Transgenic restorer rice line T1c-19 with stacked cry1C*/bar genes has low weediness potential without selection pressure

Stacked（insect and herbicide resistant） transgenic rice T1c-19 with cry1C＊/bar genes, its receptor rice Minghui 63（herein MH63） and a local two-line hybrid indica rice Fengliangyou Xiang 1（used as a control） were compared for agronomic performance under field conditions without the relevant selection pressures. Agronomic traits（plant height, tiller number, and aboveground dry biomass）, reproductive ability（pollen viability, panicle length, and filled grain number of main panicles, seed set, and grain yield）, and weediness characteristics（seed shattering, seed overwintering ability, and volunteer seedling recruitment） were used to assess the potential weediness without selection pressure of stacked transgene rice T1c-19. In wet direct-seeded and transplanted rice fields, T1c-19 and its receptor MH63 performed similarly regarding vegetative growth and reproductive ability, but both of them were significantly inferior to the control. T1c-19 did not display weed characteristics; it had weak overwintering ability, low seed shattering and failed to establish volunteers. Exogenous insect and herbicide resistance genes did not confer competitive advantage to transgenic rice T1c-19 grown in the field without the relevant selection pressures.

Occurrence pattern and morphological polymorphism of Chinese weedy rice

Rice,the main food crop in China,has been sporadically reported to suffer from weedy rice infestation.However,the overall occurrence and distribution pattern of Chinese weedy rice remains unclear because a systematic survey has not been conducted.In order to reveal the infestation of Chinese weedy rice,a field survey was conducted in 999 sampling sites all over the rice-growing regions in China from 2009 to 2016 using seven-scale visual scoring of the level of weed infestation.Weedy rice was found 39%occurrence incidence in a total of 387 sites.The sampling sites with 50%or higher overall weedy rice infestation index mainly radiated from Jiangsu,Heilongjiang,Ningxia and Guangdong to the whole East China,Northeast China,Northwest China and South China.A total of 45 morphological characters from 287 populations(collected simultaneously with the field survey)out of those occurred sites were observed and analyzed using multivariate analysis in common gardens with the same cultivation conditions in 2017 and 2019.Canonical correlation analysis showed that 45 morphological characters were significantly related to the latitude,mean temperature,minimum temperature,precipitation and mean diurnal range factors.The 287 weedy rice populations were divided into three morphological groups with climate-dependent geographical differentiation:strong tiller type only in Jiangsu,large leaf type in South China and Central China and large grain type mainly in North China.Weedy rice seriously infested rice fields and had a geography,climate and cultivated rice type-dependent morphological and biotype differentiation in China.It is suggested to pay attention to the harmfulness of weedy rice and adopt comprehensive control strategies.

Study on Damage Characteristics of Weedy Rice

In this study, several typical tralts of weedy rice and its damage charac-teristics were analyzed. The resuIts showed that the shattering of weedy rice was sometimes weaker than that of conventional rice. The newIy-harvested weedy rice seeds have certaln dormant period and a Iong active period, whiIe the conventional rice seeds have no dormant period but have a Iimited active period. In the direct seeding and intercropping rice fields where weedy rice occurs seriousIy Iast year, if not controI ed timeIy, weedy rice may caused a damage above 28%, sometimes even above 99%. After one season of cuItivation, the underground weedy rice and conventional rice seeds wiI be carbonized, Iosing their activity. The germination of underground weedy rice can be first induced, and when the Iast-season wheat is harvested, the germinated weedy rice can be kiI ed with 41% gIyphosate （3 000 mI/hm2）, thus the damage and expansion of weedy rice wiI be effectiveIy controI ed.

