Fitness correlates of crop transgene flow into weedy populations: a case study of weedy rice in China and other examples

Biotechnological advances in the production of unusual fatty acids in transgenic plants and recombinant microorganisms

Certain plants and microorganisms can produce high amounts of unusual fatty acids (UFAs) such as hydroxy, conjugated, cyclic, and very long-chain polyunsaturated fatty acids, which have distinct physicochemical properties and significant applications in the food, feed, and oleochemical industries. Since many natural sources of UFAs are not ideal for large-scale agricultural production or fermentation, it is attractive to produce them through synthetic biology. Although several UFAs have been commercially or pre-commercially produced in transgenic plants and microorganisms, their contents in transgenic hosts are generally much lower than in natural sources. Moreover, reproducing this success for a wider spectrum of UFAs has remained challenging. This review discusses recent advancements in our understanding of the biosynthesis, accumulation, and heterologous production of UFAs, and addresses the challenges and potential strategies for achieving high UFA content in engineered plants and microorganisms.

Glyphosate resistance and no fitness cost in backcross offspring of wild soybean and transgenic soybean with epsps gene

BACKGROUND

The commercial utilization of genetically modified soybeans has yielded substantial economic advantages. Nevertheless, the genetic drift towards wild soybeans is one of the main ecological risks that needs to be addressed. Previous experiments demonstrated the absence of fitness cost or florescence overlap in hybrid offspring resulting from the crossbreeding of transgenic soybean GTS40-3-2 and Zhengzhou wild soybeans. In this study, hybrid progeny was systematically crossed with wild soybeans to establish a backcross progeny system. This system was employed to evaluate the ecological risk associated with the backcross progeny of transgenic and wild soybeans.

RESULTS

The findings indicated that the offspring from the backcross exhibited glyphosate tolerance. Furthermore, the expression of foreign proteins in the backcross offspring was notably lower than in the transgenic soybean, and there was no significant difference when compared to the hybrid progeny. Parameters such as germination rate, aboveground biomass, pods per plant, full seeds per plant, and 100-grain weight exhibited no significant differences between the negative and positive lines of the backcross progenies, and no fitness cost was identified in comparison to wild soybeans. These results underscore the potential for foreign genes to propagate within other wild soybeans, which requires continuous attention.

CONCLUSIONS

The widespread adoption of genetically modified soybeans has undeniably led to substantial economic gains. However, the research findings emphasize the critical importance of addressing the ecological risks posed by genetic drift towards wild soybeans. The backcross progeny system established in this study indicates that the potential for foreign gene dissemination to wild soybean populations warrants continued attention and mitigation strategies.

Environmental impacts of genetically modified crops

Genetically modified (GM) crops have been adopted by some of the world's leading agricultural nations, but the full extent of their environmental impact remains largely unknown. Although concerns regarding the direct environmental effects of GM crops have declined, GM crops have led to indirect changes in agricultural practices, including pesticide use, agricultural expansion, and cropping patterns, with profound environmental implications. Recent studies paint a nuanced picture of these environmental impacts, with mixed effects of GM crop adoption on biodiversity, deforestation, and human health that vary with the GM trait and geographic scale. New GM or gene-edited crops with different traits would likely have different environmental and human health impacts.

Hybridization in agricultural weeds: A review from ecological, evolutionary, and management perspectives

Agricultural weeds frequently hybridize with each other or with related crop species. Some hybrid weeds exhibit heterosis (hybrid vigor), which may be stabilized through mechanisms like genome duplication or vegetative reproduction. Even when heterosis is not stabilized, hybridization events diversify weed gene pools and often enable adaptive introgression. Consequently, hybridization may promote weed evolution and exacerbate weed-crop competition. However, hybridization does not always increase weediness. Even when viable and fertile, hybrid weeds sometimes prove unsuccessful in crop fields. This review provides an overview of weed hybridization and its management implications. We describe intrinsic and extrinsic factors that influence hybrid fitness in agroecosystems. We also survey the rapidly growing literature on crop-weed hybridization and the link between hybridization and invasiveness. These topics are increasingly relevant in this era of genetic tools for crop improvement, intensive and simplified cropping systems, and globalized trade. The review concludes with suggested research priorities, including hybridization in the context of climate change, plant-insect interactions, and redesigned weed management programs. From a weed management perspective, hybridization is one of many reasons that researchers and land managers must diversify their weed control toolkits.

