Dan Skinner - Academia.edu (original) (raw)

Papers by Dan Skinner

Research paper thumbnail of Molecular structure and organization of the wheat genomic manganese superoxide dismutase gene

Genome, 2006

The genomic structure of a manganese superoxide dismutase (MnSOD) gene in wheat was elucidated by... more The genomic structure of a manganese superoxide dismutase (MnSOD) gene in wheat was elucidated by sequencing a clone from a BAC library of a stripe rust resistant wheat line. The clone was identified by hybridization with a wheat MnSOD cDNA. The gene consisted of 6 exons interrupted by 5 introns with a total length of 4770 nucleotides from the start codon to the termination codon. The wheat MnSOD gene was the longest among those sequenced from plant species. The transcription initiation site was preceded by a G+C-rich promoter without a TATA or CAAT box. The promoter contained many putative cis-acting regulatory elements, including an abscisic acid (ABA)-responsive element, a stress-responsive element, and a GC-repeat, as well as several other structural features in common with the promoter of the rice MnSOD gene. A Stowaway-like transposable element was found in intron 5 of the wheat MnSOD gene, but further investigation revealed the transposable element was not present in all copi...

Research paper thumbnail of Different Haplotypes of Vrn-1 and Fr-2 Affect Wheat Freezing Tolerance

Freezing tolerance is an important trait for temperate cereals grown in regions with severe winte... more Freezing tolerance is an important trait for temperate cereals grown in regions with severe winters. In wheat, the main loci associated with freezing tolerance are Frost resistance-1 (Fr-1)and Frost resistance-2 (Fr-2). The freezing tolerance effect of Fr-1 is believed to be a pleiotropic effect of Vrn-1. Vrn1alleles for spring growth habit result in an earlier transition to the reproductive phase, which is associated with lower levels of frost tolerance. The Fr-2locus includes a cluster of 11-13 tandem CBF genes that play important roles on the regulation of downstream Cold resistant (COR) genes. We detected two haplotypes at the Fr-A2 locus characterized by 8 SNP and 2 indels.At the Fr-B2locus we identified large deletion events that were associated with differences in freezing tolerance. A global collection of 113 common wheat accessions was used to test the association between the different haplotypes at Vrn-A1, Fr-A2, and Fr-B2 and survival in artificial freezing trials. Haplot...

Research paper thumbnail of Different Haplotypes of TaCBF-A12 Are Associated With Freezing Tolerance in Hexaploid Wheat

Extremely low temperatures in winter can cause severe damage to winter wheat. Breeding of freeze-... more Extremely low temperatures in winter can cause severe damage to winter wheat. Breeding of freeze-tolerant winter wheat is an urgent task in the face of an increasingly variable world climate. The C-repeat Binding Factor(CBF) genes TmCBF12, TmCBF14 and TmCBF15 were hypothesized to play critical roles in freezeing tolerance of T. monococcum. Orthologs of TaCBF12, TaCBF14 and TaCBF15 in the A, B, and D genomes of hexaploid wheat (T. aestivum) were sequenced within a diverse panel of 70 cultivated winter wheats collected from different parts of the world, in order to exploit haplotypes of these nine genes, if associated with freezing tolerance. One indel polymorphism and three SNPs(single nucleotide polymorphisms) in TaCBF-A12 and one in-del polymorphism and five SNPs in TaCBF-A15 were found in the diverse panel. An F2-derived F3 population of 58 individuals from winter wheat populations ‘OFW#5’/‘Eltan’ ‘OFW#5’ /‘Tiber’, was used to test the association between TaCBF-A12 haplotypes and ...

Research paper thumbnail of Measuring freezing tolerance: Survival and regrowth assays

Screening plants for freezing tolerance under tightly controlled conditions is an invaluable tech... more Screening plants for freezing tolerance under tightly controlled conditions is an invaluable technique for studying freezing tolerance and selecting for improved winterhardiness. Artificial freezing tests of cereal plants historically have used isolated crown and stem tissue prepared by "removing all plant parts 3 cm above and 0.5 cm below the crown tissue" (Fowler et al., Crop Sci 21:896-901, 1981). Here, we describe a method of conducting freezing tolerance tests using intact plants grown in small horticultural containers, including suggested methods for collecting and analyzing the data.

Research paper thumbnail of Wheat Research Progress Report Project #: 3019-5344 Title: Evaluation and Selection for Cold Tolerance in Wheat Researchers

Accomplishments and Results: (listed by objective) 1. Evaluate Washington wheat variety trials (S... more Accomplishments and Results: (listed by objective) 1. Evaluate Washington wheat variety trials (Soft Wheat and Hard Wheat Trials) 2. Evaluate cold tolerance of new breeding lines in regional nurseries. 3. Evaluate cold tolerance of advanced breeding lines. 4. Evaluate cold tolerance of F3-F5 (early generation) wheat populations that are segregating for cold tolerance and select resistant progeny. 5. Conduct artificial freeze tests after six weeks of hardening at 36 o F plus infection by soil borne diseases. 6. Identify genes controlling cold hardiness in winter wheat. 7. Identify genes controlling cold hardiness in spring wheat.

Research paper thumbnail of Using Prevosti's Distance Coefficient for Direct Statistical Analysis of Population Differences

HortScience, 2006

An enigma in the process of domestication of many of our common vegetables is what they looked li... more An enigma in the process of domestication of many of our common vegetables is what they looked like and the speed of the process at which they were transformed from the wild progenitors to the modern cultivars. Many vegetables were either domesticated in antiquity or introduced into Europe, often by trade with Africa, the Middle East, or the Americas. Based on genetic information, we often know or can deduce center of origin and the progenitor species of our common vegetables, but we do not have a record of their early history once introduced into Europe. One window to the process of domestication of vegetables is still life art from the Renaissance period. The emphasis of the art form "natura morta" emphasized realism, which allows us to, in some cases, identify species and market classes based on accurate morphological details.