Effects of Soaking Cultivated Rice Seeds with Fulvic Acid on Physiological and Ecological Properties of Weedy Rice

[Objective] This study aimed to investigate the effects of soaking cultivated rice seeds with fulvic acid （FA） on physiological and ecological properties of weedy rice in the direct seeding cultivated rice field. [Method] Weedy rice JS-Y1 and culti-vated rice Nanjing 44 were used as experimental materials for field plot trials to an-alyze the effects of soaking cultivated rice seeds with 0 （water as control）, 4, 6, 8 g/L FA on til ering dynamics, plant height, chlorophyl content, photosynthetic perfor-mance, gas exchange parameters and yield components of weedy rice at different growth stages. [Result] Among the 4 plants/m2 weedy rice plots, with the increase of FA concentration, til er number, plant height, chlorophyl content, net photosynthetic rate （Pn）, stomatal conductance （Gs） and transpiration rate （Tr） of weedy rice were reduced. Under the 4-6 g/L FA concentration, til er numbers of weedy rice at differ-ent growth stages were reduced by 13.84%-35.71% compared with control at the same density and the most significant reduction was on the 22nd d after weedy rice germination; chlorophyl contents of weedy rice at the jointing stage were significant-ly reduced by 7.90%-8.88%. Furthermore, in the plots with 4 g/L FA, weedy rice plant heights at the heading stage and grain fil ing stage were significantly reduced by 6.37%-9.10%; Pn, Gs and Tr of weedy rice at the jointing stage and grain fil ing stage were significantly reduced by 10.19%-16.05%, 12.57%-23.33% and 10.28%-19.76%, respectively; 1 000-grain weight, effective panicle number per plant and panicles weight per plant of weedy rice at the maturity stage were significantly re-duced by 3.19%, 21.21% and 27.27%, correspondingly. [Conclusion] In 4 plants/m2 weedy rice plots, because soaking cultivated rice seeds with 4 g/L FA could regu-late the growth and development of cultivated rice, the soaking with FA could change the ecological relationship between cultivated rice and weedy rice, affect weedy rice physiological and ecological properties and al eviate the competitive inhi-bition of weedy rice on cultivated rice.

Genetic Diversity and Relationship of Weedy Rice in Taizhou City, Jiangsu Province, China

Microsatellite markers and morphological characteristics were used to explore the genetic diversity and possible origin of weedy rice in Taizhou City, Jiangsu Province, China. Fifty-two weedy rice (Oryza sativa L.) accessions were compared with two wild rice, four hybrid rice and five cultivars using 22 simple sequence repeat (SSR) primer pairs. A total of 107 fragments were amplified, averaging 5.6 alleles per primer pair. The polymorphic index content (PIC) values ranged from 0.3077 to 0.7951, averaging at 0.5870. The average genetic distance of all samples ranged from 0.02 to 0.46 with an average of 0.262. The genetic distance among Taizhou weedy rice ranged from 0.03 to 0.44 with an average of 0.224. Cluster analysis showed that all the weedy rice accessions from Taizhou City were indica, and could be subdivided into different genotypes. The majority (86%) of weedy rice was most closely related to hybrid rice. The Taizhou weedy rice accessions were morphologically similar, but still could be delineated into indica or japonica group by some morphological traits. It is suggested that the levels of genetic and morphological diversities of weedy rice in Taizhou City are low and these weedy rice plants originated from the segregating progenies of hybrid rice that had naturally introgressed with cultivated rice.

Fitness of F1 hybrids between stacked transgenic rice T1c-19 with cry1C*/bar genes and weedy rice

