Genetic Structure of Oryza rufipogon Griff. Natural Populations in Malaysia: Implications for Conservation and Genetic Introgression of Cultivated Rice

Abstract

Thirty polymorphic Oryza sativa microsatellite loci (SSRs) were used to study population genetic structure of O. rufipogon Griff. natural populations in Malaysia. A total of 445 alleles were detected with an average of 14.8 alleles per locus in 176 individuals of O. rufipogon sampled from the states of Penang, Kedah, Kelantan and Terengganu where the natural populations are still found. The Kelantan population in the northeast of Peninsular Malaysia had the highest level of genetic diversity as measured by the mean number of alleles per locus, A a =7.67, average number of effective alleles, A e =5.50, percentage of polymorphic loci, P=100%, observed heterozygosity, H o =0.631 and expected heterozygosity, H e =0.798. In contrast, the Terengganu population in the east showed the lowest level of genetic diversity measured by the same criteria (A a =4.23, A e =2.10, P= 100%, H o =0.549 and H e =0.449).Model-based clustering analysis using the STRUCTURE 2.2 program placed all the individuals into 12 clusters that corresponded to the geographic sampling locations. Neighbour-joining tree was constructed based on Nei's genetic distance to further assess the genetic structure of the O. rufipogon individuals, showed good agreement (93.8%) with the model-based cluster analysis. However, the neighbour-joining tree identified subpopulations that STRUCTURE could not identify. The classification of individuals from the same populations under the same cluster supported the population differentiation. These two analyses seemed to indicate expansion of populations from the northeast of Peninsular Malaysia (Tumpat, Pasir Mas and Kota Bahru, Kelantan) not only to the immediate south of the region i.e. Terengganu but also into the northwest (i.e. Penang and Kedah) with the former being more recent. Oryza rufipogon accession IRGC105491 and O. sativa ssp. indica cultivar MR219, which were included in this study for comparisons with the local wild rice accessions, indicated that introgression of cultivated rice could change genetic composition and affect the population genetic structure of wild rice. This possibility should be carefully considered in plans to conserve this wild rice. AbbreviationsRAPD Randomly amplified polymorphic DNA RFLP Restriction fragment length polymorphism SSR Microsatellite or simple sequence repeat QTL Quantitative trait locus DNA Deoxyribonucleic acid PCR Polymerase chain reaction Communicated by: Hongwei Cai Electronic supplementary material The online version of this article (

Life‐history traits and geographical divergence in wild rice ( Oryza rufipogon ) gene pool in Indochina Peninsula region

“…The wide range of genetic variation found within and among both annual and perennial wild rice populations of the Indochina Peninsula is consistent with results reported in several studies using a diversity of genetic markers and geographical scales, within country and across the range distribution (Song et al , ; Zhou et al , ; Gao, ; Shishido et al , ; Kuroda et al , ; Zhou et al , ; Ngu et al , ; Pusadee et al , ). Combined, these results suggested that wild rice is genetically variable and still abundant in many parts of its range.…”

“…The enormous geographical range and threatened status of O . rufipogon in some regions, as well as the many international boundaries have made population level sampling from natural habitats difficult and thus limited studies to specific regions in China (Song et al , ; Zhou et al , ; Gao, ) Myanmar (Shishido et al , ), Laos (Kuroda et al , ), Malaysia (Ngu et al , ) and Thailand (Pusadee et al , ). Yet, in order to understand the population genetic structure and to determine recurrent evolutionary forces and the interplay of those forces, comparative studies across regions are still needed, particularly to understand the role of local adaptation to heterogeneous environments and its interaction with geographical differentiation.…”

Genetic Diversity and Structure ofOryza rufipogonGriff. Populations in the Philippines

“…Unlike the Philippine Rufi samples that were geographically isolated, with restricted gene flow, and that might have been predominantly reproducing asexually. In addition, the level of genetic diversity of these Rufi populations is lower compared to those reported by Zhou et al (2003) in China (Na=10.6 among 10 SSR loci, 237 samples), Prathepha (2012) in Northeastern Thailand and Laos (Na=11.8571 among 7 SSR loci, 94 samples), and Ngu et al (2010) in Malaysia (Na=14.8 alleles among 30 loci, 176 samples) despite using more SSR loci, as they had larger sample sizes which also came from several distant locations between sampled populations. *Corresponding Authors: sandyjanlabarosa@gmail.com; f.joy.jamago@cmu.edu.ph…”

Identification of quantitative trait loci for blast resistance in BC2F3 and BC2F5 advanced backcross families of rice

“…It is distributed in the marshy areas of tropical and subtropical Asia. Considerable genetic diversity has been reported within natural populations of O. rufipogon in Malaysia (Ngu et al, 2010). O. rufipogon is considered the progenitor of O. sativa.…”

“…Geographic distribution surveys of O. rufipogon conducted by the International Rice Research Institute demonstrated that O. rufipogon accession from Malaysia (OR22) exhibited resistance to blast disease (Huang et al, 2008). Gene flow from cultivated rice also occurs, which can persist in wild rice populations, change its genetic composition, and affect the population genetics of wild rice (Ngu et al, 2010). Among the characteristics of O. rufipogon IRGC105491 that implies introgression from O. sativa are its upright growth habit and slightly high number of grains per panicle.…”