A strategy to provide long-term control of weedy rice while mitigating herbicide resistance transgene flow, and its potential use for other crops with related weeds

Key Roles of De-Domestication and Novel Mutation in Origin and Diversification of Global Weedy Rice

Simple Summary

Weedy rice is a noxious weed infesting rice fields worldwide and causing tremendous losses of rice yield and quality. The control of this conspecific weed is difficult owing to abundant genetic diversity associated with its complex origins and evolution. Applying different molecular methods, we demonstrate the multiple origins of weedy rice with the major pathway from its cultivar progenitors. The origin and diversification of weedy rice are also closely associated with differentiation of indica-japonica rice varieties. In addition, novel mutations are identified, which may promote continued evolution and genetic diversity of weedy rice. Knowledge generated from this study provides deep insights into the origin and evolution of conspecific weeds, in addition to the design of effective measures to control these weeds.

Abstract

Agricultural weeds pose great challenges to sustainable crop production, owing to their complex origins and abundant genetic diversity. Weedy rice (WD) infests rice fields worldwide causing tremendous losses of rice yield/quality. To explore WD origins and evolution, we analyzed DNA sequence polymorphisms of the seed shattering genes (sh4 and qsh1) in weedy, wild, and cultivated rice from a worldwide distribution. We also used microsatellite and insertion/deletion molecular fingerprinting to determine their genetic relationship and structure. Results indicate multiple origins of WD with most samples having evolved from their cultivated progenitors and a few samples from wild rice. WD that evolved from de-domestication showed distinct genetic structures associated with indica and japonica rice differentiation. In addition, the weed-unique haplotypes that were only identified in the WD samples suggest their novel mutations. Findings in this study demonstrate the key role of de-domestication in WD origins, in which indica and japonica cultivars stimulated further evolution and divergence of WD in various agroecosystems. Furthermore, novel mutations promote continued evolution and genetic diversity of WD adapting to different environments. Knowledge generated from this study provides deep insights into the origin and evolution of conspecific weeds, in addition to the design of effective measures to control these weeds.

Quantitative and Qualitative Evaluation of Sorghum bicolor L. under Intercropping with Legumes and Different Weed Control Methods

In order to evaluate the quantity and quality of forage when intercropping forage sorghum (Sorghum bicolor L.) with lathyrus (Lathyrus sativus) and hairy vetch (Vicia villosa), and using different weed management methods such as double cropping, a factorial experiment in a randomized complete block design with three replications was carried out at the research station of the University of Zanjan over two growing seasons (2015 and 2016). In this experiment, the intercropping of forage sorghum with lathyrus and hairy vetch at six levels with single cropping of forage sorghum, lathyrus, and hairy vetch, and three weed management strategies (no weed control, full weed control, and single weed control) was evaluated. The results showed that most forage sorghum traits were significantly (p ≤ 0.05) affected by different sowing ratios. The highest fresh forage yield of sorghum (77.9 ton/ha) and lowest (49.0 ton/ha) were obtained with sorghum + 33% hairy vetch and sorghum + 100% lathyrus, respectively. Forage qualitative traits were also affected by intercropping and weed management. The highest average acid detergent fiber (ADF), neutral detergent fiber (NDF), and total ash percentage (ASH) were obtained with 100% sorghum + 66% lathyrus and 33% hairy vetch. The results showed that sorghum intercropping with 33% lathyrus led to a significant reduction in dry matter intake and relative feed value with no weed control and single weed control. This study demonstrated that, by selecting the appropriate intercropping ratios and forage legumes, we could largely control sorghum weeds in addition to improving the quantitative and qualitative yield of sorghum forage.

Sorghum bicolor x S. halepense interspecific hybridization is influenced by the frequency of 2n gametes in S. bicolor

Tetraploid johnsongrass [Sorghum halepense (L.) Pers.] is a sexually-compatible weedy relative of diploid sorghum [Sorghum bicolor (L.) Moench]. To determine the extent of interspecific hybridization between male sterile grain sorghum and johnsongrass and the ploidy of their progeny, cytoplasmic (CMS), genetic (GMS) and chemically induced male sterile lines of Tx623 and Tx631 were pollinated with johnsongrass pollen. At maturity 1% and 0.07% of the developing seeds of Tx623 and Tx631 respectively were recovered. Ninety-one percent of recovered hybrids were tetraploid and two percent were triploid, the tetraploids resulting from 2n gametes present in the sorghum female parent. Their formation appears to be genotype dependent as more tetraploids were recovered from Tx623 than Tx631. Because a tetraploid sorghum x johnsongrass hybrid has a balanced genome, they are male and female fertile providing opportunities for gene flow between the two species. Given the differences in 2n gamete formation among Tx623 and Tx631, seed parent selection may be one way of reducing the likelihood of gene flow. These studies were conducted in controlled and optimum conditions; the actual outcrossing rate in natural conditions is expected to be much lower. More studies are needed to assess the rates of hybridization, fitness, and fertility of the progeny under field conditions.

