Is all red rice found in commercial rice really Oryza sativa?
Laura K. VaughanBrian V. OttisAnn M. Prazak-HaveyConcetta BormansClay SnellerJames M. ChandlerWilliam D. Park
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All red rice found in commercial rice in the United States has traditionally been classified as Oryza sativa ssp. indica. This assumption was tested by analyzing red rice samples collected from across the southern United States rice belt with 18 simple sequence length polymorphism (SSLP) markers distributed across all 12 chromosomes. The results clearly demonstrate that the traditional classification of red rice is inadequate. Some red rice is closely related to O. sativa ssp. indica cultivated rice. However, other red rice is more closely related to O. sativa ssp. japonica. Most importantly, some red rice samples collected from Arkansas, Louisiana, Mississippi, and Texas form a distinct group that includes a number of Oryza nivara and Oryza rufipogon accessions from the National Small Grains Center. In particular, red rice samples from three states were identified that for all 18 markers are identical to the O. rufipogon accession IRGC 105491. These different classes of red rice are intermingled across the southern U.S. rice belt and within individual production fields. Oryza sativa ssp. indica-like red rice and O. rufipogon-like red rice have been found within a single 9-m2 collection site. While the classification of red rice as O. sativa ssp. indica, O. sativa ssp. japonica, or O. rufipogon using DNA markers is generally in agreement with classification based on simple morphological traits, readily observed morphological traits alone are not sufficient to reliably classify red rice. Because red rice is much more diverse than previously assumed, this diversity must be considered when developing red rice management strategies.Keywords:
Oryza rufipogon
Red rice
Oryza
Weedy rice
Several weedy red rice populations have evolved resistance to imidazolinone herbicides worldwide. The understanding of the factors related to the herbicide resistance in weedy red rice is important to prevent its occurrence in new areas where imidazolinone-resistant rice cultivars are being used, and to manage the new rice cultivars resistant to herbicides with modes of action other than the acetolactate synthase (ALS)-inhibitors that are being developed. The objectives of this study were to analyze the relationship of weedy red rice populations from southern Brazil with rice cultivars and wild Oryza species and to evaluate the occurrence of introgression from rice cultivars and seed migration as the origin of resistance to imidazolinone herbicides in weedy rice. The study was based on 27 weedy red rice populations, seven rice cultivars, and four wild Oryza species that were genotyped with 24 simple sequence repeats and three ALS -specific single-nucleotide polymorphism markers. A large proportion of the genetic variation of the weedy red rice populations was found within (74%) rather than among populations (26%). The weedy red rice populations were more closely related to the newer rice cultivars that are imidazolinone-resistant than to the older cultivars. The South American native Oryza glumaepatula and the other wild Oryza species— Oryza rufipogon, Oryza longistaminata , and Oryza glaberrima —clustered separately from weedy red rice populations, indicating a low likelihood of introgression among weedy red rice and these wild species. Seed migration was an important factor in the genetic structure of the evaluated weedy red rice populations, although gene flow by pollen from resistant cultivars was the principal reason for the spread of herbicide resistance.
Weedy rice
Red rice
Introgression
Oryza
Oryza rufipogon
Upland rice
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Oryza rufipogon
Oryza
Nuclear gene
Nuclear DNA
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Weedy rice
Oryza rufipogon
Oryza
Upland rice
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Citations (53)
Abstract Weedy red rice ( Oryza sativa spontonea ) is a persistent and problematic weed of rice culture worldwide. A major hypothesis for the mechanism of production of this weed in South and Southeast Asia is hybridization between cultivated rice ( Oryza sativa ) and wild rice ( Oryza rufipogon ). However, weedy red rice can often be found outside the range of O. rufipogon leaving questions on the origin and process behind weedy rice infestations. In the USA, weedy red rice was first documented as early as 1846 and has continued to affect rice production areas. In this study, we attempt to identify the origin and population structure of weedy red rice sampled from the USA using both DNA sequence data from a neutral nuclear locus as well as microsatellite genotype data. Results suggest that two major accessions of weedy rice exist, strawhull and blackhull, and these forms may both hybridize with the cultivated rice of the USA, O. sativa japonica . Using population assignment of multilocus genotype signatures with principal component analysis and structure , an Asian origin is supported for US weedy rice. Additionally, hybridization between strawhull and blackhull varieties was inferred and may present the opportunity for the production of new weedy forms in the future.
