Plant Pathology Faculty Research and Publications

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  • ItemOpen Access
    Variant call format (VCF) file corresponding to called single nucleotide polymorphisms (SNPs) from a set of 454 clone-corrected isolates of Fusarium graminearum (Dhakal et al., submitted)
    (2023-11-11) Dhakal, Upasana; Toomajian, Christopher; Leslie, John F.; Yue, Wei
    VCF file (fileformat=VCFv4.2, readable without specialized software) with genotyping-by-sequencing SNPs from set of 454 clone-corrected isolates of Fusarium graminearum, from the US and Uruguay. Produced by GATK software v., only biallelic SNPs retained. SNPs from this file segregated in a larger sample of over 500 isolates (some from closely related species), and what remains in this file were selected after variant quality score recalibration (vqsr).
  • ItemOpen Access
    Complete data from a mycotoxin survey conducted in western Honduras in 2017 and 2018
    (2022-10-07) Sabillón, Luis; Alvarado, Jackeline; Leiva, Alejandra; Mendoza, Rodrigo; Espinal, Raúl; Leslie, John F.; Bianchini, Andréia
    · We determined the occurrence of and exposure levels to aflatoxins and fumonisins in maize intended for human and animal consumption in food-insecure regions of western Honduras by using a monoclonal antibody-based affinity spectrofluorimetric method. · Fumonisins were detected in 614/631 samples of maize destined for human consumption at 0.3 to 41 mg/Kg. Of the 614 positive samples, 147 had fumonisin levels exceeding the U.S. FDA advisory threshold of 4.0 mg/Kg. · Aflatoxins were detected in 109 of the 631 samples with concentrations between 1.0 and 490 µg/Kg. Aflatoxin levels in 34 samples exceeded the FDA regulatory limit of 20 µg/Kg. · Aflatoxins and fumonisins co-occurred in 106/631 samples with 60 samples containing both toxins at levels greater than the FDA regulatory levels. · Samples of maize intended for animal feed had significantly higher aflatoxin and fumonisin contamination levels than those observed in samples destined for human consumption.
  • ItemOpen Access
    Effects Of Acclimation Position On Detachment Of Tethered Culex Quinquefasciatus
    (2021) Boyles, Ayden; Cooper, Anastasia; Silver, Kristopher
    Electropenetrography (EPG) allows researchers to observe, record,and quantify the feeding behaviors of arthropods. [2] EPG has beentypically used to study the relationship between plants and plant-eating arthropods. EPG involves wiring insects into electrical circuits to visualizeelectrical signals associated with each insect feeding behavior. (A) By using EPG, researchers can understand how various factors affectarthropod feeding patterns. [1] Culex quinquefasciatus (Cx. quinqs.) are known vectors of virusessuch as Rift Valley fever and Japenese encephalitis, which cansignificantly affect veterinary and human health. To safely study how viruses affect mosquito feeding behavior,detachment from the EPG wire must be zero. Since July 2021, thedetachment rate in our studies has been 0.47%. Different wiring protocols have the mosquitoes either hanging orstanding following the attachment of EPG wires, but it is not clear ifusing one method or the other results in more insect detachments.
  • ItemOpen Access
    Data sets and computer code for: Population genomics of Fusarium subglutinans and Fusarium temperatum from Argentina
    (2020-09-24) Fumero, M. Veronica; Yue, Wei; Chiotta, María L.; Chulze, Sofía N.; Leslie, John F.; Toomajian, Christopher; jfl; toomajia
    Fusarium subglutinans and Fusarium temperatum are two important fungal pathogens of maize whose distinctness as separate species has been difficult to assess. We isolated strains of these species from commercial and native maize varieties in Argentina and sequenced >28,000 GBS loci to estimate genetic variation in the sample. Our objectives were to measure genetic divergence between the species, infer demographic parameters related to their split, and describe the population structure of the sample. When analyzed together, over 30% of each species’ polymorphic sites (>2,500 sites) segregate as polymorphisms in the other. Demographic modeling confirmed the species split predated maize domestication, but subsequent between-species gene flow has occurred, with gene flow from F. subglutinans into F. temperatum greater than gene flow in the reverse direction. In F. subglutinans, little evidence exists for substructure or recent selective sweeps, but there is evidence for limited sexual reproduction. In F. temperatum, there is clear evidence for population substructure and signals of abundant recent selective sweeps, with sexual reproduction probably less common than in F. subglutinans. Both genetic variability and the relative number of polymorphisms shared between species increase near the telomeres of all 12 chromosomes, where genes related to plant-pathogen interactions often are located. Our results suggest that species boundaries between closely related Fusarium species can be porous and merit further study. Such porosity could facilitate unanticipated genetic exchange between species and enable quicker permanent responses to changes in the agro-ecosystem, e.g., pathogen-resistant host varieties, new chemical and biological control agents, and agronomic practices.
