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Sorghum has been considered a recalcitrant plant in vitro and suffers from a lack of regeneration protocols that function broadly and efficiently across a range of genotypes. This study was initiated to identify differential genotype-in vitro protocol responses across a range of bioenergy sorghum parental lines and the common grain sorghum genotype Tx430 in order to characterize response profiles for use in future genetic studies. Two different in vitro protocols, LG and WU, were used for comparisons. Distinct genotype-protocol responses were observed, and the WU protocol performed significantly better for plantlet regeneration. Most bioenergy genotypes performed as well, if not better than Tx430, with Rio and PI329311 as the top regenerating lines. Genotypes displayed protocol-dependent, differential phenolic exudation responses, as indicated by medium browning. During the callus induction phase, genotypes prone to medium browning exhibited a response on WU medium which was either equal or greater than on LG medium. Genotype- and protocol-dependent albino plantlet regeneration was also noted, with three of the bioenergy genotypes showing albino plantlet regeneration. Grassl, Rio and Pink Kafir were susceptible to albino plantlet regeneration, with the response strongly associated with the WU protocol. These bioenergy parental genotypes, and their differential responses under two in vitro protocols, provide tools to further explore and assess the role of genetic loci, candidate genes, and allelic variants in the regulation of in vitro responsiveness in sorghum.
Barry Flinn; Savanah Dale; Andrew Disharoon; Stephen Kresovich. Comparative Analysis of In Vitro Responses and Regeneration between Diverse Bioenergy Sorghum Genotypes. Plants 2020, 9, 248 .
AMA StyleBarry Flinn, Savanah Dale, Andrew Disharoon, Stephen Kresovich. Comparative Analysis of In Vitro Responses and Regeneration between Diverse Bioenergy Sorghum Genotypes. Plants. 2020; 9 (2):248.
Chicago/Turabian StyleBarry Flinn; Savanah Dale; Andrew Disharoon; Stephen Kresovich. 2020. "Comparative Analysis of In Vitro Responses and Regeneration between Diverse Bioenergy Sorghum Genotypes." Plants 9, no. 2: 248.
Sorghum has been considered a recalcitrant plant in vitro, and suffers from a lack of regeneration protocols that function broadly and efficiently across a range of genotypes. This study was initiated to identify differential genotype-in vitro protocol responses across a range of bioenergy sorghum bioenergy parental lines, in order to characterize response profiles for use in future genetic studies. Seven bioenergy sorghum genotypes were compared, along with the common grain sorghum genotype Tx430, for their in vitro regeneration responses using two different in vitro protocols, LG and WU. All genotypes displayed some level of response during in vitro culture with both protocols. Distinct genotype-protocol responses were observed, with the WU protocol significantly better for plantlet regeneration. All bioenergy genotypes, with the exception of Chinese Amber, performed as well, if not better than Tx430, with Rio and PI329311 the top regenerating lines. Genotypes displayed protocol-dependent, differential phenolic exudation responses, as indicated by medium browning. During the callus induction phase, genotypes prone to medium browning exhibited a response on WU medium which was either equal or greater than on LG medium, with Pink Kafir and PI329311 the most prone to medium browning. Genotype- and protocol-dependent albino plantlet regeneration was also noted, with three of the bioenergy genotypes showing albino plantlet regeneration. Grassl, Rio and Pink Kafir were susceptible to albino plantlet regeneration, with the response strongly associated with the WU protocol. Pink Kafir displayed the highest albino formation, with close to 25% of regenerating explants forming albino plantlets.
Barry S. Flinn; Savanah Dale; Andrew Disharoon; Stephen Kresovich. Comparative Analysis of In Vitro Responses and Regeneration Between Diverse Bioenergy Sorghum Genotypes. 2019, 1 .
AMA StyleBarry S. Flinn, Savanah Dale, Andrew Disharoon, Stephen Kresovich. Comparative Analysis of In Vitro Responses and Regeneration Between Diverse Bioenergy Sorghum Genotypes. . 2019; ():1.
Chicago/Turabian StyleBarry S. Flinn; Savanah Dale; Andrew Disharoon; Stephen Kresovich. 2019. "Comparative Analysis of In Vitro Responses and Regeneration Between Diverse Bioenergy Sorghum Genotypes." , no. : 1.
The ‘triple-blue’ cultivar of blue spruce (Picea pungens Hoopsii) is notably recalcitrant towards the realm of traditional vegetative propagation methods. Its ability to naturally proliferate is limited by ovule and embryo abortion during the growing season, leading to low viable seed yield. In this study, we established a protocol using somatic embryogenesis (SE) as a means of propagating this popular ornamental cultivar. We collected cones from Hoopsii trees at seven different timepoints throughout the growing season (mid-June to late July in Ottawa (Plant Hardiness Zone 5A)). Female megagametophytes were harvested following each collection and immature zygotic embryos were plated onto induction media. Early somatic embryos began developing from the embryonic tissue (ET) three to five weeks following induction. The highest ET initiation frequency occurred from embryos collected June 20–July 10, suggesting that developmental stage of the embryo was a significant factor in SE induction. The conversion of mature somatic embryos into plantlets (emblings) was completed in eight–ten weeks at a rate of 92.8%. In this study, we demonstrate that in vitro somatic embryogenesis using our optimized protocol is a fast and prolific method for the mass propagation of Hoopsii blue spruce. This is the first report on the production of somatic Hoopsii emblings.
Jordan J Demone; Jingqin Mao; Shen Wan; Maryam Nourimand; Äsbjörn Erik Hansen; Barry Flinn; Olivia Facchin; Alar Prost; Illimar Altosaar; Äsbörn Erik Hansen. Blue sky’s the limit? Somatic embryogenesis as a means of propagating recalcitrant blue spruce (Picea pungens) cultivar Hoopsii. 2019, 1 .
