Fragments of the key flowering gene <em>GIGANTEA</em> are associated with helitron-type sequences in the Pooideae grass <em>Lolium perenne</em>

BACKGROUND: Helitrons are a class of transposable elements which have been identified in a number of species of plants, animals and fungi. They are unique in their proposed rolling-circle mode of replication, have a highly variable copy-number and have been implicated in the restructuring of coding sequences both by their insertion into existing genes and by their incorporation of transcriptionally competent gene fragments. Helitron discovery depends on identifying associated DNA signature sequences and comprehensive evaluation of helitron contribution to a particular genome requires detailed computational analysis of whole genome sequence. Therefore, the role which helitrons have played in modelling non-model plant genomes is largely unknown. RESULTS: Cloning of the flowering gene GIGANTEA (GI) from a BAC library of the Pooideae grass Lolium perenne (perennial ryegrass) identified the target gene and several GI pseudogene fragments spanning the first five exons. Analysis of genomic sequence 5' and 3' of one these GI fragments revealed motifs consistent with helitron-type transposon insertion, specifically a putative 5'-A↓T-3' insertion site containing 5'-TC and CTAG-3' borders with a sub-terminal 16 bp hairpin. Screening of a BAC library of the closely related grass species Festuca pratensis (meadow fescue) indicated similar helitron-associated GI fragments present in this genome, as well as non-helitron associated GI fragments derived from the same region of GI. In order to investigate the possible extent of ancestral helitron-activity in L. perenne, a methylation-filtered GeneThresher(® )genomic library developed from this species was screened for potential helitron 3' hairpin sequences associated with a 3'-CTRR motif. This identified 7 potential helitron hairpin-types present between at least 9 and 51 times within the L. perenne methylation-filtered library. CONCLUSION: This represents evidence for a possible ancestral role for helitrons in modelling the genomes of Lolium and related species

Climate and human exploitation have regulated Atlantic salmon populations in the River Spey, Scotland, over the last 2000 years

Historical salmon catch records suggest that climatic variability, and more recently human exploitation, control patterns of abundance in Atlantic salmon populations. We present the first long-term (2000-year) reconstruction of Atlantic Salmon population variations based on a Marine Derived Nutrient (MDN) lake sediment record. Our record is constructed from nitrogen isotopes (δ15N) measured from a lake sediment core, which we compare with an escapement index (EI) derived from historic net catch data on major Scottish salmon rivers. We used an isotope mixing model to demonstrate that the N isotope values are likely enriched with MDN and demonstrate that Loch Insh sediments are enriched compared with a control site (Loch Vaa) that has never had exposure to salmon. We demonstrate that current adult spawner returns are around half that of historic values prior to major human exploitation. Before the onset of widespread human exploitation and habitat degradation, large fluctuations in salmon abundance are attributed to variations in North Atlantic sea surface temperature. While our data support published reconstructions of declining Atlantic salmon stocks in Northwest European rivers over the last 1000 years, rather than point to a solely human cause, the human impact appears to be overprinted on larger-scale changes in marine habitat occurring at the transition from the warmer Medieval Climatic Anomaly (MCA) to the cooler Little Ice Age (LIA)

Climate and human exploitation have regulated Atlantic salmon populations in the River Spey, Scotland, over the last 2000 years

Historical salmon catch records suggest that climatic variability, and more recently human exploitation, control patterns of abundance in Atlantic salmon populations. We present the first long-term (2000-year) reconstruction of Atlantic Salmon population variations based on a Marine Derived Nutrient (MDN) lake sediment record. Our record is constructed from nitrogen isotopes (δ15N) measured from a lake sediment core, which we compare with an escapement index (EI) derived from historic net catch data on major Scottish salmon rivers. We used an isotope mixing model to demonstrate that the N isotope values are likely enriched with MDN and demonstrate that Loch Insh sediments are enriched compared with a control site (Loch Vaa) that has never had exposure to salmon. We demonstrate that current adult spawner returns are around half that of historic values prior to major human exploitation. Before the onset of widespread human exploitation and habitat degradation, large fluctuations in salmon abundance are attributed to variations in North Atlantic sea surface temperature. While our data support published reconstructions of declining Atlantic salmon stocks in Northwest European rivers over the last 1000 years, rather than point to a solely human cause, the human impact appears to be overprinted on larger-scale changes in marine habitat occurring at the transition from the warmer Medieval Climatic Anomaly (MCA) to the cooler Little Ice Age (LIA)

Population genomics of Mediterranean oat (A. sativa) reveals high genetic diversity and three loci for heading date

KEY MESSAGE: Genomic analysis of Mediterranean oats reveals high genetic diversity and three loci for adaptation to this environment. This information together with phenotyping and passport data, gathered in an interactive map, will be a vital resource for oat genetic improvement. ABSTRACT: During the twentieth century, oat landraces have increasingly been replaced by modern cultivars, resulting in loss of genetic diversity. However, landraces have considerable potential to improve disease and abiotic stress tolerance and may outperform cultivars under low input systems. In this work, we assembled a panel of 669 oat landraces from Mediterranean rim and 40 cultivated oat varieties and performed the first large-scale population genetic analysis of both red and white oat types of Mediterranean origin. We created a public database associated with an interactive map to visualize information for each accession. The oat collection was genotyped with 17,288 single-nucleotide polymorphism (SNP) loci to evaluate population structure and linkage disequilibrium (LD); to perform a genome-wide association study (GWAs) for heading date, a key character closely correlated with performance in this drought-prone area. Population genetic analysis using both structure and PCA distinguished two main groups composed of the red and white oats, respectively. The white oat group was further divided into two subgroups. LD decay was slower within white lines in linkage groups Mrg01, 02, 04, 12, 13, 15, 23, 33, whereas it was slower within red lines in Mrg03, 05, 06, 11, 21, 24, and 28. Association analysis showed several significant markers associated with heading date on linkage group Mrg13 in white oats and on Mrg01 and Mrg08 in red oats. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00122-021-03805-2

