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Population genetics analyses of North-East Indian indigenous rice landraces revealed divergent history and alternate origin of aroma in aus group

  • Debarati Chakraborty (a1) (a2) and Avik Ray (a3)


The rice-based agriculture of the Indian subcontinent has been interwoven in the rich socio-cultural fabric of the country. Of which, bio-culturally diverse North-Eastern states nurture thousands of landraces with poorly tapped agronomic traits. In the present study, 27 standard microsatellite data from 171 rice landraces from six states were analysed to understand their genetic diversity and population structure. Further, combining with a global dataset, we determined subpopulation identity using both model-based and multivariate analyses to uncover their history. We found moderate to high genetic diversity and high differentiation [standardized GST = 0.57]. The AMOVA partitioned overall variance into within population (75%) and among population (25%). The landraces from six states remained at various degrees of differentiation (pairwise FST = 0.09–0.41). We have detected a preponderance of aus-type in a majority of aromatic landraces. Rests were japonica and admixed with a little representation of indica. The presence of aromatic aus probably implied assimilation into local culture from the primary aus growing region of Bangladesh and India. Likewise, the arrival of japonica may stem from the exchange of goods among neighbouring dynasties via Southern and Southwestern Silk routes. The shared ancestry may reflect a merger of two ancient cultures. Our analyses also uncovered the existence of aus-type short and medium grain aromatic rice predicting an origin of aroma in aus subpopulation. Collectively, it demonstrated the diversity and divergent history of the rice landraces have been shaped by various socio-cultural interactions operative over time and space.


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Aggarwal, R, Shenoy, V, Ramadevi, J, Rajkumar, R and Singh, L (2002) Molecular characterization of some Indian Basmati and other elite rice genotypes using fluorescent-AFLP. Theoretical Applied Genetics 105: 680690.
Ahuja, SC and Ahuja, U (2006) Rice in religion and tradition. In: Souvenir, 2nd International Rice Congress, Delhi, Oct 9–13.
Ahuja, U, Ahuja, SC, Thakrar, R and Singh, RK (2008a) Rice – a nutraceutical. Asian Agri-History 12: 93108.
Ahuja, U, Ahuja, SC, Thakrar, R and Rani, NS (2008b) Scented rices of India. Asian Agri-History 12: 267283.
Asem, ID, Imotomba, R, Mazumder, PB and Laishram, JM (2015) Anthocyanin content in the black scented rice (Chakhao): its impact on human health and plant defense. Symbiosis' 66: 4754.
Barker, R (2011) The origin and spread of early-ripening champa rice: it's impact on Song Dynasty China. Rice 4: 184186.
Bennett, E (1970) Adaptation in wild and cultivated plant populations. In: Frankel, OH and Bennett, E (eds) Genetic Resources in Plants – Their Exploration and Conservation. International Biological Programme Handbook No. 11. Oxford: Blackwell, pp. 115129.
Besnier, F and Glover, KA (2013) Parallelstructure: a R package to distribute parallel runs of the population genetics program STRUCTURE on multi-core computers. PLoS ONE 8: e70651.
Bhattasali, NK (1946) New lights on the history of Assam. Indian Historical Quarterly XXII, 245252.
Bhuyan, SK (1974) Anglo Assamese Relations, 1771–1826: A History of the Relations of Assam with the East India Company From 1771 to 1826, Based on Original English and Assamese Sources, 2nd edn. Gauhati: Lawyer's Book Stall.
Bray, F, Coclanis, PA, Fields-Black, E and Dagmar, S (eds). (2015) Rice: Global Networks and New Histories. USA: Cambridge University Press.
Brown, AHD (1999) The genetic structure of crop landraces and the challenge to conserve them in situ on farms. In: Brush, S (ed.) Genes in the Field. Rome: International Plant Genetic Resources Institute, pp. 2948.
Chakraborty, D, Deb, D and Ray, A (2016) An analysis of variation of the aroma gene in rice (Oryza sativa L. subsp. indica kato) landraces. Genetic Resources and Crop Evolution 63: 953959.
Chang, T (2000) Rice. In: Kiple, K and Ornelas, K (ed.) The Cambridge World History of Food. Cambridge: Cambridge University Press, pp. 132149.
Chang, TT (1976) The rice cultures. Philosophical Transactions of the Royal Societies of London B 275: 143157.