AMA StyleJordan J Demone, Jingqin Mao, Shen Wan, Maryam Nourimand, Äsbjörn Erik Hansen, Barry Flinn, Olivia Facchin, Alar Prost, Illimar Altosaar, Äsbörn Erik Hansen. Blue sky’s the limit? Somatic embryogenesis as a means of propagating recalcitrant blue spruce (Picea pungens) cultivar Hoopsii. . 2019; ():1.
Chicago/Turabian StyleJordan J Demone; Jingqin Mao; Shen Wan; Maryam Nourimand; Äsbjörn Erik Hansen; Barry Flinn; Olivia Facchin; Alar Prost; Illimar Altosaar; Äsbörn Erik Hansen. 2019. "Blue sky’s the limit? Somatic embryogenesis as a means of propagating recalcitrant blue spruce (Picea pungens) cultivar Hoopsii." , no. : 1.
Premature senescence in annual crops reduces yield, while delayed senescence, termed stay-green, imposes positive and negative impacts on yield and nutrition quality. Despite its importance, scant information is available on the genetic architecture of senescence in maize (Zea mays) and other cereals. We combined a systematic characterization of natural diversity for senescence in maize and coexpression networks derived from transcriptome analysis of normally senescing and stay-green lines. Sixty-four candidate genes were identified by genome-wide association study (GWAS), and 14 of these genes are supported by additional evidence for involvement in senescence-related processes including proteolysis, sugar transport and signaling, and sink activity. Eight of the GWAS candidates, independently supported by a coexpression network underlying stay-green, include a trehalose-6-phosphate synthase, a NAC transcription factor, and two xylan biosynthetic enzymes. Source–sink communication and the activity of cell walls as a secondary sink emerge as key determinants of stay-green. Mutant analysis supports the role of a candidate encoding Cys protease in stay-green in Arabidopsis (Arabidopsis thaliana), and analysis of natural alleles suggests a similar role in maize. This study provides a foundation for enhanced understanding and manipulation of senescence for increasing carbon yield, nutritional quality, and stress tolerance of maize and other cereals.
Rajandeep S. Sekhon; Christopher Saski; Rohit Kumar; Barry S. Flinn; Feng Luo; Timothy M. Beissinger; Arlyn J. Ackerman; Matthew W. Breitzman; William C. Bridges; Natalia De Leon; Shawn M. Kaeppler. Integrated Genome-Scale Analysis Identifies Novel Genes and Networks Underlying Senescence in Maize. The Plant Cell 2019, 31, 1968 -1989.
AMA StyleRajandeep S. Sekhon, Christopher Saski, Rohit Kumar, Barry S. Flinn, Feng Luo, Timothy M. Beissinger, Arlyn J. Ackerman, Matthew W. Breitzman, William C. Bridges, Natalia De Leon, Shawn M. Kaeppler. Integrated Genome-Scale Analysis Identifies Novel Genes and Networks Underlying Senescence in Maize. The Plant Cell. 2019; 31 (9):1968-1989.
Chicago/Turabian StyleRajandeep S. Sekhon; Christopher Saski; Rohit Kumar; Barry S. Flinn; Feng Luo; Timothy M. Beissinger; Arlyn J. Ackerman; Matthew W. Breitzman; William C. Bridges; Natalia De Leon; Shawn M. Kaeppler. 2019. "Integrated Genome-Scale Analysis Identifies Novel Genes and Networks Underlying Senescence in Maize." The Plant Cell 31, no. 9: 1968-1989.
The process of crop domestication often consists of two stages: initial domestication, where the wild species is first cultivated by humans, followed by diversification, when the domesticated species are subsequently adapted to more environments and specialized uses. Selective pressure to increase sugar accumulation in certain varieties of the cereal crop Sorghum bicolor is an excellent example of the latter; this has resulted in pronounced phenotypic divergence between sweet and grain-type sorghums, but the genetic mechanisms underlying these differences remain poorly understood. Here we present a new reference genome based on an archetypal sweet sorghum line and compare it to the current grain sorghum reference, revealing a high rate of nonsynonymous and potential loss of function mutations, but few changes in gene content or overall genome structure. We also use comparative transcriptomics to highlight changes in gene expression correlated with high stalk sugar content and show that changes in the activity and possibly localization of transporters, along with the timing of sugar metabolism play a critical role in the sweet phenotype. The high level of genomic similarity between sweet and grain sorghum reflects their historical relatedness, rather than their current phenotypic differences, but we find key changes in signaling molecules and transcriptional regulators that represent new candidates for understanding and improving sugar metabolism in this important crop.
Elizabeth A. Cooper; Zachary W. Brenton; Barry S. Flinn; Jerry Jenkins; Shengqiang Shu; Dave Flowers; Feng Luo; Yunsheng Wang; Penny Xia; Kerrie Barry; Chris Daum; Anna Lipzen; Yuko Yoshinaga; Jeremy Schmutz; Christopher Saski; Wilfred Vermerris; Stephen Kresovich. A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism. BMC Genomics 2019, 20, 1 -13.
AMA StyleElizabeth A. Cooper, Zachary W. Brenton, Barry S. Flinn, Jerry Jenkins, Shengqiang Shu, Dave Flowers, Feng Luo, Yunsheng Wang, Penny Xia, Kerrie Barry, Chris Daum, Anna Lipzen, Yuko Yoshinaga, Jeremy Schmutz, Christopher Saski, Wilfred Vermerris, Stephen Kresovich. A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism. BMC Genomics. 2019; 20 (1):1-13.