Research paper thumbnail of Use of a new technique to map the porcine ? interferon gene to Chromosome 1

Mammalian Genome, 1994

The polymerase chain reaction (PCR; Mullis et al. 1986) provides a means to amplify a single copy... more The polymerase chain reaction (PCR; Mullis et al. 1986) provides a means to amplify a single copy of DNA to literally hundreds of thousands of copies in a short time. It has been demonstrated that PCR can be performed on the surface of a slide containing cells (Yap and McGee 1991) and that the PCR process can incorporate biotin-11-dUTP into the amplification product (Weier et al. 1991). The objective of this investigation was to develop a method whereby the power of the PCR reaction could be coupled to physical gene mapping by amplifying single-copy genes in metaphase chromosome spreads, with non-isotopic detection methods to determine the site of amplification. The development of such a technique to place short, unique copy sequences that are PCR-based, such as expressed sequence tags (ESTs), microsatellites, and sequence-tagged sites (STSs), could considerably expedite the construction of gene maps of mammalian species. We describe here the application of this technique, which we have termed DISCPCR (Direct In-situ Single Copy) PCR to localize a short fragment of the porcine ~ interferon gene to a region of porcine Chromosome (Chr) 1 to which it has been previously placed by isotopic (Yerle et al. 1986) and nonisotopic (Sarmiento et al. 1993) in situ hybridization. Subsequent to the initiation of this investigation, a report appeared that further substantiates the feasibility of this approach; that report described a similar approach targeting repetitive human sequences (Gosden and Hanratty 1993). Metaphase chromosome spreads were prepared from pokeweed mitogen-stimulated lymphocytes of male pigs. The DNA sequence for the porcine o~ interferon gene (Lefevre and La Bonnardiere 1986) was used to design primers with the Primer 0.5 program (Whitehead Institute, Cambridge, Mass.). The forward primer sequence

Research paper thumbnail of Agrobacterium-Mediated Transformation of Creeping Bentgrass Using GFP as a Reporter Gene

Hereditas, 2004

Creeping bentgrass (Agrosfis palustris Huds.) is a cool season grass widely used on putting green... more Creeping bentgrass (Agrosfis palustris Huds.) is a cool season grass widely used on putting greens in golf courses. Transformation of creeping bentgrass has been conducted using microprojectile bombardment and protoplast electroporation. The objective of our study is to develop an alternative and more efficient approach in transforming the grass using Agrohucterium (strain EHA 101). This technique was effective in transforming 40-day old calli derived from mature seeds cultured on MS medium supplemented with 2,4-D, kinetin, and sucrose. Dozens of transgenic plants have been produced from two independent transformed calli. Presence of functional green fluorescence protein (GFP) was detected in leaves, stems, and roots of transgenic seedlings. Four putative transgenic plants and two control plants were randomly chosen and analyzed by Southern blot analysis. Bands corresponding to the GFP gene were clearly shown in transgenic plants. These results indicated that Agrobacterium transformation can successfully be applied to creeping bentgrass.

Research paper thumbnail of RAPD analysis of genetic variation within a collection of Monascus spp. isolated from red rice (ang-kak) and sofu

Mycological Research, 2000

ABSTRACT Genetic variation within a collection of 25 isolates of Monascus from red rice and sofu ... more ABSTRACT Genetic variation within a collection of 25 isolates of Monascus from red rice and sofu was assessed with RAPD markers using genetic distances (1-Jaccard's coefficient) calculated for all combinations of isolates. Cluster analysis based on genetic distance was performed using the Ward's minimum variance method. Five distinct clusters were revealed based on genetic distances between and among clusters. The robustness (reproducibility) of the cluster assignments was tested by resampling (bootstrap) analysis. Cluster distribution was visualized as a three-dimensional graph based on multiple correspondence analysis. A dendrogram, based on the clusters, was constructed to examine the relationships. Three clusters accounted for 21 isolates; the fourth cluster consisted of three isolates which were quite distinct from each other and all other isolates. The fifth cluster, a single isolate from Japan, was very different from all others in RAPD patterns and was used as an outgroup. Resampling analysis indicated that the 25 isolates represented four genetic lineages of red rice fungi, suggesting that a relatively narrow genetic source of Monascus isolates is used in food products in Asia.

Research paper thumbnail of Evidence of a major genetic factor conditioning freezing sensitivity in winter wheat

Plant Breeding, 2008

... 1992), 'Froid' and germplasm line ORFW were crossed in all combinat... more ... 1992), 'Froid' and germplasm line ORFW were crossed in all combinations including reciprocals. 'Froid' was developed in Montana, USA and was released in 1968 (http://www.ars-grin.gov/ cgi-bin/npgs/acc/search.pl?accid=CItr%2014486&inactive=Yes). ...