  • ItemOpen Access
    Habitat configuration matters when evaluating habitat-area effects on host–parasitoid interactions
    (2019-02-07) With, Kimberly A.; Pavuk, Daniel M.
    Higher trophic levels tend to be more sensitive to habitat fragmentation than lower trophic levels, which is why parasitism rates should decline in fragmented landscapes. Habitat loss and fragmentation (the subdivision of habitat) are typically interrelated processes, and thus, their effects are confounded in most studies. To address this, we quantified parasitism rates in pea aphids (Acyrthosiphon pisum) within an experimental model landscape system, in which we independently controlled the amount vs. the fragmentation of habitat (red clover, Trifolium pratense) within individual landscape plots (16 × 16 m). Aphid densities were generally unaffected by landscape pattern, except at the local scale for interior habitat cells within fragmented landscapes, which had significantly lower aphid densities than all other cell types. Aphid parasitism rates averaged about 40% and were significantly—albeit weakly—correlated with aphid density. Habitat amount had the greatest overall effect on parasitism rates, but fragmentation effects were evident in a shift in parasitism at intermediate habitat levels: Parasitism rates were higher in fragmented landscapes with <50% habitat, but higher in clumped landscapes with >50% habitat. Edge effects alone did not explain this shift in parasitism rates. Parasitism rates were uniformly high within edge habitat and fragmented landscapes, and thus, the shift in parasitism at intermediate habitat levels was driven by increasing parasitism rates within interior cells and clumped landscapes at higher habitat amounts. Habitat configuration is thus important for evaluating habitat-area effects on species interactions, as habitat amount only affected parasitism rates within less-fragmented landscapes in this system.
  • ItemOpen Access
    Host-Derived Artificial MicroRNA as an Alternative Method to Improve Soybean Resistance to Soybean Cyst Nematode
    (2016-12-08) Tian, B.; Li, J. R.; Oakley, T. R.; Todd, Timothy C.; Trick, Harold N.; nema; hnt; Todd, Timothy C.; Trick, Harold N.
    The soybean cyst nematode (SCN), Heterodera glycines, is one of the most important pests limiting soybean production worldwide. Novel approaches to managing this pest have focused on gene silencing of target nematode sequences using RNA interference (RNAi). With the discovery of endogenous microRNAs as a mode of gene regulation in plants, artificial microRNA (amiRNA) methods have become an alternative method for gene silencing, with the advantage that they can lead to more specific silencing of target genes than traditional RNAi vectors. To explore the application of amiRNAs for improving soybean resistance to SCN, three nematode genes (designated as J15, J20, and J23) were targeted using amiRNA vectors. The transgenic soybean hairy roots, transformed independently with these three amiRNA vectors, showed significant reductions in SCN population densities in bioassays. Expression of the targeted genes within SCN eggs were downregulated in populations feeding on transgenic hairy roots. Our results provide evidence that host-derived amiRNA methods have great potential to improve soybean resistance to SCN. This approach should also limit undesirable phenotypes associated with off-target effects, which is an important consideration for commercialization of transgenic crops.