Feral rice from introgression of weedy rice genes into transgenic herbicide-resistant hybrid-rice progeny

Pollen-mediated transgenic flow of herbicide resistance occurs bidirectionally between transgenic cultivated rice and weedy rice. The potential risk of weedy traits introgressing into hybrid rice has been underestimated and is poorly understood. In this study, two glufosinate-resistant transgenic rice varieties, hybrid rice (F1), and their succeeding generations (F2-F4) were planted for 3 years in field plots free of weedy rice adjacent to experimental weedy-rice fields. Weedy-rice-like (feral) plants that were both glufosinate-resistant and had red-pericarp seed were initially found only among the F3 generations of the two glufosinate-resistant transgenic hybrid cultivars. The composite fitness (an index based on eight productivity and weediness traits) of the feral progeny was significantly higher than that of the glufosinate-resistant transgenic hybrid (the original female parent of the feral progeny) under monoculture common garden conditions. The hybrid rice progeny segregated into individuals of variable height and extended flowering. The hybrid rice F2 generations had higher outcrossing rates by pollen reception (0.96-1.65%) than their progenitors (0.07-0.98%). The results show that herbicide-resistant weedy rice can rapidly arise by pollen-mediated gene flow from weedy to transgenic hybrid rice, and their segregating pollen-receptive progeny pose a greater agro-ecological risk than transgenic varieties. The safety assessment and management regulations for transgenic hybrid rice should take into account the risk of bidirectional gene flow.

Enhanced photosynthesis endows seedling growth vigour contributing to the competitive dominance of weedy rice over cultivated rice

BACKGROUND

Weedy rice, as one of the worst paddy field weeds worldwide, bears vigorous seedlings and dominantly competes with cultivated rice causing serious crop yield losses. To elucidate the causes of its stronger seedling vigour endowing its dominant competition with cultivated rice, comparative studies on seedling growth characteristics were conducted among six weedy rice biotypes and the two indica and japonica cultivars Shanyou-63 (SY-63) and Zhendao-8 (ZD-8), respectively, in the greenhouse.

RESULTS

Weedy rice emerged 2 to 3 days earlier, rapidly grew 1.3-1.7 cm taller daily, produced more secondary adventitious roots and greater aboveground fresh biomass than cultivated rice. Moreover, weedy rice exhibited greater photosynthetic pigment content, net photosynthetic rate, stomatal conductance, intercellular CO₂ concentration, transpiration rate, and chlorophyll fluorescence kinetic parameters. An enhanced overall photosynthetic activity in weedy rices was attributed to the combined action of a larger antenna, more active reaction centres and higher quantum yield for electron transfer beyond Q_A .

CONCLUSIONS

Enhanced photosynthesis of weedy rice at the seedling stage should be the main factor for leading to strong competitive dominance over cultivated rice. © 2016 Society of Chemical Industry.

Reduced weed seed shattering by silencing a cultivated rice gene: strategic mitigation for escaped transgenes

Transgene flow form a genetically engineered (GE) crop to its wild relatives may result in unwanted environmental consequences. Mitigating transgenes via introducing a gene that is disadvantageous to wild relatives but beneficial to crops, and is tightly-linked with the target transgenes, may provide a promising solution to limit the spread of transgenes in wild/weedy populations. Here we demonstrate a novel system with significantly reduced seed shattering in crop-weed hybrid descendants by partially silenced expression of the seed-shattering gene SH4 in cultivated rice, using artificial microRNA and antisense RNA techniques. Accordingly, fewer seeds were found in the soil of the field plots where transgenic hybrid lineages were grown. However, no differences in productivity-related traits were detected between GE and non-GE cultivated rice. To silence seed-shattering genes provides a useful strategy to reduce the potential environmental impacts caused by transgene flow from commercial GE rice to weedy rice, in addition to the control of weedy rice.