Chicago/Turabian StyleElizabeth A. Cooper; Zachary W. Brenton; Barry S. Flinn; Jerry Jenkins; Shengqiang Shu; Dave Flowers; Feng Luo; Yunsheng Wang; Penny Xia; Kerrie Barry; Chris Daum; Anna Lipzen; Yuko Yoshinaga; Jeremy Schmutz; Christopher Saski; Wilfred Vermerris; Stephen Kresovich. 2019. "A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism." BMC Genomics 20, no. 1: 1-13.
Pinus oocarpa var. oocarpa Schiede (Pinophyta, Pinales, Pinaceae subgenus Pinus) is an economically-important conifer of Mexico and Central America. Clonal propagation methods are required to capture the genetic gains obtained through traditional breeding, for the rapid production of elite stock, as well for the introduction of desirable genes via genetic engineering technologies. However, little attention has been paid to the development of tissue culture protocols for P. oocarpa. Here, we outline the clonal propagation process via somatic embryogenesis for this species.
Alejandra Lara-Chavez; Ulrika Egertsdotter; Barry S. Flinn. Oocarpa Pine (Pinus Oocarpa var. Oocarpa Schiede). Biosafety of Forest Transgenic Trees 2018, 295 -305.
AMA StyleAlejandra Lara-Chavez, Ulrika Egertsdotter, Barry S. Flinn. Oocarpa Pine (Pinus Oocarpa var. Oocarpa Schiede). Biosafety of Forest Transgenic Trees. 2018; ():295-305.
Chicago/Turabian StyleAlejandra Lara-Chavez; Ulrika Egertsdotter; Barry S. Flinn. 2018. "Oocarpa Pine (Pinus Oocarpa var. Oocarpa Schiede)." Biosafety of Forest Transgenic Trees , no. : 295-305.
Improvement and year-to-year stabilization of biomass yields are primary objectives for the development of a low-input switchgrass feedstock production system using microbial endophytes. An earlier investigation of the effect of Burkholderia phytofirmans strain PsJN on switchgrass germplasm demonstrated differential responses between genotypes. PsJN inoculation of cv. Alamo (lowland ecotype) increased the plant root system, shoot length, and biomass yields, whereas it had no beneficial effect on cv. Cave-in-Rock (upland ecotype). To understand the gene networks governing plant growth promotion responses triggered by PsJN, the gene expression profiles were analysed in these two hosts, following seedling inoculation. The Affymetrix platform switchgrass expressed sequence tag (EST) microarray chip representing 122 972 probe sets, developed by the DOE BioEnergy Science Center, was employed to assess transcript abundance at 0.5, 2, 4, and 8 DAI (days after PsJN inoculation). Approximately 20 000 switchgrass probe sets showed significant responses in either cultivar. Switchgrass identifiers were used to map 19 421 genes in MapMan software. There were apparent differences in gene expression profiling between responsive and non-responsive cultivars after PsJN inoculation. Overall, there were 14 984 and 9691 genes affected by PsJN inoculation in Alamo and Cave-in-Rock, respectively. Of these, 394 are annotated as pathogenesis-related genes. In the responsive cv. Alamo, 68 pathogenesis-related genes were affected, compared with only 10 in the non-responsive cv. Cave-in-Rock. At the very early stage at 0.5 DAI, both cultivars exhibited similar recognition and defence responses, such as genes in signalling and proteolysis, after which the defence reaction in the responsive cv. Alamo became weaker while it was sustained in non-responsive cv. Cave-in-Rock.
Alejandra Lara-Chavez; Scott Lowman; Seonhwa Kim; Yuhong Tang; Jiyi Zhang; Michael Udvardi; Jerzy Nowak; Barry Flinn; Chuansheng Mei. Global gene expression profiling of two switchgrass cultivars following inoculation withBurkholderia phytofirmansstrain PsJN. Journal of Experimental Botany 2015, 66, 4337 -4350.
AMA StyleAlejandra Lara-Chavez, Scott Lowman, Seonhwa Kim, Yuhong Tang, Jiyi Zhang, Michael Udvardi, Jerzy Nowak, Barry Flinn, Chuansheng Mei. Global gene expression profiling of two switchgrass cultivars following inoculation withBurkholderia phytofirmansstrain PsJN. Journal of Experimental Botany. 2015; 66 (14):4337-4350.
Chicago/Turabian StyleAlejandra Lara-Chavez; Scott Lowman; Seonhwa Kim; Yuhong Tang; Jiyi Zhang; Michael Udvardi; Jerzy Nowak; Barry Flinn; Chuansheng Mei. 2015. "Global gene expression profiling of two switchgrass cultivars following inoculation withBurkholderia phytofirmansstrain PsJN." Journal of Experimental Botany 66, no. 14: 4337-4350.
A potato mutant with a strong stress-response phenotype, and a partial mutant revertant, were characterized. Gene expression patterns and DNA cytosine methylation varied between these and wild-type, indicating a role for DNA cytosine methylation changes in the gene expression and visible phenotypes.
Sukhwinder S. Aulakh; Richard E. Veilleux; Guozhu Tang; Barry S. Flinn. Characterization of a potato activation-tagged mutant, nikku, and its partial revertant. Planta 2015, 241, 1481 -1495.
AMA StyleSukhwinder S. Aulakh, Richard E. Veilleux, Guozhu Tang, Barry S. Flinn. Characterization of a potato activation-tagged mutant, nikku, and its partial revertant. Planta. 2015; 241 (6):1481-1495.
Chicago/Turabian StyleSukhwinder S. Aulakh; Richard E. Veilleux; Guozhu Tang; Barry S. Flinn. 2015. "Characterization of a potato activation-tagged mutant, nikku, and its partial revertant." Planta 241, no. 6: 1481-1495.