Compared to single-trait transgenic crops, stacked transgenic plants may be more prone to become weedy, and transgene flow from stacked transgenic plants to weedy relatives may pose a potential environmental risk because these hybrids could be more advantageous under specific environmental conditions. Evaluation of the potential environmental risk caused by stacked transgenes is essential for assessing the environmental consequences caused by crop-weed transgene flow. The agronomic performance of fitness-related traits was assessed in F1+(transgene positive) hybrids(using the transgenic line T1 c-19 as the paternal parent) in monoculture and mixed planting under presence or absence glufosinate pressure in the presence or absence of natural insect pressure and then compared with the performance of F1–(transgene negative) hybrids(using the non-transgenic line Minghui 63(MH63) as the paternal parent) and their weedy rice counterparts. The results demonstrated that compared with the F1– hybrids and weedy rice counterparts, the F1+ hybrid presented higher performance(P<0.05) or non-significant changes(P>0.05) under natural insect pressure, respectively, lower performance(P<0.05) or non-significant changes(P>0.05) in the absence of insect pressure in monoculture planting, respectively. And compared to weedy rice counterparts, the F1+ hybrid presented higher performance(P<0.05) or non-significant changes(P>0.05) in the presence or absence of insect pressure in mixed planting, respectively. The F1+ hybrids presented nonsignificant changes(P>0.05) under the presence or absence glufosinate pressure under insect or non-insect pressure in monoculture planting. The all F1+ hybrids and two of three F1– hybrids had significantly lower(P<0.05) seed shattering than the weedy rice counterparts. The potential risk of gene flow from T1 c-19 to weedy rice should be prevented due to the greater fitness advantage of F1 hybrids in the majority of cases.

iTRAQ-Based Proteomics Investigation of Critical Response Proteins in Embryo and Coleoptile During Rice Anaerobic Germination

Direct-seeding of rice has become popular in recent years due to its low cost and convenience,however,hypoxic condition limits seedling establishment.In this study,weedy rice WR04-6 with high germination ability under anaerobic conditions was used as a gene donor,and we successfully improved the seedling establishment rate of rice cultivar Qishanzhan(QSZ)based on selection of a new rice line R42 from the recombinant inbred line population.R42 inherited high anaerobic germination(AG)ability,and was used for isobaric tags for relative and absolute quantitation(iTRAQ)-based comparative proteomic studies with QSZ to further explore the molecular mechanism of AG.A total of 719 differentially abundant proteins(DAPs)were shared by R42 and QSZ responded to AG,and thus defined as common response DAPs.A total of 300 DAPs that responded to AG were only identified from R42,which were defined as tolerance-specific DAPs.The common response and tolerance-specific DAPs had similar biochemical reaction processes and metabolic pathways in response to anoxic stress,however,they involved different proteins.The tolerance-specific DAPs were involved in amino acid metabolism,starch and sucrose metabolism,tricarboxylic acid cycle pathway,ethylene synthesis pathway,cell wall-associated proteins and activity of active oxygen scavenging enzyme.The in silico protein-protein interactions for the top 60 DAPs indicated that tolerance-specific DAPs had relatively independent protein interaction networks in response to an anoxic environment compared with common response DAPs.The results of physiological indicators showed thatα-amylase and superoxide dismutase activities of R42 were significantly increased under anoxic conditions compared with aerobic conditions.Multiple lines of evidence from western blot,physiological analysis and quantitatDirect seeding of rice has become popular in recent years due to its low cost and convenience,however,hypoxic conditions can limit seedling establishment.In the present study,weedy rice WR04-6 with high germination ability in anaerobic conditions was used as the gene donor and successfully improved the seedling establishment rate of rice cultivar Qishanzhan(QSZ)based on selection of a new rice line R42 from the recombinant inbred line(RIL)population.R42 inherited the had high anaerobic germination(AG)ability,which was used for the isobaric tags for relative and absolute quantitation(iTRAQ)based comparative proteomic studies with QSZ to further explore the molecular mechanism of AG.A total of 719 differentially abundant proteins(DAPs)shared by R42 and QSZ responded to AG and were thus defined as common response DAPs.A total of 300 DAPs that responded to AG were only identified from R42,which were defined as tolerance-specific DAPs.The common response and tolerance-specific DAPs had similar biochemical reaction processes and metabolic pathways in response to anoxic stress,however they involved different proteins.The 300 tolerance-specific DAPs were involved in amino acid metabolism,starch and sucrose metabolism,TCA cycle pathways,ethylene synthesis pathway,cell wall-associated proteins and activity of active oxygen scavenging enzyme.The in silico protein-protein interactions for the top 60 DAPs indicated that tolerance-specific DAPs had relatively independent protein interaction networks in response to an anoxic environment compared with common response DAPs.The results of physiological indicators showed thatα-amylase and SOD activities of R42 were significantly increased under anoxic conditions compared with aerobic conditions.Multiple lines of evidence from western blot,physiological analyses and real-time PCR jointly supported the reliability of proteomics data.In summary,our findings deepened the understanding of the molecular mechanism for the rice response to AG.ive real-time PCR jointly supported the reliability of proteomics data.In summary,our findings deepened the understanding of the molecular mechanism for the rice response to AG.