Rate of crop-weed hybridization in Sorghum bicolor × Sorghum halepense is influenced by genetic background, pollen load, and the environment

The potential for gene flow between cultivated species and their weedy relatives poses agronomic and environmental concerns, particularly when there are opportunities for the transfer of adaptive or agronomic traits such as herbicide resistance into the weedy forms. Grain sorghum (Sorghum bicolor) is an important crop capable of interspecific hybridization with its weedy relative johnsongrass (Sorghum halepense). Previous findings have shown that triploid progenies resulting from S. bicolor × S. halepense crosses typically collapse with only a few developing into mature seeds, whereas tetraploids often fully develop. The objective of this experiment was to determine the impact of S. bicolor genotype and pollen competition on the frequency of hybridization between S. bicolor and S. halepense. A total of 12 different cytoplasmic male sterile S. bicolor genotypes were compared with their respective male fertile lines across 2 years, to assess the frequency of hybridization and seed set when S. halepense served as the pollinator parent. Results indicate significant differences in the frequency of interspecific hybridization among the S. bicolor genotypes, and pollen fertility in S. bicolor reduced the rate of this interspecific hybridization by up to two orders of magnitude. Further, hybridization rates greatly varied across the two study environments. Results are helpful for developing appropriate gene flow mitigation strategies and indicate that gene flow could be reduced by the selection of appropriate seed parents for sorghum hybrids.

Global whole-genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops

Common weedy rice plants are important genetic resources for modern breeding programs because they are the closest relatives to rice cultivars and their genomes contain elite genes. Determining the utility and copy numbers of WRKY and nucleotide-binding site (NBS) resistance-related genes may help to clarify their variation patterns and lead to crop improvements. In this study, the weedy rice line LM8 was examined at the whole-genome level. To identify the Oryza sativa japonica subpopulation that LM8 belongs to, the single nucleotide polymorphisms (SNPs) of 180 cultivated and 23 weedy rice varieties were used to construct a phylogenetic tree and a principal component analysis and STRUCTURE analysis were performed. The results indicated that LM8 with admixture components from japonica (GJ) and indica (XI) belonged to GJ-admixture (GJ-adm), with more than 60% of its genetic background derived from XI-2 (22.98%), GJ-tropical (22.86%), and GJ-subtropical (17.76%). Less than 9% of its genetic background was introgressed from weedy rice. Our results also suggested LM8 may have originated in a subtropical or tropical geographic region. Moreover, the comparisons with Nipponbare (NIP) and Shuhui498 (R498) revealed many specific structure variations (SVs) in the LM8 genome and fewer SVs between LM8 and NIP than between LM8 and R498. Next, 96 WRKY and 464 NBS genes were identified and mapped on LM8 chromosomes to eliminate redundancies. Three WRKY genes (ORUFILM02g002693, ORUFILM05g002725, and ORUFILM05g001757) in group III and one RNL [including the resistance to powdery mildew 8 (RPW8) domain, NBS, and leucine rich repeats (LRRs)] type NBS gene (ORUFILM12g000772) were detected in LM8. Among the NBS genes, the RPW8 domain was detected only in ORUFILM12g000772. This gene may improve plant resistance to pathogens as previously reported. Its classification and potential utility imply LM8 should be considered as a germplasm resource relevant for rice breeding programs.

Reducing Seed Shattering in Weedy Rice by Editing SH4 and qSH1 Genes: Implications in Environmental Biosafety and Weed Control through Transgene Mitigation

Mitigating the function of acquired transgenes in crop wild/weedy relatives can provide an ideal strategy to reduce the possible undesired environmental impacts of pollen-mediated transgene flow from genetically engineered (GE) crops. To explore a transgene mitigation system in rice, we edited the seed-shattering genes, SH4 and qSH1, using a weedy rice line ("C9") that originally had strong seed shattering. We also analyzed seed size-related traits, the total genomic transcriptomic data, and RT-qPCR expression of the SH4 or qSH1 gene-edited and SH4/qSH1 gene-edited weedy rice lines. Substantially reduced seed shattering was observed in all gene-edited weedy rice lines. The single gene-edited weedy rice lines, either the SH4 or qSH1 gene, did not show a consistent reduction in their seed size-related traits. In addition, reduced seed shattering was closely linked with the weakness and absence of abscission layers and reduced abscisic acid (ABA). Additionally, the genes closely associated with ABA biosynthesis and signaling transduction, as well as cell-wall hydrolysis, were downregulated in all gene-edited weedy rice lines. These findings facilitate our deep insights into the underlying mechanisms of reduced seed shattering in plants in the rice genus Oryza. In addition, such a mitigating technology also has practical applications for reducing the potential adverse environmental impacts caused by transgene flow and for managing the infestation of weedy rice by acquiring the mitigator from GE rice cultivars through natural gene flow.

