Evaluation of genetic variation among wild rice populations in Cambodia

Abstract

A total of 448 samples in five natural populations of wild rice (Oryza rufipogon) were collected in Cambodia. They were examined using 12 SSR and two chloroplast markers to evaluate the degree of variation among populations and the genetic structure within populations. In the two annual populations, the number of plants with homozygous alleles at all 12 SSR loci were high (66.3% and 79.5%), suggesting that these plants propagate mainly through self-pollination. In the three perennial populations, no individuals had all homozygous genotypes, but redundant genotypes resulted from clonal propagation were observed. Percentages of the redundant genotypes were highly varied (3.6%, 29.2% and 86.0%). This may be due to the different stable levels of environmental conditions. As for chloroplast genome, most of the wild plants showed the same chloroplast types as most Indica-type cultivars have. However, plants with different chloroplast types were maintained, even in the same population. In tropical Asian countries, many wild rice populations were observed under similar ecological conditions examined in this study. Therefore, the present results concerning population structure will be important to further elucidate genetic features of wild rice, and will also give strong clues to utilize and conserve wild natural genetic resources.

The potentiality of rice microsatellite markers in assessment of cross-species transferability and genetic diversity of rice and its wild relatives

“…The results of the comparison in mean genetic diversity parameters among the eight genomes groups using these 70 SSR markers showed wide variations (Table 4, Figure S1). The highest N (6.243), Na (3.086), Ne (2.284) and I (0.871) among the genome groups were observed in AA genome groups, whereas the lowest of N (0.286), Na (0.371), Ne (0.371) and I (0.059) were observed in KKLL genome group; this large variation might be due to sample size and ecological factors which greatly influences on genetic differentiation among the wild rice populations (Orn et al 2015 andIshii et al 2011). The percent of polymorphic loci (%P) ranged from 8.57% in KKLL genome to 97.14% in the AA genome group.…”

Genetic diversity among perennial wild rice Oryza rufipogon Griff., in the Mekong Delta

“…This higher variation allowed a breeding program that successfully created AS996, carrying higher acid sulfate tolerance (Can & Lang, ; Khush & Virk, ; Lang et al, ). This higher degree of diversity might be due to ecological factors that have a great influence on genetic differentiation among wild rice populations (Orn et al, ). In fact, the Dong Thap wild population is distributed widely in a government conservation area at Tram Chim National Park.…”

“…The wild species of rice are widely distributed from upstream to downstream in the delta and their perennial nature makes them different from those in neighboring Cambodia (based on our field observation). Annual type is predominated around Phnom Penh area, whereas a few perennial populations were reported (Orn et al, ). Perennial type could be observed but became extinct because of the size and drastic infrastructure development.…”

“…Molecular markers have provided a powerful tool for studies of genetic diversity among crop species (Gao, 2004;Olsen & Schaal, 2001;Song, Xu, Wang, Chen, & Lu, 2003), clarifying details of population structure and genetics, and having a significant impact on in situ conservation management (Barbier, 1989;Cai et al, 2004;Ishii et al, 2011;Kaewcheenchai et al, 2018;Wang et al, 2012). In fact, such data can be sampled efficiently from natural populations to monitor the transition of population structures in nature (Gao, 2004;Gao, Shaal, Zang, Jia, & Dong, 2002;Orn et al, 2015;Qian, Tianhua, Song, & Lu, 2005;Wang et al, 2012). Since the complete chloroplast (cp) genome became available, cytoplasmic molecular tools have also been developed to clarify evolutionary processes (Chen, Nakamura, Sato, & Nakai, 1993;Kano, Watanabe, Nakamura, & Hirai, 1993;Kim et al., 2015;Masood et al, 2004;Sotowa et al, 2013;Takahashi, Sato, & Nakamura, 2008 (Wambugu, Brozynska, Furtado, Waters, & Henry, 2015;Waters, Nock, Ishikawa, Rice, & Henry, 2012).…”

Diverse genetic variation in maternal lineages with high heterogeneity among <i>in situ</i>-conserved wild rice (<i>Oryza rufipogon</i> Griff.) developed in Thailand

“…In order to conduct such efficient sampling, it is necessary to know the details of each population structure and to develop tools for precise assessment of genetic resources. Wild rice in Cambodia has also been studied to clarify the natural population structure (Orn et al 2015). Different habitats characterized by annual and perennial wild rice plants were shown to have resulted in different ranges of genetic diversity.…”