Huang T.,Boyce Thompson Institute for Plant Research |
Huang T.,Keygene Inc |
Jander G.,Boyce Thompson Institute for Plant Research
Planta | Year: 2017
Main conclusion: Whereas proline accumulates through de novo biosynthesis in plants subjected to osmotic stress, leucine, isoleucine, and valine accumulation in drought-stressedArabidopsis thalianais caused by abscisic acid-regulated protein degradation.In response to several kinds of abiotic stress, plants greatly increase their accumulation of free amino acids. Although stress-induced proline increases have been studied the most extensively, the fold-increase of other amino acids, in particular branched-chain amino acids (BCAAs; leucine, isoleucine, and valine), is often higher than that of proline. In Arabidopsis thaliana (Arabidopsis), BCAAs accumulate in response to drought, salt, mannitol, polyethylene glycol, herbicide treatment, and nitrogen starvation. Plants that are deficient in abscisic acid signaling accumulate lower amounts of BCAAs, but not proline and most other amino acids. Previous bioinformatic studies had suggested that amino acid synthesis, rather than protein degradation, is responsible for the observed BCAA increase in osmotically stressed Arabidopsis. However, whereas treatment with the protease inhibitor MG132 decreased drought-induced BCAA accumulation, inhibition of BCAA biosynthesis with the acetolactate synthase inhibitors chlorsulfuron and imazapyr did not. Additionally, overexpression of BRANCHED-CHAIN AMINO ACID TRANSFERASE2 (BCAT2), which is upregulated in response to osmotic stress and functions in BCAA degradation, decreased drought-induced BCAA accumulation. Together, these results demonstrate that BCAA accumulation in osmotically stressed Arabidopsis is primarily the result of protein degradation. After relief of the osmotic stress, BCAA homeostasis is restored over time by amino acid degradation involving BCAT2. Thus, drought-induced BCAA accumulation is different from that of proline, which is accumulated due to de novo synthesis in an abscisic acid-independent manner and remains elevated for a more prolonged period of time after removal of the osmotic stress. © 2017 Springer-Verlag GmbH Germany
DiLeo M.V.,University of California at Davis |
DiLeo M.V.,Keygene Incorporated |
Bostock R.M.,University of California at Davis |
Rizzo D.M.,University of California at Davis
PLoS ONE | Year: 2014
Phytophthora ramorum, an invasive pathogen and the causal agent of Sudden Oak Death, has become established in mixed-evergreen and redwood forests in coastal northern California. While oak and tanoak mortality is the most visible indication of P. ramorum's presence, epidemics are largely driven by the presence of bay laurel (Umbellularia californica), a reservoir host that supports both prolific sporulation in the winter wet season and survival during the summer dry season. In order to better understand how over-summer survival of the pathogen contributes to variability in the severity of annual epidemics, we monitored the viability of P. ramorum leaf infections over three years along with coincident microclimate. The proportion of symptomatic bay laurel leaves that contained viable infections decreased during the first summer dry season and remained low for the following two years, likely due to the absence of conducive wet season weather during the study period. Over-summer survival of P. ramorum was positively correlated with high percent canopy cover, less negative bay leaf water potential and few days exceeding 30°C but was not significantly different between mixed-evergreen and redwood forest ecosystems. Decreased summer survival of P. ramorum in exposed locations and during unusually hot summers likely contributes to the observed spatiotemporal heterogeneity of P. ramorum epidemics. © 2014 DiLeo et al.
DiLeo M.V.,Boyce Thompson Institute for Plant Research |
DiLeo M.V.,Robert lley Center For Agriculture And Health |
DiLeo M.V.,Keygene Inc |
den Bakker M.,Boyce Thompson Institute for Plant Research |
And 6 more authors.
Plant Genome | Year: 2014
While the greatest strength of systems biology may be to measure tens of thousands of variables across different genotypes, this simultaneously presents an enormous challenge to statistical analysis that cannot be completely solved with conventional approaches that identify and rank differences. Here we examine a diverse panel of conventional and transgenic, field-grown tomato fruits (Solanum lycopersicum L.) by liquid chromatography-mass spectrometry (LC-MS) metabolic fingerprinting. We used a progression of statistics to examine phenotypic variation observed. While clear trends were found by principal component analysis (PCA) related to genetic background and ripeness, it could not detect differences between transgenic genotypes and their nontransgenic parent variety. Partial least squares discriminant analysis (PLS-DA), a supervised method, identified 15 metabolic features of potential interest, but only five were significantly different between the transgenic lines and their nontransgenic parent. Weighted correlation network analysis (WGCNA) recognized relationships among these features and others, suggesting that a small suite of highly correlated compounds accumulated to significantly lower levels in the transgenic genotypes. We assert that metabolic fingerprinting with a series of statistical methods is an efficient and powerful approach to examine both large and small genetic effects on phenotypes of high value or interest. © Crop Science Society of America.