Chang, TT (2002) Origin, domestication, and diversification. In: Smith, CW and Dilday, RH (eds) Rice: Origin, History, Technology, and Production. New Jersey: John Wiley and Sons. pp. 326.
Choudhury, B, Khan, ML and Dayanandan, S (2013) Genetic structure and diversity of indigenous rice varieties (Oryza sativa) in Eastern Himalayan region of Northeast India. SpringerPlus 2: 228237.
Choudhury, DR, Singh, N, Singh, AK, Kumar, S, Srinivasan, K, Tyagi, RK, Ahmad, A, Singh, NK and Singh, R. (2014) Analysis of genetic diversity and population structure of rice germplasm from North-eastern region of India and development of a core germplasm set. PLoS ONE 9: e113094.
Civan, P and Brown, TA (2018) Role of genetic introgression during the evolution of cultivated rice (Oryza sativa L.). BMC Evolutionary Biology 18: 57.
Civan, P, Craig, H, Cox, CJ and Brown, TA (2015) Three geographically separate domestications of Asian rice. Nature Plants 1: 15164. 10.1038/nplants.2015.164.
Das, T and Das, AK (2014) Inventory of the traditional rice varieties in farming system of southern Assam: a case study. Indian Journal Traditional Knowledge 13: 157163.
Das, A, Kesari, V and Rangan, L (2010) Aromatic Joha rice of Assam – a review. Agricultural Reviews 31: 110.
Das, B, Sengupta, S, Parida, SK, Roy, B, Ghosh, M, Prasad, M and Ghose, TK (2013) Genetic diversity and population structure of rice landraces from Eastern and North Eastern states of India. BMC Genetics 14: 71.
Frankel, OH, Brown, AHD and Burdon, JJ (1998) The Conservation of Plant Biodiversity, 2nd edn. Cambridge: Cambridge University Press.
Fuller, DQ (2011a) Finding plant domestication in the Indian subcontinent. Current Anthropology 52: S347S362. 10.1086/658900.
Fuller, DQ (2011b) Pathways to Asian civilizations: tracing the origins and spread of rice and rice cultures. Rice 4: 7892. 10.1007/s12284-011-9078-7.
Fuller, DQ and Castillo, C (2015) Diversification and cultural construction of a crop: the case of glutinous rice and waxy cereals in the food cultures of Eastern Asia. In: Lee-Thorp, J and Katzenberg, MA (eds) The Oxford Handbook of the Archaeology of Diet. Oxford, UK: Oxford University Press.
Fuller, DQ and Lucas, L (2017) Adapting crops, landscapes, and food choices: patterns in the dispersal of domesticated plants across Eurasia. In: Boivin, N, Crassard, R and Petraglia, M (eds) Human Dispersal and Species Movement From Prehistory to the Present. Cambridge, United Kingdom: Cambridge University Press, pp. 304331.
Fuller, DQ, Sato, Y, Castillo, C, Qin, L, Weisskopf, AR, Kingwell-Banham, EJ, Song, J, Ahn, SM and Van Etten, J (2010) Consilience of genetics and archaeobotany in the entangled history of rice. Archaeological and Anthropological Sciences 2: 115131.
Fuquan, Y (2004) The ‘Ancient Tea and Horse Caravan Route,’ the ‘Silk Road’ of Southwest China. In: Silk Road Foundation Newsletter Vol. 2 No. 1.
Garris, AJ, Tai, TH, Coburn, J, Kresovich, S and McCouch, S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169: 16311638.
Geertz, C (1970) Agricultural Involution: The Process of Ecological Change in Indonesia, Vol. 11. California, USA: University of California Press.
Glaszmann, JC (1987) Isozymes and classification of Asian rice varieties. Theoretical Applied Genetics 74: 2130. 10.1007/BF00290078.
Guha, A (1967) Ahom migration: its impact on the rice economy of Medieval Assam. Artha Vijnana 2. 10.21648/arthavij/1967/v9/i2/116720.
Guha, A (1980) Little nationalism turned chauvinist: Assam's anti-foreigner upsurge, 1979-80. Economic and Political Weekly 15: 16991720.
Guha, A (1982) The medieval economy of Assam appendix. In: Raychoudhury, T and Habih, I (eds) The Cambridge Economic History of India. Cambridge: Cambridge University Press, Vol. 1, pp. 478505.
Guha, A (1984) Pre-Ahom roots and the Medieval state in Assam: a reply. Social Scientist 12: 7077.