Effects of Insect-Resistant Maize HGK60 on Community Diversity of Bacteria and Fungi in Rhizosphere Soil

The influence of biotech crops on microbial communities in rhizosphere soil is an important issue in biosafety assessments. The transgenic maize HGK60 harboring the Bt cry1Ah gene enhanced the resistance to lepidopteran pests, while the ecological risk of HGK60 maize on rhizosphere microorganisms is unclear. In this study, we comprehensively analyzed the diversity and composition of bacterial and fungal communities in the rhizosphere soil around Bt maize HGK60 and the near-isogenic non-Bt maize ZD958 at four growth stages via a high-throughput sequencing technique. The results showed that HGK60 maize unleashed temporary effects on the bacterial and fungal diversity and richness during the study plant's development, which would be restored after one cycle of plant cultivation due to the application of the same agricultural management. The differences of bacterial and fungal communities were marked by seasonality, while the different growth stage was the important factor as opposed to the cultivar contributing to the shifts in the bacterial and fungal communities' structure. This study will provide useful information regarding the impact of Bt transgenic maize on the soil microbiome and a theoretical basis for the development of a safety assessment approach for Bt maize in China.

Supporting in situ conservation of the genetic diversity of crop wild relatives using genomic technologies

The last decade has witnessed huge technological advances in genomics, particularly in DNA sequencing. Here, we review the actual and potential application of genomics in supporting in situ conservation of crop wild relatives (CWRs). In addition to helping in prioritization of protection of CWR taxa and in situ conservation sites, genome analysis is allowing the identification of novel alleles that need to be prioritized for conservation. Genomics is enabling the identification of potential sources of important adaptive traits that can guide the establishment or enrichment of in situ genetic reserves. Genomic tools also have the potential for developing a robust framework for monitoring and reporting genome‐based indicators of genetic diversity changes associated with factors such as land use or climate change. These tools have been demonstrated to have an important role in managing the conservation of populations, supporting sustainable access and utilization of CWR diversity, enhancing accelerated domestication of new crops and forensic genomics thus preventing misappropriation of genetic resources. Despite this great potential, many policy makers and conservation managers have failed to recognize and appreciate the need to accelerate the application of genomics to support the conservation and management of biodiversity in CWRs to underpin global food security. Funding and inadequate genomic expertise among conservation practitioners also remain major hindrances to the widespread application of genomics in conservation.

Fitness and Ecological Risk of Hybrid Progenies of Wild and Herbicide-Tolerant Soybeans With EPSPS Gene

Exogenous genes of transgenic crops are usually transferred to their wild-type relatives through pollen-mediated gene flow, which may change the ecological fitness and ability to invade wild populations, resulting in the weeding of wild plants and other unpredictable environmental impacts. In this study, the F₁ generation of herbicide-resistant soybeans and wild soybeans was obtained by artificial pollination, F₂ generation seeds were obtained by self-crossing, and the fitness of the parents and their F₁ and F₂ generations were tested. The foreign protein EPSPS was expressed normally in the hybrid between transgenic and wild soybeans; however, the protein expression was significantly lower than that in transgenic soybeans. The fitness of the F₁ hybrid between transgenic and wild soybeans was significantly lower than that of its parent. Compared with those of the wild soybeans, the F₂ generation soybeans improved in some fitness indices, while the emergence rate, pollen germination rate, and number of full seeds per pod, pods per plant, and full seeds per plant did not significantly differ. The aboveground biomass and 100-seed weight of the F₂ generation were higher than those of wild soybeans. Fitness among the F₂-negative plants, homozygous, and heterozygous positive plants did not significantly vary. Improved fitness and presence of foreign genes in the F₂ soybean were not significantly correlated. As the F₂ generation of transgenic and wild soybeans had no fitness cost and the flowering stage were overlapped, the foreign gene might still spread in the wild soybean population.

Increased Longevity and Dormancy of Soil-Buried Seeds from Advanced Crop–Wild Rice Hybrids Overexpressing the EPSPS Transgene

Simple Summary

Estimating the survival and reproductive ability caused by a transgene moved from a genetically engineered (GE) crop to its wild relative populations through gene flow plays an important role in assessing the potential environmental risks of the GE crop. Such estimation has essentially focused on the survival and reproduction-related characteristics above the ground, but with little attention to the GE seeds shattered in the soil seed banks. We demonstrated that the herbicide-resistant transgene overexpressing the rice endogenous EPSP enzyme increased the survival and longevity of the GE crop–wild (Oryza rufipogon) hybrid seeds in soil seed banks. In addition, enhanced survival and longevity of the GE hybrid seeds are likely associated with increases in seed dormancy and a growth hormone (auxin) via overexpressing the EPSPS transgene. Therefore, the EPSPS transgene can persist in the soil seed banks and spread in the environment, causing unwanted environmental impacts.

