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Morphological Characterization of Weedy Rice Populations from Different Regions of Asia | Zhang 1,2 | Molecular Plant Breeding

Research Article

Morphological Characterization of Weedy Rice Populations from Different Regions of Asia  

Shulin Zhang1,2 , Li Tian1 , Juan Li2 , Cong Wang1 , Dongsun  Lee2 , Renhai  Peng1 , Lijuan Chen2
1 College of Biology and Food Technology, Anyang Institute of Technology, Anyang, 455000, China
2 Rice Research Institute, Yunnan Agricultural University, Kunming, 650201, China
Author    Correspondence author
Molecular Plant Breeding, 2017, Vol. 8, No. 6   doi: 10.5376/mpb.2017.08.0006
Received: 09 Jun., 2017    Accepted: 26 Jun., 2017    Published: 28 Jul., 2017
© 2017 BioPublisher Publishing Platform
This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Zhang S.L., Tian L., Li J., Lee D.S., Peng R.H., and Chen L.J., 2017, Morphological characterization of weedy rice populations from different regions of Asia, Molecular Plant Breeding, 8(6): 52-64 (doi: 10.5376/mpb.2017.08.0006)


Weedy rice produces a low number of grains per plant and is considered undesirable in cultivated rice fields. It spreads rapidly because of its high phenotypic plasticity and seed shattering. We used the RID14 marker to identify the genotypes governing red and white pericarp color in weedy rice. We then evaluated 18 characters of 199 weedy rice accessions (5 rice-growing regions in Asia) and 24 of cultivated rice as control, and analyzed them using coefficients of variation, principal component analysis, and cluster analysis. Our results showed that weedy rice accessions and cultivated rice populations from different regions of Asia were significantly different in one or more of their morphological characteristics. Weedy rice significantly differed from cultivated rice in plant height at vegetative growth phase, and in pericarp color and seed shattering during the reproductive growth phase. According to principal component analysis, weedy rice populations were significantly separated from cultivated rice in North China, Korea, Southeast Asia, Korea, and South China. We used principal component analysis and cluster analysis to categorize weedy rice populations into 3 main groups: Group 1 from Korea and Northern China; group 2 from Southern China and Southeast Asia; and group 3 from Eastern China. This study established an index for morphological characteristics of weedy rice to facilitate its identification the fields, which are expected to provide a theoretical basis for weedy rice infestation control in Asia.

Cultivated rice (Oryza sativa L.); Cluster analysis; Principal component analysis (PCA); Weedy rice (Oryza sativa f. spontanea)


Weedy rice is widespread in several rice-growing regions of the world and is responsible for loss in economic yield. Weedy rice is classified as the same species as cultivated rice (Linghwa and Morishima, 1997) and is often called "red rice" because of its red pericarp color. Some weedy rice accessions are morphologically similar to wild rice (Oryza rufipogon) in characteristics such as black hull, red pericarp, low 1000 seed weight, good phenotypic plasticity, high seed shattering and dormancy, and inconsistent maturation time (Oka, 1988; Suh, 2008; Chung, 2010). These characters facilitate the distribution of weedy rice seriously impairing the yield of rice grain (Gressel and Valverde, 2009; Prathepha, 2009; Shivrain et al., 2009; Chung and Park, 2010). Direct-seeded rice systems contribute to the spread of weedy rice, which poses a threat to the rice growers in Asian countries including China, Malaysia, Thailand, India, Korea, the Philippines, Vietnam, and Sri Lanka (Delouche et al., 2007; Varshney and Tiwari, 2008; Prathepha, 2011; Chauhan, 2012; Mansor et al., 2012; Zhang et al., 2012a). Weedy rice has especially caused significant damage in rice growing areas of China where it has reduced the crop yield by approximately 3.4 billion kg (Liang and Qiang, 2011). Similar reports implicate weedy rice in reducing the yield of cultivated rice by one t ha-1 in Malaysia (Azmi et al., 2012; Chauhan, 2013). Weedy rice is also known as red rice in the USA and arose from Asian domesticated rice; therefore, most weedy rice studies in the US explore the evolutionary basis and population structure of weedy rice (Thurber et al., 2013; Subudhi et al., 2014). Ziska et al. (2010) reported that weedy rice shows greater competitive ability in response to rising CO2 levels, thus, deeming it a potentially serious problem of the future.