Hamilton, F and Bhuyan, SK (1987) An Account of Assam, 3rd edn. Guwahati: Department of Historical and Antiquarian Studies.
Hore, DK (2005) Rice diversity collection, conservation and management in northeastern India. Genetic Resources and Crop Evolution 52: 11291140.
Hufford, MB, Berny Mier y Teran, JC and Gepts, P (2019) Crop biodiversity: an unfinished magnum opus of nature. Annual Review of Plant Biology 70: 727751.
Jain, S, Jain, RK and McCouch, SR (2004) Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. Theoretical Applied Genetics 109: 965977.
Juliano, BO and Villareal, CP (1993) Grain Quality Evaluation of World Rices. Phillipines: International Rice Research Institute.
Khush, GS (2000) Taxonomy and origin of rice. In: Singh, RK, Singh, US and Khush, GS (eds) Aromatic Rices. New Delhi: Oxford & IBH Publishing Co., pp. 514.
Kingwell-Banham, E, Bohingamuwa, W, Perera, N, Adikari, G, Crowther, A, Fuller, DQ and Boivin, N (2018) Spice and rice: pepper, cloves and everyday cereal foods at the ancient port of Mantai, Sri Lanka. Antiquity 92: 15521570.
Kovach, MJ, Calingacion, MN, Fitzgerald, MA and McCouch, SR (2009) The origin and evolution of fragrance in rice (Oryza sativa L.). Proceedings of the National Academy of Sciences of the USA 106: 1444414449.
Kumar, TT (1988) History of Rice in India: Mythology, Culture, and Agriculture. Delhi, India: Gyan Publication House.
Lahiri, N (1991) Pre-Ahom Assam: Studies in the Inscriptions of Assam Between the Fifth and the Thirteenth Centuries AD. New Delhi, India: Munshiram Manoharlal Publishers Pvt Ltd.
Liu, X, Lister, DL, Zhao, Z, Petrie, CA, Zeng, X, Jones, PJ, Staff, RA, Pokharia, AK, Bates, J, Singh, RN and Weber, SA (2017) Journey to the east: diverse routes and variable flowering times for wheat and barley en route to prehistoric China. PLoS ONE 12: e0187405.
Lu, H, Zhang, J, Yang, Y, Yang, X, Xu, B, Yang, W, Tong, T, Jin, S, Shen, C, Rao, H and Li, X (2016) Earliest tea as evidence for one branch of the Silk Road across the Tibetan Plateau. Scientific Reports 6: 18955. 10.1038/srep18955.
Meirmans, PG and Van Tienderen, PH (2004) GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes 4: 792794.
Miller, MA, Pfeiffer, W and Schwartz, T (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE), 14 Nov. 2010, New Orleans, LA, pp. 18.
Nagaraju, J, Kathirvel, M, Ramesh Kumar, R, Siddiq, EA and Hasnain, SE (2002) Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by using fluorescence-based ISSR-PCR and SSR markers. Proceedings of the National Academy of Sciences of the USA 99: 58365841.
Neog, P, Sarma, PK, Chary, GR, Dutta, S, Rajbongshi, R, Sarmah, K, Baruah, S, Sarma, D, Sarma, MK, Borah, P and Rao, CS (2016) Building climate resilient agriculture through traditional floating rice in flash flood affected areas of the North bank plains zone of Assam. Indian Journal of Traditional Knowledge 15: 632638.
Peakall, R and Smouse, PE (2012) Genalex 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics (Oxford, England) 28: 25372539. 10.1093/bioinformatics/bts460.
Pemberton, RB (1839) Report on Bootan. Huttman, GH: Bengal Military Orphan Press.
Pingali, PL (2017) The green revolution and crop diversity. In: Hunter, D, Guarino, L, Spillane, C and McKeown, PC (eds) Routledge Handbook of Agricultural Biodiversity. New York: Routledge, pp. 213–223.
Prathepha, P (2009) The fragrance (fgr) gene in natural populations of wild rice (Oryza rufipogon Griff.). Genetic Resources and Crop Evolution 56: 1318.
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945959. 10.1111/j.1471-8286.2007.01758.x.
Rahman, ARB and Zhang, J (2013) Rayada specialty: the forgotten resource of elite features of rice. Rice 641: 4151. 10.1186/1939-8433-6-41.
Ray, A and Chakraborty, D (2018) Shattering or not shattering: that is the question in domestication of rice (Oryza sativa L.). Genetic Resources and Crop Evolution 65: 391395.