Genome-wide association study for crown rust (Puccinia coronata f. sp. avenae) and powdery mildew (Blumeria graminis f. sp. avenae) resistance in an oat (Avena sativa) collection of commercial varieties and landraces

Diseases caused by crown rust (Puccinia coronata f. sp. avenae and powdery mildew (Blumeria graminis f. sp. avenae) are among the most important constraints for the oat crop. Breeding for resistance is one of the most effective, economical, and environmentally friendly means to control these diseases. The purpose of this work was to identify elite alleles for rust and powdery mildew resistance in oat by association mapping to aid selection of resistant plants. To this aim, 177 oat accessions including white and red oat cultivars and landraces were evaluated for disease resistance and further genotyped with 31 simple sequence repeat (SSR) and 15,000 Diversity Arrays Technology (DArT) markers to reveal association with disease resistance traits. After data curation, 1712 polymorphic markers were considered for association analysis. Principal component analysis and a Bayesian clustering approach were applied to infer population structure. Five different general and mixed linear models accounting for population structure and/or kinship corrections and two different statistical tests were carried out to reduce false positive. Five markers, two of them highly significant in all models tested were associated with rust resistance. No strong association between any marker and powdery mildew resistance at the seedling stage was identified. However, one DArT sequence, oPt-5014, was strongly associated with powdery mildew resistance in adult plants. Overall, the markers showing the strongest association in this study provide ideal candidates for further studies and future inclusion in strategies of marker assisted selection

Genotype and environment affect the grain quality and yield of winter oats (Avena sativa L.)

The extent to which the quality and yield of plant varieties are influenced by the environment is important for their successful uptake by end users particularly as climatic fluctuations are resulting in environments that are highly variable from one growing season to another. The genotype-by-environment interaction (GEI) of milling quality and yield was studied using four winter oat varieties in multi-locational trials over 4 years in the U.K. Significant differences across the 22 environments were found between physical grain quality and composition as well as grain yield, with the environment having a significant effect on all of the traits measured. Grain yield was closely related to grain number m−2 whereas milling quality traits were related to grain size attributes. Considerable genotype by environment interaction was obtained for all grain quality traits and stability analysis revealed that the variety Mascani was the least sensitive to the environment for all milling quality traits measured whereas the variety Balado was the most sensitive. Examination of environmental conditions at specific within-year stages of crop development indicated that both temperature and rainfall during grain development were correlated with grain yield and β-glucan content and with the ease of removing the hull (hullability)

The Grizzly, September 8, 2005

Hurricane Katrina Devastates Louisiana • Constitution Stirs up Debate in Iraq • Music and Comedy Greet Class of 2009 • Acting Out Project • An Ursinus Freshman Excels at an Unlikely Sport • What\u27s New at the Berman? Preview of Ursinus\u27 Museum of Art • Stopping the Stork • Food Pyramid Overview • Opinions: Holloway Case Should Raise Awareness; Positives and Negatives of Freshman Orientation; My House Party Dreams; Changes Around Campus • Second Half Comeback Propels Crusaders Past Bears • Field Hockey Drops Season Openerhttps://digitalcommons.ursinus.edu/grizzlynews/1587/thumbnail.jp

The Grizzly, September 15, 2005

Gas Prices Continue to Rise • Campus and Local Community Begin Relief Efforts • Students Share Study Abroad Experiences • The Deal with the Meal Deal • One of Ursinus\u27 Own Performs Professionally • Watch Out, Employers: You Could be Next! • How Much is Too Much? Your Guide to Avoiding Portion Distortion • Excitement Building in Kaleidoscope • Beyond the Condom: Guide to Safe Sex • Opinions: New Price of Driving; Ursinus, U are Worth it • Irony of Work Study • Things They Didn\u27t Teach You at Freshman Orientation • Who Says Division III Players Can\u27t Go Pro?https://digitalcommons.ursinus.edu/grizzlynews/1692/thumbnail.jp

Analysis of Two New Arabinosyltransferases Belonging to the Carbohydrate-Active Enzyme (CAZY) Glycosyl Transferase Family1 Provides Insights into Disease Resistance and Sugar Donor Specificity

Glycosylation of small molecules is critical for numerous biological processes in plants, including hormone homeostasis, neutralization of xenobiotics, and synthesis and storage of specialized metabolites. Glycosylation of plant natural products is usually carried out by uridine diphosphate-dependent glycosyltransferases (UGTs). Triterpene glycosides (saponins) are a large family of plant natural products that determine important agronomic traits such as disease resistance and flavor and have numerous pharmaceutical applications. Most characterised plant natural product UGTs are glucosyltransferases, and little is known about enzymes that add other sugars. Here we report the discovery and characterization of AsAAT1 (UGT99D1), which is required for biosynthesis of the antifungal saponin avenacin A-1 in oat. This enzyme adds L-arabinose to the triterpene scaffold at the C-3 position, a modification critical for disease resistance. The only previously reported plant natural product arabinosyltransferase is a flavonoid arabinosyltransferase from Arabidopsis. We show that AsAAT1 has high specificity for UDP-β-L-arabinopyranose, identify two amino acids required for sugar donor specificity, and through targeted mutagenesis convert AsAAT1 into a glucosyltransferase. We further identify a second arabinosyltransferase potentially implicated in the biosynthesis of saponins that determine bitterness in soybean. Our investigations suggest independent evolution of UDP-arabinose sugar donor specificity in arabinosyltransferases in monocots and eudicots