Can herbicide safeners allow selective control of weedy rice infesting rice crops?

BACKGROUND

Rice is a major field crop of paramount importance for global food security. However, the increased adoption of more profitable and resource-efficient direct-seeded rice (DSR) systems has contributed to greater weed infestations, including weedy rice, which has become a severe problem in several Asian regions. In this study we have developed a conceptually novel method to protect rice plants at high doses of clomazone and triallate.

RESULTS

The insecticide phorate applied to rice seeds provided a substantial level of protection against the herbicides clomazone or triallate. A quantity of 15 kg phorate ha^-1 significantly increased the LD₅₀ values, which were more than twofold greater than for rice plants treated only with clomazone. A quantity of 20 kg phorate ha^-1 in combination with 2000 g triallate ha^-1 safened rice plants (80% survival) with LD₅₀ >3.4-fold greater than in phorate-untreated rice. Weed control efficacy was not lowered by the presence of phorate-treated rice seeds.

CONCLUSION

Weedy rice is one of the most damaging global weeds and a major threat to DSR systems. In this study we have developed a proof-of-concept method to allow selective weedy rice control in rice crops. We call for herbicide discovery programmes and research to identify candidate safener and herbicide combinations to achieve selective herbicide control of weedy rice and alleviate weed infestations in global rice crops. © 2016 Society of Chemical Industry.

Transgene flow: facts, speculations and possible countermeasures

Convincing evidence has accumulated that unintended transgene escape occurs in oilseed rape, maize, cotton and creeping bentgrass. The escaped transgenes are found in variant cultivars, in wild type plants as well as in hybrids of sexually compatible species. The fact that in some cases stacked events are present that have not been planted commercially, implies unintended recombination of transgenic traits. As the consequences of this continuous transgene escape for the ecosystem cannot be reliably predicted, I propose to use more sophisticated approaches of gene technology in future. If possible GM plants should be constructed using either site-directed mutagenesis or cisgenic strategies to avoid the problem of transgene escape. In cases where a transgenic trait is needed, efficient containment should be the standard approach. Various strategies available or in development are discussed. Such a cautious approach in developing novel types of GM crops will enhance the sustainable potential of GM crops and thus increase the public trust in green gene technology.

Dealing with transgene flow of crop protection traits from crops to their relatives

Genes regularly move within species, to/from crops, as well as to their con- specific progenitors, feral and weedy forms ('vertical' gene flow). Genes occasionally move to/from crops and their distantly related, hardly sexually interbreeding relatives, within a genus or among closely related genera (diagonal gene flow). Regulators have singled out transgene flow as an issue, yet non-transgenic herbicide resistance traits pose equal problems, which cannot be mitigated. The risks are quite different from genes flowing to natural (wild) ecosystems versus ruderal and agroecosystems. Transgenic herbicide resistance poses a major risk if introgressed into weedy relatives; disease and insect resistance less so. Technologies have been proposed to contain genes within crops (chloroplast transformation, male sterility) that imperfectly prevent gene flow by pollen to the wild. Containment does not prevent related weeds from pollinating crops. Repeated backcrossing with weeds as pollen parents results in gene establishment in the weeds. Transgenic mitigation relies on coupling crop protection traits in a tandem construct with traits that lower the fitness of the related weeds. Mitigation traits can be morphological (dwarfing, no seed shatter) or chemical (sensitivity to a chemical used later in a rotation). Tandem mitigation traits are genetically linked and will move together. Mitigation traits can also be spread by inserting them in multicopy transposons which disperse faster than the crop protection genes in related weeds. Thus, there are gene flow risks mainly to weeds from some crop protection traits; risks that can and should be dealt with.

Multiple tissue-specific expression of rice seed-shattering gene SH4 regulated by its promoter pSH4

BACKGROUND

Rice seed shattering is an important domestication syndrome encoded by a gene named as SH4. The coding region of SH4 has been well studied regarding its function and roles in evolution. However, its promoter has not been identified, which limited our understanding of the detailed regulatory mechanisms of this gene. It is therefore critical to characterize the promoter and study its expression pattern.

