
Barwale Foundation, Barwale Chambers, # 3-6-666, Street No. 10, Himayathnagar, Hyderabad500 029, Andhra Pradesh, India
Rahul Priyadarshi
Affiliation:
Barwale Foundation, Barwale Chambers, # 3-6-666, Street No. 10, Himayathnagar, Hyderabad500 029, Andhra Pradesh, India
Durga Khandekar
Affiliation:
Barwale Foundation, Barwale Chambers, # 3-6-666, Street No. 10, Himayathnagar, Hyderabad500 029, Andhra Pradesh, India
Rajani K Allu
Affiliation:
Barwale Foundation, Barwale Chambers, # 3-6-666, Street No. 10, Himayathnagar, Hyderabad500 029, Andhra Pradesh, India
Chitkale Hiremath
Affiliation:
Barwale Foundation, Barwale Chambers, # 3-6-666, Street No. 10, Himayathnagar, Hyderabad500 029, Andhra Pradesh, India
Raj Kumar
Affiliation:
Barwale Foundation, Barwale Chambers, # 3-6-666, Street No. 10, Himayathnagar, Hyderabad500 029, Andhra Pradesh, India
Rashmi Mohan
Affiliation:
Barwale Foundation, Barwale Chambers, # 3-6-666, Street No. 10, Himayathnagar, Hyderabad500 029, Andhra Pradesh, India
K. Ulaganathan
Affiliation:
Centre for Plant Molecular Biology, Osmania University, Hyderabad500 007, Andhra Pradesh, India
Vinay Shenoy
Affiliation:
Barwale Foundation, Barwale Chambers, # 3-6-666, Street No. 10, Himayathnagar, Hyderabad500 029, Andhra Pradesh, India
*
*Corresponding author. E-mail: akhileshsingh@barwalefoundation.org

Abstract

To maximize heterosis, it is important to understand the genetic diversity of germplasm and associate useful phenotypic traits such as fertility restoration for hybrid rice breeding. The objectives of the present study were to characterize genetic diversity within a set of rice germplasm groups using coefficient of parentage (COP) values and 58 simple sequence repeat (SSR) markers for 124 genotypes having different attributes such as resistance/tolerance to various biotic and abiotic stresses. These lines were also used for identifying prospective restorers and maintainers for wild abortive-cytoplasmic male sterile (CMS) line. The mean COP value for all the lines was 0.11, indicating that the genotypes do not share common ancestry. The SSR analysis generated a total of 268 alleles with an average of 4.62 alleles per locus. The mean polymorphism information content value was 0.53, indicating that the markers selected were highly polymorphic. Grouping based on COP analysis revealed three major clusters pertaining to the indica, tropical japonica and japonica lines. A similar grouping pattern with some variation was also observed for the SSR markers. Fertility restoration phenotype based on the test cross of the 124 genotypes with a CMS line helped identify 23 maintainers, 58 restorers and 43 genotypes as either partial maintainers or partial restorers. This study demonstrates that COP analysis along with molecular marker analysis might encourage better organization of germplasm diversity and its use in hybrid rice breeding. Potential restorers identified in the study can be used for breeding high-yielding stress-tolerant medium-duration rice hybrids, while maintainers would prove useful for developing new rice CMS lines.