Abstract

Estimating the fitness effect conferred by a transgene introgressed into populations of wild relative species from a genetically engineered (GE) crop plays an important role in assessing the potential environmental risks caused by transgene flow. Such estimation has essentially focused on the survival and fecundity-related characteristics measured above the ground, but with little attention to the fate of GE seeds shattered in the soil seed banks after maturation. To explore the survival and longevity of GE seeds in soil, we examined the germination behaviors of crop–wild hybrid seeds (F₄–F₆) from the lineages of a GE herbicide-tolerant rice (Oryzasativa) line that contains an endogenous EPSPS transgene hybridized with two wild O. rufipogon populations after the seeds were buried in soil. The results showed significantly increased germination of the GE crop–wild hybrid seeds after soil burial, compared with that of the non-GE hybrid seeds. Additionally, the proportion of dormant seeds and the content of the growth hormone auxin (indole-3-acetic acid, IAA) in the GE crop–wild hybrid seeds significantly increased. Evidently, the EPSPS transgene enhances the survival and longevity of GE crop–wild rice seeds in the soil seed banks. The enhanced survival and longevity of the GE hybrid seeds is likely associated with the increases in seed dormancy and auxin (IAA) by overexpressing the rice endogenous EPSPS transgene. Thus, the fate of GE seeds in the soil seed banks should be earnestly considered when assessing the environmental risks caused by transgene flow.

Compositional differences in hybrids between protoporphyrinogen IX oxidase (PPO)-inhibiting herbicide-resistant transgenic rice and weedy rice accessions

We characterized the metabolites in grains of transgenic protoporphyrinogen IX oxidase-inhibiting herbicide-resistant rice and weedy accessions using GC-MS and examined whether the chemical composition of their hybrids differed from that of the parents. We found that the metabolite profiles of transgenic rice and weedy rice were clearly separated. Although the metabolite profiles of F₂ progeny were partially separated from their parents, zygosity did not affect the profiles. The F₂ progeny had similar or intermediate levels of most major nutritional components compared with their parents. However, levels of galactopyranose, trehalose, xylofuranose, mannitol, and benzoic acid were higher in the F₂ progeny. Some fatty acids and organic acids also showed prominent quantitative differences between the F₂ progeny and the parents. Changes in the metabolite levels of transgenic crop-weed hybrids compared to their parents might influence not only the ecological consequences of the hybrids, but also the nutritional quality and food safety.

Expression of Bt Protein in Transgenic Bt Cotton Plants and Ecological Fitness of These Plants in Different Habitats

Fitness is one of the key parameters to evaluate the effects of transgenic plants on the ecological environment. To evaluate the ecological risk of transgenic Bt cotton plants growing in different habitats, we determined the expression of the exogenous Bt gene and the fitness of transgenic and non-transgenic cotton plants in three habitats (farmland, grassland, and shrub). We observed that the expression of Bt protein in the farmland was significantly higher than that in the natural habitat, and when the growth environment was suitable, the Bt protein expression level showed a downward trend with the advancement of the growth. There were no significant differences in plant height, aboveground biomass, and seed yield between the Bt transgenic and non-transgenic cotton plants at the same growth stage under the same habitat. Nevertheless, in different habitats, the fitness of the same cotton line showed significant differences. In the farmland habitat, the plant height, aboveground biomass, and seed yield of both transgenic cotton and its non-transgenic isoline were significantly higher than that in the other two natural habitats. The results indicate that the expression of Bt protein does not increase the fitness of the parent plants and would not cause the weeding of the recipient cotton plants.

Phylogenetic origin and dispersal pattern of Taiwan weedy rice

BACKGROUND

Knowledge of the genetic diversity and spatial structure of Taiwan weedy red rice (WRR) populations, which adapted in a transplanting system, will facilitate the design of effective methods to control this weed by tracing its origins and dispersal patterns in a given region.