RESULTS

We analyzed the 5' upstream sequences of this gene and identified a ~2.6 kb fragment with typical promoter features, which was designated as pSH4. The promoter contained a number of cis-acting elements related to abscisic acid (ABA) and a CpG island that were characteristics of multiple tissue-specific expression. We isolated and ligated pSH4 to the β-glucuronidase (GUS) reporter gene, and transformed it into a japonica rice cultivar to determine the multiple expression pattern of SH4. Histochemical location and fluorescence analyses of GUS activity of transgenic plants indicated multiple tissue-specific expression of pSH4 in the seed-pedicel junction region of mature panicles (with highest level), stems, coleoptiles of germinated seeds, and scutella of mature seeds.

CONCLUSIONS

The multiple tissue-specific expression pSH4 is categorized as a spatiotemporal promoter that drives the expression of the SH4 gene in different rice tissues, in addition to the seed-pedicel junction region. Our findings suggest that SH4 may have additional functions in the growth and development of rice, apart from its major role in seed shattering.

The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of United States weedy rice

The use of herbicide-resistant (HR) Clearfield rice (Oryza sativa) to control weedy rice has increased in the past 12 years to constitute about 60% of rice acreage in Arkansas, where most U.S. rice is grown. To assess the impact of HR cultivated rice on the herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a history of Clearfield rice. Panicles from each weedy type were harvested and tested for resistance to imazethapyr. The majority of plants sampled had at least 20% resistant offspring. These resistant weeds were 97 to 199 cm tall and initiated flowering from 78 to 128 d, generally later than recorded for accessions collected prior to the widespread use of Clearfield rice (i.e. historical accessions). Whereas the majority (70%) of historical accessions had straw-colored hulls, only 30% of contemporary HR weedy rice had straw-colored hulls. Analysis of genotyping-by-sequencing data showed that HR weeds were not genetically structured according to hull color, whereas historical weedy rice was separated into straw-hull and black-hull populations. A significant portion of the local rice crop genome was introgressed into HR weedy rice, which was rare in historical weedy accessions. Admixture analyses showed that HR weeds tend to possess crop haplotypes in the portion of chromosome 2 containing the ACETOLACTATE SYNTHASE gene, which confers herbicide resistance to Clearfield rice. Thus, U.S. HR weedy rice is a distinct population relative to historical weedy rice and shows modifications in morphology and phenology that are relevant to weed management.

Use of multicopy transposons bearing unfitness genes in weed control: four example scenarios

We speculate that multicopy transposons, carrying both fitness and unfitness genes, can provide new positive and negative selection options to intractable weed problems. Multicopy transposons rapidly disseminate through populations, appearing in approximately 100% of progeny, unlike nuclear transgenes, which appear in a proportion of segregating populations. Different unfitness transgenes and modes of propagation will be appropriate for different cases: (1) outcrossing Amaranthus spp. (that evolved resistances to major herbicides); (2) Lolium spp., important pasture grasses, yet herbicide-resistant weeds in crops; (3) rice (Oryza sativa), often infested with feral weedy rice, which interbreeds with the crop; and (4) self-compatible sorghum (Sorghum bicolor), which readily crosses with conspecific shattercane and with allotetraploid johnsongrass (Sorghum halepense). The speculated outcome of these scenarios is to generate weed populations that contain the unfitness gene and thus are easily controllable. Unfitness genes can be under chemically or environmentally inducible promoters, activated after gene dissemination, or under constitutive promoters where the gene function is utilized only at special times (e.g. sensitivity to an herbicide). The transposons can be vectored to the weeds by introgression from the crop (in rice, sorghum, and Lolium spp.) or from planted engineered weed (Amaranthus spp.) using a gene conferring the degradation of a no longer widely used herbicide, especially in tandem with an herbicide-resistant gene that kills all nonhybrids, facilitating the rapid dissemination of the multicopy transposons in a weedy population.

Gene expression related to seed shattering and the cell wall in cultivated and weedy rice

Seed shattering is an evolutionary trait that is essential to the survival of wild and weedy rice. Discovery of the qSH1 gene in rice subspecies Japonica and Sh4 in the rice subspecies Indica indicated the possibility that seed shattering is governed by major genes in a qualitative manner. However, observation of the large variability of seed shattering in weedy rice has led us to hypothesise that other genes related to abscission layer integrity could also be important in the regulation of seed shattering in rice. Gene expression 10 days after pollination and nucleotide composition revealed that qSH1 and Sh4 that are described as major players in seed shattering were not important in weedy rice. High expression of the gene OsCPL1 was positively associated with the occurrence of high seed shattering in weedy rice, which did not concur in previous studies of cultivated rice. This result is related to the absence of four SNPs and an indel in the OsCPL1 gene in weedy rice that are related to seed shattering in previous studies. Analysis of the expression of six genes related to cell wall synthesis/degradation revealed the importance of the genes OsXTH8 and OsCel9D in seed shattering in weedy rice. Therefore, in addition to qSH1 and Sh4, the genes OsCPL1, OsXTH8 and OsCel9D should be considered in studies of rice evolution and in the development of mitigation approaches of gene flow in transgenic rice.