Switchgrass (Panicum virgatum L.) is a perennial warm season grass capable of growth on marginal lands without major inputs of water and fertilizers. However, full utilization of its agronomic potential as a bioenergy crop requires improvement of its stand establishment, disease resistance, and prevention of the biomass yield variation from year to year. Our program focuses on the utilization of beneficial bacterial endophytes to enhance switchgrass performance under a low-input production system on marginal lands. We demonstrated earlier that inoculation of switchgrass cv. Alamo with a growth promoting endophyte, Burkholderia phytofirmans strain PsJN (PsJN), can significantly enhance seedling vigor and plant growth under both in vitro and greenhouse conditions. In this study, we tested the effects of PsJN bacterization of switchgrass seedlings on stand establishment, plant growth, and biomass yield in three field experiments conducted over 2 years on highly fertile prime land, and on a former tobacco farm with low fertility soil. PsJN bacterization improved growth and development of switchgrass seedlings, significantly stimulated plant root and shoot growth, and tiller number on the low fertility soil (p p p
J. Scott Lowman; Alejandra Lava-Chavez; Seonhwa Kim-Dura; Barry Flinn; Jerzy Nowak; Chuansheng Mei. Switchgrass Field Performance on Two Soils as Affected by Bacterization of Seedlings with Burkholderia phytofirmans Strain PsJN. BioEnergy Research 2014, 8, 440 -449.
AMA StyleJ. Scott Lowman, Alejandra Lava-Chavez, Seonhwa Kim-Dura, Barry Flinn, Jerzy Nowak, Chuansheng Mei. Switchgrass Field Performance on Two Soils as Affected by Bacterization of Seedlings with Burkholderia phytofirmans Strain PsJN. BioEnergy Research. 2014; 8 (1):440-449.
Chicago/Turabian StyleJ. Scott Lowman; Alejandra Lava-Chavez; Seonhwa Kim-Dura; Barry Flinn; Jerzy Nowak; Chuansheng Mei. 2014. "Switchgrass Field Performance on Two Soils as Affected by Bacterization of Seedlings with Burkholderia phytofirmans Strain PsJN." BioEnergy Research 8, no. 1: 440-449.
The potato cv. Bintje and a Bintje activation-tagged mutant, underperformer (up) were compared. Mutant up plants grown in vitro were dwarf, with abundant axillary shoot growth, greater tuber yield, altered tuber traits and early senescence compared to wild type. Under in vivo conditions, the dwarf and early senescence phenotypes of the mutant remained, but the up plants exhibited a lower tuber yield and fewer axillary shoots compared to wild type. Southern blot analyses indicated a single T-DNA insertion in the mutant, located on chromosome 10. Initial PCR-based gene expression studies indicated transcriptional activation/repression of several genes in the mutant flanking the insertion. The gene immediately flanking the right border of the T-DNA insertion, which encoded an uncharacterized Broad complex, Tramtrac, Bric-a-brac; also known as Pox virus and Zinc finger (BTB/POZ) domain-containing protein (StBTB/POZ1) containing an Armadillo repeat region, was up-regulated in the mutant. Global gene expression comparisons between Bintje and up using RNA-seq on leaves from 60 day-old plants revealed a dataset of over 1,600 differentially expressed genes. Gene expression analyses suggested a variety of biological processes and pathways were modified in the mutant, including carbohydrate and lipid metabolism, cell division and cell cycle activity, biotic and abiotic stress responses, and proteolysis.
Sukhwinder S. Aulakh; Richard E. Veilleux; Allan W. Dickerman; Guozhu Tang; Barry S. Flinn. Characterization and RNA-seq analysis of underperformer, an activation-tagged potato mutant. Plant Molecular Biology 2013, 84, 635 -658.
AMA StyleSukhwinder S. Aulakh, Richard E. Veilleux, Allan W. Dickerman, Guozhu Tang, Barry S. Flinn. Characterization and RNA-seq analysis of underperformer, an activation-tagged potato mutant. Plant Molecular Biology. 2013; 84 (6):635-658.
Chicago/Turabian StyleSukhwinder S. Aulakh; Richard E. Veilleux; Allan W. Dickerman; Guozhu Tang; Barry S. Flinn. 2013. "Characterization and RNA-seq analysis of underperformer, an activation-tagged potato mutant." Plant Molecular Biology 84, no. 6: 635-658.
K. Da; H. Farish-Williford; B. Flinn. ACCLIMATIZATION OF MICROPROPAGATED ICELANDIC POPPY 'TEMPTRESS' PLANTLETS. Acta Horticulturae 2013, 93 -98.
AMA StyleK. Da, H. Farish-Williford, B. Flinn. ACCLIMATIZATION OF MICROPROPAGATED ICELANDIC POPPY 'TEMPTRESS' PLANTLETS. Acta Horticulturae. 2013; (988):93-98.
Chicago/Turabian StyleK. Da; H. Farish-Williford; B. Flinn. 2013. "ACCLIMATIZATION OF MICROPROPAGATED ICELANDIC POPPY 'TEMPTRESS' PLANTLETS." Acta Horticulturae , no. 988: 93-98.
We developed an efficient Agrobacterium -mediated transformation method using an Ac/Ds transposon tagging construct for F. vesca and high throughput paromomycin spray assay to identify its transformants for strawberry functional genomics. Genomic resources for Rosaceae species are now readily available, including the Fragaria vesca genome, EST sequences, markers, linkage maps, and physical maps. The Rosaceae Genomic Executive Committee has promoted strawberry as a translational genomics model due to its unique biological features and transformability for fruit trait improvement. Our overall research goal is to use functional genomic and metabolic approaches to pursue high throughput gene discovery in the diploid woodland strawberry. F. vesca offers several advantages of a fleshy fruit typical of most fruit crops, short life cycle (seed to seed in 12–16 weeks), small genome size (206 Mbb/C), small plant size, self-compatibility, and many seeds per plant. We have developed an efficient Agrobacterium tumefaciens-mediated strawberry transformation method using kanamycin selection, and high throughput paromomycin spray assay to efficiently identify transgenic strawberry plants. Using our kanamycin transformation method, we were able to produce up to 98 independent kanamycin resistant insertional mutant lines using a T-DNA construct carrying an Ac/Ds transposon Launchpad system from a single transformation experiment involving inoculation of 22 leaf explants of F. vesca accession 551572 within approx. 11 weeks (from inoculation to soil). Transgenic plants with 1–2 copies of a transgene were confirmed by Southern blot analysis. Using our paromomycin spray assay, transgenic F. vesca plants were rapidly identified within 10 days after spraying.