  • ItemOpen Access
    Characterization of maize roothairless6 which encodes a D-type cellulose synthase and controls the switch from bulge formation to tip growth
    (2016-10-06) Li, L.; Hey, S.; Liu, Sanzhen Z.; Liu, Q.; McNinch, C.; Hu, H. C.; Wen, T. J.; Marcon, C.; Paschold, A.; Bruce, W.; Schnable, P. S.; Hochholdinger, F.; liu3zhen; Liu, Sanzhen
    Root hairs are tubular extensions of the epidermis. Root hairs of the monogenic recessive maize mutant roothairless 6 (rth6) are arrested after bulge formation during the transition to tip growth and display a rough cell surface. BSR-Seq in combination with Seq-walking and subsequent analyses of four independently generated mutant alleles established that rth6 encodes CSLD5 a plasma membrane localized 129 kD D-type cellulose synthase with eight transmembrane domains. Cellulose synthases are required for the biosynthesis of cellulose, the most abundant biopolymer of plant cell walls. Phylogenetic analyses revealed that RTH6 is part of a monocot specific clade of D-type cellulose synthases. D-type cellulose synthases are highly conserved in the plant kingdom with five gene family members in maize and homologs even among early land plants such as the moss Physcomitrella patens or the clubmoss Selaginella moellendorffii. Expression profiling demonstrated that rth6 transcripts are highly enriched in root hairs as compared to all other root tissues. Moreover, in addition to the strong knock down of rth6 expression in young primary roots of the mutant rth6, the gene is also significantly down-regulated in rth3 and rth5 mutants, while it is up-regulated in rth2 mutants, suggesting that these genes interact in cell wall biosynthesis.
  • ItemOpen Access
    A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A
    (2017-01-10) Balcarkova, B.; Frenkel, Z.; Skopova, M.; Abrouk, M.; Kumar, A.; Chao, S. M.; Kianian, S. F.; Akhunov, Eduard; Korol, A. B.; Dolezel, J.; Valarik, M.; eakhunov; Akhunov, Eduard
    Bread wheat has a large and complex allohexaploid genome with low recombination level at chromosome centromeric and peri-centromeric regions. This significantly hampers ordering of markers, contigs of physical maps and sequence scaffolds and impedes obtaining of high-quality reference genome sequence. Here we report on the construction of high-density and high-resolution radiation hybrid (RH) map of chromosome 4A supported by high-density chromosome deletion map. A total of 119 endosperm-based RH lines of two RH panels and 15 chromosome deletion bin lines were genotyped with 90K iSelect single nucleotide polymorphism (SNP) array. A total of 2316 and 2695 markers were successfully mapped to the 4A RH and deletion maps, respectively. The chromosome deletion map was ordered in 19 bins and allowed precise identification of centromeric region and verification of the RH panel reliability. The 4A-specific RH map comprises 1080 mapping bins and spans 6550.9 cR with a resolution of 0.13 Mb/cR. Significantly higher mapping resolution in the centromeric region was observed as compared to recombination maps. Relatively even distribution of deletion frequency along the chromosome in the RH panel was observed and putative functional centromere was delimited within a region characterized by two SNP markers.
  • ItemOpen Access
    An evaluation of the status of living collections for plant, environmental, and microbial research
    (2017-05-12) McCluskey, Kevin; Parsons, J. P.; Quach, K.; Duke, C. S.; mccluskeyk; McCluskey, Kevin
    While living collections are critical for biological research, support for these foundational infrastructure elements is inconsistent, which makes quality control, regulatory compliance, and reproducibility difficult. In recent years, the Ecological Society of America has hosted several National Science Foundation–sponsored workshops to explore and enhance the sustainability of biological research infrastructure. At the same time, the United States Culture Collection Network has brought together managers of living collections to foster collaboration and information exchange within a specific living collections community. To assess the sustainability of collections, a survey was distributed to collection scientists whose responses provide a benchmark for evaluating the resiliency of these collections. Among the key observations were that plant collections have larger staffing requirements and that living microbe collections were the most vulnerable to retirements or other disruptions. Many higher plant and vertebrate collections have institutional support and several have endowments. Other collections depend on competitive grant support in an era of intense competition for these resources. Opportunities for synergy among living collections depend upon complementing the natural strong engagement with the research communities that depend on these collections with enhanced information sharing, communication, and collective action to keep them sustainable for the future. External efforts by funding agencies and publishers could reinforce the advantages of having professional management of research resources across every discipline. © 2017 Indian Academy of Sciences
  • ItemOpen Access
    The hijacking of a receptor kinase-driven pathway by a wheat fungal pathogen leads to disease
    (2016-10-26) Shi, G. J.; Zhang, Z. C.; Friesen, T. L.; Raats, D.; Fahima, T.; Brueggeman, R. S.; Lu, S. W.; Trick, Harold N.; Liu, Z. H.; Chao, W.; Frenkel, Z.; Xu, S. S.; Rasmussen, J. B.; Faris, J. D.; hnt; Trick, Harold N.
