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Genetic Diversity of Isolated Populations of Indonesian Landraces of Rice (Oryza Sativa L.) Collected in East Kalimantan on the Island of Borneo

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Genetic Diversity of Isolated Populations of Indonesian Landraces of Rice (Oryza Sativa L.) Collected in East Kalimantan on the Island of Borneo Rice (2009) 2:80–92 DOI 10.1007/s12284-009-9023-1 Genetic Diversity of Isolated Populations of Indonesian Landraces of Rice (Oryza sativa L.) Collected in East Kalimantan on the Island of Borneo Michael J. Thomson & Nicholas R. Polato & Joko Prasetiyono & Kurniawan R. Trijatmiko & Tiur S. Silitonga & Susan R. McCouch Received: 23 October 2008 /Accepted: 2 February 2009 /Published online: 19 February 2009 # Springer Science + Business Media, LLC 2009 Abstract Although the genetic diversity of rice germplasm 20% indica, which largely correlated with the field-level has been well characterized globally, few studies have taken ecotypes: upland japonica and lowland indica. Indigenous an in-depth view of a large number of rice landraces on a knowledge from local farmers was gathered about the local scale. To better understand the relationships between names, origins, and uses of the landraces, which provides a rice genetic diversity and associated geographic and rich background to compare with the genetic relationships cultural factors, we collected and characterized 183 rice of these traditional varieties. landraces from 18 villages along the Bahau and Kayan rivers in the Indonesian province of East Kalimantan on the Keywords Rice (Oryza sativa) . Genetic diversity . island of Borneo. A genetic diversity analysis using 30 Landrace . Ecotype . SSR markers microsatellite markers detected a clear distinction between the indica and japonica varietal groups (Fst=0.59), with 80% of the landraces identified as tropical japonica and Introduction The genetic diversity of cultivated rice germplasm on a Electronic supplementary material The online version of this article (doi:10.1007/s12284-009-9023-1) contains supplementary material, global scale has been well characterized using molecular which is available to authorized users. markers (Caicedo et al. 2007; Garris et al. 2005; Glaszmann M. J. Thomson : J. Prasetiyono : K. R. Trijatmiko : T. S. Silitonga 1987; Yang et al. 1994; Yu et al. 2003). To encompass the Indonesian Center for Agricultural Biotechnology and Genetic entire range of rice diversity, these studies have sampled Resources Research and Development, rice varieties from many different rice-growing countries Jl. Tentara Pelajar 3A, around the world. Likewise, efforts to designate core Bogor 16111, Indonesia collections have employed sampling strategies to maximize N. R. Polato : S. R. McCouch (*) the genetic diversity of the subset, while minimizing the Department of Plant Breeding and Genetics, Cornell University, numbers of accessions studied to a reasonable level. 162 Emerson Hall, Consequently, while global studies will provide an excel- Ithaca, NY 14853, USA e-mail: [email protected] lent overview of the population structure of cultivated rice, they cannot provide an in-depth view of rice germplasm on Present address: a local scale, since each region will only be represented by M. J. Thomson a few varieties. Increasingly, studies have begun to Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, characterize subsets of rice germplasm at the country-wide Los Baños, Laguna, Philippines level, with molecular markers being used to describe the genetic diversity of rice within specific countries (Gao et al. Present address: 2005; Jain et al. 2004; Lu et al. 2005; Pessoa-Filho et al. N. R. Polato Department of Biology, Penn State University, 2007; Prashanth et al. 2002; Thomson et al. 2007). University Park, PA 16802, USA However, there is still a lack of data that describe molecular Rice (2009) 2:80–92 81 diversity of rice on a local scale. The most complete study rice-growing people across Asia, where rice cultivation has to date characterized a set of 692 rice landraces from the been practiced for thousands of years. Yet there is still a great province of Yunnan, China using 20 simple sequence repeat deal to learn concerning the impact of farmer practices on the (SSR) markers and found seven population sub-groups preservation, exchange, and continuing evolution of tradi- roughly corresponding to subspecies (indica/japonica), tional landraces today. This knowledge will provide an field-level ecotypes (lowland/upland), and seasonal eco- essential foundation for making decisions about the conser- types based on maturity (Zhang et al. 2007). Another study vation and use of traditional germplasm in breeding examined the diversity of 170 accessions from 14 villages programs. in Guinea and found that diversity between accessions The Green Revolution was felt throughout Asia and within the same village was the most important component greatly impacted the varietal landscape due to rapid of regional genetic diversity (Barry et al. 2007). Likewise, dissemination of high-yielding, semi-dwarf indica varieties several studies have begun to explore plant genetic that displaced many traditional landrace varieties. This diversity at a local scale in other crops, such as