Genetic Diversity in Crop Management

*Integrated View of Population Genetics*

[36] Roush TL, Granett J, Walker MA. Inheritance of gall formation relative to phylloxera resistance levels in hybrid grapevines. American Journal of Enology and Viticulture.

[38] Houel C et al. Identification of stable QTLs for vegetative and reproductive traits in the microvine (*Vitis vinifera* L.) using the 18 K Infinium chip. BMC Plant Biology.

[39] Duchêne E et al. Towards the adaptation of grapevine varieties to climate change: QTLs and candidate genes for developmental stages. Theoretical and Applied Genetics.

[40] Coupel-Ledru A et al. Reduced nighttime transpiration is a relevant breeding target for high water-use efficiency in grapevine. Proceedings of the National Academy of Sciences.

[41] Mandl K et al. A genetic map of Welschriesling × Sirius for the identification of magnesium-

[42] Costantini L et al. Berry and phenology-related traits in grapevine (*Vitis vinifera* L.): From quantitative trait loci to underlying genes. BMC

[43] Grzeskowiak L et al. Candidate loci for phenology and fruitfulness contributing to the phenotypic variability observed in grapevine. Theoretical and Applied Genetics.

Plant Biology. 2008;**8**(1):38

2013;**126**(11):2763-2776

deficiency by QTL analysis. Euphytica.

[37] Xu K et al. Genetic and QTL analysis of resistance to *Xiphinema index* in a grapevine cross. Theoretical and Applied Genetics. 2008;**116**(2):305-311

[44] Bayo Canha A. Genetic Analysis of Traits of Interest in *Vitis vinifera* Using a Progeny of Wine Grapes. PhD thesis. Universidad Politécnica de Cartagena. Colombia: Monastrell x Syrah; 2015

[45] Díaz-Riquelme J et al. Genome-wide analysis of MIKCC-type MADS box genes in grapevine. Plant Physiology.

2009;**149**(1):354-369

2007;**58**(2):234-241

2015;**15**(1):1

2012;**124**(4):623-635

2016;**113**(32):8963-8968

2006;**149**(1-2):133-144

**24**

**27**

**Chapter 3**

**Abstract**

Weedy Rice: Competitive Ability,

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

**Keywords:** genetic diversity, phenotypic diversity, rice breeding, red rice, abiotic

Weedy rice, also called as red rice because of its red pericarp, belongs to same genus and species as the cultivated rice, *Oryza sativa* L. It is one of the major weeds in rice field worldwide [1] and adulterates cultivated rice decreasing its productivity in the field and reducing crop quality due to seed contamination. Rice monocropping and direct-seeded rice system promote infestation of weedy rice, and severe infestation of weedy rice can cause up to 100% yield reduction in direct-seeded rice system [2]. Numerous weed control strategies are adopted by the farmers to control weedy rice in rice fields. Development of herbicide-tolerant rice was thought to solve the problem of weedy rice, but with the development of herbicide-resistant weeds, the value of this technology has become questionable. Management of weedy rice in rice fields is possible only through adoption of integrated weed management practice such as winter flooding, fallow tillage, and crop rotation [3]. The genus *Oryza* has 21 wild and two cultivated species. Two cultivated species include *O. sativa* the Asian rice and *O. glaberrima* the African rice, both with diploid AA genome. *O. sativa* has three major subspecies: *indica*, *japonica*, and *javanica.* Among the wild rice, nine are tetraploid (BBCC) (CCDD) and 12 are

diploid [4]. Wild rice found in nature are those derived from *O. sativa*

*Swati Shrestha, Shandrea Stallworth and Te-Ming Tseng*

Evolution, and Diversity

able to tolerate high biotic and abiotic stresses.

stress tolerance, biotic stress tolerance

**1. Introduction**

### **Chapter 3**

## Weedy Rice: Competitive Ability, Evolution, and Diversity

*Swati Shrestha, Shandrea Stallworth and Te-Ming Tseng*

### **Abstract**

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.

**Keywords:** genetic diversity, phenotypic diversity, rice breeding, red rice, abiotic stress tolerance, biotic stress tolerance

### **1. Introduction**

Weedy rice, also called as red rice because of its red pericarp, belongs to same genus and species as the cultivated rice, *Oryza sativa* L. It is one of the major weeds in rice field worldwide [1] and adulterates cultivated rice decreasing its productivity in the field and reducing crop quality due to seed contamination. Rice monocropping and direct-seeded rice system promote infestation of weedy rice, and severe infestation of weedy rice can cause up to 100% yield reduction in direct-seeded rice system [2]. Numerous weed control strategies are adopted by the farmers to control weedy rice in rice fields. Development of herbicide-tolerant rice was thought to solve the problem of weedy rice, but with the development of herbicide-resistant weeds, the value of this technology has become questionable. Management of weedy rice in rice fields is possible only through adoption of integrated weed management practice such as winter flooding, fallow tillage, and crop rotation [3].

The genus *Oryza* has 21 wild and two cultivated species. Two cultivated species include *O. sativa* the Asian rice and *O. glaberrima* the African rice, both with diploid AA genome. *O. sativa* has three major subspecies: *indica*, *japonica*, and *javanica.* Among the wild rice, nine are tetraploid (BBCC) (CCDD) and 12 are diploid [4]. Wild rice found in nature are those derived from *O. sativa*

(AA complex) and *O. Officinalis* complex (BB, CC, CCDD) [5]. *Oryza sativa* complex includes *O. rufipogon*, *O. barthii*, and *O. longistaminata*, while *O. officinalis* complex includes *O. punctata*, *O. latifolia*, and *O. officinalis.* However, weedy rice is distinct from wild rice and is believed to have been evolved through (i) hybridization among and within cultivated and wild rice, (ii) de-domestication of cultivated rice, and (iii) direct colonization of wild rice in agricultural rice fields [6].

The genus *Oryza* consists of numerous species, and studying the genetic structure of cultivated, wild, and weedy rice species is crucial for understanding the morphological and physiological characters of rice cultivars and the genes governing these characters. Proper understanding of numerous genes governing quantitative and qualitative traits in rice is essential for successful molecular breeding programs. Genetic diversity of *Oryza* can be utilized for crop improvement program by plant breeders in order to produce rice cultivars with higher yield that could meet the growing food demand.

### **2. Weedy rice: a troublesome weed**

Weedy rice (*Oryza sativa spp.) is* currently distributed worldwide, and it is known to infest the areas in and around rice fields [7]. These weedy rice tend to have many undesirable traits when compared to cultivated rice such as the ability to germinate faster, reduce yields by 90%, and persist within the soil bed for up to 10 years [8]. Conventionally, in most of the developing countries, rice is transplanted into standing water, thus providing competitive advantage to the crop and enhancing crop productivity by suppressing weeds [9]. However, with the scarcity of labor and water, there has been a significant shift from puddled transplanting (PTR) to direct-seeded rice (DSR) system in Asian countries in the past two decades [2]. In the USA, all rice fields are cultivated through highly mechanized DSR system [10]. DSR involves rice stand establishment directly by sowing seeds in the fields and uses less water and labor and emits less methane than the PTR system [11]. Although DSR has numerous advantages over the PTR, sustainability of DSR with reference to control of weedy rice is becoming questionable. Currently, weedy rice has been reported in most of the rice-growing countries like China, India, the USA, Bangladesh, Bhutan, Brazil, Nepal, Thailand, Japan, the Philippines, Korea, Thailand, Sri Lanka, Vietnam, and Malaysia (**Figure 1**) [15]. Incidence of weedy rice has increased tremendously in Malaysia following the adoption of DSR in the 1980s [12]. In Vietnam, yield loss due to weedy rice has been reported from 15 to 70% [13]. Due to its ability to behave similarly to rice, management of these weedy species without causing damage to the crop itself has proven to be an issue [14].

