Stuttgart, AR, United States
Stuttgart, AR, United States

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Gealy D.R.,Dale Bumpers National Rice Research Center | Fischer A.J.,University of California at Davis
Weed Science | Year: 2010

Assessing belowground plant competition is complex because it is very difficult to separate weed and crop roots from each other by physical methods. Alternative techniques for separating crop and weed roots from each other are needed. This article introduces a stable isotope method that can quantify the amounts of roots of rice and barnyardgrass intermixed in flooded field soils. It relies on the biological principle that rice, a C3 (photosynthetic pathway) species, discriminates more effectively than barnyardgrass, a C4 species, against a relatively rare isotopic form (13C) of CO2. This results in different 13C:12C isotope ratios (expressed as δ13C) in root tissues of the two species. δ13C values for monoculture barnyardgrass and rice grown in a standard flood-irrigated system were highly stable over 4 crop-years, averaging-13.12 ± 0.80 (SD) and-28.5 ± 0.11 (SD)‰, respectively, based on analysis by an isotope ratio mass spectrometer. Standard concentration curves relating measured δ13C values to set proportions of rice:barnyardgrass root biomass were described by linear regressions, typically with r2 values of 0.96 or greater. Quantities of intermixed rice and barnyardgrass roots sampled 0 to 5 cm deep from soil between rice rows were estimated by extrapolation from standard curves based on δ13C values. About 50 more barnyardgrass root tissue was detected in plots of Lemont long-grain rice than in weed-suppressive PI 312777 indica rice, demonstrating the feasibility of using this stable carbon isotope method in flooded rice systems. © 2010 Weed Science Society of America.


Fernandez-Pozo N.,Boyce Thompson Institute for Plant Research | Menda N.,Boyce Thompson Institute for Plant Research | Edwards J.D.,Dale Bumpers National Rice Research Center | Saha S.,Boyce Thompson Institute for Plant Research | And 10 more authors.
Nucleic Acids Research | Year: 2015

The Sol Genomics Network (SGN, http://solgenomics.net) is a web portal with genomic and phenotypic data, and analysis tools for the Solanaceae family and close relatives. SGN hosts whole genome data for an increasing number of Solanaceae family members including tomato, potato, pepper, eggplant, tobacco and Nicotiana benthamiana. The database also stores loci and phenotype data, which researchers can upload and edit with user-friendly web interfaces. Tools such as BLAST, GBrowse and JBrowse for browsing genomes, expression and map data viewers, a locus community annotation system and a QTL analysis tools are available. A new tool was recently implemented to improve Virus-Induced Gene Silencing (VIGS) constructs called the SGN VIGS tool. With the growing genomic and phenotypic data in the database, SGN is now advancing to develop new web-based breeding tools and implement the code and database structure for other species or clade-specific databases. © The Author(s) 2014.


Scheuermann K.K.,Santa Catarina State Agricultural Research and Rural Extension Agency | Jia Y.,Dale Bumpers National Rice Research Center
Phytopathology | Year: 2016

The Pi9 gene in rice, originating from Oryza minuta, is an effective resistance gene for controlling rice blast disease. However, currently available linked DNA markers do not accurately identify the function of Pi9, thus hindering its efficient incorporation into new cultivars through marker-assisted selection (MAS). In addition, no known Pi9-containing rice germplasm is available to breeders. In the present study, DNA sequence variation of Pi9 alleles and their family members was analyzed in 40 diverse rice germplasm accessions from the AA genome to develop a robust Pi9 marker. In total, 29 DNA primers of 20 to 23 nucleotides were designed and each possible combination of primer pairs was used to detect Pi9. Only one combination of DNA primers, KS28/KS6, was identified to specifically detect Pi9 in the monogenic line IRBL9-W. The presence of Pi9 was verified with the predicted Pi9-specific blast reaction. Subsequently, 201 genetically diverse mini-core rice accessions from 114 countries were screened with KS28/KS6. One germplasm, IR 9660-48-1-1-2, was identified to carry Pi9 and the function of Pi9 was verified with pathogenicity assays. This robust Pi9 marker and a rice germplasm, IR9660-48-1-1-2 (GSOR310687), carrying Pi9 can be used to improve blast resistance with a MAS approach. © 2016, American Phytopathological Society. All rights reserved.


Min B.,University of Maryland Eastern Shore | McClung A.,Dale Bumpers National Rice Research Center | Chen M.-H.,Dale Bumpers National Rice Research Center
Food Chemistry | Year: 2014

The impacts of parboiling and wet-cooking, alone and in combination, on the concentrations of lipophilic antioxidants (vitamin E and γ-oryzanol), soluble (including proanthocyanidins and anthocyanins) and cell wall-bound phenolics, and antioxidant capacities in whole grain rice from six cultivars having different bran colours were investigated. Parboiling rough and brown rice increased the concentrations of lipophilic antioxidants in whole grain rice but decreased the concentrations of total phenolics and antioxidant capacities found in the soluble fraction. After hydrothermal processing of purple bran rice, the retention of extractable anthocyanins was low, but was high for simple phenolics. For proanthocyanidins found in red bran rice, the extractable oligomers with a degree of polymerization (DP) less than 4, increased up to 6-fold; while for oligomers with DP ≥ 4 and polymers, there was a significant decrease that was positively correlated with the DP and the temperature of the processing methods. The presence of hulls helped to retain water-soluble antioxidants during parboiling.