Ray, A and Ray, R (2018) The birth of Aus agriculture in the South-eastern highlands of India – an exploratory synthesis. Ancient Asia 9: 3.
Ray, A, Deb, D, Ray, R and Chattopadhayay, B (2013) Phenotypic characters of rice landraces reveal independent lineages of short-grain aromatic indica rice. AoB Plants 5. 10.1093/aobpla/plt032.
Richharia, RH and Govindaswami, S (1990) Rices of India. Academy of Development Sciences, Kashele (Maharashtra).
Roy, S, Banerjee, A, Mawkhlieng, B, Misra, AK, Pattanayak, A, Harish, GD, Singh, SK, Ngachan, SV and Bansal, KC (2015) Genetic diversity and population structure in aromatic and quality rice (Oryza sativa L.) landraces from North-Eastern India. PLoS ONE 10: e0129607. 10.1371/journal.pone.0129607.
Roy, PS, Samal, R, Rao, GJ, Patnaik, SS, Jambhulkar, NN, Patnaik, A and Mohapatra, T (2016a) Differentiation and description of aromatic short grain rice landraces of eastern Indian state of Odisha based on qualitative phenotypic descriptors. BMC Ecology 16: 36.
Roy, S, Marndi, BC, Mawkhlieng, B, Banerjee, A, Yadav, RM, Misra, AK and Bansal, KC (2016b) Genetic diversity and structure in hill rice (Oryza sativa L.) landraces from the North-Eastern Himalayas of India. BMC Genetics 17: 107.
Salick, J (2012) Indigenous peoples conserving, managing, and creating biodiversity. In: Gepts, P, Famula, TR, Bettinger, RL, Brush, SB, Damania, AB, McGuire, PE and Qualset, CO (eds) Biodiversity in Agriculture: Domestication, Evolution, and Sustainability. Cambridge, UK: Cambridge University Press, pp. 426444.
Sanajaoba, N (1988) Manipur: Past and Present: History, Polity & Law. Vol. I of Manipur, Past and Present: The Heritage and Ordeals of a Civilization. New Delhi: Mittal Publications.
Saraswat, KS (2004) Plant economy of early farming communities. In: Singh, BP (ed.) Early Farming Communities of the Kaimur (Excavations at Senuwar). Jaipur: Publication Scheme, pp. 416535.
Saraswat, KS (2005) Agricultural background of the early farming communities in the Middle Ganga Plain. Pragdhara 15: 145177.
Sarma, M (2015) A study of migration from Bangladesh to Assam, India and its impact. Doctoral dissertation.
Schatz, MC, Maron, LG, Stein, JC, Wences, AH, Gurtowski, J, Biggers, E, Lee, H, Kramer, M, Antoniou, E, Ghiban, E and Wright, MH (2014) Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biology 15: 506522.
Singh, RK, Singh, US and Khush, GS (eds) (2000) Aromatic Rices. New Delhi, India: Oxford & IBH Pub. Co. Pvt. Ltd.
Sweeney, MT, Thomson, MJ, Cho, YG, Park, YJ, Williamson, SH, Bustamante, CD and McCouch, SR (2007) Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genetics 3: e133. doi:
Tewari, R, Srivastava, RK, Saraswat, KS, Singh, IB and Singh, KK (2006) Early farming in Lahurdewa. Puratatwa 18: 347373.
Tewari, R, Srivastava, RK, Saraswat, KS, Singh, IB and Singh, KK (2008/2009) Early farming at Lahuradewa. Pragdhara 19: 347373.
Vairavan, S, Siddiq, EA, Arunachalam, V and Swaminathan, MS (1973) A study on the nature of genetic divergence in rice from Assam and North East Himalayas. Theoretical Applied Genetics 43: 213221.
Villa, TCC, Maxted, N, Scholten, M and Ford-Lloyd, B (2005) Defining and identifying crop landraces. Plant Genetic Resources 3: 373384.
Yan, C, Yifu, S, Zuan, H, Heyi, C, Suichu, R and Sun, Y (1989) Silk Road on Land and Sea. Yunnan, China: China Pictorial Publishing.
Yang, B (2008) Between Winds and Clouds: The Southwest Silk Road: Yunnan in a Global Context. New York: Columbia University Press.
Zeven, AC (1998) Landraces: a review of definitions and classifications. Euphytica 104: 127139.


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