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 [16]. 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 [2]. In many places, farmers have altered their cropping pattern to non-rice system to manage this noxious weed [14]. Depending on the amount of infestation, weedy rice can cause yield losses

**29**

**Figure 1.**

*reported [15].*

*Weedy Rice: Competitive Ability, Evolution, and Diversity*

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 [19]. The threshold for weedy

*Weedy rice distribution worldwide. Red dots represent regions where weedy rice infestation has been* 

Competition for limited resource is the drawing force for natural selection and shaping plant communities [21]. 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 [22]. 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 [23]. 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 [24]. The study found the differential level of dormancy among weedy rice ecotypes buried under the soil at different depths, and

in the USA; plant density higher than this

*DOI: http://dx.doi.org/10.5772/intechopen.81838*

rice infestation is one to three plants/m<sup>2</sup>

**3. Competitive nature of weedy rice**

can cause significant yield loss [20].

**Figure 1.**

*Integrated View of Population Genetics*

meet the growing food demand.

**2. Weedy rice: a troublesome weed**

(AA complex) and *O. Officinalis* complex (BB, CC, CCDD) [5]. *Oryza sativa* complex includes *O. rufipogon*, *O. barthii*, and *O. longistaminata*, while *O. officinalis* complex includes *O. punctata*, *O. latifolia*, and *O. officinalis.* However, weedy rice is distinct from wild rice and is believed to have been evolved through (i) hybridization among and within cultivated and wild rice, (ii) de-domestication of cultivated rice, and (iii) direct colonization of wild rice in agricultural rice fields [6]. The genus *Oryza* consists of numerous species, and studying the genetic structure of cultivated, wild, and weedy rice species is crucial for understanding the morphological and physiological characters of rice cultivars and the genes governing these characters. Proper understanding of numerous genes governing quantitative and qualitative traits in rice is essential for successful molecular breeding programs. Genetic diversity of *Oryza* can be utilized for crop improvement program by plant breeders in order to produce rice cultivars with higher yield that could

Weedy rice (*Oryza sativa spp.) is* currently distributed worldwide, and it is known to infest the areas in and around rice fields [7]. These weedy rice tend to have many undesirable traits when compared to cultivated rice such as the ability to germinate faster, reduce yields by 90%, and persist within the soil bed for up to 10 years [8]. Conventionally, in most of the developing countries, rice is transplanted into standing water, thus providing competitive advantage to the crop and enhancing crop productivity by suppressing weeds [9]. However, with the scarcity of labor and water, there has been a significant shift from puddled transplanting (PTR) to direct-seeded rice (DSR) system in Asian countries in the past two decades [2]. In the USA, all rice fields are cultivated through highly mechanized DSR system [10]. DSR involves rice stand establishment directly by sowing seeds in the fields and uses less water and labor and emits less methane than the PTR system [11]. Although DSR has numerous advantages over the PTR, sustainability of DSR with reference to control of weedy rice is becoming questionable. Currently, weedy rice has been reported in most of the rice-growing countries like China, India, the USA, Bangladesh, Bhutan, Brazil, Nepal, Thailand, Japan, the Philippines, Korea, Thailand, Sri Lanka, Vietnam, and Malaysia (**Figure 1**) [15]. Incidence of weedy rice has increased tremendously in Malaysia following the adoption of DSR in the 1980s [12]. In Vietnam, yield loss due to weedy rice has been reported from 15 to 70% [13]. Due to its ability to behave similarly to rice, management of these weedy species without causing damage to the crop itself has proven to be an issue [14]. 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 [16]. 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 [2]. In many places, farmers have altered their cropping pattern to non-rice system to manage this noxious weed [14]. Depending on the amount of infestation, weedy rice can cause yield losses

**28**

*Weedy rice distribution worldwide. Red dots represent regions where weedy rice infestation has been reported [15].*

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 [19]. The threshold for weedy rice infestation is one to three plants/m<sup>2</sup> in the USA; plant density higher than this can cause significant yield loss [20].

## **3. Competitive nature of weedy rice**

Competition for limited resource is the drawing force for natural selection and shaping plant communities [21]. 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 [22]. 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 [23]. 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 [24]. 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 [24].

Seed shattering, which distinguishes cultivated rice from its wild forms, is variable in weedy rice [25]. 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 [26]. Shattering in weedy rice is controlled by unidentified regulatory genes distinct from wild rice, thus suggesting parallel evolution between weedy rice and wild rice [26]. Weedy rice is also generally taller than cultivated rice making them more efficient for light and space [27]. Weedy rice has higher nitrogen use efficiency causing greater yield loss in rice fields [28]. 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 [28]. 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 [29]. 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<sup>−</sup><sup>1</sup> which is the projected CO2 concentration in the middle and end of the twentieth century [30]. 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<sup>−</sup><sup>1</sup> (NaCl) salinity level [32]. 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" [33]. 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/m<sup>2</sup> [34].

### **4. Evolution of weedy rice**

There is immense diversity both among and within weedy rice populations and between weedy and cultivated rice [35–38]. 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 [39]. 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 [40]. 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.

**31**

*Weedy Rice: Competitive Ability, Evolution, and Diversity*

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 [41]. The weedy rice populations were compared to a wild rice relative, *O. rufipogon*, as well as cultivars to represent both indica and japonica biotypes. Cao et al. discovered, through genetic data, that the Liaoning cultivar, a japonica biotype, was very similar to that of weedy rice and clustered together to demonstrate this, while another Chinese japonica biotype did not follow the same clustering style. Through AMOVA analysis, the study found approximately 35% of the total genetic variation among regions, 18% within regions, and 46% within the populations. When the wild relative, *O. rufipogon*, and indica biotypes were compared to the weeds, they were further clustered from the weedy rice and Liaoning cultivar. Based on this data and the clusters presented, the authors concluded that weedy rice in the Liaoning province of China arose from the mutation and hybridization of Liaoning rice varieties [41]. This conclusion was challenged in 2010 by a paper from Ellstrand et al. stating "…if hybridization had occurred, it is likely that some *O. rufipogon* alleles would have been retained in the weedy lineages in the short time that they have been problematic" [38]. This could be true as Cao et al. found that there was a lack of heterozygosity within the weedy

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 [42]. In this study, 31 SSR markers were used to analyze 180 kinds of rice from the genus *Oryza* and 80 weedy rice and rice cultivars from the USA. The 31 SSR markers selected represented low to high polymorphism information content values to screen the population for genetic variation. Using AMOVA, the genetic variation of the 80 weedy rice and rice cultivars was 56% within populations and 44% among populations. When the study compared only the 38 weedy rice populations that were separated into three different weedy rice populations, the genetic variation was 47% within populations and 53% among populations. A large amount of genetic variability was explained by the considerable genetic variation within blackhull, awned red rice (BA+), and *Oryza sativa* with white bran (OSW). Gealy et al. also found that when comparing hull types among the red rice population, red rice with straw or blackhulls and awns were not molecularly different from one another. Gealy et al. found that many of the SSR markers used were able to differentiate between the OSW and the weedy rice. There were 12 SSR markers that produced alleles that were present in the cultivated rice with white bran that was absent in the weedy rice populations [42]. Through the study, they found that BA+ weedy rice had a greater genetic distance and more diversity than its strawhull, awnless counterparts with both varying genetically from the historic OSW population. To understand these differences, Gealy et al. also used principal component analysis to look at the clustering of populations based on genetic distance [43]. Through the analysis, they were able to find that hybrids were more closely associated with the weedy rice parent. This data was closely related to earlier studies completed by Gealy et al. [43]. Using structure analysis, genetic structure groupings were used to visualize the genetic backgrounds of weedy rice present in the USA. Six different groups were identified using STRUCTURE software by Pritchard et al. [44]. When analyzing the weedy rice population, the hybrid weedy rice fell in between strawhull,

*DOI: http://dx.doi.org/10.5772/intechopen.81838*

rice populations.