    Necrotrophic pathogens live and feed on dying tissue, but their interactions with plants are not well understood compared to biotrophic pathogens. The wheat Snn1 gene confers susceptibility to strains of the necrotrophic pathogen Parastagonospora nodorum that produce the SnTox1 protein. We report the positional cloning of Snn1, a member of the wall-associated kinase class of receptors, which are known to drive pathways for biotrophic pathogen resistance. Recognition of SnTox1 by Snn1 activates programmed cell death, which allows this necrotroph to gain nutrients and sporulate. These results demonstrate that necrotrophic pathogens such as P. nodorum hijack host molecular pathways that are typically involved in resistance to biotrophic pathogens, revealing the complex nature of susceptibility and resistance in necrotrophic and biotrophic pathogen interactions with plants.
  • ItemOpen Access
    Genotype-by-sequencing facilitates genetic mapping of a stem rust resistance locus in Aegilops umbellulata, a wild relative of cultivated wheat
    (2016-12-15) Edae, E. A.; Olivera, P. D.; Jin, Y.; Poland, Jesse A.; Rouse, M. N.; jpoland; Poland, Jesse A.
    Background: Wild relatives of wheat play a significant role in wheat improvement as a source of genetic diversity. Stem rust disease of wheat causes significant yield losses at the global level and stem rust pathogen race TTKSK (Ug99) is virulent to most previously deployed resistance genes. Therefore, the objective of this study was to identify loci conferring resistance to stem rust pathogen races including Ug99 in an Aegilops umbelluata bi-parental mapping population using genotype-by-sequencing (GBS) SNP markers. Results: A bi-parental F-2:3 population derived from a cross made between stem rust resistant accession PI 298905 and stem rust susceptible accession PI 542369 was used for this study. F2 individuals were evaluated with stem rust race TTTTF followed by testing F-2:3 families with races TTTTF and TTKSK. The segregation pattern of resistance to both stem rust races suggested the presence of one resistance gene. A genetic linkage map, comprised 1,933 SNP markers, was created for all seven chromosomes of Ae. umbellulata using GBS. A major stem rust resistance QTL that explained 80% and 52% of the phenotypic variations for TTTTF and TTKSK, respectively, was detected on chromosome 2U of Ae. umbellulata. Conclusion: The novel resistance gene for stem rust identified in this study can be transferred to commercial wheat varieties assisted by the tightly linked markers identified here. These markers identified through our mapping approach can be a useful strategy to identify and track the resistance gene in marker-assisted breeding in wheat.
  • ItemOpen Access
    Draft genome sequence of Neurospora crassa strain FGSC 73
    (2015-04-02) Baker, S. E.; Schackwitz, W.; Lipzen, A.; Martin, J.; Haridas, S.; LaButti, K.; Grigoriev, I. V.; Simmons, B. A.; McCluskey, Kevin; mccluskeyk; McCluskey, Kevin
    We report the elucidation of the complete genome of the Neurospora crassa (Shear and Dodge) strain FGSC 73, a mat-a, trp-3 mutant strain. The genome sequence around the idiotypic mating type locus represents the only publicly available sequence for a mat-a strain. 40.42 Megabases are assembled into 358 scaffolds carrying 11,978 gene models. © 2015 Baker et al.
