Comparisons of microsatellite variability and population genetic structure of two endangered wild rice species, Oryza rufipogon and O. officinalis, and their conservation implications

Gao, Li‐Zhi; Zhang, Chi-Hong

doi:10.1007/s10531-004-0537-y

Cited by 19 publications

(11 citation statements)

References 63 publications

(61 reference statements)

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“…More than two thousands microsatellite loci isolated from the genome of O. sativa (e.g., Akagi et al 1996;McCouch et al 1997;Cho et al 2000;Temnykh et al 2000) have provided promising opportunities to study genetic diversity and population structure of rice species (e.g., Gao et al 2002a;Song et al 2003;Gao 2004;Gao and Zhang 2005). In this study, we used 19 microsatellites to assess the genetic variation within 92 accessions of O. rufipogon preserved in two field gene banks.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity within Oryza rufipogon germplasms preserved in Chinese field gene banks of wild rice as revealed by microsatellite markers

Gao

Zhang

et al. 2006

Biodivers Conserv

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Nineteen microsatellite markers were employed to evaluate the genetic diversity of 92 accessions of common wild rice Oryza rufipogon Griff., which represent a significant portion of the distribution range from field gene banks of China. In comparison, a total of 57 varieties from most of the rice growing areas in China were also analyzed. The microsatellite analysis revealed a considerable amount of genetic diversity resided within the preserved wild rice germplasms. In all, the nineteen microsatellites revealed 328 alleles. The number of alleles per locus varied widely among these markers, ranging from 6 at RM242 to 30 at RM206. A comparison of the genetic parameters showed that wild rice strains preserved in the field gene banks (na = 17.27; R S = 15.66; H S = 0.86; H T = 0.852; H O = 0.307) possess much higher genetic diversity than cultivated rice varieties (na = 8.27; R S = 8.14; H S = 0.75; H T = 0.758; H O = 0.051). A total of 196 alleles detected in the wild rice could not be found in cultivated rice, suggesting that about 60% of the alleles of wild rice might be lost during the process of rice domestication. This result shows that these ex situ preserved wild rice strains are of great importance for the discovery and utilization of novel alleles in the future rice breeding practices. Considerably abundant genetic variability detected within the studied wild rice germplasms could be comparable to that previously found in a wide sampling of 47 natural populations (na = 16.17; H S = 0.67; H O = 0.229), demonstrating that developing field gene banks of wild rice is a necessary and efficient way for preserving genetic diversity of wild rice resources. To determine minimum microsatellites that could distinguish these wild rice accessions, the phylogenetic trees constructed by means of the combinations of different microsatellites suggested that the five highly polymorphic microsatellites could clearly identify these samples. High polymorphisms of rice microsatellite loci and their great resolving power will be particularly helpful for germplasm evaluation and evolutionary studies for better strengthening the conservation and utilization of genetic diversity of wild rice in the field gene banks.

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Section: Introductionmentioning

confidence: 99%

Genetic diversity within Oryza rufipogon germplasms preserved in Chinese field gene banks of wild rice as revealed by microsatellite markers

Gao

Zhang

et al. 2006

Biodivers Conserv

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“…Similar issues are raised with concerns of drug and vaccine resistance for human health, where the spatial variation in drug or vaccine use could influence the evolution of the pathogens being controlled (McLean 1995;Heinemann 1999;Gandon et al 2001). The importance of spatial variation in selective pressures for conservation genetic programs is somewhat different (Robert et al 2003;Gao and Zhang 2005;Jamieson et al 2006;Bohme et al 2007). Here, the goal is to maintain or increase genetic diversity within a population.…”

Section: Discussionmentioning

confidence: 96%

“…These issues can be of direct practical concern. For example, conservation genetics often aims to maximize the genetic diversity of endangered populations (Robert et al 2003;Gao and Zhang 2005;Jamieson et al 2006;Bohme et al 2007), and health or agricultural programs aim to minimize the fixation probability of alleles for insecticide, drug, or vaccine resistance (McLean 1995;Heinemann 1999;Scott et al 2000).…”

