Genetic Characterization of Indigenous Rice Varieties in Eastern Himalayan Region of Northeast India

doi:10.1016/S1672-6308(13)60173-0

Abstract

Abstract:

The eastern Himalayan region of Northeast (NE) India is home to a large number of indigenous rice varieties, which are traditionally classified as Oryza sativa subspecies indica, japonica or intermediate types. The classification based on traditional Cheng’s index is often inconclusive due to phenotypic plasticity of morphological characters, which are influenced by environmental conditions. We used molecular markers specific for indica and japonica subspecies to assess the degree of genetic relatedness of indigenous rice varieties in NE India. The results revealed that majority of upland (jum) and glutinous rice varieties, traditionally considered as japonica, were genetically close to the subspecies indica. All varieties of boro ecotype were found to be indica type, and only a few varieties cultivated in lowland and upland areas were japonica type. Some of the lowland varieties of the sali ecotype were intermediate between indica and japonica, and they showed a closer genetic affinity to O. rufipogon.

Key words: classification, genetic characterization, insertion and deletion marker, indica, japonica, O. sativa

Baharul Islam CHOUDHURY, Mohammed Latif KHAN, Selvadurai DAYANANDAN. Genetic Characterization of Indigenous Rice Varieties in Eastern Himalayan Region of Northeast India[J]. RICE SCIENCE, DOI: 10.1016/S1672-6308(13)60173-0 .

References

Cai X X, Liu J, Qiu Y Q, Zhao W, Song Z P, Lu B R. 2007. Differentiation of indica-japonica rice revealed by insertion/ deletion (InDel) fragments obtained from the comparative genomic study of DNA sequences between 93-11 (indica) and Nipponbare (japonica). Front Biol China, 2(3): 291–296.
Cheng K S, Lu Y X, Lou J, Huang N W, Lin G R, Wang X K. 1984. Studies on the indigenous rices in Yunnan and their utilization: II. A revised classification of Asian cultivated rice. Acta Agron Sin, 10(4): 271–280. (in Chinese with English abstract)
Cheng K S. 1993. Identification in Indica and Japonica Subspecies of Asian Cultivated Rice. Kunming: Yunnan Science and Technology Press. (in Chinese)
Doyle J J, Doyle J L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull, 19: 11–15.
Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol Ecol, 14(8): 2611–2620.
Felsenstein J. 2005. PHYLIP (Phylogeny Inference Package), version 3.6a3. Department of Genome Science. Seattle, WA: University of Washington.
Feltus F A, Wan J, Schulze S R, Estill J C, Jiang N, Paterson A H. 2004. An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res, 14: 1812–1819.
Garris A J, Tai T H, Coburn J, Kresovich S, McCouch S R. 2005. Genetic structure and diversity in Oryza sativa L. Genetics, 169(3): 1631–1638.
Glaszmann J C. 1987. Isozymes and classification of Asian rice varieties. Theor Appl Genet, 74: 21–30.
Huang X H, Kurata N, Wei X H, Wang Z X, Wang A H, Zhao Q, Zhao Y, Liu K Y, Lu H Y, Li W J, Guo Y L, Lu Y Q, Zhou C C, Fan D L, Weng Q J, Zhu C R, Huang T, Zhang L, Wang Y C, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan X P, Xu Q, Dong G J, Zhan Q L, Li C Y, Fujiyama A, Toyoda A, Lu T T, Feng Q, Qian Q, Li J Y, Han B. 2012. A map of rice genome variation reveals the origin of cultivated rice. Nature, 490: 497–501.
Khush G S. 1997. Origin, dispersal, cultivation and variation of rice. Plant Mol Biol, 35(1/2): 25–34.
Liu P, Cai X X, Lu B R. 2012. Single-seeded InDel fingerprints in rice: An effective tool for indica-japonica rice classification and evolutionary studies. J Syst Evol, 50(1): 1–11.
Long W H, Xu M H. 2002. RAPD-based genetic difference between indica rice and japonica rice. J Yunnan Agric Univ, 17(3): 245–247. (in Chinese with English abstract)
Lu B R, Cai X X, Xin J. 2009. Efficient indica and japonica rice identification based on the InDel molecular method: Its implication in rice breeding and evolutionary research. Prog Nat Sci, 19(10): 1241–1252.
Ma J X, Bennetzen J L. 2004. Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA, 101(34): 12404–12410.
Matsuo T, Futsuhara Y, Kikuchi F, Yamaguchi H. 1997. Science of the Rice Plant. Tokyo: Food and Agriculture Policy Research Center.
Nasu S, Suzuki J, Ohta R, Hasegawa K, Yui R, Kitazawa N, Monna L, Minobe Y. 2002. Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. DNA Res, 9(5): 163–171.
Oka H I. 1988. Indica-japonica differentiation of rice cultivars. In: Origin of Cultivated Rice. Tokyo: Japan Science Society Press: 141–179.
Peakall R, Smouse P E. 2006. Genealex 6: Genetic analysis in excel. Population genetic software for teaching and research. Mol Ecol Notes, 6(1): 288–295.
Pritchard J K, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155: 945–959.
Qi Y W, Zhang H L, Zhang D L, Wang M X, Sun J L, Ding L, Wang F H, Li Z C. 2009. Assessing indica-japonica differentiation of improved rice varieties using microsatellite markers. J Genet Genom, 36(5): 305–312.
Sano R, Morishima H. 1992. Indica-japonica differentiation of rice cultivars viewed from variations in key characters and isozymes, with special reference to landraces from the Himalayan hilly areas. Theor Appl Genet, 84(3/4): 266–274.
Shen Y J, Jiang H, Jin J P, Zhang Z B, Xi B, He Y Y, Wang G, Wang C, Qian L, Li X, Yu Q B, Liu H J, Chen D H, Gao J H, Huang H, Shi T L, Yang Z N. 2004. Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol, 135(3): 1198–1205.
Tang J B, Xia H A, Cao M L, Zhang X Q, Zeng W Y, Hu S N, Tong W, Wang J, Yu J, Yang H M, Zhu L H. 2004. A comparison of rice chloroplast genomes. Plant Physiol, 135(1): 412–420.
Vairavan S, Siddiq E A, Arunachalam V, Swaminathan M S. 1973. A study on the nature of genetic divergence in rice from Assam and Northeast Himalayas. Theor Appl Genet, 43(5): 213–221.
Xiong Z Y, Zhang S J, Wang Y Y, Ford-Lloyd B V, Tu M, Jin X, Wu Y, Yan H X, Yang X, Liu P, Lu B R. 2010. Differentiation and distribution of indica and japonica rice varieties along the altitude gradients in Yunnan Province of China as revealed by InDel molecular markers. Genet Resour Crop Evol, 57(6): 891–902.
Yang G P, Saghai-Maroof M A, Xu C G, Zhang Q F, Biyashev R M. 1994. Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice. Mol Gen Genet, 245: 187–194.
Yeh F C, Yang R, Boyle T. 1999. POPGENE. Version 1.31. Microsoft Window-Based Freeware for Population Genetic Analysis. Edmonton, AB, Canada: University of Alberta.
Zhang D L, Zhang H L, Wang M X, Sun J L, Qi Y W, Wang F M, Wei X H, Han L Z, Wang X K, Li Z C. 2009. Genetic structure and differentiation of Oryza sativa L. in China revealed by microsatellites. Theor Appl Genet, 119(6): 1105–1117.
Zhang Q F, Saghai-Maroof M A, Lu T Y, Shen B Z. 1992. Genetic diversity and differentiation of indica and japonica rice detected by RFLP analysis. Theor Appl Genet, 83: 495–499.

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