Research paper thumbnail of Phospholipase A Activity during Cold Acclimation of Wheat

Crop Science, 2009

Nighttime temperature is one of the major environmental factors infl uencing plant metabolic proc... more Nighttime temperature is one of the major environmental factors infl uencing plant metabolic processes. The respiration rates, membrane thermal stability (MTS), and total antioxidant capacities of leaves were investigated in rice (Oryza sativa L.) plants when exposed to high nighttime temperature (HNT) (32°C) or ambient nighttime temperature (ANT) (27°C), and with or without potential preventive exogenous effector (chemical) treatments. The exogenous effector treatments included α-tocopherol (vitamin E), glycine betaine, and salicylic acid, which play important but different roles in inducing thermal tolerance in many plant species. Plants were subjected to an HNT through use of continuously controlled infrared heaters, starting from 2000 h until 0600 h. High nighttime temperature increased respiration rates, decreased MTS, and negatively affected the yield (by 95%). Application of salicylic acid somewhat lowered the reduction in yield due to HNT (76 vs. 95%) by decreasing the respiration rates and increasing MTS and total antioxidant capacity of rice plants.

Research paper thumbnail of Phospholipid Acyl Chain and Phospholipase Dynamics during Cold Acclimation of Winter Wheat

Crop Science, 2005

on the phospholipid profiles. It has been suggested that alterations in concentration of specific... more on the phospholipid profiles. It has been suggested that alterations in concentration of specific phospholipids Phospholipid (PL) composition is known to change in plants explay a role in cold acclimation. Horvath et al. (1979) posed to cold temperature. The dynamics of PL acyl chain pairs and genes encoding phospholipase enzymes were studied in winter wheat observed an inverse relationship between survival and (Triticum aestivum L.) during cold acclimation. Mass spectrometry the loss of phosphatidylcholine by conversion to the corwas used to characterize PL dynamics, and quantitative real-time responding phosphatidic acid in field-grown wheat PCR was used to characterize phospholipase gene mRNA transcript plants. A similar conversion of phosphatidylcholine to dynamics during cold acclimation. The proportion of PLs with misphosphatidic acid was reported by De La Roche and matched acyl chains decreased concomitantly with an increase in total Andrews (1973) in plants grown at 2ЊC and morphologi-PLs during the first week of cold exposure. Proportions of mismatched cally equivalent plants grown at 24ЊC, again suggesting acyl chains then increased, while total PLs varied little. Numbers of these phospholipid dynamics are a function of plant phe-mRNA transcripts of phospholipase (PL)D, PLC, and PLA 2 increased nology rather than cold acclimation. in response to cold and remained at elevated levels throughout a 4-wk The proportion of unsaturated fatty acids, particularly period. Lysophosphatidylcholine (LPC) increased as much as 14-fold over the 5-wk period and increased significantly less in a less cold linolenic acid (18 carbons, three double bonds [18:3]), tolerant cultivar than more tolerant cultivars. It appeared that newly increased during cold acclimation at the expense of less synthesized PLs with equal-length acyl chains form a part of the initial saturated forms (De La Roche et al., 1972, 1975; Skocresponse to cold temperature; they are then modified to contain nearzowski et al., 1994; Sopin and Trunova, 1991; Willemot initial levels of mismatched acyl chains during acclimation. LPC is a and Pelletier, 1980; Willemot et al., 1977a, 1977b). Howhighly active signal molecule and PLA 2 , PLC, and PLD are involved ever, it has been demonstrated that the accumulation in generation of phospholipid-based signaling molecules; hence, it of linolenic acid per se is not required for the developappeared PL signaling is involved in initial and continuing responses ment of freezing tolerance (De La Roche, 1979). Szalai to cold temperature.

Research paper thumbnail of Freezing Tolerance-Associated Quantitative Trait Loci in the Brundage × Coda Wheat Recombinant Inbred Line Population

Crop Science, 2014

ABSTRACT Freezing tolerance is an essential trait for winter wheat cultivars. A genetic analysis ... more ABSTRACT Freezing tolerance is an essential trait for winter wheat cultivars. A genetic analysis of a Brundage x Coda winter wheat recombinant inbred line (RIL) mapping population was undertaken to identify quantitative trait loci (QTL) associated with freezing tolerance. Five-week to 6-wk old, cold-acclimated plants were frozen to -10.5, -11.5, or -12.5 degrees C. The standardized mean percentage survival of all RILs within each temperature was 61, 44, and 28%, respectively. A total of 2391 polymorphic DNA markers including 1984 single nucleotide polymorphism (SNP), 232 Diversity Array Technology (DArT), and 175 simple sequence repeat (SSR) markers were used to create a genome-wide genetic linkage map. The QTL analysis identified six QTL that were associated with freezing tolerance at either a specific temperature or a combination of temperatures. The QTL QFrbr.wak-5A was associated with freezing tolerance at all temperatures tested and was on chromosome 5AL. Further marker analysis indicates that this QTL is not an effect of known sequence polymorphisms at Vrn-A1. On the basis of map homology, QFrbr.wak-5A mapped at or near the CBF (cold binding factor) gene cluster at Fr-A2, but not an effect of TaCBF-A15, TaCBF-A14, or TaCBF-A12. Other QTL were located on chromosomes 2A, 3A, 5B, and 6D, and were significant at only specific temperatures. Identification of QTL associated with freezing tolerance may lead to useful genetic markers for marker-assisted selection, allowing for more efficient development of freezing tolerant cultivars. Additional studies of this QTL will further enhance knowledge of cold tolerance in wheat, as this QTL is not due to known sequence variation at Vrn-A1 or tested CBF genes.

