National Clonal Germplasm Repository

Corvallis, OR, United States

National Clonal Germplasm Repository

Corvallis, OR, United States
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Thekke-Veetil T.,University of Arkansas | Ho T.,University of Arkansas | Postman J.D.,National Clonal Germplasm Repository | Tzanetakis I.E.,University of Arkansas
European Journal of Plant Pathology | Year: 2017

A novel virus was discovered in a blackcurrant accession (Ribes nigrum L.) at the USDA genebank in Oregon, USA. The genome consists of two positive-sense, single-stranded RNAs with the first encoding a 197 kDa multifunctional protein with methyl transferase, helicase and RNA-dependent RNA polymerase enzymatic motifs. The second molecule encodes two putative proteins; the 39 kDa movement and 30 kDa coat proteins. Both RNAs have conserved sequences and structures at the 5′ and 3′ termini. The genome organization, sequence and phylogenetic analyses indicate that the virus is a putative new member of the genus Idaeovirus, as it consistently groups with privet leaf blotch-associated virus and raspberry bushy dwarf virus. A duplex RT-PCR assay was developed for rapid detection of both genomic RNAs simultaneously. The work presented in this communication will assure the health status of blackcurrant plants in mother blocks, nurseries and production fields alike. © 2017 Koninklijke Nederlandse Planteziektenkundige Vereniging


Verde I.,Fruit Tree Research Center | Bassil N.,National Clonal Germplasm Repository | Scalabrin S.,Instituto Of Genomica Applicata | Gilmore B.,National Clonal Germplasm Repository | And 18 more authors.
PLoS ONE | Year: 2012

Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ~75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs. The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species.


Aradhya M.K.,National Clonal Germplasm Repository | Preece J.,National Clonal Germplasm Repository | Kluepfel D.A.,University of California at Davis
Acta Horticulturae | Year: 2015

The National Clonal Germplasm Repository (NCGR) in Davis is one among the nine repositories in the National Plant Germplasm System, USDA-ARS, that is responsible for conservation of clonally propagated woody perennial subtropical and temperate fruit and nut crop germplasm. Currently the repository holds over 6500 accessions of germplasm of Actinidia (kiwi fruit), Diospyros (persimmon), Ficus (fig), Juglans (walnuts), Morus (mulberry), Olea (olive), Pistacia (pistachio), Prunus (stonefruits and almond), Punica (pomegranate), Vitis (grape), and other minor genera. Wild relatives are widely represented in these collections with about 91% of the taxa and 43% of the total accessions representing the wild gene pools. Research at the repository is mainly focused on genetic characterization of germplasm using molecular markers and morphological traits to quantify and describe genetic structure and differentiation within and among species and gene pools. Promoting the use of crop wild relatives (CWR) germplasm in genetic improvement of tree fruit and nut crops is our top priority. Presently, at the Davis repository, we are extensively utilizing Prunus and Juglans wild relatives for developing improved rootstocks with resistance to biotic and abiotic stresses. We will review and discuss the results of ongoing programs highlighting the importance of different CWRs as donors of genes for resistance to major soil borne diseases such as crown gall, Phytophthora rots, and nematodes in the rootstock improvement programs. Breeding for drought tolerance is another major thrust for which we are screening CWR germplasm to identify novel sources of drought tolerance to infuse into ongoing rootstock breeding programs.


PubMed | Lassen Canyon Nursery Breeding Program, National Clonal Germplasm Repository, Michigan State University, University of Peradeniya and 2 more.
Type: | Journal: Frontiers in plant science | Year: 2016

Much of the cost associated with marker discovery for marker assisted breeding (MAB) can be eliminated if a diverse, segregating population is generated, genotyped, and made available to the global breeding community. Herein, we present an example of a hybrid, wild-derived family of the octoploid strawberry that can be used by other breeding programs to economically find and tag useful genes for MAB. A pseudo test cross population between two wild species of Fragaria virginiana and F. chiloensis (FVC 11) was generated and evaluated for a set of phenotypic traits. A total of 106 individuals in the FVC 11 were genotyped for 29,251 single nucleotide polymorphisms (SNPs) utilizing a commercially available, genome-wide scanning platform (Affymetrix Axiom IStraw90(TW)). The marker trait associations were deduced using TASSEL software. The FVC 11 population segregating for daughters per mother, inflorescence number, inflorescence height, crown production, flower number, fruit size, yield, internal color, soluble solids, fruit firmness, and plant vigor. Coefficients of variations ranged from 10% for fruit firmness to 68% for daughters per mother, indicating an underlying quantitative inheritance for each trait. A total of 2,474 SNPs were found to be polymorphic in FVC 11 and strong marker trait associations were observed for vigor, daughters per mother, yield and fruit weight. These data indicate that FVC 11 can be used as a reference population for quantitative trait loci detection and subsequent MAB across different breeding programs and geographical locations.