The proanthocyanidin-pigmented pericarp is a characteristic feature of red rice (Oki et al., 2002) that helps in distinguishing it from wild and cultivated rice. However, the red pericarp color can only be observed post seed maturation. Classical genetics studies have shown that the genetics of red rice is controlled by two loci, namely Rd and Rc (Kinoshita, 1995; Kato et al., 2006). The pericarp is brown-pigmented when Rc is present alone and is colorless when Rd is present alone; however, the presence of both Rd and Rc impart red color to the pericarp. The white pericarp of cultivated rice is a result of a 14-bp gene deletion in exon 6, which causes the loss of gene function and no pigmentation in the pericarp. Yang et al. (2009a; 2009b) suggested that developing functional markers of the red pericarp gene of weedy rice could enable the identification of red pericarp of weedy rice at any stage. This would also avoid the limitation on the growth phase of weedy rice and color confusion caused by the level of ripening in manual identification processes. Genetic diversity and plasticity of a species contribute to their establishment in different environments and have been the focus of many studies (Yu et al., 2005; Cao et al., 2006; Prathepha, 2011) in weedy rice. These studies describe the diversity of trait characteristics and genetic structure of weedy rice in various regions (Linghwa and Morishima, 1997; Suh et al., 1997; Zhao et al., 2008; Liu and Liu, 2011; Liu et al., 2012; Zhang et al., 2012b), but they are limited to a single province or a region.


Weedy rice poses a major challenge during hand-picking of weeds in rice fields mainly because its morphological characteristics are similar to cultivated rice in the vegetative phase and wild rice in the reproductive stage. Therefore, it is important to have an index – based on morphological characteristics – for identifying weedy rice at an early stage in the cultivated and wild rice fields. The current measures to prevent and control weedy rice – using pure seeds, crop rotation, varietal choice, water management and chemical control methods are unsatisfactory, because many seed producers, farmers, and scientists cannot effectively distinguish weedy rice and cultivated rice in the early growth stages. Chemical control with herbicides adversely impacts cultivated rice, negatively impacts the environment, and is sometimes ineffective for removing weedy rice (Hoagaland, 1978). Moreover, the plant characters system of weedy rice from different regions are still lacking and new weedy rice resources may be produced through gene flow between related species, causing more difficulties in its prevention and control (Chen et al., 2001; Xiong et al., 2012; Xu et al., 2012). We hypothesize that early identification of weedy rice plants based on their morphological features will provide farmers with a simple, efficient and economical solution for management of weedy rice in fields. Therefore, we conducted the present study with the following objectives: (i) to assess the morphological variability of weedy rice and its distribution in the Asian rice area: (ii) to find underlying structures of the collected populations by identifying groups related to distinctive morphological characters and (iii) to evaluate the impact of morphological variability on weedy rice management strategies.


1 Results and Analysis

1.1 Identification of phenotypes and genotypes for pericarp color of weedy rice from different regions

The seeds of most accessions from a particular region showed a red pericarp. The pericarp color of 84.4% of the Asian weedy rice accessions was red or brown (from light to dark) while that of 15.6% was white (Figure 1). There was significant variation in the pericarp color of weedy rice accessions from a particular region (Table 1).