Christopher J. Pantazis; Sarah Fisk; Kerri Mills; Barry Flinn; Vladimir Shulaev; Richard E. Veilleux; Yinghui Dan. Development of an efficient transformation method by Agrobacterium tumefaciens and high throughput spray assay to identify transgenic plants for woodland strawberry (Fragaria vesca) using NPTII selection. Plant Cell Reports 2012, 32, 329 -337.
AMA StyleChristopher J. Pantazis, Sarah Fisk, Kerri Mills, Barry Flinn, Vladimir Shulaev, Richard E. Veilleux, Yinghui Dan. Development of an efficient transformation method by Agrobacterium tumefaciens and high throughput spray assay to identify transgenic plants for woodland strawberry (Fragaria vesca) using NPTII selection. Plant Cell Reports. 2012; 32 (3):329-337.
Chicago/Turabian StyleChristopher J. Pantazis; Sarah Fisk; Kerri Mills; Barry Flinn; Vladimir Shulaev; Richard E. Veilleux; Yinghui Dan. 2012. "Development of an efficient transformation method by Agrobacterium tumefaciens and high throughput spray assay to identify transgenic plants for woodland strawberry (Fragaria vesca) using NPTII selection." Plant Cell Reports 32, no. 3: 329-337.
The relative expression of developmentally regulated genes was analyzed during zygotic embryo development in Pinus taeda and somatic embryo development/maturation in P. taeda and Pinus oocarpa. The following four embryo samples were studied: zygotic pro-embryos and somatic embryogenic suspensor masses; round/globular, early cotyledonary, and late cotyledonary. The relative transcript levels of six genes of interest: legumin-/vicilin-like, group 4 late embryogenesis abundant, homeodomain-leucine zipper I, 26S proteasome regulatory subunit S2, and clavata-like, associated with different aspects of embryo development, were analyzed by real-time PCR. In both pine species, the relative transcript levels for legumin-/vicilin-like storage proteins and the late embryogenesis abundant protein accumulated gradually through somatic embryo maturation, in contrast to zygotic embryos, where transcripts increased significantly to their highest levels at the late cotyledonary stage. The homeodomain-leucine zipper I relative transcript accumulation pattern differed between somatic and zygotic embryos. This difference was attributed to differences in cell-type compositions between the embryogenic suspensor masses and pro-embryos. Additionally, in P. oocarpa, the transcript levels of homeodomain-leucine zipper I remained high after the transfer of somatic embryos to maturation conditions, but declined during maturation in P. taeda. The highest 26S proteasome regulatory subunit S2 relative transcript levels in P. taeda were in round/globular somatic and zygotic embryos and in embryogenic suspensor masses and round/globular P. oocarpa somatic embryos. Finally, the relative transcripts levels for the clavata-like gene were more predominant in round/globular, early cotyledonary, and embryogenic suspensor masses in P. taeda and P. oocarpa, respectively. Somatic embryos exhibited relative gene expression patterns similar to their zygotic counterparts, although some differences were noted between zygotic and somatic embryos, as well as between the different pine somatic embryo systems.
Alejandra Lara-Chavez; Ulrika Egertsdotter; Barry S. Flinn. Comparison of gene expression markers during zygotic and somatic embryogenesis in pine. In Vitro Cellular & Developmental Biology - Animal 2012, 48, 341 -354.
AMA StyleAlejandra Lara-Chavez, Ulrika Egertsdotter, Barry S. Flinn. Comparison of gene expression markers during zygotic and somatic embryogenesis in pine. In Vitro Cellular & Developmental Biology - Animal. 2012; 48 (3):341-354.
Chicago/Turabian StyleAlejandra Lara-Chavez; Ulrika Egertsdotter; Barry S. Flinn. 2012. "Comparison of gene expression markers during zygotic and somatic embryogenesis in pine." In Vitro Cellular & Developmental Biology - Animal 48, no. 3: 341-354.
Burkholderia phytofirmans strain PsJN is a highly effective plant-beneficial endophyte. We have used a combination of capillary electrophoresis and methylation-sensitive amplification length polymorphism (CE-MSAP) analysis to investigate the potato genomic DNA cytosine methylation changes that occur in response to PsJN bacterization. Six weeks after PsJN inoculation, over 6800 loci were identified and assessed in two in vitro grown potato varieties, the strongly-responsive Red Pontiac and the poorly-responsive Superior. Compared to non-bacterized control, bacterized Red Pontiac exhibited little change in the overall cytosine methylation, although methylation polymorphisms did occur. In contrast, poorly-responsive Superior exhibited significantly higher levels of overall cytosine methylation and a decrease in the number of non-methylated sites in the bacterized plants compared to controls. Superior had significantly higher DNA methylation and DNA hyper-methylation than Red Pontiac, suggesting that enhanced DNA loci methylation is involved in the suppression of PsJN-induced plant growth stimulation. Several DNA fragments, corresponding to different open reading frames exhibiting methylation polymorphisms in Red Pontiac or Superior were sequenced. Gene expression analysis of a subset of those genes was carried out using real time PCR. We identified several genes whose transcript levels were either enhanced or decreased in response to PsJN in a variety-specific way, as well as genes that were specifically enhanced in both varieties in response to the endophyte.