Research paper thumbnail of Freezing Tolerance of Winter Wheat Plants Frozen In Saturated Soil

Field Crops Research, 2009

Research paper thumbnail of Quantitative Real-Time PCR Method to Detect Changes In Specific Transcript and Total RNA Amounts

Electronic Journal of Biotechnology, 2004

Research paper thumbnail of Post-Acclimation Transcriptome Adjustment is a Major Factor In Freezing Tolerance of Winter Wheat

Functional & integrative genomics, 2009

Cold-acclimated winter wheat plants were slowly frozen to -10 degrees C, and then the temperature... more Cold-acclimated winter wheat plants were slowly frozen to -10 degrees C, and then the temperature was either maintained at -10 degrees C or was lowered further to -12 degrees C. Expression levels of a total of 423 genes were significantly altered in these treatments; genes upregulated outnumbered those downregulated by about a 9:1 ratio. Sixty-eight genes were upregulated at least fivefold in all freezing treatments; 17 of these 68 encoded transcription factors including C-repeat binding factor (Cbf), WRKY, or other Zn-finger proteins, indicating strong upregulation of genes involved in transcription regulation. Sixteen of the 68 highly upregulated genes encoded kinases, phosphatases, calcium trafficking-related proteins, or glycosyltransferases, indicating upregulation of genes involved in signal transduction. Six genes encoding chlorophyll a/b binding-like proteins were upregulated uniquely in response to the -12 degrees C treatment, suggesting a protective role of pigment-binding proteins in freezing stress response. Most genes responded similarly in the very freezing tolerant cultivar Norstar and in the moderately freezing tolerant Tiber, but some genes responded in opposite fashion in the two cultivars. These results showed that wheat crowns actively adapt as the temperature declines to potentially damaging levels, and genetic variation for this ability exists among cultivars.

Research paper thumbnail of Mechanism of Extreme Genetic Recombination In Weedy Amaranthus Hybrids

Weed Science, 2003

... The authors thank Dr. Michael Horak for initiating this research, Dr. Peter Kulakow for advic... more ... The authors thank Dr. Michael Horak for initiating this research, Dr. Peter Kulakow for advice on propagating greenhouse interspecific crosses, and Denise Wetzel for providing Figure 1. We also thank the USDA National Research Initiative (97-35315-4203) and Kansas State ...

Research paper thumbnail of Genetic Diversity In South American Colletotrichum Gloeosporioides Isolates From Stylosanthes Guianensis, a Tropical Forage Legume

European Journal of …, 1999

The degree of genetic diversity of 127 Colletotrichum gloeosporioides isolates from Stylosanthes ... more The degree of genetic diversity of 127 Colletotrichum gloeosporioides isolates from Stylosanthes guianensis genotypes in South America was measured at the molecular level by random amplified polymorphic DNA (RAPD) with nine arbitrary primers of 10 bases, and by restriction fragment length polymorphism (RFLP) with a non-LTR (long terminal repeats) retrotransposon DNA sequence. The RAPD products revealed scorable polymorphism among the isolates, and a total of 80 band positions were scored. Sixty-three of the 127 isolates were clustered into 13 distinct lineages usually correlating with geographic origin. Where isolates from various regions were clustered together, most had identical host genotype origin. The pathogen population sampled from Carimagua, Colombia, a long-time Stylosanthes breeding and selection site, with a savanna ecosystem, was highly diverse. A set of 12 S. guianensis genotype differentials was used to characterize pathogenic variability of 104 isolates and their virulence patterns were grouped into 57 pathotypes. However, when they were tested on four Australian differentials, they grouped into 11 pathotypes. As shown in previous studies, no strict correlations existed between genetic diversity measured by RAPD or RFLP, and pathotype defined by pathogenicity pattern on the differentials. Southern blot analysis of the 127 isolates revealed 23 hybridizing fragments, resulting in 41 fingerprint patterns among the 127 isolates. Relationships between RFLP and RAPD variables were examined using Spearman's Rank Correlation Coefficient, which showed that the two measures of genotypic variation are in agreement.

Research paper thumbnail of Interspecific Hybridization and Gene Flow of ALS Resistance In Amaranthus Species

???welcome.guest??? Sign In | Register. Search within: This issue. Advanced Search. Volume 49, Is... more ???welcome.guest??? Sign In | Register. Search within: This issue. Advanced Search. Volume 49, Issue 5 (September 2001). ...

Research paper thumbnail of Alteration of Antioxidant Enzyme Gene Expression During Cold Acclimation of Near-Isogenic Wheat Lines

Plant Science, 2003

Background: It has been reported that radical oxygen species (ROS) production increased drastical... more Background: It has been reported that radical oxygen species (ROS) production increased drastically during ageing. This increase in ROS had negative effects on many age-related diseases. In this study, we investigated the effects of ageing and exercise on antioxidant gene expression in Fisher rats and the mechanism of chronic exercise on ROS generation related to ageing. Methods: After a standard diet, young and old male Fischer rats were assigned to sedentary control groups (young control group: YC, old control group: OC) and exercise training groups (young exercised group: YE, old exercised group: OE). After a 12-week treadmill exercise training in the exercise training groups, antioxidant gene expression (catalase, glutathione peroxidase) in the liver and muscle was measured by RT-PCR (reverse transcriptionpolymerase chain reaction). Results: Liver catalase mRNA expression was lower in the old group compared with that in the young group. However, this remained unchanged post-exercise. Liver glutathione peroxidase mRNA expression was not different between the young and old groups and remained unchanged in both these groups. The expression of catalase mRNA in the soleus muscle was significantly lower in the old control rats compared with that in the young rats. Exercise significantly increased catalase mRNA expression in the soleus in both the young and old rats. The expression of glutathione peroxidase mRNA in the soleus was lower in the old control rats than in the young. Exercise significantly increased glutathione peroxidase mRNA expression in both young and old rats. Conclusion: This study showed that chronic exercise could be an important contributor to the recovery in the decline of certain antioxidant gene expressions in both young and aged rats. Long-term exercise may positively affect metabolic diseases by modulating antioxidant gene expression.