  • ItemOpen Access
    The Small GTPase MoSec4 Is Involved in Vegetative Development and Pathogenicity by Regulating the Extracellular Protein Secretion in Magnaporthe oryzae
    (2016-06-03) Zheng, H. K.; Chen, S. M.; Chen, X. F.; Liu, S. Y.; Dang, X.; Yang, C. D.; Giraldo, M. C.; Oliveira-Garcia, E.; Zhou, J.; Wang, Z. H.; Valent, Barbara; bvalent; Valent, Barbara
    The Rab GTPase proteins play important roles in the membrane trafficking, and consequently protein secretion and development of eukaryotic organisms. However, little is known about the function of Rab GTPases in Magnaporthe oryzae. To further explore the function of Rab GTPases, we deleted the ortholog of the yeast Sec4p protein in M. oryzae, namely MoSEC4. The Delta Mosec4 mutant is defective in polarized growth and conidiation, and it displays decreased appressorium turgor pressure and attenuated pathogenicity. Notably, the biotrophic invasive hyphae produced in rice cells are more bulbous and compressed in the Delta Mosec4 mutant. Further studies showed that deletion of the MoSEC4 gene resulted in decreased secretion of extracellular enzymes and mislocalization of the cytoplasmic effector PWL2-mCherry-NLS. In accordance with a role in secretion, the GFP-MoSec4 fusion protein mainly accumulates at tips of growing vegetative hyphae. Our results suggest that the MoSec4 protein plays important roles in the secretion of extracellular proteins and consequently hyphal development and pathogenicity in the rice blast fungus.
  • ItemOpen Access
    Wheat quality improvement at CIMMYT and the use of genomic selection on it
    (2016-12-01) Guzman, C.; Pena, R. J.; Singh, R.; Autrique, E.; Dreisigacker, S.; Crossa, J.; Rutkoski, J.; Poland, Jesse A.; Battenfield, S.; jpoland; Poland, Jesse A.
    The International Center for Maize and Wheat Improvement (CIMMYT) leads the Global Wheat Program, whose main objective is to increase the productivity of wheat cropping systems to reduce poverty in developing countries. The priorities of the program are high grain yield, disease resistance, tolerance to abiotic stresses (drought and heat), and desirable quality. The Wheat Chemistry and Quality Laboratory has been continuously evolving to be able to analyze the largest number of samples possible, in the shortest time, at lowest cost, in order to deliver data on diverse quality traits on time to the breeders formaking selections for advancement in the breeding pipeline. The participation of wheat quality analysis/selection is carried out in two stages of the breeding process: evaluation of the parental lines for new crosses and advanced lines in preliminary and elite yield trials. Thousands of lines are analyzed which requires a big investment in resources. Genomic selection has been proposed to assist in selecting for quality and other traits in breeding programs. Genomic selection can predict quantitative traits and is applicable to multiple quantitative traits in a breeding pipeline by attaining historical phenotypes and adding high-density genotypic information. Due to advances in sequencing technology, genome-wide single nucleotide polymorphism markers are available through genotyping-by-sequencing at a cost conducive to application for genomic selection. At CIMMYT, genomic selection has been applied to predict all of the processing and end-use quality traits regularly tested in the spring wheat breeding program. These traits have variable levels of prediction accuracy, however, they demonstrated that most expensive traits, dough rheology and baking final product, can be predicted with a high degree of confidence. Currently it is being explored how to combine both phenotypic and genomic selection to make more efficient the genetic improvement for quality traits at CIMMYT spring wheat breeding program. (C) 2016 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license.