Kedong Da; Jerzy Nowak; Barry Flinn. Potato cytosine methylation and gene expression changes induced by a beneficial bacterial endophyte, Burkholderia phytofirmans strain PsJN. Plant Physiology and Biochemistry 2012, 50, 24 -34.
AMA StyleKedong Da, Jerzy Nowak, Barry Flinn. Potato cytosine methylation and gene expression changes induced by a beneficial bacterial endophyte, Burkholderia phytofirmans strain PsJN. Plant Physiology and Biochemistry. 2012; 50 (1):24-34.
Chicago/Turabian StyleKedong Da; Jerzy Nowak; Barry Flinn. 2012. "Potato cytosine methylation and gene expression changes induced by a beneficial bacterial endophyte, Burkholderia phytofirmans strain PsJN." Plant Physiology and Biochemistry 50, no. 1: 24-34.
Switchgrass is one of the most promising bioenergy crop candidates for the US. It gives relatively high biomass yield and can grow on marginal lands. However, its yields vary from year to year and from location to location. Thus it is imperative to develop a low input and sustainable switchgrass feedstock production system. One of the most feasible ways to increase biomass yields is to harness benefits of microbial endophytes. We demonstrate that one of the most studied plant growth promoting bacterial endophytes, Burkholderia phytofirmans strain PsJN, is able to colonize and significantly promote growth of switchgrass cv. Alamo under in vitro, growth chamber, and greenhouse conditions. In several in vitro experiments, the average fresh weight of PsJN-inoculated plants was approximately 50% higher than non-inoculated plants. When one-month-old seedlings were grown in a growth chamber for 30 days, the PsJN-inoculated Alamo plants had significantly higher shoot and root biomass compared to controls. Biomass yield (dry weight) averaged from five experiments was 54.1% higher in the inoculated treatment compared to non-inoculated control. Similar results were obtained in greenhouse experiments with transplants grown in 4-gallon pots for two months. The inoculated plants exhibited more early tillers and persistent growth vigor with 48.6% higher biomass than controls. We also found that PsJN could significantly promote growth of switchgrass cv. Alamo under sub-optimal conditions. However, PsJN-mediated growth promotion in switchgrass is genotype specific. Our results show B. phytofirmans strain PsJN significantly promotes growth of switchgrass cv. Alamo under different conditions, especially in the early growth stages leading to enhanced production of tillers. This phenomenon may benefit switchgrass establishment in the first year. Moreover, PsJN significantly stimulated growth of switchgrass cv. Alamo under sub-optimal conditions, indicating that the use of the beneficial bacterial endophytes may boost switchgrass growth on marginal lands and significantly contribute to the development of a low input and sustainable feedstock production system.
Seonhwa Kim; Scott Lowman; Guichuan Hou; Jerzy Nowak; Barry Flinn; Chuansheng Mei. Growth promotion and colonization of switchgrass (Panicum virgatum) cv. Alamo by bacterial endophyte Burkholderia phytofirmans strain PsJN. Biotechnology for Biofuels 2012, 5, 37 -37.
AMA StyleSeonhwa Kim, Scott Lowman, Guichuan Hou, Jerzy Nowak, Barry Flinn, Chuansheng Mei. Growth promotion and colonization of switchgrass (Panicum virgatum) cv. Alamo by bacterial endophyte Burkholderia phytofirmans strain PsJN. Biotechnology for Biofuels. 2012; 5 (1):37-37.
Chicago/Turabian StyleSeonhwa Kim; Scott Lowman; Guichuan Hou; Jerzy Nowak; Barry Flinn; Chuansheng Mei. 2012. "Growth promotion and colonization of switchgrass (Panicum virgatum) cv. Alamo by bacterial endophyte Burkholderia phytofirmans strain PsJN." Biotechnology for Biofuels 5, no. 1: 37-37.
R.E. Veilleux; T. Oosumi; P.A. Wadl; A.J. Baxter; S.H. Holt; J.J. Ruiz-Rojas; J. Pattison; B. Flinn; Yinghui Dan; C. Nessler; V. Shulaev. INSERTIONAL MUTAGENESIS IN THE DIPLOID STRAWBERRY (FRAGARIA VESCA). Acta Horticulturae 2012, 49 -54.
AMA StyleR.E. Veilleux, T. Oosumi, P.A. Wadl, A.J. Baxter, S.H. Holt, J.J. Ruiz-Rojas, J. Pattison, B. Flinn, Yinghui Dan, C. Nessler, V. Shulaev. INSERTIONAL MUTAGENESIS IN THE DIPLOID STRAWBERRY (FRAGARIA VESCA). Acta Horticulturae. 2012; (941):49-54.
Chicago/Turabian StyleR.E. Veilleux; T. Oosumi; P.A. Wadl; A.J. Baxter; S.H. Holt; J.J. Ruiz-Rojas; J. Pattison; B. Flinn; Yinghui Dan; C. Nessler; V. Shulaev. 2012. "INSERTIONAL MUTAGENESIS IN THE DIPLOID STRAWBERRY (FRAGARIA VESCA)." Acta Horticulturae , no. 941: 49-54.