Zwick M.E.,Emory University |
Zwick M.E.,Biological Defense Research Directorate |
Joseph S.J.,Emory University |
Didelot X.,University of Oxford |
And 18 more authors.
Genome Research | Year: 2012
The key genes required for Bacillus anthracis to cause anthrax have been acquired recently by horizontal gene transfer. To understand the genetic background for the evolution of B. anthracis virulence, we obtained high-redundancy genome sequences of 45 strains of the Bacillus cereus sensu lato (s.l.) species that were chosen for their genetic diversity within the species based on the existing multilocus sequence typing scheme. From the resulting data, we called more than 324,000 new genes representing more than 12,333 new gene families for this group. The core genome size for the B. cereus s.l. group was ∼1750 genes, with another 2150 genes found in almost every genome constituting the extended core. There was a paucity of genes specific and conserved in any clade. We found no evidence of recent large-scale gene loss in B. anthracis or for unusual accumulation of nonsynonymous DNA substitutions in the chromosome; however, several B. cereus genomes isolated from soil and not previously associated with human disease were degraded to various degrees. Although B. anthracis has undergone an ecological shift within the species, its chromosome does not appear to be exceptional on a macroscopic scale compared with close relatives.
Munkvold J.D.,Cornell University |
Munkvold J.D.,Keygene Inc |
Laudencia-Chingcuanco D.,U.S. Department of Agriculture |
Sorrells M.E.,Cornell University
Genetics | Year: 2013
Quantitative phenotypic traits are influenced by genetic and environmental variables as well as the interaction between the two. Underlying genetic · environment interaction is the influence that the surrounding environment exerts on gene expression. Perturbation of gene expression by environmental factors manifests itself in alterations to gene co-expression networks and ultimately in phenotypic plasticity. Comparative gene co-expression networks have been used to uncover biological mechanisms that differentiate tissues or other biological factors. In this study, we have extended consensus and differential Weighted Gene Co-Expression Network Analysis to compare the influence of different growing environments on gene co-expression in the mature wheat (Triticum aestivum) embryo. This network approach was combined with mapping of individual gene expression QTL to examine the genetic control of environmentally static and variable gene expression. The approach is useful for gene expression experiments containing multiple environments and allowed for the identification of specific gene co-expression modules responsive to environmental factors. This procedure identified conserved coregulation of gene expression between environments related to basic developmental and cellular functions, including protein localization and catabolism, vesicle composition/trafficking, Golgi transport, and polysaccharide metabolism among others. Environmentally unique modules were found to contain genes with predicted functions in responding to abiotic and biotic environmental variables. These findings represent the first report using consensus and differential Weighted Gene Coexpression Network Analysis to characterize the influence of environment on coordinated transcriptional regulation. © 2013 by the Genetics Society of America.
Williams K.,Cornell University |
Munkvold J.,KeyGene Inc. |
Sorrells M.,Cornell University
Euphytica | Year: 2013
Digital image analysis (DIA) is widely used for describing plant organ shape. However, the various types of shape descriptors that can be generated using DIA may identify different loci in genetic analyses. The purpose of this study was to evaluate two different DIA approaches to quantifying wheat seed shape for exploring trait correlations and quantitative trait loci (QTL) mapping. Phenotypic data were produced using the software programs ImageJ (National Institutes of Health, USA, http://rsbweb. nih. gov/ij/) and SHAPE (Hiroyoshi Iwata, http://lbm. ab. a. u-tokyo. ac. jp/≃iwata/shape/). ImageJ generates measures of length, width, perimeter, and area that can be used to describe dimensions of objects, whereas SHAPE generates elliptic Fourier descriptors (EFDs) to capture shape variation such as roughness, asymmetric skewing, or other two-dimensional aspects not encompassed by axes or distinctions in overall object area. There were significant differences in the results of the QTL analysis depending on the DIA software used. The use of EFDs to characterize horizontal measures of seed shape in wheat identified more QTL with higher LOD scores than length to width ratio. Additionally, the entire three dimensional shape of the seed described using two images in different orientations was shown to identify seed shape QTL that co-located with flour yield (FLYLD) and would go undetected based solely on a two dimensional image of the seed. Both methods identified QTL for length, width, thickness, and vertical perimeter that were co-localized with QTL for FLYLD. © 2012 Springer Science+Business Media B.V.