  • ItemOpen Access
    Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp tritici isolates revealed by the comparative gene co-expression network and genome analyses
    (2017-04-12) Rutter, William B.; Salcedo, Andres; Akhunova, Alina; He, Fei; Wang, Shichen C.; Liang, Hanquan Q.; Bowden, Robert L.; Akhunov, Eduard; eakhunov; akhunova; Akhunov, Eduard; Akhunova, Alina
    Background: Two opposing evolutionary constraints exert pressure on plant pathogens: one to diversify virulence factors in order to evade plant defenses, and the other to retain virulence factors critical for maintaining a compatible interaction with the plant host. To better understand how the diversified arsenals of fungal genes promote interaction with the same compatible wheat line, we performed a comparative genomic analysis of two North American isolates of Puccinia graminis f. sp. tritici (Pgt). Results: The patterns of inter-isolate divergence in the secreted candidate effector genes were compared with the levels of conservation and divergence of plant-pathogen gene co-expression networks (GCN) developed for each isolate. Comprative genomic analyses revealed substantial level of interisolate divergence in effector gene complement and sequence divergence. Gene Ontology (GO) analyses of the conserved and unique parts of the isolate-specific GCNs identified a number of conserved host pathways targeted by both isolates. Interestingly, the degree of inter-isolate sub-network conservation varied widely for the different host pathways and was positively associated with the proportion of conserved effector candidates associated with each sub- network. While different Pgt isolates tended to exploit similar wheat pathways for infection, the mode of plant-pathogen interaction varied for different pathways with some pathways being associated with the conserved set of effectors and others being linked with the diverged or isolate-specific effectors. Conclusions: Our data suggest that at the intra-species level pathogen populations likely maintain divergent sets of effectors capable of targeting the same plant host pathways. This functional redundancy may play an important role in the dynamic of the "arms-race" between host and pathogen serving as the basis for diverse virulence strategies and creating conditions where mutations in certain effector groups will not have a major effect on the pathogen's ability to infect the host.
  • ItemOpen Access
    Canopy Temperature and Vegetation Indices from High-Throughput Phenotyping Improve Accuracy of Pedigree and Genomic Selection for Grain Yield in Wheat
    (2016-07-06) Rutkoski, J.; Poland, Jesse A.; Mondal, S.; Autrique, E.; Perez, L. G.; Crossa, J.; Reynolds, M.; Singh, R.; jpoland; Poland, Jesse A.
    Genomic selection can be applied prior to phenotyping, enabling shorter breeding cycles and greater rates of genetic gain relative to phenotypic selection. Traits measured using high-throughput phenotyping based on proximal or remote sensing could be useful for improving pedigree and genomic prediction model accuracies for traits not yet possible to phenotype directly. We tested if using aerial measurements of canopy temperature, and green and red normalized difference vegetation index as secondary traits in pedigree and genomic best linear unbiased prediction models could increase accuracy for grain yield in wheat, Triticum aestivum L., using 557 lines in five environments. Secondary traits on training and test sets, and grain yield on the training set were modeled as multivariate, and compared to univariate models with grain yield on the training set only. Cross validation accuracies were estimated within and across-environment, with and without replication, and with and without correcting for days to heading. We observed that, within environment, with unreplicated secondary trait data, and without correcting for days to heading, secondary traits increased accuracies for grain yield by 56% in pedigree, and 70% in genomic prediction models, on average. Secondary traits increased accuracy slightly more when replicated, and considerably less when models corrected for days to heading. In across-environment prediction, trends were similar but less consistent. These results show that secondary traits measured in high-throughput could be used in pedigree and genomic prediction to improve accuracy. This approach could improve selection in wheat during early stages if validated in early-generation breeding plots.
  • ItemOpen Access
    Construction of a map-based reference genome sequence for barley, Hordeum vulgare L
    (2017-04-27) Beier, S.; Himmelbach, A.; Colmsee, C.; Zhang, X. Q.; Barrero, R. A.; Zhang, Q. S.; Li, L.; Bayer, M.; Bolser, D.; Taudien, S.; Groth, M.; Felder, M.; Hastie, A.; Simkova, H.; Stankova, H.; Vrana, J.; Chan, S. K.; Munoz-Amatriain, M.; Ounit, R.; Wanamaker, S.; Schmutzer, T.; Aliyeva-Schnorr, L.; Grasso, S.; Tanskanen, J.; Sampath, D.; Heavens, D.; Cao, S. J.; Chapman, B.; Dai, F.; Han, Y.; Li, H.; Li, X.; Lin, C. Y.; McCooke, J. K.; Tan, C.; Wang, S. B.; Yin, S. Y.; Zhou, G. F.; Poland, Jesse A.; Bellgard, M. I.; Houben, A.; Dolezel, J.; Ayling, S.; Lonardi, S.; Langridge, P.; Muehlbauer, G. J.; Kersey, P.; Clark, M. D.; Caccamo, M.; Schulman, A. H.; Platzer, M.; Close, T. J.; Hansson, M.; Zhang, G. P.; Braumann, I.; Li, C. D.; Waugh, R.; Scholz, U.; Stein, N.; Mascher, M.; jpoland; Poland, Jesse A.
    Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. `Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).
  • ItemOpen Access
    Complete genome sequence of the African strain AXO1947 of Xanthomonas oryzae pv. oryzae
    (2016-02-11) Huguet-Tapia, J. C.; Peng, Zhou; Yang, B.; Yin, Z.; Liu, Sanzhen; White, F. F.; liu3zhen; Liu, Sanzhen
    Xanthomonas oryzae pv. oryzae is the etiological agent of bacterial rice blight. Three distinct clades of X. oryzae pv. oryzae are known. We present the complete annotated genome of the African clade strain AXO194 using long-read single-molecule PacBio sequencing technology. The genome comprises a single chromosome of 4,674,975 bp and encodes for nine transcriptional activator-like (TAL) effectors. The approach and data presented in this announcement provide information for complex bacterial genome organization and the discovery of new virulence effectors, and they facilitate target characterization of TAL effectors. © 2016 Huguet-Tapia et al.
  • ItemOpen Access
    The challenges faced by living stock collections in the USA
    (2017-03-07) McCluskey, Kevin; Boundy-Mills, K.; Dye, G.; Ehmke, E.; Gunnell, G. F.; Kiaris, H.; Richmond, M. P.; Yoder, A. D.; Zeigler, D. R.; Zehr, S.; Grotewold, E.; mccluskeyk; McCluskey, Kevin
    Many discoveries in the life sciences have been made using material from living stock collections. These collections provide a uniform and stable supply of living organisms and related materials that enhance the reproducibility of research and minimize the need for repetitive calibration. While collections differ in many ways, they all require expertise in maintaining living organisms and good logistical systems for keeping track of stocks and fulfilling requests for specimens. Here, we review some of the contributions made by living stock collections to research across all branches of the tree of life, and outline the challenges they face.
  • ItemOpen Access
    A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize
    (2017-05-10) Mei, W. B.; Liu, Sanzhen Z.; Schnable, J. C.; Yeh, C. T.; Springer, N. M.; Schnable, P. S.; Barbazuk, W. B.; liu3zhen; Liu, Sanzhen
    Identifying and characterizing alternative splicing (AS) enables our understanding of the biological role of transcript isoform diversity. This study describes the use of publicly available RNA-Seq data to identify and characterize the global diversity of AS isoforms in maize using the inbred lines B73 and Mo17, and a related species, sorghum. Identification and characterization of AS within maize tissues revealed that genes expressed in seed exhibit the largest differential AS relative to other tissues examined. Additionally, differences in AS between the two genotypes B73 and Mo17 are greatest within genes expressed in seed. We demonstrate that changes in the level of alternatively spliced transcripts (intron retention and exon skipping) do not solely reflect differences in total transcript abundance, and we present evidence that intron retention may act to fine-tune gene expression across seed development stages. Furthermore, we have identified temperature sensitive AS in maize and demonstrate that drought-induced changes in AS involve distinct sets of genes in reproductive and vegetative tissues. Examining our identified AS isoforms within B73 X Mo17 recombinant inbred lines (RILs) identified splicing QTL (sQTL). The 43.3% of cis-sQTL regulated junctions are actually identified as alternatively spliced junctions in our analysis, while 10 Mb windows on each side of 48.2% of trans-sQTLs overlap with splicing related genes. Using sorghum as an out-group enabled direct examination of loss or conservation of AS between homeologous genes representing the two subgenomes of maize. We identify several instances where AS isoforms that are conserved between one maize homeolog and its sorghum ortholog are absent from the second maize homeolog, suggesting that these AS isoforms may have been lost after the maize whole genome duplication event. This comprehensive analysis provides new insights into the complexity of AS in maize.