Wang M.,University of Arizona |
Yu Y.,University of Arizona |
Haberer G.,Helmholtz Center Munich |
Marri P.R.,Dow AgroSciences |
And 30 more authors.
Nature Genetics | Year: 2014
The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes. © 2014 Nature America, Inc. All rights reserved.
Chia J.-M.,Cold Spring Harbor Laboratory |
Song C.,BGI Shenzhen |
Bradbury P.J.,Cornell University |
Bradbury P.J.,U.S. Department of Agriculture |
And 47 more authors.
Nature Genetics | Year: 2012
Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize. © 2012 Nature America, Inc. All rights reserved.
Perea H.,University of Nebraska - Lincoln |
Strelkoff T.S.,Research Hydraulic Engineer |
Adamsen F.J.,Urban Irrigation Water Testing and Consulting |
Hunsaker D.J.,Us Arid Land Agricultural Research Center |
Clemmens A.J.,Research Hydraulic Engineer and Center Director
Journal of Irrigation and Drainage Engineering | Year: 2010
A cross-section-averaged advection-dispersion equation (ADE) model was developed to simulate the transport of fertilizer in furrow irrigation. The advection and dispersion processes were solved separately at each time step by implementing a method of characteristics with cubic-spline interpolation and a time-weighted finite-difference scheme, respectively. The upstream boundary condition was a prescribed concentration. Downstream, a zero-flux boundary condition during advance and a concentration gradient following completion of advance were prescribed. Local pseudosteady state was assumed in order to apply Fischer's longitudinal dispersion equation under nonuniform and unsteady furrow flow conditions. Statistical parameters were used to evaluate the ADE model performance. © 2010 ASCE.
Wang G.,University of California |
Bronson K.F.,Us Arid Land Agricultural Research Center |
Thorp K.R.,Us Arid Land Agricultural Research Center |
Mon J.,Us Arid Land Agricultural Research Center |
Badaruddin M.,University of Arizona
Crop Science | Year: 2014
Simple and rapid methods are needed to measure durum wheat (Triticum durum L.) nitrogen (N) status and make on-site N application decisions for increased crop yield and grain quality. Although chlorophyll meters (SPAD meters) have been widely tested for cereal crop N management, significant variation in SPAD meter readings among growing seasons, locations, and crop cultivars makes them challenging. Experiments with six durum wheat cultivars and six N fertilizer rates were conducted in Arizona in the 2010-2011 and 2011-2012 growing seasons to test whether multiple leaf SPAD readings on the same plants can improve estimation of crop N status by SPAD meters. The relationships between N nutrition index (NNI) and SPAD readings on the most recent fully expanded leaves (SPAD1), Sufficiency Index or normalized SPAD index (SI), Normalized difference SPAD index (NDSPAD), and the differences in SPAD readings between the second most recent and most recent fully expanded leaves (SPAD21) were compared. The results showed SPAD1 varied with growing season, growth stage, and durum wheat cultivar. All three indices, SI, NDSPAD, and SPAD21, improved the prediction of durum wheat N status compared to SPAD1. The SI measured at Feekes 10.5 or mean SI over growth stages (Feekes 5, 10, and 10.5) performed better than the other three indices in predicting crop yield. This study suggests that using SPAD21 can improve the effectiveness of the SPAD meter compared to SPAD1 and that SPAD21 can be as effective as SI without requirement of reference plots in durum wheat N management. © Crop Science Society of America.
Clemmens A.J.,WEST Consultants Inc. |
Clemmens A.J.,Us Arid Land Agricultural Research Center |
Litrico X.,Lyonnaise des Eaux Recherche |
Litrico X.,IRSTEA |
And 2 more authors.
Journal of Irrigation and Drainage Engineering | Year: 2011
The integrator-delay (ID) model is commonly used to model canal pools that do not exhibit resonance behavior. Simple step tests are often used to estimate ID model parameters; namely, delay time and backwater surface area. These step tests change the canal inflow at the upstream end of the pool and observe water depth variations at the downstream end. Some knowledge of the canal pool characteristics are needed to determine the amount of flow change and its duration. Auto tune variation (ATV) is one method for determining the duration of these step tests. Pools that are under backwater over their entire length tend to exhibit oscillations attributable to resonance waves. Random Binary Sequence (RBS) tests have been used to determine the resonance frequency of such pools, for which step tests with different durations are used. RBS tests are difficult to implement in practice and may not provide the resonance frequency. The intent of this paper is to demonstrate on a real canal that the ATV method can determine both the resonance frequency and the resonance-peak height for canal pools whose water levels oscillate. © 2012 American Society of Civil Engineers.
Ottman M.J.,University of Arizona |
Kimball B.A.,Us Arid Land Agricultural Research Center |
White J.W.,Us Arid Land Agricultural Research Center |
Wall G.W.,Us Arid Land Agricultural Research Center
Agronomy Journal | Year: 2012
Possible future increases in atmospheric temperature may threaten wheat (Triticum aestivum L.) production and food security. The purpose of this research is to determine the response of wheat growth to supplemental heating and to seasonal air temperature from an unusually wide range of planting dates. A field study was conducted at Maricopa, AZ, where wheat was planted from September to May over a 2-yr period for a total of 12 planting dates. Supplemental heating was provided for 6 of the 12 planting dates using infrared heaters placed above the crop which increased canopy temperature by 1.3°C during the day and 2.7°C during the night. Grain yield declined 42 g m -2 (6.9%) per 1°C increase in seasonal temperature above 16.3°C. Supplemental heating had no effect on grain yield for plantings in winter (Dec./Jan.) since temperatures were near optimum (14.9°C). However, in spring (Mar.) plantings where temperature (22.2°C) was above optimum, supplemental heating decreased grain yield from 510 to 368 g m -2. Supplemental heating had the greatest effect in the early fall plantings (Sept./Oct.) when temperature was slightly below optimum (13.8°C) and mid-season frost limited the yield of unheated plots to only 3 g m -2 whereas yield of heated plots was 435 g m -2. Thus, possible future increases in temperature may decrease wheat yield for late plantings and shift optimum planting windows to earlier dates in areas of the world similar to the desert southwest of the United States.© 2012 by the American Society of Agronomy.
