Genetic diversity of weedy rice (
Weedy rice is conspecific, the most troublesome weed of cultivated rice identified as a threat to global rice production. The weed has inherited high reproductive ability and high dormancy by outcrossing with modern rice cultivars and wild cultivars, respectively. Traits such as rapid growth, high tillering, enhanced ability to uptake fertilizers, asynchronous maturation, seed shattering, and long dormancy periods make weedy rice more competitive than cultivated rice. Weedy rice infesting rice fields are morphologically diverse with different hull color, awn length, plant height, and variable tiller number. Morphological diversity in weedy rice can be attributed to its high genetic diversity. Introgression of alleles from cultivated rice into weedy has resulted in high genetic and morphological diversity in weedy rice. Although variations among weedy rice populations make them difficult to control, on the brighter side, competitive nature of weedy rice could be considered as raw genetic materials for rice breeding program to develop vigorous rice plants able to tolerate high biotic and abiotic stresses.
- genetic diversity
- phenotypic diversity
- rice breeding
- red rice
- abiotic stress tolerance
- biotic stress tolerance
Weedy rice, also called as red rice because of its red pericarp, belongs to same genus and species as the cultivated rice,
2. Weedy rice: a troublesome weed
Weedy rice (
According to Allston, the first weedy red rice was reported in the USA as early as 1800 as seed contaminants from Asia and since then has been affecting rice crop by limiting its yield . Weedy rice share common gene pool with cultivated rice making them morphologically similar to cultivated rice but have high seed shattering and differential dormancy, making them difficult to control weeds in the rice fields. Some of the unfavorable traits possessed by weedy rice are long culm lengths, high tillering capacity, light leaf color, weak culms, red pericarp, highly shattering seeds, and high degree of seed dormancy [2, 17, 18]. It is difficult to control weedy rice because they mimic cultivated rice morphologically, biochemically, and physiologically. Physical weed management is difficult as weedy rice is morphologically similar to cultivated rice in early stages, and chemical weed management is limited as herbicides controlling weedy rice also kill rice plant . In many places, farmers have altered their cropping pattern to non-rice system to manage this noxious weed . Depending on the amount of infestation, weedy rice can cause yield losses varying from 50 to 60% under moderate infestation to 70–80% under heavy infestation. In Arkansas, the highest rice-producing state in the USA, economic loss due to weedy rice has been estimated to be $274/hectare . The threshold for weedy rice infestation is one to three plants/m2 in the USA; plant density higher than this can cause significant yield loss .
3. Competitive nature of weedy rice
Competition for limited resource is the drawing force for natural selection and shaping plant communities . Weeds compete with crop for nutrients, space, and light, thus decreasing yield potential of crop. Traits of weedy rice such as taller growth habit, higher tillering, and higher nutrient use efficiency make it dominant and more competitive than the crop . The success of weedy rice as weeds can be attributed to its high dormancy as they can remain viable in soil for a long period of time and emerge when conditions are favorable . Noldin et al., in 2006, conducted an experiment to evaluate the dormancy and longevity of various weedy rice biotypes from four states in the USA . The study found the differential level of dormancy among weedy rice ecotypes buried under the soil at different depths, and all of them were more viable than commercial rice cultivar. Five weedy ecotypes had viable seeds even after 36 months of burial in the soil. The commercial rice seeds were nonviable after 5 months of burial in the soil. Weedy rice therefore has greater viability than cultivated rice under certain environmental conditions and can emerge from deeper soil surface, thus developing a robust soil seedbank .