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confidence: 99%

The Fixation of Locally Beneficial Alleles in a Metapopulation

2008

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Extinction, recolonization, and local adaption are common in natural spatially structured populations. Understanding their effect upon genetic variation is important for systems such as genetically modified organism management or avoidance of drug resistance. Theoretical studies on the effect of extinction and recolonization upon genetic variance started appearing in the 1970s, but the role of local adaption still has no good theoretical basis. Here we develop a model of a haploid species in a metapopulation in which a locally adapted beneficial allele is introduced. We study the effect of different spatial patterns of local adaption, and different metapopulation dynamics, upon the fixation probability of the beneficial allele. Controlling for the average selection pressure, we find that a small area of positive selection can significantly increase the global probability of fixation. However, local adaption becomes less important as extinction rate increases. Deme extinction and recolonization have a spatial smoothing effect that effectively reduces spatial variation in fitness.T HE fixation of novel alleles is a longstanding research topic, with work on panmictic populations dating back to the beginning of population genetics (Fisher 1922;Wright 1931). Fixation quantifies the dynamics of a rare allele by describing the probability and the expected time for it to increase to a significant frequency within a population (through selective forces or genetic drift). Fixation is therefore an important factor in determining genetic diversity and the rate of evolution. A low fixation probability and a short fixation time will produce a low genetic diversity where single alleles successively sweep through a population. A high fixation probability, or a long fixation time, will tend to increase the number of alleles segregating in a population, thus increasing genetic diversity. These issues can be of direct practical concern. For example, conservation genetics often aims to maximize the genetic diversity of endangered populations (Robert et al. 2003;Gao and Zhang 2005;Jamieson et al. 2006;Bohme et al. 2007), and health or agricultural programs aim to minimize the fixation probability of alleles for insecticide, drug, or vaccine resistance (McLean 1995;Heinemann 1999;Scott et al. 2000).Few populations can truly be described as panmictic. Populations are often spatially fragmented and form a metapopulation system (Hanski and Gaggiotti 2004), with individual fragments going extinct and later being recolonized by migrants from surrounding populations.In a metapopulation many factors can vary from deme to deme, such as the selective advantage of an allele, s, the frequency of an allele, or the force of genetic drift. Under certain circumstances the spatial structure of a metapopulation has no effect, and fixation probability will be the same as that for a panmictic population (Maruyama 1970;Nagylaki 1982). In an ideal, panmictic population where individual reproductive success follows a Poisson distribution with mea...

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“…Despite many SSR studies on the cultivated rice and its closely related wild species Ishii et al, 2000;Gao et al, 2002;Zhou et al, 2003;Garris et al, 2005), relatively few studies have been undertaken on the population genetics of the B-and C-genome species using SSRs (Gao and Zhang, 2005). Of the four diploid species in this study, O. officinalis maintained the highest diversity (P-71.4%, A=2.71, He-0.565), folk)wed by O. eichingeri (P=57.1%, A=1.71, He=0.376), O. punctata (P=57.1%, A=2.14, He=0.272) and O. rhizomatis (P=42.9%, A=1.43, He=0.222) ( Table 2).…”

Section: Genetic Diversitymentioning

confidence: 99%

“…For example, Zhou et al (2003) revealed much higher level of genetic diversity in the Chinese populations of the Agenome O. rufipogon using 10 SSR primers (P-100%, A=10.6, He=0.787). Recently, Gao and Zhang (2005) applied six and seven SSR loci to investigate the genetic structure of six populations throughout the range of the Chinese O. rufipogon and O. officinalis, respectively. They found that O. rufipogon possessed higher levels of genetic diversity (P=100%, He=0.580) than O. officinalis (P=57.1%, He=0.283).…”

Section: Genetic Diversitymentioning

confidence: 99%

Genetic diversity and evolutionary relationships ofOryza species with the B- and C-genomes as revealed by SSR markers

et al. 2006

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Genetic diversity and evolutionary relationships of 72 accessions representing six species with the B-, C-, and BC-genomes in the genus Oryza were investigated by seven microsatellite markers. Of four diploid species, Oryza officinalis maintained the highest diversity (P=71.4%, He=0.565), followed by Oryza eichingeri (P=57.1%, He=0.376), Oryza punctata (P=57.1%, He=0.272) and Oryza rhizomatis (P=42.9%, He=0.222). In comparison, a higher level of genetic diversity was revealed in the tetraploid (P=71.4%, He=0.461-0.637). UPGMA dendrograms based on genetic distance revealed an obvious genetic differentiation between Asian and African races of O. eichingeri. Three BBCC species clustered with different accessions of the diploid O. punctata, suggestive of their multiple origins. The results inferred from the dendrogram suggested that diploid species, O. officinalis and African O. eichingeri might be the C-genome donors for tetraploid species, Oryza minuta and O. punctata, respectively, while the C-genome ancestor of Oryza malampuzhaensis seemed to be either O. rhizomatis or the Sri Lankan O. eichingeri species. The genetic relationship among the CC and BBCC species further indicated that the tetraploid species with the BC-genome have originated independently, at least three times in history. In addition, we have demonstrated successful cross-species amplification of seven rice SSR loci across Oryza species with B-and C-genomes.

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Comparisons of microsatellite variability and population genetic structure of two endangered wild rice species, Oryza rufipogon and O. officinalis, and their conservation implications

Cited by 19 publications

References 63 publications

Genetic diversity within Oryza rufipogon germplasms preserved in Chinese field gene banks of wild rice as revealed by microsatellite markers

Genetic diversity within Oryza rufipogon germplasms preserved in Chinese field gene banks of wild rice as revealed by microsatellite markers

The Fixation of Locally Beneficial Alleles in a Metapopulation

Genetic diversity and evolutionary relationships ofOryza species with the B- and C-genomes as revealed by SSR markers

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