Research paper thumbnail of Molecular structure and organization of the wheat genomic manganese superoxide dismutase gene

Genome, 2006

The genomic structure of a manganese superoxide dismutase (MnSOD) gene in wheat was elucidated by... more The genomic structure of a manganese superoxide dismutase (MnSOD) gene in wheat was elucidated by sequencing a clone from a BAC library of a stripe rust resistant wheat line. The clone was identified by hybridization with a wheat MnSOD cDNA. The gene consisted of 6 exons interrupted by 5 introns with a total length of 4770 nucleotides from the start codon to the termination codon. The wheat MnSOD gene was the longest among those sequenced from plant species. The transcription initiation site was preceded by a G+C-rich promoter without a TATA or CAAT box. The promoter contained many putative cis-acting regulatory elements, including an abscisic acid (ABA)-responsive element, a stress-responsive element, and a GC-repeat, as well as several other structural features in common with the promoter of the rice MnSOD gene. A Stowaway-like transposable element was found in intron 5 of the wheat MnSOD gene, but further investigation revealed the transposable element was not present in all copi...

Research paper thumbnail of Different Haplotypes of Vrn-1 and Fr-2 Affect Wheat Freezing Tolerance

Freezing tolerance is an important trait for temperate cereals grown in regions with severe winte... more Freezing tolerance is an important trait for temperate cereals grown in regions with severe winters. In wheat, the main loci associated with freezing tolerance are Frost resistance-1 (Fr-1)and Frost resistance-2 (Fr-2). The freezing tolerance effect of Fr-1 is believed to be a pleiotropic effect of Vrn-1. Vrn1alleles for spring growth habit result in an earlier transition to the reproductive phase, which is associated with lower levels of frost tolerance. The Fr-2locus includes a cluster of 11-13 tandem CBF genes that play important roles on the regulation of downstream Cold resistant (COR) genes. We detected two haplotypes at the Fr-A2 locus characterized by 8 SNP and 2 indels.At the Fr-B2locus we identified large deletion events that were associated with differences in freezing tolerance. A global collection of 113 common wheat accessions was used to test the association between the different haplotypes at Vrn-A1, Fr-A2, and Fr-B2 and survival in artificial freezing trials. Haplot...

Research paper thumbnail of Different Haplotypes of TaCBF-A12 Are Associated With Freezing Tolerance in Hexaploid Wheat

Extremely low temperatures in winter can cause severe damage to winter wheat. Breeding of freeze-... more Extremely low temperatures in winter can cause severe damage to winter wheat. Breeding of freeze-tolerant winter wheat is an urgent task in the face of an increasingly variable world climate. The C-repeat Binding Factor(CBF) genes TmCBF12, TmCBF14 and TmCBF15 were hypothesized to play critical roles in freezeing tolerance of T. monococcum. Orthologs of TaCBF12, TaCBF14 and TaCBF15 in the A, B, and D genomes of hexaploid wheat (T. aestivum) were sequenced within a diverse panel of 70 cultivated winter wheats collected from different parts of the world, in order to exploit haplotypes of these nine genes, if associated with freezing tolerance. One indel polymorphism and three SNPs(single nucleotide polymorphisms) in TaCBF-A12 and one in-del polymorphism and five SNPs in TaCBF-A15 were found in the diverse panel. An F2-derived F3 population of 58 individuals from winter wheat populations ‘OFW#5’/‘Eltan’ ‘OFW#5’ /‘Tiber’, was used to test the association between TaCBF-A12 haplotypes and ...

Research paper thumbnail of Measuring freezing tolerance: Survival and regrowth assays

Screening plants for freezing tolerance under tightly controlled conditions is an invaluable tech... more Screening plants for freezing tolerance under tightly controlled conditions is an invaluable technique for studying freezing tolerance and selecting for improved winterhardiness. Artificial freezing tests of cereal plants historically have used isolated crown and stem tissue prepared by "removing all plant parts 3 cm above and 0.5 cm below the crown tissue" (Fowler et al., Crop Sci 21:896-901, 1981). Here, we describe a method of conducting freezing tolerance tests using intact plants grown in small horticultural containers, including suggested methods for collecting and analyzing the data.

Research paper thumbnail of Wheat Research Progress Report Project #: 3019-5344 Title: Evaluation and Selection for Cold Tolerance in Wheat Researchers

Accomplishments and Results: (listed by objective) 1. Evaluate Washington wheat variety trials (S... more Accomplishments and Results: (listed by objective) 1. Evaluate Washington wheat variety trials (Soft Wheat and Hard Wheat Trials) 2. Evaluate cold tolerance of new breeding lines in regional nurseries. 3. Evaluate cold tolerance of advanced breeding lines. 4. Evaluate cold tolerance of F3-F5 (early generation) wheat populations that are segregating for cold tolerance and select resistant progeny. 5. Conduct artificial freeze tests after six weeks of hardening at 36 o F plus infection by soil borne diseases. 6. Identify genes controlling cold hardiness in winter wheat. 7. Identify genes controlling cold hardiness in spring wheat.

Research paper thumbnail of Using Prevosti's Distance Coefficient for Direct Statistical Analysis of Population Differences

HortScience, 2006

An enigma in the process of domestication of many of our common vegetables is what they looked li... more An enigma in the process of domestication of many of our common vegetables is what they looked like and the speed of the process at which they were transformed from the wild progenitors to the modern cultivars. Many vegetables were either domesticated in antiquity or introduced into Europe, often by trade with Africa, the Middle East, or the Americas. Based on genetic information, we often know or can deduce center of origin and the progenitor species of our common vegetables, but we do not have a record of their early history once introduced into Europe. One window to the process of domestication of vegetables is still life art from the Renaissance period. The emphasis of the art form "natura morta" emphasized realism, which allows us to, in some cases, identify species and market classes based on accurate morphological details.