Seed shattering, which distinguishes cultivated rice from its wild forms, is variable in weedy rice . In weedy rice, the abscission layer degrades earlier as compared to cultivated rice, leading to earlier shattering and increasing its fitness for survival in the environment . Shattering in weedy rice is controlled by unidentified regulatory genes distinct from wild rice, thus suggesting parallel evolution between weedy rice and wild rice . Weedy rice is also generally taller than cultivated rice making them more efficient for light and space . Weedy rice has higher nitrogen use efficiency causing greater yield loss in rice fields . Thus, in fields infested with weedy rice, the application of nitrogen fertilizers may not lead to an eventual increase in rice yields; instead, the weedy rice plants grow bigger and compete more aggressively with rice resulting in rice plants with lower yield . Nitrogen accumulation is higher in weedy rice than in cultivated rice in “nutrient-deficient” conditions, suggesting a more efficient nutrient uptake mechanism in weedy rice than cultivated rice . In addition to higher nutrient response, weedy rice also has higher stress tolerance [30, 31]. Unlike commercial rice varieties, weedy rice can perform better in unfavorable environmental conditions such as higher carbon dioxide, lower nutrient supply, and high/low temperature, indicating that they have higher capability of enduring stress than cultivated rice and, therefore, thrive better in stressful environment. Weedy rice ecotypes have higher leaf area and root weight when grown at carbon dioxide level of 500 μmol mol−1 which is the projected CO2 concentration in the middle and end of the twentieth century . In saline conditions, growth and germination of most plant species are reduced; however, weedy rice accessions have higher germination index and seedling vigor than commercial rice at 16 dSm−1 (NaCl) salinity level . A weed-crop competition modeled by Pantone and Baker showed that weedy rice is more dominant than cultivated rice and competitive ability of one weedy rice plant is equivalent to three plants of an old commercial rice variety “Mars” . Ottis et al. studied the interference potential of weedy rice on five rice cultivars (CL161, Cocodrie, LaGrue, Lemont, and XL8) and demonstrated that yield reduction of rice cultivars ranged from 100 to 755 kg/ha for every weedy rice plant/m2 .
4. Evolution of weedy rice
There is immense diversity both among and within weedy rice populations and between weedy and cultivated rice [35, 36, 37, 38]. Studying the differences in weedy rice populations in relation to phenological and morphological traits will help us better understand the evolution of weedy traits. There are a number of hypotheses that speak to the origination of weedy rice. These hypotheses include the following: weedy rice is a crop mimic of rice similar to a wild relative, it is a hybrid of natural crosses between wild and cultivated rice, and it is merely an evolved taxon from cultivated rice . In areas inhabited by wild rice, De-Wet and Harlan believed that weedy rice arose from the selection of wild rice to agricultural habits for consumption . While this may be true for areas with a prominent wild rice population, it does not address the prevalence of this weedy species in areas uninhabited by wild rice. Recent genetic studies point to specific examples of the evolutionary pathways of weedy rice.
Over the last 20 years, studies conducted on weedy rice have increased due to the increased infestation in rice fields. In 2006, Cao et al. noticed the resurgence of weedy rice and set out to conduct a molecular study utilizing 20 simple sequence repeat (SSR) markers and 30 different populations of weedy rice to identify the evolution of weeds in China’s Liaoning province . The weedy rice populations were compared to a wild rice relative,
Weedy rice can also be referred to as red rice due to the presence of a red pericarp not often witnessed within the cultivated rice. To determine if the presence of a red pericarp was a characteristic of weedy rice or cultivated rice, Gealy et al. used SSR markers to differentiate between weedy rice present in the Southeastern USA, cultivated rice, and hybrids . In this study, 31 SSR markers were used to analyze 180 kinds of rice from the genus
5. Weedy rice diversity
5.1 Morphological diversity of weedy rice
Weedy rice exhibits high genetic and phenotypic diversity, and this diversity is dependent on the ecotype and habitat . Weedy rice from different regions of Asia (Malaysia, the Philippines, Thailand, and Vietnam) varied in terms of grain characteristics and growth response under competition with cultivated rice . The Philippines weedy rice produced the highest grain yield, while a higher growth potential was observed in weedy rice from Vietnam; weedy rice from Thailand was the shortest. Weedy rice from major rice-growing areas of Ampara District, Sri Lanka, were found to be morphologically diverse in terms of tiller number, plant height, and panicle number . In Peninsular Malaysia, the weedy rice can be divided into four major clusters based on their morphological variation: (1) awned black and brownhull derived from wild