Type
Research Article
Copyright
Copyright © NIAB 2014 

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References

Ahmadikhah, A, Karlov, GI, Nematzadeh, GH and GhasemiBezdi, K (2007) Inheritance of the fertility restoration and genotyping of rice lines at the restoring fertility (Rf) loci using molecular markers. International Journal of Plant Production 1: 1321.Google Scholar
Almanza-Pinzón, MI, Khairallah, M, Fox, PN and Warburton, ML (2003) Comparison of molecular markers and coefficients of parentage for the analysis of genetic diversity among spring bread wheat accessions. Euphytica 130: 7786.Google Scholar
Bazrkar, L, Ali, AJ, Babaeian, NA, Ebadi, AA, Allahgholipour, M, Kazemitabar, K and Nematzadeh, G (2008) Tagging of four fertility restorer loci for wild abortive cytoplasmic male sterility system in rice (Oryza sativa L.) using microsatellite markers. Euphytica 164: 669677.Google Scholar
Bernier, J, Kumar, A, Ramaiah, V, Spaner, D and Atlin, G (2007) A large-effect QTL for grain yield under reproductive-stage drought stress in upland rice. Crop Science 47: 505516.Google Scholar
Brar, DS, Zhu, YG, Ahmed, MI, Jachuk, PJ and Virmani, SS (1998) Diversifying the CMS system to improve the sustainability of hybrid rice technology. In: Virmani, SS, Siddiq, EA and Muralidharan, K (eds) Advances in Hybrid Rice Technology. Proceedings of the 3rd International Symposium on Hybrid Rice, 14–16 November 1996, Hyderabad, India . Los Baños, Philippines: International Rice Research Institute, pp. 129145.Google Scholar
Cheema, KK, Grewal, NK, Vikal, Y, Das, A, Sharma, R, Lore, JS, Bhatia, D, Mahajan, R, Gupta, V and Singh, K (2008) A novel bacterial blight resistance gene from Oryza nivara, mapped to 38 kb region on chromosome 4L and transferred to Oryza sativa L. Genetics Research 90: 397407.Google Scholar
Cox, TS, Lookhart, GL, Walker, DE, Harrell, LG, Albers, LD and Rodgers, DM (1985) Genetic relationships among hard red winter wheat cultivars as evaluated by pedigree analysis and gliadin polyacrylamide gel electrophoretic patterns. Crop Science 25: 10581063.Google Scholar
Dellaporta, SL, Wood, J and Hicks, JB (1983) A plant DNA minipreparation: version II. Plant Molecular Biology Reporter 1: 1921.Google Scholar
Duan, SH, Mao, JN and Zhu, YG (2002) Genetic variation of main restorer lines of hybrid rice in China was revealed by microsatellite markers. Acta Genetica Sinica 29: 250254.Google Scholar
Fujii, S and Toriyama, K (2005) Molecular mapping of the fertility restorer gene for ms-CW-type cytoplasmic male sterility of rice. Theoretical and Applied Genetics 111: 696701.Google Scholar
Glaszmann, JC, Kilian, B, Upadhyaya, HD and Varshney, RK (2010) Accessing genetic diversity for crop improvement. Current Opinion in Plant Biology 13: 17.Google Scholar
Gu, K, Tian, D, Yang, F, Wu, L, Sreekala, C, Wang, D, Wang, GL and Yin, Z (2004) High-resolution genetic mapping of Xa27(t), a new bacterial blight resistance gene in rice, Oryza sativa L. Theoretical and Applied Genetics 108: 800807.Google Scholar
Hossain, S, Singh, AK and Zaman, FU (2010) Genetics of fertility restoration of ‘WA’-based cytoplasmic male sterility system in rice (Oryza sativa) using indica/japonica derivative restorers. ScienceAsia 36: 9499.Google Scholar
Jena, KK, Jeung, JU, Lee, JH, Choi, HC and Brar, DS (2006) High-resolution mapping of a new brown planthopper (BPH) resistance gene, Bph18(t), and marker-assisted selection for BPH resistance in rice (Oryza sativa L.). Theoretical and Applied Genetics 112: 288297.Google Scholar
Khush, GS and Jena, KK (2009) Current status and future prospects for research on blast resistance in rice (Oryza sativa L.). In: Wang, GL and Valent, B (eds) Advances in Genetics, Genomics and Control of Rice Blast Disease. Netherlands: Springer, pp. 110.Google Scholar
Kobayashi, N, Yanoria, MJT, Tsunematsu, H, Kato, H, Imbe, T and Fukuta, Y (2007) Development of new sets of international standard differential varieties for blast resistance in rice (Oryza sativa L.). Japan Agricultural Research Quarterly 41: 3137.Google Scholar
Kumari, SL, Valarmathi, G, Joseph, T, Kankamany, MT and Nayar, NK (1997) Rice varieties of Kerala as restorers and maintainers for wild abortive cytoplasmic male sterile lines. International Rice Research Newsletter 22: 1112.Google Scholar