Research paper thumbnail of Use of a new technique to map the porcine ? interferon gene to Chromosome 1

Mammalian Genome, 1994

The polymerase chain reaction (PCR; Mullis et al. 1986) provides a means to amplify a single copy... more The polymerase chain reaction (PCR; Mullis et al. 1986) provides a means to amplify a single copy of DNA to literally hundreds of thousands of copies in a short time. It has been demonstrated that PCR can be performed on the surface of a slide containing cells (Yap and McGee 1991) and that the PCR process can incorporate biotin-11-dUTP into the amplification product (Weier et al. 1991). The objective of this investigation was to develop a method whereby the power of the PCR reaction could be coupled to physical gene mapping by amplifying single-copy genes in metaphase chromosome spreads, with non-isotopic detection methods to determine the site of amplification. The development of such a technique to place short, unique copy sequences that are PCR-based, such as expressed sequence tags (ESTs), microsatellites, and sequence-tagged sites (STSs), could considerably expedite the construction of gene maps of mammalian species. We describe here the application of this technique, which we have termed DISCPCR (Direct In-situ Single Copy) PCR to localize a short fragment of the porcine ~ interferon gene to a region of porcine Chromosome (Chr) 1 to which it has been previously placed by isotopic (Yerle et al. 1986) and nonisotopic (Sarmiento et al. 1993) in situ hybridization. Subsequent to the initiation of this investigation, a report appeared that further substantiates the feasibility of this approach; that report described a similar approach targeting repetitive human sequences (Gosden and Hanratty 1993). Metaphase chromosome spreads were prepared from pokeweed mitogen-stimulated lymphocytes of male pigs. The DNA sequence for the porcine o~ interferon gene (Lefevre and La Bonnardiere 1986) was used to design primers with the Primer 0.5 program (Whitehead Institute, Cambridge, Mass.). The forward primer sequence

Research paper thumbnail of Agrobacterium-Mediated Transformation of Creeping Bentgrass Using GFP as a Reporter Gene

Hereditas, 2004

Creeping bentgrass (Agrosfis palustris Huds.) is a cool season grass widely used on putting green... more Creeping bentgrass (Agrosfis palustris Huds.) is a cool season grass widely used on putting greens in golf courses. Transformation of creeping bentgrass has been conducted using microprojectile bombardment and protoplast electroporation. The objective of our study is to develop an alternative and more efficient approach in transforming the grass using Agrohucterium (strain EHA 101). This technique was effective in transforming 40-day old calli derived from mature seeds cultured on MS medium supplemented with 2,4-D, kinetin, and sucrose. Dozens of transgenic plants have been produced from two independent transformed calli. Presence of functional green fluorescence protein (GFP) was detected in leaves, stems, and roots of transgenic seedlings. Four putative transgenic plants and two control plants were randomly chosen and analyzed by Southern blot analysis. Bands corresponding to the GFP gene were clearly shown in transgenic plants. These results indicated that Agrobacterium transformation can successfully be applied to creeping bentgrass.

Research paper thumbnail of RAPD analysis of genetic variation within a collection of Monascus spp. isolated from red rice (ang-kak) and sofu

Mycological Research, 2000

ABSTRACT Genetic variation within a collection of 25 isolates of Monascus from red rice and sofu ... more ABSTRACT Genetic variation within a collection of 25 isolates of Monascus from red rice and sofu was assessed with RAPD markers using genetic distances (1-Jaccard's coefficient) calculated for all combinations of isolates. Cluster analysis based on genetic distance was performed using the Ward's minimum variance method. Five distinct clusters were revealed based on genetic distances between and among clusters. The robustness (reproducibility) of the cluster assignments was tested by resampling (bootstrap) analysis. Cluster distribution was visualized as a three-dimensional graph based on multiple correspondence analysis. A dendrogram, based on the clusters, was constructed to examine the relationships. Three clusters accounted for 21 isolates; the fourth cluster consisted of three isolates which were quite distinct from each other and all other isolates. The fifth cluster, a single isolate from Japan, was very different from all others in RAPD patterns and was used as an outgroup. Resampling analysis indicated that the 25 isolates represented four genetic lineages of red rice fungi, suggesting that a relatively narrow genetic source of Monascus isolates is used in food products in Asia.

Research paper thumbnail of Evidence of a major genetic factor conditioning freezing sensitivity in winter wheat

Plant Breeding, 2008

... 1992), 'Froid' and germplasm line ORFW were crossed in all combinat... more ... 1992), 'Froid' and germplasm line ORFW were crossed in all combinations including reciprocals. 'Froid' was developed in Montana, USA and was released in 1968 (http://www.ars-grin.gov/ cgi-bin/npgs/acc/search.pl?accid=CItr%2014486&inactive=Yes). ...