Chen G.-Q.,Shanghai JiaoTong University | Ren L.,Shanghai JiaoTong University | Zhang J.,Shanghai JiaoTong University | Reed B.M.,National Clonal Germplasm Repository | And 2 more authors.
Cryobiology | Year: 2015

Plant recovery status after cryopreservation by vitrification had a negative relationship to the oxidative stress induced by reactive oxygen species (ROS). Arabidopsis thaliana seedlings germinated for 48h or 72h with different survival tolerances were examined at five steps of cryopreservation, to determine the role of ROS (O2 -, H2O2 and OH) and antioxidant systems (SOD, POD, CAT, AsA and GSH) in cryo-injury. In addition, the effects of the steps on membrane lipid peroxidation were studied using malondialdehyde (MDA) as an indicator. The results indicated that H2O2-induced oxidative stress at the steps of dehydration and rapid warming was the main cause of cryo-injury of 48-h seedlings (high survival rate) and 72-h seedlings (no survival). The H2O2 was mainly generated in cotyledons, shoot tips and roots of seedlings as indicated by Amplex Red staining. Low survival of 72-h seedlings was associated with severe membrane lipid peroxidation, which was caused by increased OH generation activity and decreased SOD activity. The antioxidant-related gene expression by qRT-PCR and physiological assays suggested that the antioxidant system of 48-h seedlings were activated by ROS, and they mounted a defense against oxidative stress. A high level of ROS led to the weakening of the antioxidant system of 72-h seedlings. Correlation analysis indicated that enhanced antioxidant enzymes activities contributed to the high survival rate of 48-h seedlings, which could reflect by cryopreservation of antioxidant mutant seedlings. This model system indicated that elevated CAT activity and AsA content were determinants of cryogenic stress tolerance, whose manipulation could improve the recovery of seedlings after cryopreservation. © 2014 Elsevier Inc.


Ren L.,Shanghai JiaoTong University | Zhang D.,Shanghai JiaoTong University | Jiang X.-N.,Beijing Forestry University | Gai Y.,Beijing Forestry University | And 3 more authors.
Plant Science | Year: 2013

Cryopreservation can be a safe and cost-effective tool for the long-term storage of plant germplasm. In Arabidopsis, the ability to recover from cryogenic treatment was lost as growth progressed. Growth could be restored in 48-h seedlings, whereas 72-h seedlings died after cryogenic treatment. Why seedling age and survival are negatively correlated is an interesting issue. A comparative transcriptomics was performed to screen differentially expressed genes between 48- and 72-h seedlings after exposure to cryoprotectant. Among differentially expressed genes, oxidative stress response genes played important roles in cryoprotectant treatment, and peroxidation was a key factor related to cell survival. Seedlings underwent more peroxidation at 72-h than at 48-h. A comprehensive analysis indicated that peroxidation injured membrane systems leading to photophosphorylation and oxidative phosphorylation damage. Furthermore, the apoptosis-like events were found in cryogenic treatment of Arabidopsis seedlings. 48- and 72-h seedlings underwent different degrees of membrane lipid peroxidation during cryoprotectant treatment, and reducing the injury of oxidative stress was an important factor to successful cryopreservation. This study provided a novel insight of genetic regulatory mechanisms in cryopreservation, and established an excellent model to test and evaluate the effect of exogenous antioxidants and conventional cryoprotectants in plant cryopreservation. © 2013 Elsevier Ireland Ltd.


PubMed | National Clonal Germplasm Repository and Shanghai JiaoTong University
Type: Journal Article | Journal: Plant cell reports | Year: 2015

Elevated antioxidant status and positive abiotic stress response in dehydration enhance cell resistance to cryoinjury, and controlling oxidative damage via reactive oxygen species homeostasis maintenance leads to high survival. Cryoprotectants are important for cell survival in cryopreservation, but high concentrations can also cause oxidative stress. Adding vitamin C to the cryoprotectant doubled the survival ratio in Arabidopsis thaliana 60-h seedlings (seedlings after 60-h germination) cryopreservation. In this study, the metabolites and transcriptional profiling of 60-h seedlings were analyzed in both the control cryopreservation procedure (CCP) and an improved cryopreservation procedure (ICP) to reveal the mechanism of plant cell response to oxidative stress from cryopreservation. Reactive oxygen species (ROS) and peroxidation levels reached a peak after rapid cooling-warming in CCP, which were higher than that in ICP. In addition, gene regulation was significantly increased in CCP and decreased in ICP during rapid cooling-warming. Before cryogenic treatment, the number of specifically regulated genes was nearly 10 times higher in ICP dehydration than CCP dehydration. Among these genes, DREBs/CBFs were beneficial to cope with cryoinjury, and calcium-binding protein, OXI1, WRKY and MYB family members as key factors in ROS signal transduction activated the ROS-producing and ROS-scavenging networks including AsA-GSH and GPX cycles involved in scavenging H2O2. Finally, elevated antioxidant status and oxidative stress response in the improved dehydration enhanced seedling resistance to cryogenic treatment, maintained ROS homeostasis and improved cell recovery after cryopreservation.