### *Weedy Rice: Competitive Ability, Evolution, and Diversity DOI: http://dx.doi.org/10.5772/intechopen.81838*

*Integrated View of Population Genetics*

of 500 μmol mol<sup>−</sup><sup>1</sup>

for every weedy rice plant/m<sup>2</sup>

**4. Evolution of weedy rice**

pathways of weedy rice.

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 [24]. Seed shattering, which distinguishes cultivated rice from its wild forms, is variable in weedy rice [25]. 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 [26]. Shattering in weedy rice is controlled by unidentified regulatory genes distinct from wild rice, thus suggesting parallel evolution between weedy rice and wild rice [26]. Weedy rice is also generally taller than cultivated rice making them more efficient for light and space [27]. Weedy rice has higher nitrogen use efficiency causing greater yield loss in rice fields [28]. 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 [28]. 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 [29]. 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

which is the projected CO2 concentration in the middle and

(NaCl)

end of the twentieth century [30]. 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<sup>−</sup><sup>1</sup>

There is immense diversity both among and within weedy rice populations and between weedy and cultivated rice [35–38]. 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 [39]. 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 [40]. 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

salinity level [32]. 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" [33]. 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

[34].

**30**

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 [41]. The weedy rice populations were compared to a wild rice relative, *O. rufipogon*, as well as cultivars to represent both indica and japonica biotypes. Cao et al. discovered, through genetic data, that the Liaoning cultivar, a japonica biotype, was very similar to that of weedy rice and clustered together to demonstrate this, while another Chinese japonica biotype did not follow the same clustering style. Through AMOVA analysis, the study found approximately 35% of the total genetic variation among regions, 18% within regions, and 46% within the populations. When the wild relative, *O. rufipogon*, and indica biotypes were compared to the weeds, they were further clustered from the weedy rice and Liaoning cultivar. Based on this data and the clusters presented, the authors concluded that weedy rice in the Liaoning province of China arose from the mutation and hybridization of Liaoning rice varieties [41]. This conclusion was challenged in 2010 by a paper from Ellstrand et al. stating "…if hybridization had occurred, it is likely that some *O. rufipogon* alleles would have been retained in the weedy lineages in the short time that they have been problematic" [38]. This could be true as Cao et al. found that there was a lack of heterozygosity within the weedy rice populations.

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 [42]. In this study, 31 SSR markers were used to analyze 180 kinds of rice from the genus *Oryza* and 80 weedy rice and rice cultivars from the USA. The 31 SSR markers selected represented low to high polymorphism information content values to screen the population for genetic variation. Using AMOVA, the genetic variation of the 80 weedy rice and rice cultivars was 56% within populations and 44% among populations. When the study compared only the 38 weedy rice populations that were separated into three different weedy rice populations, the genetic variation was 47% within populations and 53% among populations. A large amount of genetic variability was explained by the considerable genetic variation within blackhull, awned red rice (BA+), and *Oryza sativa* with white bran (OSW). Gealy et al. also found that when comparing hull types among the red rice population, red rice with straw or blackhulls and awns were not molecularly different from one another. Gealy et al. found that many of the SSR markers used were able to differentiate between the OSW and the weedy rice. There were 12 SSR markers that produced alleles that were present in the cultivated rice with white bran that was absent in the weedy rice populations [42]. Through the study, they found that BA+ weedy rice had a greater genetic distance and more diversity than its strawhull, awnless counterparts with both varying genetically from the historic OSW population. To understand these differences, Gealy et al. also used principal component analysis to look at the clustering of populations based on genetic distance [43]. Through the analysis, they were able to find that hybrids were more closely associated with the weedy rice parent. This data was closely related to earlier studies completed by Gealy et al. [43]. Using structure analysis, genetic structure groupings were used to visualize the genetic backgrounds of weedy rice present in the USA. Six different groups were identified using STRUCTURE software by Pritchard et al. [44]. When analyzing the weedy rice population, the hybrid weedy rice fell in between strawhull,

awnless and blackhull, awned weedy rice. This outcome was expected given the data presented on genetic variation and principal component analysis. The same results were observed when all rice in the study were combined together suggesting that the selected SSR markers by Gealy et al. were able to capture enough genetic variability to differentiate the origination of sampled weedy rice present within the USA [42]. Gealy et al. went further and compared their findings to those of Cao et al. notating that US weedy rice was qualitatively different from those found in the Liaoning province of China. While US weedy rice was genetically different from historical rice grown in the USA, they were more closely related to *O. sativa*, *nivara*, or *rufipogon* species, but Liaoning weedy rice populations were related to rice grown in the area and *japonica* biotypes from other regions [42]. These findings could be related to the selection of SSR markers used in the study by Cao et al. lacking the ability to capture as much genetic variation present in their population [42]. While Gealy et al. used 31 SSR markers and Cao et al. used 20 SSR markers, the quality of markers may not have been to the same degree as Gealy et al.

## **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 [45]. 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 [46]. 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 [47]. 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 *Oryza* population, (2) strawhull awnless weedy rice derived from rice cultivars with high shattering, (3) brownhull weedy rice, and (4) weedy rice of mixed weedy morphotype inferring multiple origin [48]. Similarly, weedy rice from major rice-cultivating areas of Italy can be awned, awnless, or mucronate. The highest variability was observed among awned weedy rice ecotypes than the awnless in terms of flag leaf length, 1000 seed weight, and germination rates [49]. In Arkansas, morphological characteristics varied among the two weedy rice ecotypes and within each ecotype (**Figure 2**) [45]. Blackhull weedy rice ecotype showed greater variation in traits than strawhull weedy rice. Plant height among blackhull accessions ranged from as short as 75 cm to as tall as 190 cm. The range of plant height in strawhull was greater (46–189 cm), but on an average, they were slightly shorter than blackhull weedy rice. Flag leaf lengths were longer in strawhull, 38 cm, than in blackhull weedy rice, 34 cm. Tillering capacity of blackhull weedy rice (mean = 105 tillers per plant) was higher than strawhull (mean = 95 tillers per plant). Also, weedy rice accessions from northeastern region of Arkansas flowered earlier than other regions in Arkansas. As the weedy rice is conspecific species of rice with AA genome, it has traits of both cultivated and wild rice. Weedy rice, being closely related to cultivated rice, has a tendency to pollinate with cultivated rice and produce progeny of different phenotypes [50]. Thus, weedy rice all over the world have

**33**

**Table 1.**

*markers.*

**Figure 2.**

*2008–2009.*

*Oryza sativa* f. *spontanea*

**Species Geographical** 

*Oryza sativa* L. Liaoning province, China

**location**

*Oryza sativa* L. Northeast Asia SSR He = 0.748

Awnless red rice Arkansas, USA SSR Average genetic

Awned red rice Arkansas, USA SSR Average genetic

*Oryza sativa* Arkansas, USA SSR Nei's genetic distance

Red rice Uruguay AFLP Average of 25.6 bands per

*Genetic diversity of weedy rice (Oryza sativa) from different regions of the world as detected by molecular* 

*Weedy Rice: Competitive Ability, Evolution, and Diversity*

variable phenotype as they can readily exchange genetic information with

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) [50–54]. Of these SSR markers are most commonly

*Weedy rice of different hull color and awn length collected from various rice fields of Arkansas, USA, in* 

**Marker used**

Northeastern China SSR Heterozygosity (H*e*) = 0.313

*Oryza sativa* L. Italy SSR He = 0.295 Grimm et al.

**Genetic diversity Reference**

Cao et al. [41]

Mao-bai et al. [51]

Gealy et al. [59]

Gealy et al. [59]

Shivrain et al. [54]

Federici et al. [57]

[56]

Shannon's diversity index

SSR He = 0.053 Yu et al. [52]

(I) = 0.572

I = 0.434

distance = 0.2

distance = 0.33

(GD) = 0.7

primer pair

**5.2 Genetic diversity of weedy rice and its gene flow potential**

*DOI: http://dx.doi.org/10.5772/intechopen.81838*

nearby cultivated rice plants.

variable phenotype as they can readily exchange genetic information with nearby cultivated rice plants.