A model of the relationship between weedy rice seed-bank dynamics and rice-crop infestation and damage in Jiangsu Province, China

BACKGROUND

A heavy infestation of weedy rice leading to no harvested rice has never been predicted in China due to a lack of knowledge about the weedy rice seed bank. We studied the seed-bank dynamics of weedy rice for three consecutive years and analyzed the relationship between seed-bank density and population density in order to predict future weedy rice infestations of direct-seeded rice at six sites along the Yangtze River in Jiangsu Province, China.

RESULTS

The seed-bank density of weedy rice in all six sites displayed an increasing trend with seasonal fluctuations. Weedy rice seeds found in the 0-10 cm soil layer contributed most to seedling emergence. An exponential curve expressed the relationship between cultivated rice yield loss and adult weedy rice density. Based on data collected during the weedy rice life-cycle, a semi-empirical mathematic model was developed that fits well with the experimental data in a way that could be used to predict seed-bank dynamics.

CONCLUSIONS

By integrating the semi-empirical model and the exponential curve, weedy rice infestation levels and crop losses can be predicted based on the seed-bank dynamics so that a practical control can be adopted before rice planting.

A novel 5-enolpyruvoylshikimate-3-phosphate (EPSP) synthase transgene for glyphosate resistance stimulates growth and fecundity in weedy rice (Oryza sativa) without herbicide

Understanding evolutionary interactions among crops and weeds can facilitate effective weed management. For example, gene flow from crops to their wild or weedy relatives can lead to rapid evolution in recipient populations. In rice (Oryza sativa), transgenic herbicide resistance is expected to spread to conspecific weedy rice (Oryza sativa f. spontanea) via hybridization. Here, we studied fitness effects of transgenic over-expression of a native 5-enolpyruvoylshikimate-3-phosphate synthase (epsps) gene developed to confer glyphosate resistance in rice. Controlling for genetic background, we examined physiological traits and field performance of crop-weed hybrid lineages that segregated for the presence or absence of this novel epsps transgene. Surprisingly, we found that transgenic F2 crop-weed hybrids produced 48-125% more seeds per plant than nontransgenic controls in monoculture- and mixed-planting designs without glyphosate application. Transgenic plants also had greater EPSPS protein levels, tryptophan concentrations, photosynthetic rates, and per cent seed germination compared with nontransgenic controls. Our findings suggest that over-expression of a native rice epsps gene can lead to fitness advantages, even without exposure to glyphosate. We hypothesize that over-expressed epsps may be useful to breeders and, if deployed, could result in fitness benefits in weedy relatives following transgene introgression.

Could abiotic stress tolerance in wild relatives of rice be used to improve Oryza sativa?

Oryza sativa and Oryza glaberrima have been selected to acquire and partition resources efficiently as part of the process of domestication. However, genetic diversity in cultivated rice is limited compared to wild Oryza species, in spite of 120,000 genotypes being held in gene banks. By contrast, there is untapped diversity in the more than 20 wild species of Oryza, some having been collected from just a few coastal locations (e.g. Oryza schlechteri), while others are widely distributed (e.g. Oryza nivara and Oryza rufipogon). The extent of DNA sequence diversity and phenotypic variation is still being established in wild Oryza, with genetic barriers suggesting a vast range of morphologies and function even within species, such as has been demonstrated for Oryza meridionalis. With increasing climate variability and attempts to make more marginal land arable, abiotic and biotic stresses will be managed over the coming decades by tapping into the genetic diversity of wild relatives of O. sativa. To help create a more targeted approach to sourcing wild rice germplasm for abiotic stress tolerance, we have created a climate distribution map by plotting the natural occurrence of all Oryza species against corresponding temperature and moisture data. We then discuss interspecific variation in phenotype and its significance for rice, followed by a discussion of ways to integrate germplasm from wild relatives into domesticated rice.