PubMed | National Clonal Germplasm Repository and Shanghai JiaoTong University
Type: Journal Article | Journal: Cryobiology | Year: 2015

Plant recovery status after cryopreservation by vitrification had a negative relationship to the oxidative stress induced by reactive oxygen species (ROS). Arabidopsis thaliana seedlings germinated for 48 h or 72 h with different survival tolerances were examined at five steps of cryopreservation, to determine the role of ROS (O2(-), H2O2 and OH) and antioxidant systems (SOD, POD, CAT, AsA and GSH) in cryo-injury. In addition, the effects of the steps on membrane lipid peroxidation were studied using malondialdehyde (MDA) as an indicator. The results indicated that H2O2-induced oxidative stress at the steps of dehydration and rapid warming was the main cause of cryo-injury of 48-h seedlings (high survival rate) and 72-h seedlings (no survival). The H2O2 was mainly generated in cotyledons, shoot tips and roots of seedlings as indicated by Amplex Red staining. Low survival of 72-h seedlings was associated with severe membrane lipid peroxidation, which was caused by increased OH generation activity and decreased SOD activity. The antioxidant-related gene expression by qRT-PCR and physiological assays suggested that the antioxidant system of 48-h seedlings were activated by ROS, and they mounted a defense against oxidative stress. A high level of ROS led to the weakening of the antioxidant system of 72-h seedlings. Correlation analysis indicated that enhanced antioxidant enzymes activities contributed to the high survival rate of 48-h seedlings, which could reflect by cryopreservation of antioxidant mutant seedlings. This model system indicated that elevated CAT activity and AsA content were determinants of cryogenic stress tolerance, whose manipulation could improve the recovery of seedlings after cryopreservation.


Uchendu E.E.,Oregon State University | Uchendu E.E.,University of Guelph | Muminova M.,Tashkent Institute of Chemical Technology | Gupta S.,Tissue Culture and Cryopreservation Unit | Reed B.M.,National Clonal Germplasm Repository
In Vitro Cellular and Developmental Biology - Plant | Year: 2010

Regrowth of plants after cryopreservation varies, and resulting regrowth ranges from poor to excellent. Oxidative stress is a potential cause of damage in plant tissues. Antioxidants and anti-stress compounds may improve regrowth by preventing or repairing the damage. Lipoic acid (LA), glutathione (GSH), glycine betaine (GB), and polyvinylpyrrolidone (PVP) were tested during cryopreservation of shoot tips using the plant vitrification solution 2 (PVS2) protocol. Two in vitro-grown blackberry cultivars were cold acclimated and then cryopreserved in liquid nitrogen (LN). The antioxidant and anti-stress compounds were added at four critical steps of the protocol: pretreatment, loading, rinsing, and regrowth. Three out of the four compounds significantly improved regrowth of cryopreserved shoot tips. Regrowth ranged from 40% to 50% for controls to >80% for treated shoot tips. LA (4-8 mM) produced high regrowth at pretreatment, loading, and rinsing for 'Chehalem' and at all steps for 'Hull Thornless'. Recovery improved at all steps with GSH (0.16 mM) and GB (10 mM). PVP had a neutral or negative impact on regrowth. Overall addition of LA, GSH, and GB improved regrowth by ̃25% over the shoot tips cryopreserved using the regular PVS2 protocol (control). This study shows that adding non-vitamin antioxidants and anti-stress compounds during the PVS2-vitrification protocol improves regrowth of shoot cultures following cryopreservation. We recommend inclusion of antioxidants as part of standard cryopreservation protocols. © 2010 The Society for In Vitro Biology.


Parchert K.J.,University of New Mexico | Spilde M.N.,University of New Mexico | Porras-Alfaro A.,University of New Mexico | Porras-Alfaro A.,Western Illinois University | And 2 more authors.
Geomicrobiology Journal | Year: 2012

Rock varnish is a darkly pigmented coating rich in manganese oxides. Though microbes inhabit varnish deposits, it is unclear whether they are involved in varnish formation. The fungal communities of rock varnish and adjacent rock sites with no visible varnish deposits were examined. Microcolonial fungi were identified at all sampling sites, and were associated with manganese oxides in patches of incipient varnish at non-varnish sites. Fungi were closely related to manganese-oxidizing genera and seventeen isolates oxidized manganese in culture, producing six distinct manganese-oxide morphologies. Our results indicate that microcolonial fungi may play a crucial role in rock varnish formation. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental file. © 2012 Copyright Taylor and Francis Group, LLC.

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