## **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) [50–54]. Of these SSR markers are most commonly

### **Figure 2.**

*Integrated View of Population Genetics*

have been to the same degree as Gealy et al.

**5.1 Morphological diversity of weedy rice**

**5. Weedy rice diversity**

awnless and blackhull, awned weedy rice. This outcome was expected given the data presented on genetic variation and principal component analysis. The same results were observed when all rice in the study were combined together suggesting that the selected SSR markers by Gealy et al. were able to capture enough genetic variability to differentiate the origination of sampled weedy rice present within the USA [42]. Gealy et al. went further and compared their findings to those of Cao et al. notating that US weedy rice was qualitatively different from those found in the Liaoning province of China. While US weedy rice was genetically different from historical rice grown in the USA, they were more closely related to *O. sativa*, *nivara*, or *rufipogon* species, but Liaoning weedy rice populations were related to rice grown in the area and *japonica* biotypes from other regions [42]. These findings could be related to the selection of SSR markers used in the study by Cao et al. lacking the ability to capture as much genetic variation present in their population [42]. While Gealy et al. used 31 SSR markers and Cao et al. used 20 SSR markers, the quality of markers may not

Weedy rice exhibits high genetic and phenotypic diversity, and this diversity is dependent on the ecotype and habitat [45]. 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 [46]. 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 [47]. 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 *Oryza* population, (2) strawhull awnless weedy rice derived from rice cultivars with high shattering, (3) brownhull weedy rice, and (4) weedy rice of mixed weedy morphotype inferring multiple origin [48]. Similarly, weedy rice from major rice-cultivating areas of Italy can be awned, awnless, or mucronate. The highest variability was observed among awned weedy rice ecotypes than the awnless in terms of flag leaf length, 1000 seed weight, and germination rates [49]. In Arkansas, morphological characteristics varied among the two weedy rice ecotypes and within each ecotype (**Figure 2**) [45]. Blackhull weedy rice ecotype showed greater variation in traits than strawhull weedy rice. Plant height among blackhull accessions ranged from as short as 75 cm to as tall as 190 cm. The range of plant height in strawhull was greater (46–189 cm), but on an average, they were slightly shorter than blackhull weedy rice. Flag leaf lengths were longer in strawhull, 38 cm, than in blackhull weedy rice, 34 cm. Tillering capacity of blackhull weedy rice (mean = 105 tillers per plant) was higher than strawhull (mean = 95 tillers per plant). Also, weedy rice accessions from northeastern region of Arkansas flowered earlier than other regions in Arkansas. As the weedy rice is conspecific species of rice with AA genome, it has traits of both cultivated and wild rice. Weedy rice, being closely related to cultivated rice, has a tendency to pollinate with cultivated rice and produce progeny of different phenotypes [50]. Thus, weedy rice all over the world have

**32**

*Weedy rice of different hull color and awn length collected from various rice fields of Arkansas, USA, in 2008–2009.*


### **Table 1.**

*Genetic diversity of weedy rice (Oryza sativa) from different regions of the world as detected by molecular markers.*

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 [41]. Weedy rice from Northeast Asia are genetically diverse with high Shannon's information index of 0.748 and heterozygosity of 0.434 [51]. Among RAPD and SSR markers, SSR were superior to RAPD in detecting genetic diversity among weedy rice populations [52]. Weedy rice, weedy rice-cultivated rice hybrids, and rice cultivars can be distinguished using microsatellite SSR markers [53]. Molecular studies using SSR confirmed the differentiation of the two weedy rice ecotypes from Arkansas, USA [54]. 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 [54]. 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 *O. sativa* indica and *O. sativa* aus, instead of the commonly cultivated rice in the USA, *O. sativa* japonica [55]. Similar results were also observed by Londo and Schaal where most of the weedy rice clustered together with *O. sativa* aus. These results suggest that the US weedy rice evolved from *O. sativa* indica and aus rather than *O. sativa* japonica [38]. Genetic diversity of weedy rice from major rice-growing areas of Italy using 19 SSR markers was found to be relatively high with heterozygosity of 0.295 and average alleles of 3.368 [56]. Weedy rice from Uruguay is grouped into three distinct clusters based on their geographical location indicating similar characteristics of plants from similar location [57]. Great diversity in weedy rice accessions from different parts of the world supports the hypothesis that these are derived from natural hybridization among and within the cultivated and wild rice. It should be noted that not all blackhull, brownhull, and strawhull accessions are similar in terms of their genetic makeup or morphology. Their distinct characteristics can significantly affect management strategies that are adopted for controlling weedy rice making the control of weedy rice difficult.

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 [50]. Gene flow frequency from cultivated rice to wild rice (*O. rufipogon*) can be as high as 2.94% [58]. However, most of the gene flow studies have revealed outcrossing rate of up to 1% in *Oryza* species [59]. The variation in gene flow frequency in different studies reveals that the rate of gene flow between cultivated rice and their wild relatives depends upon various factors like weather conditions, density of infestation, and flowering synchrony. Studies have shown a possibility of crop-to-wild gene flow between *Oryza* species. As the infestation of weedy rice is increasing with change in rice production systems and climate change, the problem can become more severe in the future. Thus, steps should be taken to control weedy rice in the rice field, or it might have negative impacts on crop yield as well as the ecology of the area.

**35**

provided the original work is properly cited.

Swati Shrestha, Shandrea Stallworth and Te-Ming Tseng\* Mississippi State University, Mississippi State, Mississippi, USA

\*Address all correspondence to: t.tseng@msstate.edu

*Weedy Rice: Competitive Ability, Evolution, and Diversity*

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

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

*DOI: http://dx.doi.org/10.5772/intechopen.81838*

**6. Conclusions**

**Acknowledgements**

**Conflict of interest**

Station.

interest.

**Author details**

© 2018 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/ by/3.0), which permits unrestricted use, distribution, and reproduction in any medium,

## **6. Conclusions**

*Integrated View of Population Genetics*

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 [41]. Weedy rice from Northeast Asia are genetically diverse with high Shannon's information index of 0.748 and heterozygosity of 0.434 [51]. Among RAPD and SSR markers, SSR were superior to RAPD in detecting genetic diversity among weedy rice populations [52]. Weedy rice, weedy rice-cultivated rice hybrids, and rice cultivars can be distinguished using microsatellite SSR markers [53]. Molecular studies using SSR confirmed the differentiation of the two weedy rice ecotypes from Arkansas, USA [54]. 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 [54]. 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 *O. sativa* indica and *O. sativa* aus, instead of the commonly cultivated rice in the USA, *O. sativa* japonica [55]. Similar results were also observed by Londo and Schaal where most of the weedy rice clustered together with *O. sativa* aus. These results suggest that the US weedy rice evolved from *O. sativa* indica and aus rather than *O. sativa* japonica [38]. Genetic diversity of weedy rice from major rice-growing areas of Italy using 19 SSR markers was found to be relatively high with heterozygosity of 0.295 and average alleles of 3.368 [56]. Weedy rice from Uruguay is grouped into three distinct clusters based on their geographical location indicating similar characteristics of plants from similar location [57]. Great diversity in weedy rice accessions from different parts of the world supports the hypothesis that these are derived from natural hybridization among and within the cultivated and wild rice. It should be noted that not all blackhull, brownhull, and strawhull accessions are similar in terms of their genetic makeup or morphology. Their distinct characteristics can significantly affect management strategies that are adopted for

controlling weedy rice making the control of weedy rice difficult.