Gene flow from transgenic rice to red rice (Oryza sativa L.) in the field

In this study, we simulate a transgenic rice crop highly infested with red rice to examine transgene transfer from a transgenic line (A2504) resistant to glufosinate ammonium to cohabitant red rice. The red rice was sown along with the transgenic line at the highest density found in naturally infested crops in the region. Agricultural practices similar to those used to control red rice infestation in northern Italy rice fields were used to reproduce the local rice production system. During the first 2 years, the field was treated with herbicide at the appropriate time; in the first year the dosage of herbicide was three times the recommended amount. In this first year, detectable red rice plants that escaped herbicide treatment were manually removed. Nevertheless, two herbicide-resistant hybrid plants (named 101 and 104) were identified in the experimental field during the second year of cultivation. Phenotypic and molecular characterisation suggests the hybrid nature of these two plants, deriving from crossing events involving A2504, respectively, with red rice (plant 101) and the buffer cultivar Gladio (plant 104). The progeny of two subsequent generations of the two plants were examined and the presence of the transgene detected, indicating stable transfer of the transgene across generations. In conclusion, despite control methods, red rice progeny tolerant to the herbicide can be expected following use of transgenic rice and, consequently, difficulties in controlling this weed with chemicals will emerge in a relatively short time.

Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China

As a weed of rice paddy fields, weedy rice has spread worldwide. In northern China, the expansion of weedy rice has been rapid over the past two decades. Its evolutionary history and adaptive mechanisms are poorly understood. Evolutionary relationships between northern weedy rice and rice cultivars were analyzed using presumed neutral markers sampled across the rice genome. Genes involved in rice domestication were evaluated for their potential roles in weedy rice adaptation. Seed longevity, a critical trait of weedy rice, was examined in an F(2) population derived from a cross between weedy rice and a rice cultivar to evaluate weedy rice adaptation and the potential effect of candidate genes. Weedy rice in northern China was not derived directly from closely related wild Oryza species or from the introgression of indica subspecies. Introgression with local cultivars, coupled with selection that maintained weedy identity, shaped the evolution of weedy rice in northern China. Weedy rice is a unique system with which to investigate how weedy plants adapt to an agricultural environment. Our finding that extensive introgression from local cultivars, combined with the continuing ability to maintain weedy genes, is characteristic of weedy rice in northern China provides a clue for the field control of weedy rice.

Green revolution trees: semidwarfism transgenes modify gibberellins, promote root growth, enhance morphological diversity, and reduce competitiveness in hybrid poplar

Semidwarfism has been used extensively in row crops and horticulture to promote yield, reduce lodging, and improve harvest index, and it might have similar benefits for trees for short-rotation forestry or energy plantations, reclamation, phytoremediation, or other applications. We studied the effects of the dominant semidwarfism transgenes GA Insensitive (GAI) and Repressor of GAI-Like, which affect gibberellin (GA) action, and the GA catabolic gene, GA 2-oxidase, in nursery beds and in 2-year-old high-density stands of hybrid poplar (Populus tremula × Populus alba). Twenty-nine traits were analyzed, including measures of growth, morphology, and physiology. Endogenous GA levels were modified in most transgenic events; GA(20) and GA(8), in particular, had strong inverse associations with tree height. Nearly all measured traits varied significantly among genotypes, and several traits interacted with planting density, including aboveground biomass, root-shoot ratio, root fraction, branch angle, and crown depth. Semidwarfism promoted biomass allocation to roots over shoots and substantially increased rooting efficiency with most genes tested. The increased root proportion and increased leaf chlorophyll levels were associated with changes in leaf carbon isotope discrimination, indicating altered water use efficiency. Semidwarf trees had dramatically reduced growth when in direct competition with wild-type trees, supporting the hypothesis that semidwarfism genes could be effective tools to mitigate the spread of exotic, hybrid, and transgenic plants in wild and feral populations.