sorghum study focused on an isolated region on the island of Borneo and millet in Africa (Adoukonou-Sagbadja et al. 2007; populated by traditional hunter-gatherers who also practice Barnaud et al. 2007). As additional studies detail rice rice cultivation. We were interested to examine the genetic genetic diversity on a local scale, the complex interaction structure and diversity of the rice varieties that were being between rice diversity and human cultivation practices can grown by these villagers and to determine whether they still be better understood. cultivated exclusively traditional landraces or whether there Rice landraces have been shaped by the interplay was any evidence that Green Revolution varieties had been between adaptation to the local environment and selection introduced in the region. imposed by farmers who determine which varieties will be There are a number of important issues concerning crop grown each year. This is in contrast to wild rice genetic diversity and its relationship to local cultures that populations, which proliferate based on their ability to can only be answered by intensively studying traditional survive and compete under natural conditions. Natural varieties collected from a geographically isolated region populations tend to be more stable than cultivars in their (one that has not been affected by the introduction of geographic distributions because the forces of natural modern varieties). For example, how do the landraces in an selection generally lead to gradual changes over evolution- isolated region reflect the ethnic history, cultural prefer- ary time. Several studies carried out on wild rice popula- ences, and production practices of local farmers? How long tions in China have characterized the local diversity of have these varieties been cultivated by people in the Oryza rufipogon and found varying degrees of differenti- village? Are the genetic relationships among local landraces ation within and between local populations (Song et al. defined more by geographical proximity, or does the 2003; Xu et al. 2006; Zhou et al. 2003). In contrast, the dynamic exchange of germplasm within and between accelerated evolution provided by intense artificial selection regions play a greater role? Which specific plant and/or and seed exchanges among local farmers has led to grain characters are selectively maintained and valued by dramatic changes in the genetics of cultivated crops in a local cultures? How do farmers decide what varieties to relatively short time frame (<10,000 years). While the story plant every year? Carefully focused germplasm collection of rice domestication is still being unraveled based on trips are needed to explore the intricacies and dynamics of interpretations of geographic and phylogenetic data (Caicedo rice genetic diversity on a local scale and to provide a more et al. 2007; Londo et al. 2006) and analysis of cloned detailed view of the rice varieties adapted to a specific set domestication genes (Kovach et al. 2007; Sweeney et al. of local environments and cultural expectations. 2007), it appears that rice was domesticated from diverse To begin to answer some of these questions, we gene pools and that gene flow among sub-populations and initiated a collection trip to a remote region in the with wild ancestral populations has created a complex series interior of Borneo with the goal of collecting indigenous of events leading to the modern day fabric of rice diversity landraces along with corresponding information from (Sang and Ge 2007;SweeneyandMcCouch2007), although local farmers (Fig. 1). We selected the Bahau River to the possibility of a single domestication event is still debated focus the collection trip due to its isolated location and (Gao and Innan 2008; Vaughan et al. 2008). While the because a previous survey in 1993 had interviewed local relationships between the earliest domesticates and indige- farmers and identified 35 distinct rice landraces grown in nous landraces surviving in rice-growing regions today are the village of Apau Ping (Setyawati 2003). This region of still unclear, signatures of shared ancestry, selection, and East Kalimantan, which is partially encompassed by the introgression are written in the genomes of traditional Kayan Mentarang National Park covering 1.6 million varieties. Over many generations, rice has become an hectares, is sparsely populated by several thousand essential component of the local cultures and customs of indigenous people collectively called the Dayak. The 82 Rice (2009) 2:80–92 Fig. 1 Location of the three geographic regions from which Villages of the rice accessions were collected Upper Bahau River: 1. Apua Ping on the Indonesian province of 1 2 2. Long Berini Bahau 3 Tarakan East Kalimantan on the island of 3. Long Kemuat River 4 Long Peso 5 10 12 Borneo: including five villages 4. Long Alango 6 Tanjung Selor 7 from the Upper Bahau river, 5. Long Tebulo 8 9 11 four villages from the lower Long Bia Bahau river, and the remaining Villages of the Kayan from villages along the lower Lower Bahau River: River Kayan river. 6. Long Uli 7. Long Peleran East Kalimantan 8. Long Pujungan 9. Long Aran Villages of the Mahakam Lower Kayan River: River 10. Long Peso 11. Long Bia Samarinda 12.
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