5.2 Genetic diversity of weedy rice and its gene flow potential
Morphological diversity in weedy rice can be attributed to its high genetic diversity. The genetic diversity of rice has been estimated using various markers like random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), and simple sequence repeats (SSR) [50, 51, 52, 53, 54]. Of these SSR markers are most commonly used as they are readily available, easy to use, highly polymorphic, and less expensive and give accurate results (Table 1). Genetic diversity of weedy rice populations from Liaoning province using SSR markers was found to be relatively high with He value of 0.313, and 35% of genetic variation was among regions . Weedy rice from Northeast Asia are genetically diverse with high Shannon’s information index of 0.748 and heterozygosity of 0.434 . Among RAPD and SSR markers, SSR were superior to RAPD in detecting genetic diversity among weedy rice populations . Weedy rice, weedy rice-cultivated rice hybrids, and rice cultivars can be distinguished using microsatellite SSR markers . Molecular studies using SSR confirmed the differentiation of the two weedy rice ecotypes from Arkansas, USA . Strawhull weedy rice were genetically distant compared to blackhull weedy rice. A higher genetic diversity within blackhull weedy rice (D = 0.76) was estimated compared to strawhull (D = 0.68). US weedy rice has high genetic diversity with nucleotide diversity (Pi) = 1.48 per Kb, thus indicating their higher potential to evolve . Within weedy rice populations, the blackhull group showed higher nucleotide diversity (Pi = 0.66) than strawhull group (Pi = 0.56). Weedy rice was found to be closely related to
|Species||Geographical location||Marker used||Genetic diversity||Reference|
|Northeastern China||SSR||Heterozygosity (H|
Shannon’s diversity index (I) = 0.572
|Cao et al. |
|Northeast Asia||SSR||He = 0.748|
I = 0.434
|Mao-bai et al. |
|Liaoning province, China||SSR||He = 0.053||Yu et al. |
|Awnless red rice||Arkansas, USA||SSR||Average genetic distance = 0.2||Gealy et al. |
|Awned red rice||Arkansas, USA||SSR||Average genetic distance = 0.33||Gealy et al. |
|Arkansas, USA||SSR||Nei’s genetic distance (GD) = 0.7||Shivrain et al. |
|Italy||SSR||He = 0.295||Grimm et al. |
|Red rice||Uruguay||AFLP||Average of 25.6 bands per primer pair||Federici et al. |
Weedy rice and cultivated rice being closely related to each other have chances of exchanging genetic information. Gene flow from wild species to crop and vice versa has increasing practical implication with development of herbicide-resistant and genetically engineered crops. Transfer of genes conferring biotic and abiotic stress tolerance in crops to the wild species may pose great ecological threat. Thus, gene flow frequency between weedy rice and rice cultivars should be kept in mind while using weedy rice species for rice improvement programs. Studies have shown noticeable gene flow potential between weedy rice, wild rice, and cultivated rice. Gene flow frequency between weedy rice and cultivated rice ranged from 0.011 to 0.046% and between wild rice and cultivated rice ranged from 1.21 to 2.19% approximately . Gene flow frequency from cultivated rice to wild rice (
The research discussed above shows that weedy rice is one of the most successful weeds in rice due to key weedy traits including high seed dormancy and longevity, high seed shattering, high nutrient uptake and nitrogen use efficiency, more tillers, high panicle number and biomass, and tolerance to stresses including herbicides. For successful implementation of management strategies for weedy rice, the physiological and genetic basis of these competitive traits needs to be understood. Further, understanding the mechanism and genetic basis of these competitive traits may provide unique information for rice improvement owing to its close relationship with cultivated rice. However, numerous pros and cons associated with the use of the wild relatives for crop improvement program should be considered before using weedy rice as raw genetic material for developing robust rice cultivars.
This work is supported by the National Institute of Food and Agriculture, US Department of Agriculture, and Hatch Projects under accession number 230060 and is a contribution of the Mississippi Agricultural and Forestry Experiment Station.
Conflict of interest
The authors declare that this work was presented in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.