Figure 1 The pericarp color of some weedy rice accessions and cultivars (Zhang et al., 2015)

Note: 1: Cultivar KDML105 from Thailand; 2~7: Red pericarp weedy rice accessions from Myanmar, Korea, Ningxia, Hainan and Guangxi province in China, Philippines; 8: Brown spots and red pericarp weedy rice accession from Jiangsu province in China; 9: Light brown weedy rice accession from Liaoning province in China; 10: Brown weedy rice accession from Myanmar



Table 1 Pericarp color and number of weedy rice from different rice areas of Asia


We conducted the genotypic analysis of the weedy rice accessions using the RID14 marker. RID14 was identified in accessions with red and white pericarp colors. A 154bp fragment was identified by red pericarp color while a 140 bp fragment was identified as white (Figure 2). Genotypic pericarp color identification of all accessions of weedy rice was highly consistent except for the weedy rice accessions for east north regions, which showed red pericarp, had a genetic marker for white.



Figure 2 Identification of pericarp genotype of some cultivars, weedy rice and wild rice accessions by using the primer RID14; 1~4: Cultivated rice varieties; 5~8: Representative weedy rice accessions (Korea 1933, China Heidiaogu, Korea Sharei, China Ludao); 9~13: White pericarp weedy rice accessions; 14~15: Wild rice accession; Abbreviation: M, Marker I(shulin zhang et al, 2015 ).


1.2 Comparison of major biological characteristics of weedy and cultivated rice from different regions in Asia

Analysis of 18 characters in 204 weedy rice accessions revealed that Asian weedy rice from different rice regions showed different characteristics (Table 2). The variation coefficients of weedy rice from different regions varied in the following order: East China > South Korea > Southeast Asia > South China > North China > indica cultivated rice > japonica cultivated rice. Thus, there is a larger variation in weedy rice than in cultivated rice. We studied nine plant traits and nine panicle traits in weedy rice accessions as compared with japonica and indica cultivars. Our data show that the morphological characteristics of each weedy rice accession varied significantly as compared with cultivated rice. Thus, each accession varied in one or more morphological characteristic as compared with cultivated rice. The most striking differences were observed with respect to pericarp color and shattering; these traits enable the quick and easy identification of weedy rice in cultivated rice fields. Weedy rice from Southeast Asia and Korea were significantly taller than japonica rice and showed a significantly different basal leaf sheath color. Weedy rice from Northern China were significantly taller than Asian japonica cultivated rice while the flag leaf length and plant height of the East China weedy rice were significantly less than that of indica rice. Weedy rice from South China showed a significantly lower panicle number as compared with indica rice. Weedy rice plants from different regions (except those from East China) were taller and had more tillers than cultivated rice during the vegetative growth phase. The ligule color did not vary significantly among weedy rice accessions and as compared to cultivated rice. All of the nine panicle traits of weedy rice of various origins were significantly different from that of indica and japonica cultivated rice. Weedy rice from Northeast China was significantly different from indica and japonica in all characters except for lemma and palea pubescence and grain length; thus, making it easier to identify this accession in fields.



Table 2 Comparison of morphological characters of weedy rice and cultivated rice from different rice areas of Asian


1.3 Principal component analysis of the major agronomic characters of weedy rice from different rice regions

The 18 morphological characteristics of weedy rice from various regions and the cultivated rice populations (Table 3) were further analyzed by Principal component analysis (Figure 3). Our data showed that 71.89% of the total variation was present in the eighth principal component. The first principal component explained 16.8%% of the variation and was positively correlated with awn length and lemma, tip, awn, hull and pericarp colors. On the other hand, the first component was negatively correlated with grain length, basal leaf sheath color, flag leaf attitude and length; however, it showed a low degree of correlation with other traits such as grain width, panicle number, plant height, panicle thresh ability , collar color, ligule color and color. We further noted 11.8% of the total variation of the second principal component, which was significantly positively correlated with grain length, flag leaf length and plant height. The second component was significantly negatively correlated with awn-related characters (awn length and color), grain length, and flag leaf length, but in low degree of correlation with other traits. The Third principal component accounted for 10.3% of the variation and had a positive correlation with awn-related characters (awn length, awn color). A total of 8.22% of the variation and was positively correlated with flag leaf length and basal Leaf sheath color. There was 7.93%, 6.54%, 5.4% and 5.1% variation in panicle threshability, panicle number, collar color and sterile lemma color as shown by principal component fifth, sixth, seventh and eighth .Therefore, our results revealed that the major characters of weedy rice from different rice regions of Asia are awn-related traits, grain length, and flag leaf length.