Weedy red rice has novel sources of resistance to biotic stress

Weedy red rice(Oryza sativa;WRR),a close relative of cultivated rice,is a highly competitive weed that commonly infests rice fields and can also naturally interbreed with rice.Useful genes for biotic stress have been maintained in WRR and can be explored for breeding.Here we describe genetic and physiological traits of WRR that can be beneficial in preventing major rice diseases.Rice blast,caused by the hemibiotrophic fungal pathogen Magnaporthe oryzae,and sheath blight disease,caused by the necrotrophic pathogen Rhizoctonia solani,are the two most damaging biotic stresses of rice.Many major and minor resistance genes and QTL have been identified in cultivated and wild rice relatives.However,novel QTL were recently found in the two major U.S.biotypes of WRR,blackhull-awned(BH)and strawhullawnless(SH),suggesting that WRR has evolved novel genetic mechanisms to cope with these biotic stresses.Twenty-eight accessions of WRR(PI 653412–PI 653439)from the southern USA were characterized and placed in the National Small Grains Collection,and are available for identification of novel genetic factors to prevent biotic stress.

Weed growth, herbicide efficacy, and rice productivity in dry seeded paddy field under different wheat stubble management methods

To ascertain the influence of wheat stubble management options and chemical weed control methods on weed growth and productivity of dry direct-seeded fine rice, a two years' field study was undertaken at the Agronomic Research Farm, University of Agriculture, Faisalabad, Pakistan in 2013 and 2014. Different wheat stubble management methods, viz., incorporation, burning and retention were executed during seed-bed preparation. While, herbicide treatments comprised of a weed check, weed free, pendimethalin followed by tank mixture of fenoxaprop p-ethyl+ethoxysulfuron ethyl, and bispyribac sodium followed by tank mixture of fenoxaprop p-ethyl+ethoxysulfuron ethyl. Results revealed that weed control efficacy of both herbicide treatments ranged from 84 to 94%. Herbicide treatments significantly reduced weed density(88–90%) and dry weight(86–88%), while improved the rice growth attributes compared with weed check. Application of bispyribac sodium followed by tank mixture of fenoxaprop p-ethyl+ethoxysulfuron ethyl in stubble retention recorded 226 and 273% increase in kernel yield over weedy check in 2013 and 2014, respectively. In stubble incorporation, pendimethalin followed by tank mixture of fenoxaprop p-ethyl+ethoxysulfuron ethyl was more effective in increasing(256–293%) rice yields over weedy check. Among different treatment combinations, the maximum net benefits(1 397.49^(–1) 472.22 USD ha^(–1)), net returns(636–700 USD ha^(–1)), benefit cost ratio(1.77^(–1).83) and marginal rate of return(2 187–2 330%) were recorded with the application of bispyribac sodium followed by fenoxaprop p-ethyl+ethoxysulfuron ethyl in stubble retention. In crux, application of bispyribac sodium followed by tank mixture of fenoxaprop p-ethyl+ethoxysulfuron ethyl in stubble retention is efficient approach to control weeds, and get maximum rice productivity and net economic returns under dry seeded system.