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 [50]. Gene flow frequency from cultivated rice to wild rice

(*O. rufipogon*) can be as high as 2.94% [58]. However, most of the gene flow studies have revealed outcrossing rate of up to 1% in *Oryza* species [59]. The variation in gene flow frequency in different studies reveals that the rate of gene flow between cultivated rice and their wild relatives depends upon various factors like weather conditions, density of infestation, and flowering synchrony. Studies have shown a possibility of crop-to-wild gene flow between *Oryza* species. As the infestation of weedy rice is increasing with change in rice production systems and climate change, the problem can become more severe in the future. Thus, steps should be taken to control weedy rice in the rice field, or it might have negative impacts on crop yield

**34**

as well as the ecology of the area.

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.

## **Acknowledgements**

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.

## **Author details**

Swati Shrestha, Shandrea Stallworth and Te-Ming Tseng\* Mississippi State University, Mississippi State, Mississippi, USA

\*Address all correspondence to: t.tseng@msstate.edu

© 2018 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/ by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

## **References**

[1] Norsworthy JK, Bond J, Scott RC. Weed management practices and needs in Arkansas and Mississippi rice. Weed Technology. 2013;**27**:623-630. DOI: 10.1614/WT-D-12-00172.1

[2] Ziska LH, Gealy DR, Burgos N, Caicedo AL, Gressel J, Lawton-Rauh AL, et al. Weedy (red) rice: An emerging constraint to global rice production. Advances in Agronomy. 2015;**129**:181-228. DOI: 10.1016/bs.agron.2014.09.003

[3] Burgos NR, Shivrain VK, Scott RC, Mauromoustakos A, Kuk YI, Sales MA, et al. Differential tolerance of weedy red rice (*Oryza sativa* L.) from Arkansas, USA to glyphosate. Crop Protection. 2011;**30**:986-994. DOI: 10.1016/j. cropro.2011.03.024

[4] Khush GS. Origin, dispersal, cultivation and variation of rice. Plant Molecular Biology. 2002;**35**:25-34. DOI: 10.1023/A:1005810616885

[5] Singh K, Kumar V, Saharawat YS, Gathala M, Ladha JK, Chauhan BS. Weedy rice: An emerging threat for direct-seeded rice production systems in India. Rice Research. 2013;**1**(1):1000106. DOI: 10.4172/jrr.1000106

[6] Kanapeckas KL, Vigueira CC, Ortiz A, Gettler KA, Burgos NR, Fischer AJ, et al. Escape to ferality: The endoferal origin of weedy rice from crop rice through de-domestication. PLoS One. 2016;**11**(9):e0162676. DOI: 10.1371/ journal.pone.0162676

[7] Nadir S, Xiong H-B, Zhu Q, Zhang X-L, Xu H-Y, Li J, et al. Weedy rice in sustainable rice production. A review. Agronomy for Sustainable Development. 2017;**37**:1-14. DOI: 10.1007/s13593-017-0456-4

[8] Ferrero A. Weedy Rice, Biological Features and Control. FAO Plant Production and Protection Paper (FAO); 2003

[9] Muthayya S, Sugimoto JD, Montgomery S, Maberly GF. An overview of global rice production, supply, trade, and consumption. Annals of the New York Academy of Sciences. 2014;**1324**:7-14. DOI: 10.1111/ nyas.12540

[10] Akita S. Direct rice-seeding culture in the United States. Farming Japan. 1991;**26**:20-26

[11] Liu H, Hussain S, Zheng M, Peng S, Huang J, Cui K, et al. Dry direct-seeded rice as an alternative to transplanted-flooded rice in Central China. Agronomy for Sustainable Development. 2015;**35**:285-294. DOI: 10.1007/s13593-014-0239-0

[12] Vaughan DA, Sanchez PL, Ushiki J, Kaga A, Tomooka N. Asian rice and weedy rice–evolutionary perspectives. In: Crop Ferality and Volunteerism. Boca Raton, USA: CRC Press; 2005. pp. 257-277

[13] Chin DV. Weedy rice situation in Vietnam. In: FAO Report. Global Workshop on Red Rice Control. Varadero, Cuba: Food and Agricultural Organization; 1999. pp. 67-74

[14] Chauhan BS. Strategies to manage weedy rice in Asia. Crop Protection. 2013;**48**:51-56. DOI: 10.1016/j. cropro.2013.02.015

[15] Chen LJ, Suh HS. Weedy rice— Origin and Dissemination. China: Yunnan Science and Technology Press; 2015. p. 234

[16] Allston RF. The rice plant. University of Michigan Humanities Text Initiative. 1846;**1**:320-256

[17] Tseng TM, Burgos NR, Alcober EAL, Shivrain VK. Inter- and intrapopulation variation in dormancy of *Oryza sativa* L. (weedy red rice) and

**37**

*Weedy Rice: Competitive Ability, Evolution, and Diversity*

[26] Thurber CS, Hepler PK, Caicedo AL. Timing is everything: Early degradation of abscission layer is associated with increased seed shattering in US weedy rice. BMC Plant Biology. 2011;**11**:14. DOI: 10.1186/1471-2229-11-14

[27] Anuwar Nur Hidayatul SA, Mazlan N, Engku Ahmad KEA, Juraimi AS, Yusop MR. A comparative study of vegetative and reproductive growth of local weedy and Clearfield® rice varieties in Malaysia. Journal of ISSAAS.

2014;**20**:41-51. ISSN: 0859-3132

10.1016/j.fcr.2006.03.009

10.2134/agronj2007.0324

journal.pone.0132100

10.12692/ijb/9.3.122-128

[31] Bevilacqua CB, Basu S, Pereira A, Tseng TM, Zimmer PD, Burgos NR. Analysis of stress-responsive gene expression in cultivated and weedy Rice differing in cold stress tolerance. PLoS One. 2015;**10**:e0132100. DOI: 10.1371/

[32] Uddin MK, Dandan HM, Alidin AH. Salinity effects on germination of malaysian rice varieties and weedy rice biotypes. World Academy of Science, Engineering and Technology, International Journal of Bioengineering and Life Sciences. 2015;**2**:724. DOI:

[28] Burgos NR, Norman RJ, Gealy DR, Black H. Competitive N uptake between rice and weedy rice. Field Crops Research. 2006;**99**:96-105. DOI:

[29] Sales MA, Burgos NR, Shivrain VK, Murphy B, Gbur EE. Morphological and physiological responses of weedy red rice (*Oryza sativa* L.) and cultivated rice (*O. sativa*) to N supply. American Journal of Plant Sciences. 2011;**2**: 569-577. DOI: 10.4236/ajps.2011.24068

[30] Ziska LH, McClung A. Differential response of cultivated and weedy (red) rice to recent and projected increases in atmospheric carbon dioxide. Agronomy Journal. 2008;**100**:1259-1263. DOI:

*DOI: http://dx.doi.org/10.5772/intechopen.81838*

allelic variation of dormancy-linked loci. Weed Research. 2013;**53**:440-451.

[18] Tseng TM, Shivrain VK, Lawton-Rauh A, Burgos NR. Dormancylinked population structure of weedy rice (*Oryza sativa*). Weed Science. 2017;**66**:331-339. DOI: 10.1017/

[19] Burgos NR, Norsworthy JK, Scott RC, Smith KL. Red rice (*Oryza sativa*) status after 5 years of imidazolinoneresistant rice technology in Arkansas. Weed Technology. 2008;**22**:200-208.