Sequence polymorphisms in wild, weedy, and cultivated rice suggest seed-shattering locus sh4 played a minor role in Asian rice domestication

The predominant view regarding Asian rice domestication is that the initial origin of nonshattering involved a single gene of large effect, specifically, the sh4 locus via the evolutionary replacement of a dominant allele for shattering with a recessive allele for reduced shattering. Data have accumulated to challenge this hypothesis. Specifically, a few studies have reported occasional seed-shattering plants from populations of the wild progenitor of cultivated rice (Oryza rufipogon complex) being homozygous for the putative "nonshattering" sh4 alleles. We tested the sh4 hypothesis for the domestication of cultivated rice by obtaining genotypes and phenotypes for a diverse set of samples of wild, weedy, and cultivated rice accessions. The cultivars were fixed for the putative "nonshattering" allele and nonshattering phenotype, but wild rice accessions are highly polymorphic for the putative "nonshattering" allele (frequency ∼26%) with shattering phenotype. All weedy rice accessions are the "nonshattering" genotype at the sh4 locus but with shattering phenotype. These data challenge the widely accepted hypothesis that a single nucleotide mutation ("G"/"T") of the sh4 locus is the major driving force for rice domestication. Instead, we hypothesize that unidentified shattering loci are responsible for the initial domestication of cultivated rice through reduced seed shattering.

Persistence of sunflower crop traits and fitness in Helianthus petiolaris populations

Transgenic plants have increased interest in the study of crop gene introgression in wild populations. Genes (or transgenes) conferring adaptive advantages persist in introgressed populations, enhancing competitiveness of wild or weedy plants. This represents an ecological risk that could increase problems of weed control. Introgression of cultivar alleles into wild plant populations via crop-wild hybridisations is primarily governed by their fitness effect. To evaluate this, we studied the second generation of seven wild-crop interspecific hybrids between weedy Helianthus petiolaris and cultivated sunflower, H. annuus var. macrocarpus. The second generation comprised open-pollinated progeny and backcrosses to the wild parent, mimicking crosses that occur in natural situations. We compared a number of morphological, life history and fitness traits. Multivariate analysis showed that the parental species H. annuus and H. petiolaris differed in a number of morphological traits, while the second hybrid generation between them was intermediate. Sunflower crop introgression lowered fitness of interspecific hybrids, but fitness parameters tended to recover in the following generation. Relative frequency of wild/weedy and introgressed plants was estimated through four generations, based on male and female parent fitness. In spite of several negative selection coefficients observed in the second generation, introgressed plants could be detected in stands of <100 weedy H. petiolaris populations. The rapid recovery of fecundity parameters leads to prediction that any trait conferring an ecological advantage will diffuse into the wild or weedy population, even if F1 hybrids have low fitness.

Transgenes for insect resistance reduce herbivory and enhance fecundity in advanced generations of crop-weed hybrids of rice

Gene flow from transgenic crops allows novel traits to spread to sexually compatible weeds. Traits such as resistance to insects may enhance the fitness of weeds, but few studies have tested for these effects under natural field conditions. We created F₂ and F₃ crop–weed hybrid lineages of genetically engineered rice (Oryza sativa) using lines with two transgene constructs, cowpea trypsin inhibitor (CpTI) and a Bt transgene linked to CpTI (Bt/CpTI). Experiments conducted in Fuzhou, China, demonstrated that CpTI alone did not significantly affect fecundity, although it reduced herbivory. In contrast, under certain conditions, Bt/CpTI conferred up to 79% less insect damage and 47% greater fecundity relative to nontransgenic controls, and a 44% increase in fecundity relative to the weedy parent. A small fitness cost was detected in F₃ progeny with Bt/CpTI when grown under low insect pressure and direct competition with transgene-negative controls. We conclude that Bt/CpTI transgenes may introgress into co-occurring weedy rice populations and contribute to greater seed production when target insects are abundant. However, the net fitness benefits that are associated with Bt/CpTI could be ephemeral if insect pressure is lacking, for example, because of widespread planting of Bt cultivars that suppress target insect populations.

Locus-dependent selection in crop-wild hybrids of lettuce under field conditions and its implication for GM crop development

Gene escape from crops has gained much attention in the last two decades, as transgenes introgressing into wild populations could affect the latter's ecological characteristics. However, different genes have different likelihoods of introgression. The mixture of selective forces provided by natural conditions creates an adaptive mosaic of alleles from both parental species. We investigated segregation patterns after hybridization between lettuce (Lactuca sativa) and its wild relative, L. serriola. Three generations of hybrids (S1, BC1, and BC1S1) were grown in habitats mimicking the wild parent's habitat. As control, we harvested S1 seedlings grown under controlled conditions, providing very limited possibility for selection. We used 89 AFLP loci, as well as more recently developed dominant markers, 115 retrotransposon markers (SSAP), and 28 NBS loci linked to resistance genes. For many loci, allele frequencies were biased in plants exposed to natural field conditions, including over-representation of crop alleles for various loci. Furthermore, Linkage disequilibrium was locally changed, allegedly by selection caused by the natural field conditions, providing ample opportunity for genetic hitchhiking. Our study indicates that when developing genetically modified crops, a judicious selection of insertion sites, based on knowledge of selective (dis)advantages of the surrounding crop genome under field conditions, could diminish transgene persistence.