Transgene Flow from Glufosinate-Resistant Rice to Improved and Weedy Rice in China

The development of transgenic rice with novel traits in China can increase rice productivity, but transgene flow to improved or weedy rice has become a major concern. We aimed to evaluate the potential maximum frequencies of transgene flow from glufosinate-resistant rice to improved rice cultivars and weedy rice. Treatments were arranged in randomized complete blocks with three replicates. Experiments were conducted between 2009 and 2010 at the Center for Environmental Safety Supervision and Inspection for Genetically Modified Plants, China National Rice Research Institute, Hangzhou, China. Glufosinate-resistant japonica rice 99-1 was the pollen donor. The pollen recipients were two inbred japonica rice （Chunjiang 016 and Xiushui 09）, two inbred indica rice （Zhongzu 14 and Zhongzao 22）, two indica hybrid rice （Zhongzheyou 1 and Guodao 1）, and one weedy indica rice （Taizhou weedy rice）. The offspring of recipients were planted in the field and sprayed with a commercial dose of glufosinate. Leaf tissues of survivors were analyzed by polymerase chain reaction to detect the presence of the transgene. The frequency of gene flow ranged from 0 to 0.488%. In 2009, the order of gene flow frequency was as follows： weedy rice 〉 Chunjiang 016 〉 Xiushui 09 and Zhongzu 14 〉 Guodao 1, Zhongzheyou 1 and Zhongzao 22. Gene flow frequencies were generally higher in 2009 than in 2010, but did not differ significantly among rice materials. Gene flow frequency was the highest in weedy rice followed by the inbred japonica rice. The risk of gene flow differed significantly between years and year-to-year variance could mask risk differences among pollen recipients. Gene flow was generally lesser in taller pollen recipients than in shorter ones, but plant height only accounted for about 30% of variation in gene flow. When flowering synchrony was maximized, as in this study, low frequencies of gene flow occurred from herbicide-resistant japonica rice to other cultivars and weedy rice. Averaged across years, the risk of gene flow to weedy rice was higher than that of improved rice and hybrids. Greater resources must be dedicated to the management of remnant weedy rice in fields planted with herbicide-resistant rice, and to prevent the evolution of resistant weedy rice populations.

Evaluation of Population Structure, Genetic Diversity and Origin of Northeast Asia Weedy Rice Based on Simple Sequence Repeat Markers

Weedy rice exerts a severe impact on rice production by competing for sunlight, water and nutrients. This study assayed the population structure, genetic diversity and origin of Northeast Asia weedy rice by using 48 simple sequence repeat markers. The results showed that weedy rice in Northeast Asia had a high genetic diversity, with Shannon＇s diversity index （I） of 0.748 and the heterozygosity （He） of 0.434. In each regional population, I value varied widely. The widest range of I （0.228-0.489） was observed in the weedy rice of Eastern China, which was larger than that of Northeast China and Korea （0.168-0.270）. The F-statistics of regional populations （Fis, Fit and Fst） also showed higher values in the weedy rice of Eastern China than those of Northeast China and Korea All weedy rice accessions were grouped into two clusters in the unweighted pair group method with arithmetic mean cluster analysis dendrogram, namely Eastern China branch and Northeastern China plus Korea branch. There was significant differentiation in genetic characteristics in weedy rice of northeastern and eastern Asia, especially in Eastern China.