[20] Smith RJ Jr. Weed thresholds in southern US rice, *Oryza sativa*. Weed Technology. 1988;**2**:232-241. DOI: 10.1017/S0890037X00030505

[21] Whittaker RH. Dominance and diversity in land plant communities: Numerical relations of species express the importance of competition in community function and evolution. Science. 1965;**147**:250-260. DOI: 10.1126/science.147.3655.250

[22] Estorninos LE Jr, Gealy DR, Talbert RE. Growth response of Rice (*Oryza sativa*) and red Rice (*O. sativa*) in a replacement series study. Weed Technology. 2002;**16**:401-406. DOI: 10.1614/0890-037X(2002)016[0401:GR

[23] Goss WL, Brown E. Buried red rice seed. Journal of the American Society of Agronomy. 1939;**31**:633-637. ISSN:

[24] Noldin JA, Chandler JM, McCauley GN. Seed longevity of red rice ecotypes

[25] Ratnasekera D. Weedy rice: A threat to rice production in Sri Lanka. Journal of the University of Ruhuna. 2015;**3**: 2-13. DOI: 10.4038/jur.v3i1.7859

buried in soil. Planta Daninha. 2006;**24**:611-620. DOI: 10.1590/ S0100-83582006000400001

OROS]2.0.CO;2

0095-965

DOI: 10.1614/WT-07-075.1

DOI: 10.1111/wre.12044

wsc.2017.86

*Weedy Rice: Competitive Ability, Evolution, and Diversity DOI: http://dx.doi.org/10.5772/intechopen.81838*

allelic variation of dormancy-linked loci. Weed Research. 2013;**53**:440-451. DOI: 10.1111/wre.12044

[18] Tseng TM, Shivrain VK, Lawton-Rauh A, Burgos NR. Dormancylinked population structure of weedy rice (*Oryza sativa*). Weed Science. 2017;**66**:331-339. DOI: 10.1017/ wsc.2017.86

[19] Burgos NR, Norsworthy JK, Scott RC, Smith KL. Red rice (*Oryza sativa*) status after 5 years of imidazolinoneresistant rice technology in Arkansas. Weed Technology. 2008;**22**:200-208. DOI: 10.1614/WT-07-075.1

[20] Smith RJ Jr. Weed thresholds in southern US rice, *Oryza sativa*. Weed Technology. 1988;**2**:232-241. DOI: 10.1017/S0890037X00030505

[21] Whittaker RH. Dominance and diversity in land plant communities: Numerical relations of species express the importance of competition in community function and evolution. Science. 1965;**147**:250-260. DOI: 10.1126/science.147.3655.250

[22] Estorninos LE Jr, Gealy DR, Talbert RE. Growth response of Rice (*Oryza sativa*) and red Rice (*O. sativa*) in a replacement series study. Weed Technology. 2002;**16**:401-406. DOI: 10.1614/0890-037X(2002)016[0401:GR OROS]2.0.CO;2

[23] Goss WL, Brown E. Buried red rice seed. Journal of the American Society of Agronomy. 1939;**31**:633-637. ISSN: 0095-965

[24] Noldin JA, Chandler JM, McCauley GN. Seed longevity of red rice ecotypes buried in soil. Planta Daninha. 2006;**24**:611-620. DOI: 10.1590/ S0100-83582006000400001

[25] Ratnasekera D. Weedy rice: A threat to rice production in Sri Lanka. Journal of the University of Ruhuna. 2015;**3**: 2-13. DOI: 10.4038/jur.v3i1.7859

[26] Thurber CS, Hepler PK, Caicedo AL. Timing is everything: Early degradation of abscission layer is associated with increased seed shattering in US weedy rice. BMC Plant Biology. 2011;**11**:14. DOI: 10.1186/1471-2229-11-14

[27] Anuwar Nur Hidayatul SA, Mazlan N, Engku Ahmad KEA, Juraimi AS, Yusop MR. A comparative study of vegetative and reproductive growth of local weedy and Clearfield® rice varieties in Malaysia. Journal of ISSAAS. 2014;**20**:41-51. ISSN: 0859-3132

[28] Burgos NR, Norman RJ, Gealy DR, Black H. Competitive N uptake between rice and weedy rice. Field Crops Research. 2006;**99**:96-105. DOI: 10.1016/j.fcr.2006.03.009

[29] Sales MA, Burgos NR, Shivrain VK, Murphy B, Gbur EE. Morphological and physiological responses of weedy red rice (*Oryza sativa* L.) and cultivated rice (*O. sativa*) to N supply. American Journal of Plant Sciences. 2011;**2**: 569-577. DOI: 10.4236/ajps.2011.24068

[30] Ziska LH, McClung A. Differential response of cultivated and weedy (red) rice to recent and projected increases in atmospheric carbon dioxide. Agronomy Journal. 2008;**100**:1259-1263. DOI: 10.2134/agronj2007.0324

[31] Bevilacqua CB, Basu S, Pereira A, Tseng TM, Zimmer PD, Burgos NR. Analysis of stress-responsive gene expression in cultivated and weedy Rice differing in cold stress tolerance. PLoS One. 2015;**10**:e0132100. DOI: 10.1371/ journal.pone.0132100

[32] Uddin MK, Dandan HM, Alidin AH. Salinity effects on germination of malaysian rice varieties and weedy rice biotypes. World Academy of Science, Engineering and Technology, International Journal of Bioengineering and Life Sciences. 2015;**2**:724. DOI: 10.12692/ijb/9.3.122-128

**36**

2003

*Integrated View of Population Genetics*

[1] Norsworthy JK, Bond J, Scott RC. Weed management practices and needs in Arkansas and Mississippi rice. Weed Technology. 2013;**27**:623-630. DOI:

[9] Muthayya S, Sugimoto JD, Montgomery S, Maberly GF. An overview of global rice production, supply, trade, and consumption. Annals of the New York Academy of Sciences. 2014;**1324**:7-14. DOI: 10.1111/

[10] Akita S. Direct rice-seeding culture in the United States. Farming Japan.

[11] Liu H, Hussain S, Zheng M, Peng S, Huang J, Cui K, et al. Dry direct-seeded rice as an alternative to transplanted-flooded rice in Central China. Agronomy for Sustainable Development. 2015;**35**:285-294. DOI:

10.1007/s13593-014-0239-0

[12] Vaughan DA, Sanchez PL, Ushiki J, Kaga A, Tomooka N. Asian rice and weedy rice–evolutionary perspectives. In: Crop Ferality and Volunteerism. Boca Raton, USA: CRC Press; 2005.

[13] Chin DV. Weedy rice situation in Vietnam. In: FAO Report. Global Workshop on Red Rice Control. Varadero, Cuba: Food and Agricultural

[14] Chauhan BS. Strategies to manage weedy rice in Asia. Crop Protection. 2013;**48**:51-56. DOI: 10.1016/j.

[15] Chen LJ, Suh HS. Weedy rice— Origin and Dissemination. China: Yunnan Science and Technology Press;

[16] Allston RF. The rice plant.

Initiative. 1846;**1**:320-256

University of Michigan Humanities Text

[17] Tseng TM, Burgos NR, Alcober EAL, Shivrain VK. Inter- and

intrapopulation variation in dormancy of *Oryza sativa* L. (weedy red rice) and

Organization; 1999. pp. 67-74

cropro.2013.02.015

2015. p. 234

nyas.12540

1991;**26**:20-26

pp. 257-277

10.1614/WT-D-12-00172.1

**References**

cropro.2011.03.024

[2] Ziska LH, Gealy DR, Burgos N, Caicedo AL, Gressel J, Lawton-Rauh AL, et al. Weedy (red) rice: An emerging constraint to global rice production. Advances in Agronomy. 2015;**129**:181-228. DOI: 10.1016/bs.agron.2014.09.003

[3] Burgos NR, Shivrain VK, Scott RC, Mauromoustakos A, Kuk YI, Sales MA, et al. Differential tolerance of weedy red rice (*Oryza sativa* L.) from Arkansas, USA to glyphosate. Crop Protection. 2011;**30**:986-994. DOI: 10.1016/j.

[4] Khush GS. Origin, dispersal, cultivation and variation of rice. Plant Molecular Biology. 2002;**35**:25-34. DOI:

[5] Singh K, Kumar V, Saharawat YS, Gathala M, Ladha JK, Chauhan BS. Weedy rice: An emerging threat for direct-seeded rice production systems in India. Rice Research. 2013;**1**(1):1000106.