Research paper thumbnail of Phospholipase A Activity during Cold Acclimation of Wheat

Crop Science, 2009

Nighttime temperature is one of the major environmental factors infl uencing plant metabolic proc... more Nighttime temperature is one of the major environmental factors infl uencing plant metabolic processes. The respiration rates, membrane thermal stability (MTS), and total antioxidant capacities of leaves were investigated in rice (Oryza sativa L.) plants when exposed to high nighttime temperature (HNT) (32°C) or ambient nighttime temperature (ANT) (27°C), and with or without potential preventive exogenous effector (chemical) treatments. The exogenous effector treatments included α-tocopherol (vitamin E), glycine betaine, and salicylic acid, which play important but different roles in inducing thermal tolerance in many plant species. Plants were subjected to an HNT through use of continuously controlled infrared heaters, starting from 2000 h until 0600 h. High nighttime temperature increased respiration rates, decreased MTS, and negatively affected the yield (by 95%). Application of salicylic acid somewhat lowered the reduction in yield due to HNT (76 vs. 95%) by decreasing the respiration rates and increasing MTS and total antioxidant capacity of rice plants.

Research paper thumbnail of Phospholipid Acyl Chain and Phospholipase Dynamics during Cold Acclimation of Winter Wheat

Crop Science, 2005

on the phospholipid profiles. It has been suggested that alterations in concentration of specific... more on the phospholipid profiles. It has been suggested that alterations in concentration of specific phospholipids Phospholipid (PL) composition is known to change in plants explay a role in cold acclimation. Horvath et al. (1979) posed to cold temperature. The dynamics of PL acyl chain pairs and genes encoding phospholipase enzymes were studied in winter wheat observed an inverse relationship between survival and (Triticum aestivum L.) during cold acclimation. Mass spectrometry the loss of phosphatidylcholine by conversion to the corwas used to characterize PL dynamics, and quantitative real-time responding phosphatidic acid in field-grown wheat PCR was used to characterize phospholipase gene mRNA transcript plants. A similar conversion of phosphatidylcholine to dynamics during cold acclimation. The proportion of PLs with misphosphatidic acid was reported by De La Roche and matched acyl chains decreased concomitantly with an increase in total Andrews (1973) in plants grown at 2ЊC and morphologi-PLs during the first week of cold exposure. Proportions of mismatched cally equivalent plants grown at 24ЊC, again suggesting acyl chains then increased, while total PLs varied little. Numbers of these phospholipid dynamics are a function of plant phe-mRNA transcripts of phospholipase (PL)D, PLC, and PLA 2 increased nology rather than cold acclimation. in response to cold and remained at elevated levels throughout a 4-wk The proportion of unsaturated fatty acids, particularly period. Lysophosphatidylcholine (LPC) increased as much as 14-fold over the 5-wk period and increased significantly less in a less cold linolenic acid (18 carbons, three double bonds [18:3]), tolerant cultivar than more tolerant cultivars. It appeared that newly increased during cold acclimation at the expense of less synthesized PLs with equal-length acyl chains form a part of the initial saturated forms (De La Roche et al., 1972, 1975; Skocresponse to cold temperature; they are then modified to contain nearzowski et al., 1994; Sopin and Trunova, 1991; Willemot initial levels of mismatched acyl chains during acclimation. LPC is a and Pelletier, 1980; Willemot et al., 1977a, 1977b). Howhighly active signal molecule and PLA 2 , PLC, and PLD are involved ever, it has been demonstrated that the accumulation in generation of phospholipid-based signaling molecules; hence, it of linolenic acid per se is not required for the developappeared PL signaling is involved in initial and continuing responses ment of freezing tolerance (De La Roche, 1979). Szalai to cold temperature.

Research paper thumbnail of Freezing Tolerance-Associated Quantitative Trait Loci in the Brundage × Coda Wheat Recombinant Inbred Line Population

Crop Science, 2014

ABSTRACT Freezing tolerance is an essential trait for winter wheat cultivars. A genetic analysis ... more ABSTRACT Freezing tolerance is an essential trait for winter wheat cultivars. A genetic analysis of a Brundage x Coda winter wheat recombinant inbred line (RIL) mapping population was undertaken to identify quantitative trait loci (QTL) associated with freezing tolerance. Five-week to 6-wk old, cold-acclimated plants were frozen to -10.5, -11.5, or -12.5 degrees C. The standardized mean percentage survival of all RILs within each temperature was 61, 44, and 28%, respectively. A total of 2391 polymorphic DNA markers including 1984 single nucleotide polymorphism (SNP), 232 Diversity Array Technology (DArT), and 175 simple sequence repeat (SSR) markers were used to create a genome-wide genetic linkage map. The QTL analysis identified six QTL that were associated with freezing tolerance at either a specific temperature or a combination of temperatures. The QTL QFrbr.wak-5A was associated with freezing tolerance at all temperatures tested and was on chromosome 5AL. Further marker analysis indicates that this QTL is not an effect of known sequence polymorphisms at Vrn-A1. On the basis of map homology, QFrbr.wak-5A mapped at or near the CBF (cold binding factor) gene cluster at Fr-A2, but not an effect of TaCBF-A15, TaCBF-A14, or TaCBF-A12. Other QTL were located on chromosomes 2A, 3A, 5B, and 6D, and were significant at only specific temperatures. Identification of QTL associated with freezing tolerance may lead to useful genetic markers for marker-assisted selection, allowing for more efficient development of freezing tolerant cultivars. Additional studies of this QTL will further enhance knowledge of cold tolerance in wheat, as this QTL is not due to known sequence variation at Vrn-A1 or tested CBF genes.