Study on Difference in Cold Tolerance Between Weedy Rice and Cultivated Rice in Heilongjiang Province of China

A long-red awn weedy rice and rice cultivars named Ken99004（ZCI）, Crossing-503（ZC2）, Ken Sticky Rice（ZC3）, Shashani（ZC4）, Long-Grain Aromatic Rice（ZC5） were used to study typical wild traits of weedy rice and to identify the cold resistance of all genotypes. The results showed that the stem of long-red awn weedy rice was the weakest. No difference was found in the early stage of rice growth, e.g. the vegetable growth stage, between long-red awn weedy rice and other rice cultivars in the stem rigidity, but in the later stage, or reproductive growth stage, their leaves and stems were senescent rapidly because of the speedy supply of nutrients for panicle growth, meanwhile the rigidity of stem was reduced sharply just as withered weeds. The germination rate of long- red awn weedy rice was the highest in cold condition, and in turn were ZCI, ZC2, ZC3, ZC4, ZC5, respectively. The performances of genotypes in cold tolerance were identical, those with a high ability of germination in low temperature also showed a strong cold tolerance in main traits in whole growth period, the order from strong to weak in the extent of cold tolerance were long-red awn weedy rice, ZCl, ZC2, ZC3, ZC4, ZC5, respectively

Weedy Rice(Oryza sativa L.)Problem in Rice(Oryza sativa L.)Based Cropping Systems in the Philippines

A study was undertaken in February 2012 to understand the knowledge and practices of rice farmers about weedy rice in two municipalities of Iloilo, Philippines. The specific objectives of the study were to establish what rice farmers know about weedy rice, examine rice farmers’ practices in managing weedy rice, and recommend policies on weedy rice management based on the results of the study. Farmers’ knowledge of weedy rice did not differ much between two villages. Results showed that 41% from the second most affected village and 33% from the most affected village thought that weedy rice cannot reduce the market value of the harvested rice. Majority of the farmers (68%) responded that awns can be absent in some weedy rice and about 40% of the farmers did not know that seeds of weedy rice have dormancy. Cutting the weedy rice panicles at harvest, as the best way of reducing weedy rice, was practiced by majority of the respondents (82%) from the most affected village. Our study suggests that there is a need to increase awareness about weedy rice among Asian farmers.

Allele Types of Rc Gene of Weedy Rice from Jiangsu Province, China

Weedy rice （Oryza sativa f. spontanea）, the predominant type of which has a red pericarp, seriously inhibits growth and yield of direct-seeded rice in Jiangsu Province, China. In this study, we randomly selected 10 weedy rice accessions from 10 plots in Jiangsu, and then sequenced the full lengths of their Rc genes （approximately 6.4 kb）. In addition, we collected 166 different full-length Rc genes in the Oryza genus from the literature and from GenBank. A collinearity sequence analysis showed that the 10 weedy rice accessions from Jiangsu all had the same wild-type allele of the Rc gene. Single nucleotide polymorphisms indicated that the nucleotide polymorphisms （π= 0.19） and the proportion of segregation sites （ew = 0.28） of the Rc genes in the 10 weedy rice accessions from Jiangsu were higher than those in 56 weedy rice accessions from USA （π = 0.09 and θw = 0.07）. Haplotype and phylogenetic analyses showed that the Rc genes of weedy rice accessions from Jiangsu were not revertants of the rc gene found in Asian cultivated rice （O. sativa） varieties with white pericarp. In addition, Rc gene sequences of the rice varieties Lvdao from Lianyungang, Jiangsu and Tangdao from Anhui were more similar to those of cultivated rice than to the weedy rice from Jiangsu. These findings support the continued quarantine of weedy rice and clarify the evolutionary mechanism of the red pericarp found in the weedy rice of Jiangsu.

The Distribution of Riparian Corridor Plants and the Relations to River Water Salinity along Perai River,Penang,Malaysia