Albrecht E.,Keygene Inc. |
Zhang D.,U.S. Department of Agriculture |
Mays A.D.,Keygene Inc. |
Saftner R.A.,U.S. Department of Agriculture |
Stommel J.R.,U.S. Department of Agriculture
BMC Genetics | Year: 2012
Background: The exotic pepper species Capsicum baccatum, also known as the aji or Peruvian hot pepper, is comprised of wild and domesticated botanical forms. The species is a valuable source of new genes useful for improving fruit quality and disease resistance in C. annuum sweet bell and hot chile pepper. However, relatively little research has been conducted to characterize the species, thus limiting its utilization. The structure of genetic diversity in a plant germplasm collection is significantly influenced by its ecogeographical distribution. Together with DNA fingerprints derived from AFLP markers, we evaluated variation in fruit and plant morphology of plants collected across the species native range in South America and evaluated these characters in combination with the unique geography, climate and ecology at different sites where plants originated.Results: The present study mapped the ecogeographic distribution, analyzed the spatial genetic structure, and assessed the relationship between the spatial genetic pattern and the variation of morphological traits in a diverse C. baccatum germplasm collection spanning the species distribution. A combined diversity analysis was carried out on the USDA-ARS C. baccatum germplasm collection using data from GIS, morphological traits and AFLP markers. The results demonstrate that the C. baccatum collection covers wide geographic areas and is adapted to divergent ecological conditions in South America ranging from cool Andean highland to Amazonia rainforest. A high level of morphological diversity was evident in the collection, with fruit weight the leading variable. The fruit weight distribution pattern was compatible to AFLP-based clustering analysis for the collection. A significant spatial structure was observed in the C. baccatum gene pool. Division of the domesticated germplasm into two major regional groups (Western and Eastern) was further supported by the pattern of spatial population structure.Conclusions: The results reported improve our understanding of the combined effects of geography, ecology and human intervention on organization of the C. baccatum genepool. The results will facilitate utilization of C. baccatum for crop improvement and species conservation by providing a framework for efficient germplasm collection management and guidance for future plant acquisitions. © 2012 Albrecht et al.; licensee BioMed Central Ltd.
Albrecht E.,Keygene Inc. |
Zhang D.,U.S. Department of Agriculture |
Saftner R.A.,U.S. Department of Agriculture |
Stommel J.R.,U.S. Department of Agriculture
Genetic Resources and Crop Evolution | Year: 2012
Capsicum baccatum is one of five domesticated pepper species which, despite its morphological and ecological variability, has been underexploited for germplasm improvement. Utilizing a broad spectrum of domesticated and wild C. baccatum germplasm, we utilize AFLP markers to describe the species' molecular diversity and population structure in the South American gene pool. Analysis of molecular variance (AMOVA) revealed greater genetic diversity in the wild form of C. baccatum (C. baccatum var. baccatum) than in the domesticated form of the species (C. baccatum var. pendulum). Both Bayesian and distance based clustering analysis, as well as principal coordinates analysis (PCA), concordantly demonstrated admixture/shared ancestry between wild and cultivated C. baccatum botanical varieties. Two principal genetic groups were identified in the domesticated C. baccatum accessions largely based on their geographic distribution in South America. One group was predominated by accessions from the western territories of the species' distribution (Peru, Colombia, Ecuador, Bolivia, Chile and northwestern Argentina) and the second by accessions from the eastern regions, Paraguay and eastern Argentina). The two genetic groups overlapped in the geographic location of present-day Bolivia. The grouping pattern suggested that C. baccatum was domesticated in multiple sites and that its evolution took two lineages followed by lineage differentiation. The wild accessions most closely related to the cultigens were found in the highlands of Peru and Bolivia, which support the early hypothesis that this region is one of the domestication sites of this species. A Bayesian assignment analysis demonstrated that Brazilian wild forms of C. baccatum were genetically distant to all other accessions and made little to no contribution to the domesticated genepool. Moreover, results of clustering analysis suggested that C. baccatum likely originated from present day Paraguay. Analysis of inter-specific relationships across selected Capsicum species supported independent lineages for the two crossability groups within Capsicum, the baccatum species-complex (including C. baccatum) and the annuum species-complex (including C. annuum, C. chinense and C. frutescens). However, the results did not support taxonomic distinction of C. baccatum var. umbilicatum from C. baccatum var. pendulum. The present study provides new insights into the domestication of C. baccatum. The results will be useful for identifying accessions for crop improvement and guiding the development of in situ and ex situ conservation programs. © 2011 Springer Science+Business Media B.V. (outside the USA).
PubMed | Keygene Inc. and Keygene N.V.
Type: Comment | Journal: Current biology : CB | Year: 2016
Introduction of apomixis, asexual reproduction through seeds, into crop species has the potential to dramatically transform plant breeding. A new study demonstrates that traits can be stably transferred between generations in newly produced apomictic lines, and heralds a breeding revolution needed to increase food production for the growing planet.