Research paper thumbnail of Freezing Tolerance of Winter Wheat Plants Frozen In Saturated Soil

Field Crops Research, 2009

Research paper thumbnail of Quantitative Real-Time PCR Method to Detect Changes In Specific Transcript and Total RNA Amounts

Electronic Journal of Biotechnology, 2004

Research paper thumbnail of Post-Acclimation Transcriptome Adjustment is a Major Factor In Freezing Tolerance of Winter Wheat

Functional & integrative genomics, 2009

Cold-acclimated winter wheat plants were slowly frozen to -10 degrees C, and then the temperature... more Cold-acclimated winter wheat plants were slowly frozen to -10 degrees C, and then the temperature was either maintained at -10 degrees C or was lowered further to -12 degrees C. Expression levels of a total of 423 genes were significantly altered in these treatments; genes upregulated outnumbered those downregulated by about a 9:1 ratio. Sixty-eight genes were upregulated at least fivefold in all freezing treatments; 17 of these 68 encoded transcription factors including C-repeat binding factor (Cbf), WRKY, or other Zn-finger proteins, indicating strong upregulation of genes involved in transcription regulation. Sixteen of the 68 highly upregulated genes encoded kinases, phosphatases, calcium trafficking-related proteins, or glycosyltransferases, indicating upregulation of genes involved in signal transduction. Six genes encoding chlorophyll a/b binding-like proteins were upregulated uniquely in response to the -12 degrees C treatment, suggesting a protective role of pigment-binding proteins in freezing stress response. Most genes responded similarly in the very freezing tolerant cultivar Norstar and in the moderately freezing tolerant Tiber, but some genes responded in opposite fashion in the two cultivars. These results showed that wheat crowns actively adapt as the temperature declines to potentially damaging levels, and genetic variation for this ability exists among cultivars.

Research paper thumbnail of Mechanism of Extreme Genetic Recombination In Weedy Amaranthus Hybrids

Weed Science, 2003

... The authors thank Dr. Michael Horak for initiating this research, Dr. Peter Kulakow for advic... more ... The authors thank Dr. Michael Horak for initiating this research, Dr. Peter Kulakow for advice on propagating greenhouse interspecific crosses, and Denise Wetzel for providing Figure 1. We also thank the USDA National Research Initiative (97-35315-4203) and Kansas State ...

Research paper thumbnail of Genetic Diversity In South American Colletotrichum Gloeosporioides Isolates From Stylosanthes Guianensis, a Tropical Forage Legume

European Journal of …, 1999

The degree of genetic diversity of 127 Colletotrichum gloeosporioides isolates from Stylosanthes ... more The degree of genetic diversity of 127 Colletotrichum gloeosporioides isolates from Stylosanthes guianensis genotypes in South America was measured at the molecular level by random amplified polymorphic DNA (RAPD) with nine arbitrary primers of 10 bases, and by restriction fragment length polymorphism (RFLP) with a non-LTR (long terminal repeats) retrotransposon DNA sequence. The RAPD products revealed scorable polymorphism among the isolates, and a total of 80 band positions were scored. Sixty-three of the 127 isolates were clustered into 13 distinct lineages usually correlating with geographic origin. Where isolates from various regions were clustered together, most had identical host genotype origin. The pathogen population sampled from Carimagua, Colombia, a long-time Stylosanthes breeding and selection site, with a savanna ecosystem, was highly diverse. A set of 12 S. guianensis genotype differentials was used to characterize pathogenic variability of 104 isolates and their virulence patterns were grouped into 57 pathotypes. However, when they were tested on four Australian differentials, they grouped into 11 pathotypes. As shown in previous studies, no strict correlations existed between genetic diversity measured by RAPD or RFLP, and pathotype defined by pathogenicity pattern on the differentials. Southern blot analysis of the 127 isolates revealed 23 hybridizing fragments, resulting in 41 fingerprint patterns among the 127 isolates. Relationships between RFLP and RAPD variables were examined using Spearman's Rank Correlation Coefficient, which showed that the two measures of genotypic variation are in agreement.

Research paper thumbnail of Interspecific Hybridization and Gene Flow of ALS Resistance In Amaranthus Species

???welcome.guest??? Sign In | Register. Search within: This issue. Advanced Search. Volume 49, Is... more ???welcome.guest??? Sign In | Register. Search within: This issue. Advanced Search. Volume 49, Issue 5 (September 2001). ...

Research paper thumbnail of Alteration of Antioxidant Enzyme Gene Expression During Cold Acclimation of Near-Isogenic Wheat Lines

Plant Science, 2003

Background: It has been reported that radical oxygen species (ROS) production increased drastical... more Background: It has been reported that radical oxygen species (ROS) production increased drastically during ageing. This increase in ROS had negative effects on many age-related diseases. In this study, we investigated the effects of ageing and exercise on antioxidant gene expression in Fisher rats and the mechanism of chronic exercise on ROS generation related to ageing. Methods: After a standard diet, young and old male Fischer rats were assigned to sedentary control groups (young control group: YC, old control group: OC) and exercise training groups (young exercised group: YE, old exercised group: OE). After a 12-week treadmill exercise training in the exercise training groups, antioxidant gene expression (catalase, glutathione peroxidase) in the liver and muscle was measured by RT-PCR (reverse transcriptionpolymerase chain reaction). Results: Liver catalase mRNA expression was lower in the old group compared with that in the young group. However, this remained unchanged post-exercise. Liver glutathione peroxidase mRNA expression was not different between the young and old groups and remained unchanged in both these groups. The expression of catalase mRNA in the soleus muscle was significantly lower in the old control rats compared with that in the young rats. Exercise significantly increased catalase mRNA expression in the soleus in both the young and old rats. The expression of glutathione peroxidase mRNA in the soleus was lower in the old control rats than in the young. Exercise significantly increased glutathione peroxidase mRNA expression in both young and old rats. Conclusion: This study showed that chronic exercise could be an important contributor to the recovery in the decline of certain antioxidant gene expressions in both young and aged rats. Long-term exercise may positively affect metabolic diseases by modulating antioxidant gene expression.