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.

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.

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.

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.

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.

Weedy Rice Evolution:De-domestication or Semi-domestication?

Weeds,especially close relatives of crops,pose severe threats to agricultural production worldwide.As an evolutionary"evil twin"of cultivated rice,weedy rice(Oryza sativa f.spontanea)has emerged as a pernicious weed that evolved with strong growth and reproductive advantages,such as easy seed shattering and long seed dormancy,strong competitiveness for depriving resources,and robust environmental adaptability,to outcompete cultivated rice in the paddy field(Figure 1).

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.

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.

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.