The focus of the current project was to establish somatic embryogenesis protocols for the tropical pine species Pinus oocarpa using immature zygotic embryos (ZEs) as explants. Somatic embryogenesis is best supported by mimicking natural seed–embryo developmental conditions, through a tissue culture medium formulation based on the mineral content of the seed nutritive tissue [megagametophyte (MG)]. A novel culture medium (P. oocarpa medium, PO) was tested in combination with different plant growth regulator (PGR) concentrations and compared with standard Pinus taeda media for the initiation of somatic embryogenesis from immature ZEs of P. oocarpa. Immature MGs containing immature ZEs of two mother trees were used with 12 and 8% extrusion rates for mother tree genotypes 3 and 5, respectively. In both mother trees the percentage capture was 2%. Multiplication of two captured cell lines (T5C2S01 and T5C1S12) was improved by lowering the concentrations of PGRs to 2.5 µM each 2,4-dichlorophenoxyacetic acid and abscisic acid (ABA) plus 1.0 µM each 6-benzylaminopurine and kinetin. Mature somatic embryos formed on 40 µM ABA, 6% (w/v) maltose, 12% (w/v) PEG 8000 and 0.6% (w/v) Phytagel. While PO medium appeared suboptimal for somatic embryo induction, it did exhibit potential for enhanced culture proliferation and subsequent improved maturation with cell line T5C2S01, where microscopic analysis revealed better embryo morphology on PO medium than on 1250 medium. However, this enhancement was not observed with cell line T5C1S12. Germination was preceded by partial desiccation for a period of 2–3 weeks before transferring the embryos to germination medium. Germination was observed after 7 days under low light, and apical primordia slowly expanded after transfer to ex vitro conditions. To our knowledge, this is the first report on the production of somatic seedlings in P. oocarpa.
Alejandra Lara-Chavez; Barry S. Flinn; Ulrika Egertsdotter. Initiation of somatic embryogenesis from immature zygotic embryos of Oocarpa pine (Pinus oocarpa Schiede ex Schlectendal). Tree Physiology 2011, 31, 539 -554.
AMA StyleAlejandra Lara-Chavez, Barry S. Flinn, Ulrika Egertsdotter. Initiation of somatic embryogenesis from immature zygotic embryos of Oocarpa pine (Pinus oocarpa Schiede ex Schlectendal). Tree Physiology. 2011; 31 (5):539-554.
Chicago/Turabian StyleAlejandra Lara-Chavez; Barry S. Flinn; Ulrika Egertsdotter. 2011. "Initiation of somatic embryogenesis from immature zygotic embryos of Oocarpa pine (Pinus oocarpa Schiede ex Schlectendal)." Tree Physiology 31, no. 5: 539-554.
The International Strawberry Sequencing Consortium reports the draft genome of the woodland strawberry (Fragaria vesca). The genome of this diploid species should serve as a reference genome for the Fragaria genus, as the cultivated strawberry (Fragaria × ananassa) is an octoploid where F. vesca is predicted to be a subgenome donor. The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to ×39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted.
Vladimir Shulaev; Daniel J Sargent; Ross N Crowhurst; Todd C Mockler; Otto Folkerts; Arthur L Delcher; Pankaj Jaiswal; Keithanne Mockaitis; Aaron Liston; Shrinivasrao P Mane; Paul Burns; Thomas M Davis; Janet P Slovin; Nahla Bassil; Roger Hellens; Clive Evans; Tim Harkins; Chinnappa Kodira; Brian Desany; Oswald R Crasta; Roderick V Jensen; Andrew C Allan; Todd Michael; Joao Setubal; Jean-Marc Celton; Jasper Rees; Kelly P Williams; Sarah H Holt; Juan Jairo Ruiz Rojas; Mithu Chatterjee; Bo Liu; Herman Silva; Lee Meisel; Avital Adato; Sergei A Filichkin; Michela Troggio; Roberto Viola; Tia-Lynn Ashman; Hao Wang; Palitha Dharmawardhana; Justin Elser; Rajani Raja; Henry D Priest; Douglas W Bryant Jr; Samuel E Fox; Scott Givan; Larry J Wilhelm; Sushma Naithani; Alan Christoffels; David Y Salama; Jade Carter; Elena Lopez Girona; Anna Zdepski; Wenqin Wang; Randall A Kerstetter; Wilfried Schwab; Schuyler S Korban; Jahn Davik; Amparo Monfort; Beatrice Denoyes; Pere Arus; Ron Mittler; Barry Flinn; Asaph Aharoni; Jeffrey L Bennetzen; Steven Salzberg; Allan W Dickerman; Riccardo Velasco; Mark Borodovsky; Richard E Veilleux; Kevin M Folta. The genome of woodland strawberry (Fragaria vesca). Nature Genetics 2010, 43, 109 -116.
AMA StyleVladimir Shulaev, Daniel J Sargent, Ross N Crowhurst, Todd C Mockler, Otto Folkerts, Arthur L Delcher, Pankaj Jaiswal, Keithanne Mockaitis, Aaron Liston, Shrinivasrao P Mane, Paul Burns, Thomas M Davis, Janet P Slovin, Nahla Bassil, Roger Hellens, Clive Evans, Tim Harkins, Chinnappa Kodira, Brian Desany, Oswald R Crasta, Roderick V Jensen, Andrew C Allan, Todd Michael, Joao Setubal, Jean-Marc Celton, Jasper Rees, Kelly P Williams, Sarah H Holt, Juan Jairo Ruiz Rojas, Mithu Chatterjee, Bo Liu, Herman Silva, Lee Meisel, Avital Adato, Sergei A Filichkin, Michela Troggio, Roberto Viola, Tia-Lynn Ashman, Hao Wang, Palitha Dharmawardhana, Justin Elser, Rajani Raja, Henry D Priest, Douglas W Bryant Jr, Samuel E Fox, Scott Givan, Larry J Wilhelm, Sushma Naithani, Alan Christoffels, David Y Salama, Jade Carter, Elena Lopez Girona, Anna Zdepski, Wenqin Wang, Randall A Kerstetter, Wilfried Schwab, Schuyler S Korban, Jahn Davik, Amparo Monfort, Beatrice Denoyes, Pere Arus, Ron Mittler, Barry Flinn, Asaph Aharoni, Jeffrey L Bennetzen, Steven Salzberg, Allan W Dickerman, Riccardo Velasco, Mark Borodovsky, Richard E Veilleux, Kevin M Folta. The genome of woodland strawberry (Fragaria vesca). Nature Genetics. 2010; 43 (2):109-116.