Transgene introgression in crop relatives: molecular evidence and mitigation strategies

Incorporation of crop genes into wild and weedy relative populations (i.e. introgression) has long been of interest to ecologists and weed scientists. Potential negative outcomes that result from crop transgene introgression (e.g. extinction of native wild relative populations; invasive spread by wild or weedy hosts) have not been documented, and few examples of transgene introgression exist. However, molecular evidence of introgression from non-transgenic crops to their relatives continues to emerge, even for crops deemed low-risk candidates for transgene introgression. We posit that transgene introgression monitoring and mitigation strategies are warranted in cases in which transgenes are predicted to confer selective advantages and disadvantages to recipient hosts. The utility and consequences of such strategies are examined, and future directions provided.

Disease-reducing effect of Chromolaena odorata extract on sheath blight and other rice diseases

Sheath blight caused by Rhizoctonia solani (teleomorph: Thanatephorus cucumeris) is a major cause of crop loss in intensive rice production systems. No economically viable control methods have been developed. We screened aqueous extracts of common herbal plants that could reduce sheath blight lesions and found that foliar spraying and seed soaking application of extracts of either fresh or dried leaves of Chromolaena odorata gave up to 68% reduction in sheath blight lesion lengths under controlled and semi-field conditions. The observed reductions were not dependent on growth conditions of C. odorata and rice cultivar. The effect was observed until 21 days after inoculation and was not dependent on microbial activity. Under semi-field conditions, extracts also reduced severity of other important rice diseases, i.e., blast (Pyricularia oryzae) using foliar spray (up to 45%), brown spot (Bipolaris oryzae) using seed treatment (up to 57%), and bacterial blight (Xanthomonas oryzae pv. oryzae) using both application methods (up to 50%).

Evaluating biological containment strategies for pollen-mediated gene flow

Several biological containment methods have been developed to reduce pollen dispersal; many of them only have a proof of concept in a model plant species. This review focuses on biological containment measures which were tested for their long-term efficiency at the greenhouse or field scale level, i.e. plastid transformation, transgene excission, cleistogamy and cytoplasmic male sterility (CMS). Pollen-mediated gene transfer in transplastomic tobacco could occur at very low frequencies if the predominant mode of inheritance is maternal. Transgene excision from tobacco pollen can be made highly efficient by coexpression of two recombinases. For cleistogamous oilseed rape it was shown that some flowers were partially open depending on genotypes, environment and recording dates. Reports on the stability of CMS in maize and sunflower indicated that there is a high variability for different genotypes under different environmental conditions and over successive years. But for both crop types some stable lines could be selected. These data demonstrate that the biological containment methods discussed are very promising for reducing gene flow but that no single containment strategy provides 100% reduction. However, the necessary efficiency of biological containment methods depends on the level of containment required. The containment level may need to be higher for safety purposes (e.g. production of special plant-made pharmaceuticals), while much lower containment levels may already be sufficient to reach coexistence goals. It is concluded that where pollen-mediated gene flow must be prevented altogether, combinations of complementary containment systems will be required.

Advances in plant molecular farming

Plant molecular farming (PMF) is a new branch of plant biotechnology, where plants are engineered to produce recombinant pharmaceutical and industrial proteins in large quantities. As an emerging subdivision of the biopharmaceutical industry, PMF is still trying to gain comparable social acceptance as the already established production systems that produce these high valued proteins in microbial, yeast, or mammalian expression systems. This article reviews the various cost-effective technologies and strategies, which are being developed to improve yield and quality of the plant-derived pharmaceuticals, thereby making plant-based production system suitable alternatives to the existing systems. It also attempts to overview the different novel plant-derived pharmaceuticals and non-pharmaceutical protein products that are at various stages of clinical development or commercialization. It then discusses the biosafety and regulatory issues, which are crucial (if strictly adhered to) to eliminating potential health and environmental risks, which in turn is necessary to earning favorable public perception, thus ensuring the success of the industry.