Table 3 Principal component analysis of morphological characters



Figure 3 Distribute of Weedy rice and cultivated rice from different rice areas of Asian s on the first and second principal component


We represented all populations in a bi-dimensional space of the first two components yet it was not possible to identify well-separated groups of populations. This was despite the fact that East China populations were less dispersed than those of North of China, which were concentrated around slightly positive values of the first component (Figure 3). Similarly, Southeast Asia, Korea, and South China populations were largely spread from negative to positive values of both components but could not be identified as separate groups.


1.4 Cluster analysis of weedy rice from different rice regions based on agronomic traits

We performed a two-step cluster analysis performed on five rice regions where weedy rice is grown. The standardized data of five panicle characters (awn length, awn color, pericarp color, grain length, and grain width) and six plant characters (plant height, panicle number, shattering, flag leaf length and basal leaf sheath color) was categorized into three groups (Table 4). Group 1 mainly included weedy rice from North China and South Korea, at the distribution frequencies of 96% and 100%, respectively, with few or no populations from other regions. Thus, the characters having a significant impact on the group are grain length, flag leaf length, awn color and pericarp color (Figure 4-1; Figure 5A), i.e., long and brown awn, red pericarp, and very short grain and flag leaf. Weedy rice from South China and Southeast Asia were included in group 2 at the distribution of frequency of 94% with few or no populations from other regions. Tall plants, strong grain shattering, and long flag leaf and grain have a significant impact on the categorization (Figure 4-2; Figure 5B). Group 3 mainly included Asian cultivated rice and weedy rice from East China at distribution frequencies of 100% and 98%, respectively. Thus, cluster analysis suggests awnless and white pericarp are the most significant characters impacting grouping of cultivated rice (Figure 4-3; Figure 5C).



Table 4 Cluster analysis of weedy rice and cultivated rice from different rice areas of Asian



Figure 4 Variables that mainly contributed to the formation of cluster 1, 2, 3; Histograms represent the Student’t values of each variable, while dashed lines refer to the significant critical values



Figure 5 Weedy rice comparisons with cultivated rice in the field

Note A: weedy rice weedy rice from North China and South Korea have long and brown awn, red pericarp characters; B: weedy rice have tall plants, strong grain shattering, and long flag leaf characters; C: weedy rice from is very similar with cultivated rice


2 Discussion

We used a co-dominant molecular marker RID14, to analyze pericarp color in 199 weedy rice and 24 cultivated rice accessions. All cultivated rice had white pericarp and weedy rice mostly had red pericarp, but some accessions showed white pericarp too. These results corroborated the manual seed evaluation and identification results paving the ground for establishing a technical system for weedy rice identification. Since, weedy rice and cultivated rice are very similar, it is difficult to distinguish them at the seedling and early tillering stages in the field. Therefore, RID14 enables the early identification of the genotype of weedy rice and provides the basis for weedy rice infestation forecast (Gealy et al., 2002). The molecular identification result for one of the red pericarp materials was deletion type, probably because pericarp color of this material is controlled by a gene other than RC gene, but further research is needed to prove this hypothesis. Vaughan et al. (2001) stated that the red pericarp is the wild trait while white pericarp is the result of evolution. However, almost in all cases, white pericarp is a result of mutation in the transcription factor of the Rc gene (Sweeney et al., 2007), which contradicts the genetic diversity of cultivated rice. Therefore, analysis of the red pericarp gene of weedy rice will help elucidate the molecular evolutionary mechanisms of weedy rice.