Chicago/Turabian StyleVladimir Shulaev; Daniel J Sargent; Ross N Crowhurst; Todd C Mockler; Otto Folkerts; Arthur L Delcher; Pankaj Jaiswal; Keithanne Mockaitis; Aaron Liston; Shrinivasrao P Mane; Paul Burns; Thomas M Davis; Janet P Slovin; Nahla Bassil; Roger Hellens; Clive Evans; Tim Harkins; Chinnappa Kodira; Brian Desany; Oswald R Crasta; Roderick V Jensen; Andrew C Allan; Todd Michael; Joao Setubal; Jean-Marc Celton; Jasper Rees; Kelly P Williams; Sarah H Holt; Juan Jairo Ruiz Rojas; Mithu Chatterjee; Bo Liu; Herman Silva; Lee Meisel; Avital Adato; Sergei A Filichkin; Michela Troggio; Roberto Viola; Tia-Lynn Ashman; Hao Wang; Palitha Dharmawardhana; Justin Elser; Rajani Raja; Henry D Priest; Douglas W Bryant Jr; Samuel E Fox; Scott Givan; Larry J Wilhelm; Sushma Naithani; Alan Christoffels; David Y Salama; Jade Carter; Elena Lopez Girona; Anna Zdepski; Wenqin Wang; Randall A Kerstetter; Wilfried Schwab; Schuyler S Korban; Jahn Davik; Amparo Monfort; Beatrice Denoyes; Pere Arus; Ron Mittler; Barry Flinn; Asaph Aharoni; Jeffrey L Bennetzen; Steven Salzberg; Allan W Dickerman; Riccardo Velasco; Mark Borodovsky; Richard E Veilleux; Kevin M Folta. 2010. "The genome of woodland strawberry (Fragaria vesca)." Nature Genetics 43, no. 2: 109-116.
Extracellular matrix (ECM) modifications occur during plant growth, development, and in response to environmental stimuli. Key modulators of ECM modification in vertebrates, the extracellular matrix metalloproteinases (MMPs), have also been described in a few plants. Here, we report the identification of Loblolly pine (Pinus taeda) Pta1-MMP and its characterization during seed development and germination. Pta1-MMP protein has the structural characteristics of other plant MMPs, the recombinant protein exhibits Zn(2+)-dependent protease activity, and is inhibited by EDTA and the active site-binding hydroxamate inhibitor GM6001. The Pta1-MMP gene is expressed in both embryo and megagametophyte, with transcript levels increasing in both during the period from proembryo to early cotyledonary stage, then declining during late embryogenesis and maturation drying. Protein extracts exhibited similar developmental-stage MMP-like activity. Seed germination was stimulated by GA(3) and inhibited by ABA, and the timing of germination completion was mirrored by the presence of MMP-like protease activity in both water- and GA(3)-imbibed embryos. Pta1-MMP gene transcript levels increased in association with radicle protrusion for both GA(3)- and water-treated embryos, in agreement with MMP-like activity. In contrast, by 11 days after imbibition, Pta1-MMP gene transcripts in ABA-treated embryos were at levels similar to the other treatments, although MMP-like activity was not observed. The application of GM6001 during Loblolly pine seed germination inhibited radicle protrusion. Our results suggest that MMP activity may be involved in ECM modification, facilitating the cell division and expansion required during seed development, germination completion, and subsequent seedling establishment.
Supriya M. Ratnaparkhe; E. M. Ulrika Egertsdotter; Barry S. Flinn. Identification and characterization of a matrix metalloproteinase (Pta1-MMP) expressed during Loblolly pine (Pinus taeda) seed development, germination completion, and early seedling establishment. Planta 2009, 230, 339 -354.
AMA StyleSupriya M. Ratnaparkhe, E. M. Ulrika Egertsdotter, Barry S. Flinn. Identification and characterization of a matrix metalloproteinase (Pta1-MMP) expressed during Loblolly pine (Pinus taeda) seed development, germination completion, and early seedling establishment. Planta. 2009; 230 (2):339-354.
Chicago/Turabian StyleSupriya M. Ratnaparkhe; E. M. Ulrika Egertsdotter; Barry S. Flinn. 2009. "Identification and characterization of a matrix metalloproteinase (Pta1-MMP) expressed during Loblolly pine (Pinus taeda) seed development, germination completion, and early seedling establishment." Planta 230, no. 2: 339-354.
Considerable functional genomic resources have been developed by the potato research community in the past decade, including expressed sequence tag (EST) libraries, SAGE libraries, microarrays, molecular-function maps, and mutant populations. This article reviews the types, characteristics, strengths, limitations, and appropriate applications of these resources for genomic research and discusses perspectives on future directions. This wide selection of resources available to potato researchers complements efforts to sequence the entire genome and advances made in the development of saturated genetic maps. Key words: Solanum, potato, genomics, expressed sequence tag, microarray, longSAGE, data mining
Xiu-Qing Li; Rebecca Griffiths; David De Koeyer; Charlotte Rothwell; Vicki Gustafson; Sharon Regan; Barry Flinn. Functional genomic resources for potato. Canadian Journal of Plant Science 2008, 88, 573 -581.
AMA StyleXiu-Qing Li, Rebecca Griffiths, David De Koeyer, Charlotte Rothwell, Vicki Gustafson, Sharon Regan, Barry Flinn. Functional genomic resources for potato. Canadian Journal of Plant Science. 2008; 88 (4):573-581.
Chicago/Turabian StyleXiu-Qing Li; Rebecca Griffiths; David De Koeyer; Charlotte Rothwell; Vicki Gustafson; Sharon Regan; Barry Flinn. 2008. "Functional genomic resources for potato." Canadian Journal of Plant Science 88, no. 4: 573-581.