White J.W.,Us Arid Land Agricultural Research Center |
Dierig D.A.,National Center for Genetic Resources Preservation
Journal of Plant Registrations | Year: 2011
Descriptions of new germplasm published in the Journal of Plant Registrations (JPR), and previously in Crop Science, are important vehicles for informing researchers about advances in plant breeding. Launched in 2007, JPR introduced a format that allowed more detailed descriptions of registrations; however, an informal review suggests that further improvements are possible. This paper explores these suggestions. To support our arguments, we assessed the new format by reviewing 234 papers from JPR, focusing on 106 papers (53 each in the old-Crop Science-and new-JPR-formats) for cultivar releases in 14 self-pollinated crops. We examined genealogies (pedigrees), breeding processes, experimental techniques, phenotypes, and genotypes. In the new format, there was more extensive information on the chronology of the breeding process, the expected area of adaptation, experimental techniques, the quantification of phenotypes, and citation of web-based reports. Nonetheless, improvement appeared possible, including by (i) documenting genealogies in databases structured for breeding records; (ii) quantifying the degree of relatedness to other germplasm; (iii) describing the breeding process in tables that include key dates, population types and sizes, and numbers of test environments; (iv) describing adaptation through standardized scales, environmental classifications, or quantitative responses; (v) providing genotypic data; and (vi) providing access to supplementary materials from databases or Internet resources. © Crop Science Society of America.
Parsons E.P.,Purdue University |
Popopvsky S.,Israel Agricultural Research Organization |
Lohrey G.T.,Purdue University |
Lu S.,King Abdullah University of Science and Technology |
And 5 more authors.
Physiologia Plantarum | Year: 2012
To understand the role of fruit cuticle lipid composition in fruit water loss, an advanced backcross population, the BC2F2, was created between the Capsicum annuum (PI1154) and the Capsicum chinense (USDA162), which have high and low post-harvest water loss rates, respectively. Besides dramatic differences in fruit water loss, preliminary studies also revealed that these parents exhibited significant differences in both the amount and composition of their fruit cuticle. Cuticle analysis of the BC2F2 fruit revealed that although water loss rate was not strongly associated with the total surface wax amount, there were significant correlations between water loss rate and cuticle composition. We found a positive correlation between water loss rate and the amount of total triterpenoid plus sterol compounds, and negative correlations between water loss and the alkane to triterpenoid plus sterol ratio. We also report negative correlations between water loss rate and the proportion of both alkanes and aliphatics to total surface wax amount. For the first time, we report significant correlations between water loss and cutin monomer composition. We found positive associations of water loss rate with the total cutin, total C16 monomers and 16-dihydroxy hexadecanoic acid. Our results support the hypothesis that simple straight-chain aliphatic cuticle constituents form more impermeable cuticular barriers than more complex isoprenoid-based compounds. These results shed new light on the biochemical basis for cuticle involvement in fruit water loss. © 2012 Physiologia Plantarum.
van Overloop P.J.,Technical University of Delft |
Miltenburg I.J.,Technical University of Delft |
Bombois X.,Technical University of Delft |
Clemmens A.J.,Us Arid Land Agricultural Research Center |
And 3 more authors.
Control Engineering Practice | Year: 2010
This article describes a way to determine the properties of resonance (reflecting) waves in open water channels. For channels that are sensitive to resonances, information about the first resonance mode is required for controller and filter design. This research applies standard system identification techniques and is tested on an actual channel at the Central Arizona Irrigation and Drainage District, Eloy, AZ. The identification experiment results in good estimations of the frequency and magnitude of the first resonance peak of the open water channel. © 2010 Elsevier Ltd.
PubMed | West Virginia University, Israel Agricultural Research Organization, Us Arid Land Agricultural Research Center and Purdue University
Type: Journal Article | Journal: TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik | Year: 2016
Molecular markers linked to QTLs controlling post-harvest fruit water loss in pepper may be utilized to accelerate breeding for improved shelf life and inhibit over-ripening before harvest. Bell pepper (Capsicum annuum L.) is an important vegetable crop world-wide. However, marketing is limited by the relatively short shelf life of the fruit due to water loss and decay that occur during prolonged storage. Towards breeding pepper with reduced fruit post-harvest water loss (PWL), we studied the genetic, physiological and biochemical basis for natural variation of PWL. We performed quantitative trait locus (QTL) mapping of fruit PWL in multiple generations of an interspecific cross of pepper, which resulted in the identification of two linked QTLs on chromosome 10 that control the trait. We further developed near-isogenic lines (NILs) for characterization of the QTL effects. Transcriptome analysis of the NILs allowed the identification of candidate genes associated with fruit PWL-associated traits such as cuticle biosynthesis, cell wall metabolism and fruit ripening. Significant differences in PWL between the NILs in the immature fruit stage, differentially expressed cuticle-associated genes and differences in the content of specific chemical constituents of the fruit cuticle, indicated a likely influence of cuticle composition on the trait. Reduced PWL in the NILs was associated with delayed over-ripening before harvest, low total soluble solids before storage, and reduced fruit softening after storage. Our study enabled a better understanding of the genetic and biological processes controlling natural variation in fruit PWL in pepper. Furthermore, the genetic materials and molecular markers developed in this study may be utilized to breed peppers with improved shelf life and inhibited over-ripening before harvest.