Morphological methods are the most intuitive and basic methods used in the study of genetic diversity of plants. Analysis of botanical characters and morphological characters allows us to have an overall understanding of the extent of rich variation in the resources, providing important information for control and utilization. Our study of 18 characters of weedy rice from five rice cultivation regions in Asia and compared cultivated rice from corresponding sites of origin showed a high level of variation in weedy and cultivated rice. In general, weedy rice from various regions was taller than cultivated rice and had a higher number of panicles making these useful criteria distinguish weedy rice in the vegetative growth stage. We observed that weedy rice has vigorous vegetative growth and stronger tillering ability than cultivated rice making it dominant in competing with cultivated rice, which is in line with many previous studies (Yu et al., 2005; Zou, 2008). Weedy rice differs from locally cultivated rice in pericarp color and shattering at the reproductive growth stage. The caryopsis of weedy rice is mostly red due to pigmentation, which is one of the significant characteristics to distinguish weedy rice (Li et al., 2006; Pan et al., 2007). Most types of weedy rice have the tendency to shatter at ripeness ensuring the continuity of weedy rice seeds in farmland.


Principal component analysis of weedy rice and cultivated rice populations from the five Asian regions determined that the cumulative total contribution of the first two principal components was 30.2%. These were seed-related characters (awn length, awn color, hull color, pericarp color, lemma color and lemma and palea pubescence color) and plant characters (plant height, flag leaf length and basal leaf sheath color). Our results corroborated two previous studies (Zhang et al., 2004; Wu et al., 2010) that reported four principal components including plant factor, panicle shape factor, seed weight factor, and panicle number in weedy rice from South Korea, and Jiangsu and Liaoning of China. Chung and Paek (2003) speculated that the abovementioned characteristics are of significant biological importance in weedy rice.


We categorized the clustering weedy rice populations from the five cultivation regions into three groups (Table 5). Weedy rice from North China and South Korea comprised one group, having long and brown awn, red pericarp, and very short grain and flag leaf, which is similar to locally grown japonica cultivated rice. This group probably evolved from degraded local cultivars. Weedy rice from South China and Southeast Asia comprised another group. This group has tall plant, strong shattering, long flag leaf and grain, which are the characteristics of common wild rice suggesting that its origin might be related to wild rice. Weedy rice from East China and cultivated rice were categorized as a more diverse group, indicating more significant differentiation. Weedy rice in this group can be indica-like or japonica-like, but their botanical and morphological similarities to local indica cultivars or japonica cultivars are evident; thus, implying their correlation with local cultivars. However, more in-depth studies are necessary to identify the exact origin of rice accessions. Overall, the germplasm resources of weedy rice in Asia are rich and widely distributed with complex variations, diverse groups and low genetic stability (Suh et al., 1997; Zhang et al., 2004; Zhao et al., 2008). Biological characteristics can clarify typical weedy rice types and provide a theoretical basis for its prevention and control. Moreover, related species materials for gene flow studies in the environmental safety assessment of genetically modified rice, and valuable resistance genes should be explored as breeding materials (Lu and Snow, 2005; Gu et al., 2006; Rong et al., 2007).



Table 5 Main morphological characters of t clustering weedy rice populations from different regions


3 Materials and Methods

3.1 Seed collection

A total of 199 weedy rice accessions were sampled from China, Korea, and Southeast Asia, all of which comprise 80% of the total Asian rice cultivated area. Among these, 140 accessions were obtained from Shenyang Agriculture University and the China National Rice Research Institute, collected between 2008 and 2010 from rice-growing regions of China. These accessions were from nine provinces of China (Liaoning, Heilongjiang, Jilin, Ningxia, Jiangsu, Guangdong, Guangxi, Yunnan and Hainan) and covered China's three major rice-growing regions: North China, Middle of China and South China and the sample method described by zhang et al. (2015). Twenty-three accessions were from South Korea region and 36 were from the Southeast Asian countries (Sri Lanka, India, Bhutan, Nepal, Philippines, Laos, Myanmar, Vietnam, Malaysia, and Cambodia) (Table 6). Both Korean and Southeastern accessions were obtained from the Wild Crop Germplasm Bank, College of Natural Resources, Yeungnam University, Korea. A total of 24 cultivated rice entries including 16 indica and eight japonica entries from weedy rice origin area were used as reference (Table 6).