Lapitan, VC, Brar, DS, Abe, T and Redoña, ED (2007) Assessment of genetic diversity of Philippine rice cultivars carrying good quality traits using SSR markers. Breeding Science 57: 263270.CrossRefGoogle Scholar
Liu, K and Muse, SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 21282129.Google Scholar
Mackill, DJ and Bonman, JM (1992) Inheritance of blast resistance in near-isogenic lines of rice. Phytopathology 82: 746749.CrossRefGoogle Scholar
Ma, G and Yuan, L (2003) Hybrid rice achievement and development in China. In: Virmani, SS, Mao, CX and Hardy, B (eds) Hybrid Rice for Food Security, Poverty Alleviation, and Environmental Protection. Proceedings of 4th International Symposium on Hybrid Rice, 14–17 May, 2002, Hanoi, Vietnam . Los Baños, Philippines: International Rice Research Institute, pp. 247256.Google Scholar
Malarvizhi, D, Thiyagarajan, K, Manonmani, S and Sankar, PD (2003) Fertility restoration behavior of promising CMS lines in rice (Oryza sativa L.). Indian Journal of Agricultural Research 37: 259263.Google Scholar
McLaren, CG, Bruskiewich, RM, Portugal, AM and Cosico, AB (2005) The International Rice Information System. A platform for meta-analysis of rice crop data. Plant Physiology 139: 637642.Google Scholar
Messmer, MM, Melchinger, AE, Herrmann, RG and Boppenmaier, J (1993) Relationship among early European maize inbreds: II. Comparison of pedigree and RFLP data. Crop Science 33: 944950.Google Scholar
Mishra, GP, Singh, RK, Mohapatra, T, Singh, AK, Prabhu, KV, Zaman, FU and Sharma, RK (2003) Molecular mapping of a gene for fertility restoration of wild abortive (WA) cytoplasmic male sterility using a basmati rice restorer line. Journal of Plant Biochemistry and Biotechnology 12: 3742.Google Scholar
Murphy, JP, Cox, TS and Rodgers, DM (1986) Cluster analysis of red winter wheat cultivars based upon coefficient of parentage. Crop Science 2: 672676.Google Scholar
Natarajkumar, P, Sujatha, K, Laha, GS, Viraktamath, BC, Reddy, CS, Mishra, B, Balachandran, SM, Ram, T, Srinivasarao, K, Hari, Y and Sundaram, RM (2010) Identification of a dominant bacterial blight resistance gene from Oryza nivara and its molecular mapping. Rice Genetics Newsletter 25: 5456.Google Scholar
Nematzadeh, GA and Kiani, G (2010) Genetic analysis of fertility restoration genes for WA type cytoplasmic male sterility in Iranian restorer rice line DN-33-18. African Journal of Biotechnology 9: 62736277.Google Scholar
Perrier, X and Jacquemond-Collet, JP (2006) DARwin software. Available at: http://darwin.cirad.fr/darwin/.Google Scholar
Ram, T, Laha, GS, Gautam, SK, Deen, R, Madhav, MS, Brar, DS and Viraktamath, BC (2010 a) Identification of new gene introgressed from Oryza brachyantha with broad-spectrum resistance to bacterial blight of rice in India. Rice Genetics Newsletter 25: 57.Google Scholar
Ram, T, Deen, R, Gautam, SK, Ramesh, K, Rao, YK and Brar, DS (2010 b) Identification of new genes for Brown Planthopper resistance in rice introgressed from O. glaberrima and O. minuta . Rice Genetics Newsletter 25: 6769.Google Scholar
Saitou, N and Nei, M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406425.Google Scholar
Salgotra, RK, Katoch, PC and Kaushik, RP (2002) Identification of restorers and maintainers for cytoplasmic genic male sterile lines of rice. Oryza 39: 5557.Google Scholar
Sattari, M, Kathiresa, A, Gregorio, GB and Virmani, SS (2008) Comparative genetic analysis and molecular mapping of fertility restoration genes for WA, Dissi, and Gambiaca cytoplasmic male sterility systems in rice. Euphytica 160: 305315.CrossRefGoogle Scholar
Schut, JW, Qi, X and Stam, P (1997) Association between relationship measures based on AFLP markers, pedigree data and morphological traits in barley. Theoretical and Applied Genetics 95: 11611168.Google Scholar
Sheeba, NK, Viraktamath, BC, Sivaramakrishnan, S, Gangashetti, MG, Khera, P and Sundaram, RM (2009) Validation of molecular markers linked to fertility restorer gene(s) for WA-CMS lines of rice. Euphytica 167: 217227.CrossRefGoogle Scholar