Ziska L.H.,U.S. Department of Agriculture | Gealy D.R.,Dale Bumpers National Rice Research Center | Tomecek M.B.,U.S. Department of Agriculture | Jackson A.K.,Dale Bumpers National Rice Research Center | Black H.L.,Dale Bumpers National Rice Research Center
PLoS ONE | Year: 2012

Although recent and projected increases in atmospheric carbon dioxide can alter plant phenological development, these changes have not been quantified in terms of floral outcrossing rates or gene transfer. Could differential phenological development in response to rising CO2 between genetically modified crops and wild, weedy relatives increase the spread of novel genes, potentially altering evolutionary fitness? Here we show that increasing CO2 from an early 20th century concentration (300 μmol mol-1) to current (400 μmol mol-1) and projected, mid-21st century (600 μmol mol-1) values, enhanced the flow of genes from wild, weedy rice to the genetically altered, herbicide resistant, cultivated population, with outcrossing increasing from 0.22% to 0.71% from 300 to 600 μmol mol-1. The increase in outcrossing and gene transfer was associated with differential increases in plant height, as well as greater tiller and panicle production in the wild, relative to the cultivated population. In addition, increasing CO2 also resulted in a greater synchronicity in flowering times between the two populations. The observed changes reported here resulted in a subsequent increase in rice dedomestication and a greater number of weedy, herbicide-resistant hybrid progeny. Overall, these data suggest that differential phenological responses to rising atmospheric CO2 could result in enhanced flow of novel genes and greater success of feral plant species in agroecosystems.


Gross B.L.,Washington University in St. Louis | Reagon M.,University of Massachusetts Amherst | Hsu S.-C.,Washington University in St. Louis | Caicedo A.L.,University of Massachusetts Amherst | And 2 more authors.
Molecular Ecology | Year: 2010

Weedy forms of crop species infest agricultural fields worldwide and are a leading cause of crop losses, yet little is known about how these weeds evolve. Red rice (Oryza sativa), a major weed of cultivated rice fields in the US, is recognized by the dark-pigmented grain that gives it its common name. Studies using neutral molecular markers have indicated a close relationship between US red rice and domesticated rice, suggesting that the weed may have originated through reversion of domesticated rice to a feral form. We have tested this reversion hypothesis by examining molecular variation at Rc, the regulatory gene responsible for grain pigmentation differences between domesticated and wild rice. Loss-of-function mutations at Rc account for the absence of proanthocyanidin pigments in cultivated rice grains, and the major rc domestication allele has been shown to be capable of spontaneous reversion to a functional form through additional mutations at the Rc locus. Using a diverse sample of 156 weedy, domesticated and wild Oryzas, we analysed DNA sequence variation at Rc and its surrounding 4 Mb genomic region. We find that reversion of domestication alleles does not account for the pigmented grains of weed accessions; moreover, we find that haplotypes characterizing the weed are either absent or very rare in cultivated rice. Sequences from genomic regions flanking Rc are consistent with a genomic footprint of the rc selective sweep in cultivated rice, and they are compatible with a close relationship of red rice to Asian Oryzas that have never been cultivated in the US. © 2010 Blackwell Publishing Ltd.


Chen M.-H.,Rice Research Unit | Fjellstrom R.G.,Dale Bumpers National Rice Research Center | Christensen E.F.,Rice Research Unit | Bergman C.J.,University of Nevada, Las Vegas
Molecular Breeding | Year: 2010

Four Waxy haplotypes, previously identified as each having a different combination of three single nucleotide polymorphisms (SNPs) in the Waxy gene, were highly correlated with apparent amylose content and pasting properties, which are important grain quality traits for predicting cooked rice (Oryza sativa L.) texture and processing properties (Chen et al. in J Cereal Sci 47:536-545, 2008a; Chen et al. in J Cereal Sci 48:781-788, 2008b). Three allele-specific PCR markers were developed to genotype the three aforementioned functional SNPs in a single PCR amplification. Each marker contained two allele-specific primers and one common primer. For each marker, the two allele-specific primers differed by one base at the 3′-end to provide discrimination of SNP alleles, and were labeled with unique fluorescence probes. An additional mismatched base, the third base from the 3′-end, was inserted in some allele-specific primers to increase selectivity. The amplification step of the PCR thermal cycling program was initially set for 20× touch-down cycles with the annealing temperature of the first cycle approximately 6°C above the thermal melting temperature of all three primers at a touch-down rate of -0.3°C per cycle, and followed by 25× regular thermal cycles with the annealing temperature at their thermal melting temperature. The allelic genotypes for each SNP were distinguished from each other by both their differential primer-allele fluorescences and their amplification product lengths. The simplicity of these assays makes it easy to utilize these markers as part of a marker-assisted selection strategy in rice breeding programs selecting for these important grain quality traits. © 2010 US Government.