Weedy rice
Oryza rufipogon
Red rice
Oryza
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S hivrain VK, B urgos NR, A grama HA, L awton ‐R auh A, L u B, S ales MA, B oyett V, G ealy DR & M oldenhauer KAK (2010). Genetic diversity of weedy red rice ( Oryza sativa ) in Arkansas, USA. Weed Research 50 , 289–302. Summary Weedy red rice ( Oryza sativa ) is a problematic weed in cultivated rice. About 50% of US rice is produced in Arkansas and 60% of these fields have some red rice infestation. Red rice populations are morphologically and phenologically diverse. We hypothesise that red rice in Arkansas has high genetic diversity, which underlies its wide phenotypic diversity, and that some alleles from cultivated rice have been introgressed into red rice during more than a century of coexistence. We tested 137 red rice accessions from four ecological zones in Arkansas and 36 cultivars that have been grown in Arkansas in the past century. Twenty‐seven rice microsatellite primers, distributed across 12 chromosomes, were used to generate molecular markers. The overall Nei’s genetic distance (GD) of red rice accessions was 0.70. Rice grown in the last century had an overall GD of 0.26. The awnless strawhull red rice was genetically distant from blackhull (GD = 0.55) and brownhull (GD = 0.60) red rice types. Nei’s GD between blackhull and brownhull red rice was 0.42. Brownhull and blackhull formed one genotypic cluster, whereas the majority of strawhull red rice formed another cluster. Within blackhull red rice, the GD was 0.76, whereas for awnless strawhull it was 0.68, 0.75 for awned strawhull and 0.80 for brownhull types. The gene diversity of blackhull and strawhull correlated with zone of origin. A quarter of the red rice accessions share common alleles with cultivated rice. A diverse complex of weedy populations has evolved in a region devoid of other weedy and wild Oryza species.
Weedy rice
Red rice
Oryza
Upland rice
Aromatic rice
Genetic distance
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Red rice from the southern United States was collected and analyzed using Simple Sequence Length Polymorphism (SSLP) markers in an effort to test the assumption that red rice is Oryza sativa ssp. indica. The 18 markers used are distributed across all 12 chromosomes of the rice genome and can be used to distinguish between sibling cultivars. The results indicate that traditional classification of red rice based on morphological characteristics alone is inadequate. Some red rice was closely related to Oryza sativa ssp. indica, while other red rice was more closely related to Oryza sativa ssp. japonica. Some red rice samples collected from Arkansas, Louisiana, Mississippi, and Texas are very closely related to the noxious weed, Oryza rufipogon accession IRGC 105491. This research revealed that different classes of red rice are intermingled across the southern United States rice belt. Within individual commercial production fields, Oryza sativa ssp. indica-like red rice and Oryza rufipogon-like red rice can be found within a single 9 m² collection site. In 2000 and 2001, studies were conducted at several locations across the Texas rice-producing region with imidazolinone tolerant rice to determine the most efficacious sequential application rate and timing of imazethapyr for control of red rice and other weeds. At Beaumont, red rice and barnyardgrass control was greater than 94% with 0.07, 0.09 and 0.10 kg/ha preplant incorporated or preemergence followed by at least 0.04 kg/ha early postemergence on a clay soil. Broadleaf signalgrass control near Eagle Lake showed that preplant incorporated and preemergence applications followed by early postemergence applications provided greater than 86% control in 2000, and greater than 90% control in 2001. Sequential postemergence applications at Beaumont resulted in greater than 95% red rice and barnyardgrass control when 0.04 kg/ha late postemergence followed any early postemergence application. Sequential postemergence applications controlled broadleaf signalgrass greater than 98% in both years. Red rice control at Lissie on a fine sandy loam soil was at least 98% with all sequential treatments. Crop injury was found to be a function of the postemergence application in all studies. Crop yields were not reduced by early season crop injury from imazethapyr applications, regardless of soil type.
Red rice
Oryza rufipogon
Oryza
Weedy rice
Eleusine indica
Paddy field
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Weedy red rice is a highly troublesome weed of rice in the United States and throughout the world. Effective management of this weed has remained challenging to U.S. farmers, partly because of the biological diversity among red rice populations, resistance to or avoidance of control measures, and genetic similarities with crop rice that allow crossing between the two plant types. The aim of this research was to identify simple sequence repeat (SSR) marker loci that will unambiguously differentiate between U.S. weedy red rice, commercial rice cultivars, and their hybrids, to characterize the genetic diversity and structure of U.S. weedy red rice accessions in relation to Oryza collections from international sources, and to relate genetic and geographic variability within U.S. weedy red rice. Thirty-one SSR markers were used to analyze 180 worldwide Oryza entries and 80 U.S. weedy red rice and U.S. rice cultivars. Twenty-six of the 31 SSR marker loci were highly informative with respect to genetic distinctions between U.S. weedy red rice and U.S. rice cultivars. U.S. red rice are accessions clustered into two main SSR-based collections, awnless strawhull (SA−) and awned blackhull (BA+), according to genetic distance analysis and principal coordinate analysis. Genetic structure analysis clearly identified SA− and BA+ red rice, rice–red rice hybrids, commercial japonica rice cultivars, indica rice, and a number of international and wild Oryza spp. standards (e.g., Oryza nivara , Oryza rufipogon , and Oryza glaberrima ) as genetically distinct groups. U.S. SA− red rice exhibited greater spatial structure than did BA+ in that the genetic makeup of SA− accessions changed nearly twice as much with geographic distance as compared to BA+. However, the overall genetic variability within SA− red rice accessions was less than for BA+ accessions, suggesting that the SA− types may be genetically less compatible than BA+ types with other Oryza plants such as rice or other red rice types present in U.S. rice fields. Several of the awned red rice entries exhibited evidence of natural hybridization with different red rice types. Our results suggest that the SA− and BA+ red rice collections have different genetic backgrounds. SA− accessions generally associated most closely with indica -like red- or white-bran Oryza sativa cultivar standards, while BA+ accessions generally associated more closely with O. nivara or O. nivara –like O. sativa entries. Although the U.S. red rice accessions appear not to have descended directly from introductions of the worldwide Oryza standards analyzed, an Oryza red-pericarp entry from Niger (UA 1012; PI 490783) was genetically very similar to some U.S. BA+ accessions.