Ecological surveys were carried out to investigate the distribution and characterization of riparian corridor plants along the Perai River,Penang,Malaysia from July 2007 to March 2008.Surveys were design to represent horizon-tal sections of the river starting from the river mouth towards the upper reaches for 20 km.A total of 84 species of plants from 30 families were recorded.They consisted of 28 species of standing plants(plants with height of more than 1 m)and 56 species of weedy plants(plants with height of less than 1 m).Standing plants consisted of ferns,palms,herbs,shrubs and mangroves while weedy plants comprised of aroids,grasses,sedges and broad leaf weed.Species abundance and dominance for each zone were relatively different.Dominant species was determined using Important Species Index(ISI).Based on ISI,the important species of standing plants were Sonneratia alba,Acrostichum aureum,Nypa fruti-cans,Avicennia marina,Rhizophora apiculata,Acrostichum speciosum and Rhizophora mucronata.Weedy plants were dominated by Mikania micrantha,Cryptocoryne ciliata,Wedelia trilobata and Asystasia intrusa.The distribution of the corridor plant species was closely related to the pattern of river water salinity measurements.The distribution of mangrove species with tolerance and adaptation to seawater appeared as follows:Avicennia marina,Rhizophora apiculata,Rhizo-phora mucronata,Sonneratia alba,Nypa fructicans,Acrostichum aureum and Acrostichum speciosum.

Most Tibetan weedy barleys originated via recombination between Btr1 and Btr2 in domesticated barley

Tibetan weedy barleys reside at the edges of qingke(hulless barley)fields in Tibet(Xizang).The spikes of these weedy barleys contain or lack a brittle rachis,with either two-or six-rowed spikes and either hulled or hulless grains at maturity.Although the brittle rachis trait of Tibetan weedy barleys is similar to that of wild barley(Hordeum vulgare ssp.spontaneum Thell.),these plants share genetic similarity with domesticated barley.The origin of Tibetan weedy barleys continues to be debated.Here,we show that most Tibetan weedy barleys originated from cross-pollinated hybridization of domesticated barleys,followed by hybrid self-pollination and recombination between Non-brittle rachis 1(btr1)and 2(btr2).We discovered the specific genetic ancestry of these weedy barleys in South Asian accessions.Tibetan weedy barleys exhibit lower genetic diversity than wild and Chinese landraces/cultivars and share a close relationship with qingke,genetically differing from typical eastern and western barley populations.We classified Tibetan weedy barleys into two groups,brittle rachis(BR)and non-brittle rachis(NBR);these traits align with the haplotypes of the btr1 and btr2 genes.Whereas wild barleys carry haplotype combinations of Btr1 and Btr2,each showing lower proportions in a population,the recombinant haplotype BTR2H8+BTR1H24 is predominant in the BR group.Haplotype block analysis based on whole-genome sequencing revealed two recombination breakpoints,which are present in 80.6%and 16.8%of BR acces-sions according to marker-assisted analysis.Hybridization events between wild and domesticated barley were rarely detected.Thesefindings support the notion that Tibetan weedy barleys originated via recom-bination between Btr1 and Btr2 in domesticated barley.

Evolutionary Genomics of Weedy Rice in the USA

Red rice Is an Interfertlle, weedy form of cultivated rice （Oryza sativa L.） that competes aggressively with the crop In the southern US, reducing yields and contaminating harvests. No wild Oryza species occur In North America and the weed has been proposed to have evolved through multiple mechanisms, Including ＂de-domestication＂ of US crop cultlvars, accidental introduction of Asian weeds, and hybridization between US crops and Asian wild/weedy Oryza strains. The phenotype of US red rice ranges from ＂crop mimics＂, which share some domestication traits with the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity have Indicated that many weed strains are closely related to Asian taxa （Including indica and aus rice varieties, which have never been cultivated In the US, and the Asian crop progenitor O. ruflpogon）, whereas others show genetic similarity to the tropical Japonica varieties cultivated In the southern US. Herein, we review what Is known about the evolutionary origins and genetic diversity of US red rice and describe an ongoing research project to further characterize the evolutionary genomlcs of this aggressive weed.

Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game

Crop weediness,especially that of weedy rice(Oryza sativa f.spontanea),remains mysterious.Weedy rice possesses robust ecological adaptability;however,how this strain originated and gradually formed proprietary genetic features remains unclear?Here,we demonstrate that weedy rice at Asian high latitudes(WRAH)is phylogenetically well defined and possesses unselected genomic characteristics in many divergence regions between weedy and cultivated rice.We also identified novel quantitative trait loci underlying weedy-specific traits,and revealed that a genome block on the end of chromosome 1 is associated with rice weediness.To identify the genomic modifications underlying weedy rice evolution,we generated the first de novo assembly of a high-quality weedy rice genome(WR04-6),and conducted a comparative genomics study between WR04-6 with other rice reference genomes.Multiple lines of evidence,including the results of demographic scenario comparisons,suggest that differentiation between weedy rice and cultivated rice was initiated by genetic improvement of cultivated rice and that the essence of weediness arose through semi-domestication.A plant height model further implied that the origin of WRAH can be modeled as an evolutionary game and indicated that strategy-based selection driven by fitness shaped its genomic diversity.

Efficacy of insect-resistance Bt/Cp TI transgenes in F5–F7generations of rice crop–weed hybrid progeny: implications for assessing ecological impact of transgene flow

Ecological impact of transgene flow into pop- ulations of wild/weedy relatives is associated with fitness effects in hybrid progeny. Most studies assessing fitness effects focus essentially on early-generation hybrid progeny. However, whether the transgenes remain effective and durable in advanced generations of hybrid progeny remains unclear. We conducted a common garden experi- ment with Fs-F7 hybrid progeny derived from crosses between insect-resistant transgenic （Bt/CpTI） rice and weedy rice, to examine their insect resistance and fitness effects of transgenes on progeny. Hybrid progeny were grown under different insect pressures and cultivation modes where insect damage and fitness-related traits were measured in the same growth season. Plants with transgenes showed significantly lower insect damage （10 % vs. 32 %） and higher fecundity （551 vs. 392 seeds/plant） than those without transgenes in the efficacy of transgenes Fs-F7 populations, suggesting for insect resistance. Fitness benefits of the transgenes were similar among the Fs-F7 populations, indicating the stability of transgenic effects. A positive correlation between insect index and fecundity change was detected, stressing the important role of ambient insect pressures in assessing fitness effects caused by insect-resistance transgenes. Our results have important implications for assessing ecological impacts caused by transgene flow to wild/weedy relatives. For cost-effec- tiveness, the experimental estimation of fitness effects is probably sufficient based on data from hybrids in early generations. Given that fitness effects of insect-resistance transgenes are associated with ambient insect pressure, ecological risk assessment on transgene flow should consider this variable in experimental design, reasonably reflecting actual situations in wild/weedy populations.

Population genomic analysis reveals domestication of cultivated rye from weedy rye

Rye(Secale cereale)is an important crop with multiple uses and a valuable genetic resource for wheat breeding.However,due to its complex genome and outcrossing nature,the origin of cultivated rye remains elusive.The geneticist N.I.Vavilov proposed that cultivated rye had been domesticated from weedy rye,rather than directly from wild species like other crops.Unraveling the domestication history of rye will extend our understanding of crop evolution and upend our inherent understanding of agricultural weeds.To this end,in this study we generated the 8.5 Tb of whole-genome resequencing data from 116 worldwide accessions of wild,weedy,and cultivated rye,and demonstrated that cultivated rye was domesticated directly from weedy relatives with a similar but enhanced genomic selection by humans.We found that a repertoire of genes that experienced artificial selection is associated with important agronomic traits,including shattering,grain yield,and disease resistance.Furthermore,we identified a composite introgression in cultivated rye from the wild perennial Secale strictum and detected a 2-Mb introgressed fragment containing a candidate ammonium transporter gene with potential effect on the grain yield and plant growth of rye.Taken together,our findings unravel the domestication history of cultivated rye,suggest that interspecific introgression serves as one of the likely causes of obscure species taxonomy of the genus Secale,and provide an important resource for future rye and wheat breeding.