Orshinsky A.M.,Ohio State University | Hu J.,Ohio State University | Opiyo S.O.,Ohio State University | Reddyvari-Channarayappa V.,Dale Bumpers National Rice Research Center | And 2 more authors.
PLoS ONE | Year: 2012

Sclerotinia homoeocarpa causes dollar spot disease, the predominate disease on highly-maintained turfgrass. Currently, there are major gaps in our understanding of the molecular interactions between S. homoeocarpa and creeping bentgrass. In this study, 454 sequencing technology was used in the de novo assembly of S. homoeocarpa and creeping bentgrass transcriptomes. Transcript sequence data obtained using Illumina's first generation sequencing-by-synthesis (SBS) were mapped to the transcriptome assemblies to estimate transcript representation in different SBS libraries. SBS libraries included a S. homoeocarpa culture control, a creeping bentgrass uninoculated control, and a library for creeping bentgrass inoculated with S. homoeocarpa and incubated for 96 h. A Fisher's exact test was performed to determine transcripts that were significantly different during creeping bentgrass infection with S. homoeocarpa. Fungal transcripts of interest included glycosyl hydrolases, proteases, and ABC transporters. Of particular interest were the large number of glycosyl hydrolase transcripts that target a wide range of plant cell wall compounds, corroborating the suggested wide host range and saprophytic abilities of S. homoeocarpa. Several of the multidrug resistance ABC transporters may be important for resistance to both fungicides and plant defense compounds. Creeping bentgrass transcripts of interest included germins, ubiquitin transcripts involved in proteasome degradation, and cinnamoyl reductase, which is involved in lignin production. This analysis provides an extensive overview of the S. homoeocarpa-turfgrass pathosystem and provides a starting point for the characterization of potential virulence factors and host defense responses. In particular, determination of important host defense responses may assist in the development of highly resistant creeping bentgrass varieties. © 2012 Orshinsky et al.


Jia Y.,Dale Bumpers National Rice Research Center | Jia M.H.,Dale Bumpers National Rice Research Center | Wang X.,China Jiliang University | Liu G.,University of Arkansas
PLoS ONE | Year: 2012

Understanding linkage block size and molecular mechanisms of recombination suppression is important for plant breeding. Previously large linkage blocks ranging from 14 megabases to 27 megabases were observed around the rice blast resistance gene Pi-ta in rice cultivars and backcross progeny involving an indica and japonica cross. In the present study, the same linkage block was further examined in 456 random recombinant individuals of rice involving 5 crosses ranging from F2 to F10 generation, with and without Pi-ta containing genomic indica regions with both indica and japonica germplasm. Simple sequence repeat markers spanning the entire chromosome 12 were used to detect recombination break points and to delimit physical size of linkage blocks. Large linkage blocks ranging from 4.1 megabases to 10 megabases were predicted from recombinant individuals involving genomic regions of indica and japonica. However, a significantly reduced block from less than 800 kb to 2.1megabases was identified from crosses of indica with indica rice regardless of the existence of Pi-ta. These findings suggest that crosses of indica and japonica rice have significant recombination suppression near the centromere on chromosome 12.


Jia Y.,Dale Bumpers National Rice Research Center | Moldenhauer K.,University of Stuttgart
Journal of Plant Registrations | Year: 2010

The major blast resistance (R) genes Pi-ta, Pi-ks, Pi-kh have been effectively deployed in rice (Oryza sativa L.) in the southern USA for preventing disease caused by the predominant U.S. races of Magnaporthe oryzae Cav. [=Magnaporthe grisea (Herbert) Barr.]. In the present study, the codominant single nucleotide length polymorphism DNA marker for the Pi-ta gene, and the simple sequence repeat markers, RM144 and RM224, that cosegregate with two alleles of the Pi-k gene, Pi-ks and Pi-ks, were used for R identification in a F10 recombinant inbred line population. This population (Reg. no. MP-3, NSL 452303) was derived from the cross RU9101001/'Katy'. This population composed of 235 individual lines was jointly released on 24 Apr. 2009 by the USDA-ARS and the University of Arkansas Division of Agriculture Arkansas Agriculture Experiment Station. R gene containing RIL lines were verified with standard pathogenicity assays by means of a set of differential races of M. oryzae in the USA. One hundred eighty-two pure lines were identified from the population with the Pi-ta, Pi-ks, and Pi-kh genes. A total of 56 had Pi-ta and Pi-ks, 51 lines had Pi-ks, 27 had Pi-kh, and 48 lines had Pi-kh and Pi-ta. These monogenic and digenic rice lines with the major blast R genes are expected to be useful for studying effects of each R gene singly and in combination for their epistatic interaction with yield and for introducing blast resistance with marker assisted selection. © Crop Science Society of America.

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