RESULTS

Taiwan WRR is genetically most similar to Taiwan indica cultivars and landraces according to genetic distance. The inbreeding coefficient of the Taiwan WRR population is greater than 0.8, which is similar to the inbred cultivars. The ancestry coefficients map suggests a dispersal pattern of long-distance and seed-mediated contamination across Taiwan, often from warmer, earlier-planted regions to cooler, later-planted regions. Parentage analysis of Taiwan WRR revealed that mostly early indica landraces and indica cultivars were present in the genetic pool; in rare cases temperate japonica was present. Based on the above results, the phylogenetic origin of most Taiwan weedy rice appears to be from hybrid progenies of old cultivated red rice accessions crossed with 'DGWG'. The inbreeding coefficient trend of the six TWR clusters suggests a temporal shift from 'old' indica landraces with red bran (high inbreeding coefficient) to modern indica varieties (low inbreeding coefficient).

CONCLUSION

Although there were sustained efforts to remove these old red rice accessions from paddy fields before 1945, some farmers continued to use low purity seed. This practice, along with volunteer cultivation of these old varieties in the second cropping season, apparently has facilitated the long-distance, seed-mediated contamination of rice seed, and the increase in weedy rice seed in paddy soil. © 2019 Society of Chemical Industry.

Genetic Engineering and Editing of Plants: An Analysis of New and Persisting Questions

Genetic engineering is a molecular biology technique that enables a gene or genes to be inserted into a plant's genome. The first genetically engineered plants were grown commercially in 1996, and the most common genetically engineered traits are herbicide and insect resistance. Questions and concerns have been raised about the effects of these traits on the environment and human health, many of which are addressed in a pair of 2008 and 2009 Annual Review of Plant Biology articles. As new science is published and new techniques like genome editing emerge, reanalysis of some of these issues, and a look at emerging issues, is warranted. Herein, an analysis of relevant scientific literature is used to present a scientific perspective on selected topics related to genetic engineering and genome editing.

The application of gene splitting technique for controlling transgene flow in rice

Controlling transgene flow in China is important, as this country is part of the center of origin of rice. A gene-splitting technique based on intein-mediated trans-splicing represents a new strategy for controlling transgene flow via biological measures. In this study, the G2-aroA gene which provides glyphosate tolerance was split into an N-terminal and a C-terminal region, which were then fused to intein N and intein C of the Ssp DnaE intein, ultimately forming EPSPSn:In and Ic:EPSPSc fusion genes, respectively. These fusion genes were subsequently transformed into the rice cultivar Zhonghua 11 via the Agrobacterium-mediated method. The two split gene fragments were then introduced into the same rice genome by genetic crossings. Glyphosate tolerance analysis revealed that the functional target protein was reconstituted by Ssp DnaE intein-mediated trans-splicing and that the resultant hybrid rice was glyphosate tolerant. The reassembly efficiency of the split gene fragments ranged from 67 to 91% at the molecular level, and 100% of the hybrid F1 progeny were glyphosate tolerant. Transgene flow experiments showed that when the split gene fragments are inserted into homologous chromosomes, the gene-splitting technique can completely avoid the escape of the target trait to the environment. This report is the first on the reassembly efficiency and effectiveness of transgene flow containment via gene splitting in rice. This study provides not only a new biological strategy for controlling rice transgene flow but also a new method for cultivating hybrid transgenic rice.

High-throughput sequencing analysis of microbial community diversity in response to indica and japonica bar-transgenic rice paddy soils

Potential environmental risks of genetically modified (GM) crops have raised concerns. To better understand the effect of transgenic rice on the bacterial community in paddy soil, a field experiment was carried out using pairs of rice varieties from two subspecies (indica and japonica) containing bar transgene with herbicide resistance and their parental conventional rice. The 16S rRNA gene of soil genomic DNA from different soil layers at the maturity stage was sequenced using high-throughput sequencing on the Illumina MiSeq platform to explore the microbial community diversity among different rice soils. There were no significant differences in diversity indices between transgenic japonica rice and its sister conventional rice (japonica pair) among different soil layers, but, significant differences was observed between transgenic indica rice and its conventional rice (indica pair) in the topsoil layer around concentrated rice roots according to the ace diversity index. Though the japonica rice soil and indica rice soil were shared several key genera, including Rivibacter, Anaeromyxobacter, Roseomonas, Geobacter, Thiobacillus, Clostridium, and Desulfobulbus, the primary bacterial genera in indica rice soil were different from those in japonica rice. Synechococcus and Dechloromonas were present in japonica rice samples, while Chloronema, Flexibacter, and Blastocatella were observed in indica rice soil. Moreover, the abundance of genera between GM and non-GM varieties in japonica rice was significantly different from indica rice, and several bacterial communities influenced these differences. Anaerovorax was more abundant in transgenic japonica rice soil than conventional rice soil, while it was deficient in transgenic indica rice soil compared to conventional rice soil, and opposite responses to Deferrisoma were in that of indica rice. Thus, we concluded that transgenic indica and japonica rice had different effects on soil bacteria compared with their corresponding sister conventional rice. However, these composition and abundance difference only occurred for a few genera but had no effect on the primary genera and soil characteristics were mainly contributed to these differences. Thus, differences in bacterial community structure can be ignored when evaluating the impacts of transgenic rice in the complex soil microenvironment.