Table 6 Weedy and cultivated rice used in the study 

3.2 Field experiment

Weedy rice (n=199) and cultivated rice (n=24) seeds were planted in the experimental field (where weedy rice were never planted before) of the Rice Research Institute of Yunnan Agricultural University (altitude 320 meters) in February 2013, and were covered with a white film. All of the seedlings were transplanted on March 25: One seedling per hole with row spacing 30 cm × 16.6 cm; there were three rows of each population, and each row was 2 m in length. The field was managed in the same way as the local production fields.


3.3 Morphological evaluations

All weedy rice accessions and cultivated varieties were evaluated at various growth stages: Stem elongation-booting, anthesis, milk development, dough development, ripening, and after harvest. A total of 18 morphological characters (Table 7) were chosen, using a combination of the IRRI Standard Evaluation System for Rice (IRRI, 2002) and the Standard Evaluation system for weedy rice (Suh et al., 2003). The evaluation was carried out at specific growth stages depending on the characters selected. Awn length, seed length, and width were measured in 50 seeds per accession. Pericarp color was identified after manually dehusking the rice and also by using the InDl marker RID14 (Yang et al., 2009a).



Table 7 Morphological characters used to evaluate weedy and cultivated rice 


RID14 was identified by using the primer sequences RID14-For: 5'-TCCAGGCACCACACAGAGA-3'andRID14-Rev: 5'-GGCACTGAAATCACCTTGG-3', (synthesized by Shanghai Sangon Biotech). Leaf total DNA was extracted using CTAB method (Song et al., 2003). The PCR reaction system (13 μL) contained 2 ×power Taq PCR MasterMix (TaKaRa China Inc., Dalian, Liaoning) 6.5 μL, ddH2O 4.9 μL, forward and reverse primer, 0.3 μL (10 pmol/mL) each, and DNA template 1 μL (20~40 ng). PCR reaction was carried out using the following program: An initial denaturation step at 94ºC for 4min; denaturation at 94ºC for 20 s; annealing at 50ºC for 20 s; extension at 72ºC for 20 s; all for 35 cycles; and finally an extension step at 72ºC for 10 min. PCR products were separated and analyzed on a 3.5% agarose gel using electrophoresis and visualized system.


3.4 Statistical analyses

The average values of every character of all weedy rice accessions characters from different regions were analyzed. We used SPSS18.0 software to perform significance tests. Software Minitab (R) 15.1 ( was applied to perform principal component analysis(PCA) on the average values of plant characters of all samples from different regions, and two-dimensional principal component scatter plots were generated using principal component 1 and principal component 2 as the X-axis and Y-axis, respectively. In order to better tap the groups of weedy rice from various regions and the major affected traits, two-step cluster analysis was performed using SPSS18.0 software.


Authors' contributions

Shulin Zhang carried out the molecular genetic studies and and drafted the manuscript, Li Tian and Juan Li participated in the data collection. Dongsun Lee participated in the design of the study and performed the statistical analysis. Lijuan Chen and Renhai Peng conceived of the study, and participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.



We appreciate the kind donation of rice germplasm by the Wild Crop Germplasm Bank, College of Natural Resources, Yeungnam University, Korea. This study was supported by a grant from the National Natural Science Foundation of China (30860057 and 31260257) and Key scientific research project of Higher Education in Henan Province (16A210044).



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Molecular Plant Breeding
• Volume 8
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