Jun Rong

Evidences of introgression from cultivated rice to Oryza rufipogon (Poaceae) populations based on SSR fingerprinting: implications for wild rice differentiation and conservation

Crop-to-wild introgression may play an important role in evolution of wild species. Asian cultivated rice (Oryzaxa0sativa L.) is of a particular concern because of its cross-compatibility with the wild ancestor, O.xa0rufipogon Griff. The distribution of cultivated rice and O.xa0rufipogon populations is extensively sympatric, particularly in Asia where many wild populations are surrounded by rice fields. Consequently, gene flow from cultivated rice may have a potential to alter genetic composition of wild rice populations in close proximity. In this study, we estimated introgression of cultivated rice with O.xa0rufipogon based on analyses of 139 rice varieties (86 indica and 53 japonica ecotypes) and 336 wild individuals from 11 O.xa0rufipogon populations in China. DNA fingerprinting based on 17xa0selected rice simple sequence repeat (SSR) primer pairs was adopted to measure allelic frequencies in rice varieties and O.xa0rufipogon samples, and to estimate genetic associations between wild and cultivated rice through cluster analysis. We detected consanguinity of cultivated rice in O.xa0rufipogon populations according to the admixture model of the STRUCTURE program. The analyses showedz that four wild rice populations, DX-P1, DX-P2, GZ-P2, and HL-P, contained some rare alleles that were commonly found in the rice varieties examined. In addition, the four wild rice populations that scattered among the rice varieties in the cluster analysis showed a closer affinity to the cultivars than the other wild populations. This finding supports the contention of substantial gene flow from crop to wild species when these species occur close to each other. The introgressive populations had slightly higher genetic diversity than those that were isolated from rice. Crop-to-wild introgression may have accumulative impacts on genetic variations in wild populations, leading to significant differentiation in wild species. Therefore, effective measure should be taken to avoid considerable introgression from cultivated rice, which may influence the effective in-situ conservation of wild rice species.

Modelling pollen-mediated gene flow in rice: risk assessment and management of transgene escape.

Fast development and commercialization of genetically modified plants have aroused concerns of transgene escape and its environmental consequences. A model that can effectively predict pollen-mediated gene flow (PMGF) is essential for assessing and managing risks from transgene escape. A pollen-trap method was used to measure the wind-borne pollen dispersal in cultivated rice and common wild rice, and effects of relative humidity, temperature and wind speed on pollen dispersal were estimated. A PMGF model was constructed based on the pollen dispersal pattern in rice, taking outcrossing rates of recipients and cross-compatibility between rice and its wild relatives into consideration. Published rice gene flow data were used to validate the model. Pollen density decreased in a simple exponential pattern with distances to the rice field. High relative humidity reduced pollen dispersal distances. Model simulation showed an increased PMGF frequency with the increase of pollen source size (the area of a rice field), but this effect levelled off with a large pollen-source size. Cross-compatibility is essential when modelling PMGF from rice to its wild relatives. The model fits the data well, including PMGF from rice to its wild relatives. Therefore, it can be used to predict PMGF in rice under diverse conditions (e.g. different outcrossing rates and cross-compatibilities), facilitating the determination of isolation distances to minimize transgene escape. The PMGF model may be extended to other wind-pollinated plant species such as wheat and barley.

Inferring population history from fine-scale spatial genetic analysis in Oryza rufipogon (Poaceae).

Determining the genetic structure of an in situ conserved population can provide insight into the dynamics of population genetic processes associated with successful plant conservation. We used 21 microsatellite loci to analyse the genetic relationships among individuals (n= 813) collected from a small Oryza rufipogon population conserved since 1993 in Hunan Province of China. The analysis revealed four distinct genetic subpopulations (FST= 0.145) without geographic isolation. One subpopulation was composed of possible introgressed individuals, two subpopulations were composed of seed recruits and their descendants, and the fourth subpopulation consisted of reintroduced individuals, seed recruits and their descendants. Positive spatial genetic structures were detected by spatial autocorrelation statistics at the population (c. 63 m) and subpopulation levels (11–30 m), but the degree of autocorrelation was stronger at the population level. These results showed that prejudging the cryptic structure is important before autocorrelation analysis for the entire population. Our study suggests that population history can be a significant determinant on population structure for plant restoration projects.

Normal expression of insect-resistant transgene in progeny of common wild rice crossed with genetically modified rice: its implication in ecological biosafety assessment

Transgene outflow from genetically modified (GM) rice to its wild relatives may cause undesirable ecological consequences. Understanding the level of transgene expression in wild rice following gene flow is important for assessing such consequences, providing that transgene escape from GM rice cannot be prevented. To determine the expression of a transgene in common wild rice (Oryza rufipogon), we analyzed the content of Cry1Ac protein in three GM rice lines containing a Bt transgene, their F1 hybrids with common wild rice and F2 progeny at different growth stages, using the sandwich enzyme-linked immunosorbent assay. The average content of Cry1Ac protein in leaf samples of the wild rice lines ranged between 0.016 and 0.069% during the entire growth period, whereas that in stems varied between 0.12 and 0.39%. A great variation in Cry1Ac protein content was detected among individuals of F1 hybrids and F2 progeny, with some wild individuals showing higher level of Bt toxin than the cultivated GM rice. The results suggest that the Bt transgene can express normally in the interspecific hybrids between insect-resistant GM rice and common wild rice, and may have similar effects on the target insects as in GM rice.

Population clonal diversity and fine-scale genetic structure in Oryza officinalis (Poaceae) from China, implications for in situ conservation

Population clonal diversity and fine-scale genetic structure of Oryza officinalis Wall. ex Watt, an endangered species in China recently experiencing habitat degradation, was estimated using inter simple sequence repeat markers. We analyzed the genetic variations of 440 samples exhaustively collected from nine O. officinalis populations. Relatively rich clonal diversity and poor genetic variation were found in the extant populations. We found that the number of genets, the percentage of polymorphic loci, and gene diversity decreased with population decline, suggesting that habitat degradation will lead to further genetic depletion of O. officinalis populations. A pronounced spatial genetic structure occurs at both the ramet and genet levels in several larger populations, which is the result of clonal growth and concomitant inbreeding. The in situ conserved population PS holds much more genotypes than other populations with the similar population size, which might have more seedling recruitments from the soil seed bank due to habitat disturbance, suggesting a moderate disturbance combined with habitat degradation-avoiding measures are effective for in situ conservation of this species.