When West Meets East: The Origins and Spread of Weedy Rice Between Continental and Island Southeast Asia

Weedy crop relatives are among the world’s most problematic agricultural weeds, and their ability to rapidly evolve can be enhanced by gene flow from both domesticated crop varieties and wild crop progenitor species. In this study, we examined the role of modern commercial crop cultivars, traditional landraces, and wild relatives in the recent emergence and proliferation of weedy rice in East Malaysia on the island of Borneo. This region of Malaysia is separated from the Asian continent by the South China Sea, and weedy rice has become a major problem there more recently than on the Malaysian peninsular mainland. Using 24 polymorphic SSR loci and genotype data from the awn-length domestication gene An-1, we assessed the genetic diversity, population structure and potential origins of East Malaysian weeds; 564 weedy, cultivated and wild rice accessions were analyzed from samples collected in East Malaysia, Peninsular Malaysia and neighboring countries. While there is considerable evidence for contributions of Peninsular Malaysian weed ecotypes to East Malaysian populations, we find that local crop cultivars and/or landraces from neighboring countries are also likely contributors to the weedy rice infestations. These findings highlight the implications of genetic admixture from different cultivar source populations in the spread of weedy crop relatives and the urgent need for preventive measurements to maintain sustainable crop yields.

The Genomics of Oryza Species Provides Insights into Rice Domestication and Heterosis

Here, we review recent progress in genetic and genomic studies of the diversity of Oryza species. In recent years, unlocking the genetic diversity of Oryza species has provided insights into the genomics of rice domestication, heterosis, and complex traits. Genome sequencing and analysis of numerous wild rice (Oryza rufipogon) and Asian cultivated rice (Oryza sativa) accessions have enabled the identification of genome-wide signatures of rice domestication and the unlocking of the origin of Asian cultivated rice. Moreover, similar studies on genome variations of African rice (Oryza glaberrima) cultivars and their closely related wild progenitor Oryza barthii accessions have provided strong evidence to support a theory of independent domestication in African rice. Integrated genomic approaches have efficiently investigated many heterotic loci in hybrid rice underlying yield heterosis advantages and revealed the genomic architecture of rice heterosis. We conclude that in-depth unlocking of genetic variations among Oryza species will further enhance rice breeding.

Fitness Cost of Transgenic cry1Ab/c Rice Under Saline-Alkaline Soil Condition

The environmental release and biosafety of transgenic Bt crops have attracted global attention. China has a large area of saline-alkali land, which is ideal for large-scale production of Bt transgenic rice. Therefore an understanding of the fitness of Bt transgenic rice in saline-alkaline soils and the ability to predict its long-term environmental effects are important for the future sustainable use of these crops. In the present study, we aimed to evaluate the fitness of cry1Ab/c transgenic rice in both farmland and natural ecosystems. Transgenic cry1Ab/c rice Huahui1, for which a national biosafety certificate was obtained, was grown on normal farmland and saline-alkaline soils in a glass greenhouse. The expression pattern of exogenous Cry1Ab/c protein, and vegetative and reproductive fitness of rice were assessed. The expression of the exogenous Cry1Ab/c protein in the transgenic rice grown on saline-alkaline soil was lower than that in the strain grown on farmland soil. Under both the soil conditions, vegetative growth abilities, as evaluated by tiller number and biomass, and reproductive growth abilities, as measured by filled grain number and filled grain weight per plant, showed a significantly higher fitness cost for Huahui1 than that for the parental rice Minghui63 grown under the same soil conditions. In saline-alkaline soil, the fitness cost of Huahui1was moderately higher than that of Minghui63. Therefore, the ecological risk of cry1Ab/c transgenic rice is not expected to be higher than that of parental rice Minghui63 if the former escapes into natural saline-alkaline soil. The results of the present study provide a scientific basis to improve environmental safety assessment of the insect-resistant transgenic rice strain Huahui1 before commercialization.