[6] Kanapeckas KL, Vigueira CC, Ortiz A, Gettler KA, Burgos NR, Fischer AJ, et al. Escape to ferality: The endoferal origin of weedy rice from crop rice through de-domestication. PLoS One. 2016;**11**(9):e0162676. DOI: 10.1371/

[7] Nadir S, Xiong H-B, Zhu Q, Zhang X-L, Xu H-Y, Li J, et al. Weedy rice in sustainable rice production. A review. Agronomy for Sustainable Development. 2017;**37**:1-14. DOI: 10.1007/s13593-017-0456-4

[8] Ferrero A. Weedy Rice, Biological Features and Control. FAO Plant

Production and Protection Paper (FAO);

10.1023/A:1005810616885

DOI: 10.4172/jrr.1000106

journal.pone.0162676

[33] Pantone DJ, Baker JB. Weed-crop competition models and responsesurface analysis of red rice competition in cultivated rice: A review. Crop Science. 1991;**31**:1105-1110. DOI: 10.2135/cropsci1991.0011183X0031000 50003x

[34] Ottis BV, Smith KL, Scott RC, Talbert RE. Rice yield and quality as affected by cultivar and red rice (*Oryza sativa*) density. Weed Science. 2005;**53**:499-504. DOI: 10.1614/ WS-04-154R

[35] Londo JP, Schaal BA. Origins and population genetics of weedy red rice in the USA. Molecular Ecology. 2007;**16**:4523-4535. DOI: 10.1111/j.1365-294X.2007.03489.x

[36] Kanapeckas KL, Tseng TM, Vigueira CC, Ortiz A, JrBridges WC, Burgos NR, et al. Contrasting patterns of variation in weedy traits and unique crop features in divergent populations of US weedy rice (*Oryza sativa* sp.) in Arkansas and California. Pest Management Science;**2017, 74**:1404-1415. DOI: 10.1002/ps.4820

[37] Burgos NR, Singh V, Tseng TM, Black H, Young ND, Huang Z, et al. The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of United States weedy rice. Plant Physiology. 2014;**114**:242719. DOI: 10.1104/ pp.114.242719

[38] Tseng TM. Genetic diversity of seed dormancy and molecular evolution of weedy red rice [PhD dissertation]. University of Arkansas; 2013. Available from: http://scholarworks.uark.edu/ etd/595

[39] Ellstrand NC, Heredia SM, Leak-Garcia JA, et al. Crops gone wild: Evolution of weeds and invasives from domesticated ancestors. Evolutionary Applications. 2010;**3**(5-6):494-504. DOI: 10.1111/j.1752-4571.2010.00140.x

[40] De-Wet JMJ, Harlan JR. Weeds and domesticates: Evolution in the man-made habitat. Economic Botany. 1975;**29**:99. DOI: 10.1007/ BF02863309

[41] Cao Q, Lu B-R, Xia H, Rong J, Sala F, Spada A, et al. Genetic diversity and origin of weedy rice (*Oryza sativa* f. *spontanea*) populations found in North-Eastern China revealed by simple sequence repeat (SSR) markers. Annals of Botany. 2006;**98**:1241-1252. DOI: 10.1093/aob/mcl210

[42] Gealy DR, Agrama HA, Eizenga GC. Exploring genetic and spatial structure of U.S. weedy red rice (*Oryza sativa*) in relation to rice relatives worldwide. Weed Science. 2009;**57**(06):627-643. DOI: 10.1614/ WS-09-018.1

[43] Gealy DR. Gene movement between rice (*Oryza sativa*) and weedy rice (*Oryza sativa*): A U.S. temperate rice perspective. In: Gressel J, editor. Crop Ferality and Volunteerism. Boca Raton, FL: CRC Press; 2005. pp. 323-354. DOI: 10.1201/9781420037999.ch20

[44] Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;**155**:945-959

[45] Shivrain VK, Burgos NR, Scott RC, Gbur EE Jr, Estorninos LE Jr, McClelland MR. Diversity of weedy red rice (*Oryza sativa* L.) in Arkansas, USA in relation to weed management. Crop Protection. 2010;**29**(7):721-730. DOI: 10.1016/j.cropro.2010.02.010

[46] Chauhan BS, Johnson DE. The role of seed ecology in improving weed management strategies in the tropics. Advances in Agronomy. 2010;**105**: 221-262. DOI: 10.1016/S0065-2113 (10)05006-6

[47] Perera UIP, Senanayake SGJN, Ratnasekera WADPR. Morphological diversity of weedy rice accessions

**39**

*Weedy Rice: Competitive Ability, Evolution, and Diversity*

(*Oryza sativa*) in Arkansas, USA. Weed Research. 2010;**50**:289-302. DOI: 10.1111/j.1365-3180.2010.00780.x

[55] Reagon M, Thurber CS, Gross BL, Olsen KM, Jia Y, Caicedo AL. Genomic patterns of nucleotide diversity in divergent populations of US weedy rice. BMC Evolutionary Biology. 2010;**10**:180.

DOI: 10.1186/1471-2148-10-180

10.1002/ece3.848

WT02-100

[56] Grimm A, Fogliatto S, Nick P, Ferrero A, Vidotto F. Microsatellite markers reveal multiple origins for Italian weedy rice. Ecology and Evolution. 2013;**3**:4786-4798. DOI:

[57] Federici MT, Vaughan D, Norihiko T, Kaga A, Xin WW, Koji D, et al. Analysis of Uruguayan weedy rice genetic diversity using AFLP molecular markers. Electronic Journal of Biotechnology. 2001;**4**:5-6. DOI: 10.2225/vol4-issue3-fulltext-3

[58] Song ZP, Zhu YG, Chen JK. Gene flow from cultivated rice to the wild species *Oryza rufipogon* under experimental field conditions. New Phytologist. 2003;**157**:67-665. DOI: 10.1046/j.1469-8137.2003.00699.x

[59] Gealy DR, Mitten DH, Rutger JN. Gene flow between red rice (*Oryza sativa*) and herbicide-resistant rice (*O. sativa*): Implications for weed management. Weed Technology. 2003;**17**:627-645. DOI: 10.1614/

*DOI: http://dx.doi.org/10.5772/intechopen.81838*

collected in Ampara district. In: Proceedings of International Forestry and Environment Symposium. 2012. p. 15. DOI: 10.31357/fesympo.v15i0.

[48] Sudianto E, Neik TX, Tam SM, Chuah TS, Idris AA, Olsen KM, et al. Morphology of Malaysian weedy rice (*Oryza sativa*): Diversity, origin and implications for weed management. Weed Science. 2016;**64**:501-512. DOI:

[49] Fogliatto S, Vidotto F, Ferrero A. Morphological characterization of Italian weedy rice (*Oryza sativa*) populations. Weed Research. 2012;**52**:60-69. DOI: 10.1111/j.1365-3180.2011.00890.x

[50] Chen LJ, Lee DS, Song ZP, Suh HS, Lu BR. Gene flow from cultivated rice (*Oryza sativa*) to its weedy and wild relatives. Annals of Botany. 2004;**93**: 67-73. DOI: 10.1093/aob/mch006

[51] Mao-bai L, Hui W, Li-ming C. Evaluation of population structure, genetic diversity and origin of Northeast

Asia weedy rice based on simple sequence repeat markers. Rice Science. 2015;**22**:180-188. DOI: 10.1016/j.

[52] Yu GQ, Bao Y, Shi CH, Dong CQ, Ge S. Genetic diversity and population differentiation of Liaoning weedy rice detected by RAPD and SSR markers. Biochemical Genetics. 2005;**43**:261-270.