Weedy rice
Red rice
Oryza
Oryza rufipogon
Upland rice
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Citations (45)
All red rice found in commercial rice in the United States has traditionally been classified as Oryza sativa ssp. indica. This assumption was tested by analyzing red rice samples collected from across the southern United States rice belt with 18 simple sequence length polymorphism (SSLP) markers distributed across all 12 chromosomes. The results clearly demonstrate that the traditional classification of red rice is inadequate. Some red rice is closely related to O. sativa ssp. indica cultivated rice. However, other red rice is more closely related to O. sativa ssp. japonica. Most importantly, some red rice samples collected from Arkansas, Louisiana, Mississippi, and Texas form a distinct group that includes a number of Oryza nivara and Oryza rufipogon accessions from the National Small Grains Center. In particular, red rice samples from three states were identified that for all 18 markers are identical to the O. rufipogon accession IRGC 105491. These different classes of red rice are intermingled across the southern U.S. rice belt and within individual production fields. Oryza sativa ssp. indica-like red rice and O. rufipogon-like red rice have been found within a single 9-m2 collection site. While the classification of red rice as O. sativa ssp. indica, O. sativa ssp. japonica, or O. rufipogon using DNA markers is generally in agreement with classification based on simple morphological traits, readily observed morphological traits alone are not sufficient to reliably classify red rice. Because red rice is much more diverse than previously assumed, this diversity must be considered when developing red rice management strategies.
Oryza rufipogon
Red rice
Oryza
Weedy rice
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Citations (121)
Indica-japonica differentiation is the most significant genetic variation among varietal types of Asian cultivated rice(Oryza sativa L.).Despite its important roles in the domestication process of Asian cultivated rice,the mechanisms of indica-japonica differentiation are still unclear.One of the hypotheses stresses that the differentiation of indica-japonica has occurred in the wild ancestral species.In order to investigate the indica-japonica genetic variation in all wild relatives in the genus Oryza,50 typical and rice cultivars and 348 wild Oryza accessions from 35 countries were included in the study using 34 indica-japonica specified InDel primer pairs.The results indicated that significant indica-japonica differentiation occurred in Asian cultivated rice,and some indica and japonica types were also found in some of the O.rufipogon complex.However,no such differentiation were detected in other Oryza species.The geographical distribution pattern of indica and japonica types in the O.rufipogon complex is associated with the geographical distribution of and rice varieties.Given the wild accessions were collected in habitats adjacent to the fields of cultivated rice,we believe that the indica and japonica types in O.rufipogon complex is more likely generated by the introgression from the respective indica or japonica rice varieties historically.
Oryza rufipogon
Indel
Introgression
Oryza
Japonica rice
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Abstract Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed based on neutral markers and analyses of domestication genes for hull color and seed shattering. Here, we examined variation in pericarp (bran) color and its molecular basis to address how this trait evolved in Malaysian weeds and its possible role in weed adaptation. Functional alleles of the Rc gene confer proanthocyanidin pigmentation of the pericarp, a trait found in most wild and weedy Oryzas and associated with seed dormancy; nonfunctional rc alleles were strongly favored during rice domestication, and most cultivated varieties have nonpigmented pericarps. Phenotypic characterizations of 52 Malaysian weeds revealed that most strains are characterized by the pigmented pericarp; however, some weeds have white pericarps, suggesting close relationships to cultivated rice. Phylogenetic analyses indicate that the Rc haplotypes present in Malaysian weeds likely have at least three distinct origins: wild O. rufipogon, white-pericarp cultivated rice, and red-pericarp cultivated rice. These diverse origins contribute to high Rc nucleotide diversity in the Malaysian weeds. Comparison of Rc allelic distributions with other rice domestication genes suggests that functional Rc alleles may confer particular fitness benefits in weedy rice populations, for example, by conferring seed dormancy. This may promote functional Rc introgression from local wild Oryza populations.
Weedy rice
Introgression
Oryza rufipogon
Red rice
Oryza
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Citations (38)