Influence of intergenotypic competition on multigenerational persistence of abiotic stress resistance transgenes in populations of Arabidopsis thaliana

Reducing crop losses due to abiotic stresses is a major target of agricultural biotechnology that will increase with climate change and global population growth. Concerns, however, have been raised about potential ecological impacts if transgenes become established in wild populations and cause increased competitiveness of weedy or invasive species. Potential risks will be a function of transgene movement, population sizes, and fitness effects on the recipient population. While key components influencing gene flow have been extensively investigated, there have been few studies on factors subsequent to transgene movement that can influence persistence and competitiveness. Here, we performed multiyear, multigenerational, assessment to examine fitness effects and persistence of three mechanistically different abiotic stress tolerance genes: C-repeat binding factor 3/drought responsive element binding factor 1a (CBF3/DREB1a); Salt overly sensitive 1 (SOS1); and Mannose-6-phosphate reductase (M6PR). Transgenic Arabidopsis thaliana overexpressing these genes were grown in pure populations and in competition with wild-type (WT) parents for six generations spanning a range of field environment conditions. Growth, development, biomass, seed production, and transgene frequency were measured at each generation. Seed planted for each generation was obtained from the previous generation as would occur during establishment of a new genotype in the environment. The three transgenes exhibited different fitness effects and followed different establishment trajectories. In comparison with pure populations, CBF3 lines exhibited reduced dry weight, seed yield, and viable seed yield, relative to WT background. In contrast, overexpression of SOS1 and M6PR did not significantly impact productivity measures in pure populations. In competition with WT, negative fitness effects were magnified. Transgene frequencies were significantly reduced for CBF3 and SOS1 while frequencies of M6PR appeared to be subject to genetic drift. These studies demonstrate the importance of fitness effects and intergenotype competition in influencing persistence of transgenes conferring complex traits.

Gene flow in Argentinian sunflowers as revealed by genotyping-by-sequencing data

Gene flow can have several different applied consequences, ranging from extinction to the escape of transgenes to the evolution of weedy or invasive lineages. Here, we describe patterns of hybridization and gene flow involving domesticated and wild sunflowers in Argentina. To address the risks of introgression of variants from the cultivated sunflower into invasive wild Helianthus, we used genotyping‐by‐sequencing (GBS) to genotype 182 samples from 11 sites in Argentina, along with previously published data from samples from the native range (North America), to determine the native source populations of the Argentinian samples and to detect admixture. We unexpectedly discovered two distinctive forms of H. petiolaris in Argentina, one from H. petiolaris subsp. petiolaris as expected, but the other from an unknown source. Extensive admixture was observed among Argentinian sunflowers, largely confirming phenotypic predictions. While many hybrids are F1s, there were signals consistent with introgression from the domesticated sunflower into H. petiolaris. Whether this introgression is incidental or a causal driver of invasiveness is not yet clear, but it seems likely that genes found in the domesticated sunflower genome (whether engineered or not) will quickly find their way into wild Argentinian sunflower populations.

Non-random transmission of parental alleles into crop-wild and crop-weed hybrid lineages separated by a transgene and neutral identifiers in rice

It is essential to assess environmental impact of transgene flow from genetically engineered crops to their wild or weedy relatives before commercialization. Measuring comparative trials of fitness in the transgene-flow-resulted hybrids plays the key role in the assessment, where the segregated isogenic hybrid lineages/subpopulations with or without a transgene of the same genomic background are involved. Here, we report substantial genomic differentiation between transgene-present and -absent lineages (F₂-F₃) divided by a glyphosate-resistance transgene from a crop-wild/weed hybrid population in rice. We further confirmed that such differentiation is attributed to increased frequencies of crop-parent alleles in transgenic hybrid lineages at multiple loci across the genome, as estimated by SSR (simple sequence repeat) markers. Such preferential transmission of parental alleles was also found in equally divided crop-wild/weed hybrid lineages with or without a particular neutral SSR identifier. We conclude that selecting either a transgene or neutral marker as an identifier to create hybrid lineages will result in different genomic background of the lineages due to non-random transmission of parental alleles. Non-random allele transmission may misrepresent the outcomes of fitness effects. We therefore propose seeking other means to evaluate fitness effects of transgenes for assessing environmental impact caused by crop-to-wild/weed gene flow.