DOI: 10.1007/s10528-005-5218-3

[53] Gealy DR, Tai TH, Sneller CH. Identification of red rice, rice, and hybrid populations using microsatellite markers. Weed Science. 2002;**50**:333-339. DOI:

10.1614/0043-1745(2002)050[0333,IOR

[54] Shivrain VK, Burgos NR, Agrama HA, Lawton-Rauh A, Lu B, Sales MA, et al. Genetic diversity of weedy red rice

rsci.2015.02.001

RRA]2.0.CO;2

10.1614/WS-D-15-00168.1

180.g87

*Weedy Rice: Competitive Ability, Evolution, and Diversity DOI: http://dx.doi.org/10.5772/intechopen.81838*

collected in Ampara district. In: Proceedings of International Forestry and Environment Symposium. 2012. p. 15. DOI: 10.31357/fesympo.v15i0. 180.g87

*Integrated View of Population Genetics*

50003x

WS-04-154R

10.1002/ps.4820

pp.114.242719

etd/595

[33] Pantone DJ, Baker JB. Weed-crop competition models and responsesurface analysis of red rice competition in cultivated rice: A review. Crop Science. 1991;**31**:1105-1110. DOI: 10.2135/cropsci1991.0011183X0031000

[40] De-Wet JMJ, Harlan JR. Weeds and domesticates: Evolution in the man-made habitat. Economic Botany. 1975;**29**:99. DOI: 10.1007/ BF02863309

[41] Cao Q, Lu B-R, Xia H, Rong J, Sala F, Spada A, et al. Genetic diversity and origin of weedy rice (*Oryza sativa* f. *spontanea*) populations found in North-Eastern China revealed by simple sequence repeat (SSR) markers. Annals of Botany. 2006;**98**:1241-1252. DOI:

[42] Gealy DR, Agrama HA, Eizenga GC. Exploring genetic and spatial structure of U.S. weedy red rice (*Oryza sativa*) in relation to rice relatives worldwide. Weed Science. 2009;**57**(06):627-643. DOI: 10.1614/

[43] Gealy DR. Gene movement between rice (*Oryza sativa*) and weedy rice (*Oryza sativa*): A U.S. temperate rice perspective. In: Gressel J, editor. Crop Ferality and Volunteerism. Boca Raton, FL: CRC Press; 2005. pp. 323-354. DOI:

[44] Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;**155**:945-959

[45] Shivrain VK, Burgos NR, Scott RC, Gbur EE Jr, Estorninos LE Jr, McClelland MR. Diversity of weedy red rice (*Oryza sativa* L.) in Arkansas, USA in relation to weed management. Crop Protection. 2010;**29**(7):721-730. DOI:

10.1016/j.cropro.2010.02.010

(10)05006-6

[46] Chauhan BS, Johnson DE. The role of seed ecology in improving weed management strategies in the tropics. Advances in Agronomy. 2010;**105**: 221-262. DOI: 10.1016/S0065-2113

[47] Perera UIP, Senanayake SGJN, Ratnasekera WADPR. Morphological diversity of weedy rice accessions

10.1201/9781420037999.ch20

10.1093/aob/mcl210

WS-09-018.1

[34] Ottis BV, Smith KL, Scott RC, Talbert RE. Rice yield and quality as affected by cultivar and red rice (*Oryza sativa*) density. Weed Science. 2005;**53**:499-504. DOI: 10.1614/

[35] Londo JP, Schaal BA. Origins and population genetics of weedy red rice in the USA. Molecular Ecology. 2007;**16**:4523-4535. DOI: 10.1111/j.1365-294X.2007.03489.x

[36] Kanapeckas KL, Tseng TM, Vigueira CC, Ortiz A, JrBridges WC, Burgos NR, et al. Contrasting patterns of variation in weedy traits and unique crop features in divergent populations of US weedy rice (*Oryza sativa* sp.) in Arkansas and California. Pest Management Science;**2017, 74**:1404-1415. DOI:

[37] Burgos NR, Singh V, Tseng TM, Black H, Young ND, Huang Z, et al. The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of United States weedy rice. Plant Physiology. 2014;**114**:242719. DOI: 10.1104/

[38] Tseng TM. Genetic diversity of seed dormancy and molecular evolution of weedy red rice [PhD dissertation]. University of Arkansas; 2013. Available from: http://scholarworks.uark.edu/

[39] Ellstrand NC, Heredia SM, Leak-Garcia JA, et al. Crops gone wild: Evolution of weeds and invasives from domesticated ancestors. Evolutionary Applications. 2010;**3**(5-6):494-504. DOI: 10.1111/j.1752-4571.2010.00140.x

**38**

[48] Sudianto E, Neik TX, Tam SM, Chuah TS, Idris AA, Olsen KM, et al. Morphology of Malaysian weedy rice (*Oryza sativa*): Diversity, origin and implications for weed management. Weed Science. 2016;**64**:501-512. DOI: 10.1614/WS-D-15-00168.1

[49] Fogliatto S, Vidotto F, Ferrero A. Morphological characterization of Italian weedy rice (*Oryza sativa*) populations. Weed Research. 2012;**52**:60-69. DOI: 10.1111/j.1365-3180.2011.00890.x

[50] Chen LJ, Lee DS, Song ZP, Suh HS, Lu BR. Gene flow from cultivated rice (*Oryza sativa*) to its weedy and wild relatives. Annals of Botany. 2004;**93**: 67-73. DOI: 10.1093/aob/mch006

[51] Mao-bai L, Hui W, Li-ming C. Evaluation of population structure, genetic diversity and origin of Northeast Asia weedy rice based on simple sequence repeat markers. Rice Science. 2015;**22**:180-188. DOI: 10.1016/j. rsci.2015.02.001

[52] Yu GQ, Bao Y, Shi CH, Dong CQ, Ge S. Genetic diversity and population differentiation of Liaoning weedy rice detected by RAPD and SSR markers. Biochemical Genetics. 2005;**43**:261-270. DOI: 10.1007/s10528-005-5218-3

[53] Gealy DR, Tai TH, Sneller CH. Identification of red rice, rice, and hybrid populations using microsatellite markers. Weed Science. 2002;**50**:333-339. DOI: 10.1614/0043-1745(2002)050[0333,IOR RRA]2.0.CO;2

[54] Shivrain VK, Burgos NR, Agrama HA, Lawton-Rauh A, Lu B, Sales MA, et al. Genetic diversity of weedy red rice (*Oryza sativa*) in Arkansas, USA. Weed Research. 2010;**50**:289-302. DOI: 10.1111/j.1365-3180.2010.00780.x

[55] Reagon M, Thurber CS, Gross BL, Olsen KM, Jia Y, Caicedo AL. Genomic patterns of nucleotide diversity in divergent populations of US weedy rice. BMC Evolutionary Biology. 2010;**10**:180. DOI: 10.1186/1471-2148-10-180

[56] Grimm A, Fogliatto S, Nick P, Ferrero A, Vidotto F. Microsatellite markers reveal multiple origins for Italian weedy rice. Ecology and Evolution. 2013;**3**:4786-4798. DOI: 10.1002/ece3.848

[57] Federici MT, Vaughan D, Norihiko T, Kaga A, Xin WW, Koji D, et al. Analysis of Uruguayan weedy rice genetic diversity using AFLP molecular markers. Electronic Journal of Biotechnology. 2001;**4**:5-6. DOI: 10.2225/vol4-issue3-fulltext-3

[58] Song ZP, Zhu YG, Chen JK. Gene flow from cultivated rice to the wild species *Oryza rufipogon* under experimental field conditions. New Phytologist. 2003;**157**:67-665. DOI: 10.1046/j.1469-8137.2003.00699.x

[59] Gealy DR, Mitten DH, Rutger JN. Gene flow between red rice (*Oryza sativa*) and herbicide-resistant rice (*O. sativa*): Implications for weed management. Weed Technology. 2003;**17**:627-645. DOI: 10.1614/ WT02-100

**41**

Section 4

Population Genetics for

Conservation Studies

Section 4