Siddiq, EA (1996) Current status and future outlook for hybrid rice technology in India. In: Ahmed, MI, Viraktamath, BC, Ramesha, MS and Vijaya Kumar, CHM (eds) Hybrid Rice Technology. Hyderabad, India: Directorate of Rice Research, ICAR, pp. 127.Google Scholar
Singh, DK and Singh, R (2000) Identification of parental lines for rice hybrid at Varanasi location. Oryza 20: 201205.Google Scholar
Singh, RK, Gregorio, GB and Ismail, AM (2008) Breeding rice varieties with tolerance to salt stress. Journal of the Indian Society of Coastal Agricultural Research 26: 1621.Google Scholar
Smartt, J (1981) Evolving gene pool in crop plants. Euphytica 30: 415418.Google Scholar
Song, WY, Wang, GL, Chen, LL, Kim, HS, Pi, LY, Holsten, T, Gardner, J, Wang, B, Zhao, WX, Zhu, LH, Fauquet, C and Ronald, P (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21 . Science 270: 18041806.CrossRefGoogle ScholarPubMed
Souza, E and Sorrells, ME (1988) Coefficients of Parentage for North American Oat Cultivars Released from 1951 to 1986. Ithaca, NY: Cornell University Agricultural Experiment Station.Google Scholar
Souza, E and Sorrells, ME (1989) Pedigree analysis of North American oat cultivars released from 1951 to 1985. Crop Science 29: 595601.Google Scholar
St. Martin, SK (1982) Effective population size for the soybean improvement program in maturity groups 00 to IV. Crop Science 22: 151152.Google Scholar
Tan, GX, Ren, X, Weng, QM, Shi, ZY, Zhu, LL and He, GC (2004) Mapping of a new resistance gene to bacterial blight in rice line introgressed from Oryza officinalis . Acta Genetica Sinica 31: 724729.Google Scholar
Van-Beuningen, LT and Busch, RH (1997) Genetic diversity among North American spring wheat cultivars: I. Analysis of the coefficients of parentage matrix. Crop Science 37: 570579.Google Scholar
Varaprasad, GS and Rani, SN (2010) Assessment of genetic diversity among basmati and non-basmati aromatic rices of India using SSR markers. Current Science 99: 221226.Google Scholar
Virmani, SS (2003) Advances in hybrid rice research and development in the tropics. In: Virmani, SS, Mao, CX and Hardy, B (eds) 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 Baños, Philippines: International Rice Research Institute, pp. 720.Google Scholar
Wang, C, Wen, G, Lin, X and Zhang, D (2009) Identification and fine mapping of a new bacterial blight resistance gene, Xa31(t) in rice. European Journal of Plant Pathology 123: 235240.Google Scholar
Wang, S and Lu, Z (2006) Genetic diversity among parental lines of indica hybrid rice (Oryza sativa L.) in China based on coefficient of parentage. Plant Breeding 125: 606612.Google Scholar
Wang, W, Vinocur, B and Altman, A (2007) Plant responses to drought, salinity and extreme temperatures towards genetic engineering for stress tolerance. Planta 218: 114.Google Scholar
Witcombe, JR, Hollington, PA, Howarth, CJ, Reader, S and Steele, KA (2008) Breeding for abiotic stresses for sustainable agriculture. Philosophical Transactions of the Royal Society B: Biological Sciences 363: 703716.Google Scholar
Xie, F (2009) Priorities of IRRI hybrid rice breeding. In: Xie, F and Hardy, B (eds) Accelerating Hybrid Rice Development. Los Baños, Philippines: International Rice Research Institute, pp. 4961.Google Scholar
Zeng, L, Kwon, T, Liu, X, Wilson, C, Grieve, CM and Gregorio, GB (2004) Genetic diversity analyzed microsatellite markers among rice (Oryza sativa L.) genotypes with different adaptations to saline soils. Plant Science 166: 12751285.Google Scholar
Zhang, Q (2007) Strategies for developing Green Super Rice. Proceedings of the National Academy of Science United States of America 104: 1640216409.Google Scholar
Zhang, Q, Lin, SC, Zhao, BY, Wang, CL, Yang, WC, Zhou, YI, Li, DY, Chen, CB and Zhu, LH (1998) Identification and tagging a new gene for resistance to bacterial blight (Xanthomonas oryzae pv. oryzae) from O. rufipogon . Rice Genetics Newsletter 15: 138.Google Scholar
Zhou, XL, Carter, TE Jr, Cui, Z, Miyazaki, S and Burton, JW (2002) Genetic diversity in Japanese soybean cultivars based on coefficient of parentage. Crop Science 42: 13311342.Google Scholar
Zhuang, JY, Qian, HR, Lu, J, Lin, HX and Zheng, KL (1997) RFLP variation among commercial rice germplasms in China. Journal of Genetics and Breeding 51: 263268.Google Scholar
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