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.

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.

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.

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.