Genetically engineered rice endogenous 5-enolpyruvoylshikimate-3-phosphate synthase (epsps) transgene alters phenology and fitness of crop-wild hybrid offspring

Genetically engineered (GE) rice endogenous epsps (5-enolpyruvoylshikimate-3-phosphate synthase) gene overexpressing EPSPS can increase glyphosate herbicide-resistance of cultivated rice. This type of epsps transgene can enhance the fecundity of rice crop-weed hybrid offspring in the absence of glyphosate, stimulating great concerns over undesired environmental impacts of transgene flow to populations of wild relatives. Here, we report the substantial alteration of phenology and fitness traits in F1-F3 crop-wild hybrid descendants derived from crosses between an epsps GE rice line and two endangered wild rice (Oryza rufipogon) populations, based on the common-garden field experiments. Under the glyphosate-free condition, transgenic hybrid lineages showed significantly earlier tillering and flowering, as well as increased fecundity and overwintering survival/regeneration abilities. In addition, a negative correlation was observed between the contents of endogenous EPSPS of wild, weedy, and cultivated rice parents and fitness differences caused by the incorporation of the epsps transgene. Namely, a lower level of endogenous EPSPS in the transgene-recipient populations displayed a more pronounced enhancement in fitness. The altered phenology and enhanced fitness of crop-wild hybrid offspring by the epsps transgene may cause unwanted environmental consequences when this type of glyphosate-resistance transgene introgressed into wild rice populations through gene flow.

Signatures of adaptation in the weedy rice genome

Crop domestication provided the calories that fueled the rise of civilization. For many crop species, domestication was accompanied by the evolution of weedy crop relatives, which aggressively outcompete crops and reduce harvests. Understanding the genetic mechanisms that underlie the evolution of weedy crop relatives is critical for agricultural weed management and food security. Here we use whole-genome sequences to examine the origin and adaptation of the two major strains of weedy rice found in the United States. We find that de-domestication from cultivated ancestors has had a major role in their evolution, with relatively few genetic changes required for the emergence of weediness traits. Weed strains likely evolved both early and late in the history of rice cultivation and represent an under-recognized component of the domestication process. Genomic regions identified here that show evidence of selection can be considered candidates for future genetic and functional analyses for rice improvement.

Model-based calculating tool for pollen-mediated gene flow frequencies in plants

The potential social-economic and environmental impacts caused by transgene flow from genetically engineered (GE) crops have stimulated worldwide biosafety concerns. To determine transgene flow frequencies resulted from pollination is the first critical step for assessing such impacts, in addition to the determination of transgene expression and fitness in crop-wild hybrid descendants. Two methods are commonly used to estimate pollen-mediated gene flow (PMGF) frequencies: field experimenting and mathematical modeling. Field experiments can provide relatively accurate results but are time/resource consuming. Modeling offers an effective complement for PMGF experimental assessment. However, many published models describe PMGF by mathematical equations and are practically not easy to use. To increase the application of PMGF modeling for the estimation of transgene flow, we established a tool to calculate PMGF frequencies based on a quasi-mechanistic PMGF model for wind-pollination species. This tool includes a calculating program displayed by an easy-operating interface. PMGF frequencies of different plant species can be quickly calculated under different environmental conditions by including a number of biological and wind speed parameters that can be measured in the fields/laboratories or obtained from published data. The tool is freely available in the public domain (http://ecology.fudan.edu.cn/userfiles/cn/files/Tool_Manual.zip). Case studies including rice, wheat, and maize demonstrated similar results between the calculated frequencies based on this tool and those from published PMGF data. This PMGF calculating tool will provide useful information for assessing and monitoring social-economic and environmental impacts caused by transgene flow from GE crops. This tool can also be applied to determine the isolation distances between GE and non-GE crops in a coexistence agro-ecosystem, and to ensure the purity of certified seeds by setting proper isolation distances among field production plots.

Development of Bt Rice and Bt Maize in China and Their Efficacy in Target Pest Control

Rice and maize are important cereal crops that serve as staple foods, feed, and industrial material in China. Multiple factors constrain the production of both crops, among which insect pests are an important one. Lepidopteran pests cause enormous yield losses for the crops annually. In order to control these pests, China plays an active role in development and application of genetic engineering (GE) to crops, and dozens of GE rice and GE maize lines expressing insecticidal proteins from the soil bacterium Bacillus thuringiensis (Bt) have been developed. Many lines have entered environmental release, field testing, and preproduction testing, and laboratory and field experiments have shown that most of the Bt rice and Bt maize lines developed in China exhibited effective control of major target lepidopteran pests on rice (Chilo suppressalis, Scirpophaga incertulas, and Cnaphalocrocismedinalis) and maize (Ostrinia furnacalis), demonstrating bright prospects for application. However, none of these Bt lines has yet been commercially planted through this writing in 2016. Challenges and perspectives for development and application of Bt rice and maize in China are discussed. This article provides a general context for colleagues to learn about research and development of Bt crops in China, and may shed light on future work in this field.