Browsing by Subject "barley"
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Item Analysis of ergosterol in single kernel and ground grain by gas chromatography-mass spectrometry(Journal of Agricultural and Food Chemistry, 2006-05-11) Steffenson, Brian; Dong, Yanhong; Mirocha, Chester JA method for analyzing ergosterol in a single kernel and ground barley and wheat was developed using gas chromatography−mass spectrometry (GC-MS). Samples were saponified in methanolic KOH. Ergosterol was extracted by “one step” hexane extraction and subsequently silylated by N-trimethylsilylimidazole/trimethylchlorosilane (TMSI/TMCS) reagent at room temperature. The recoveries of ergosterol from ground barley were 96.6, 97.1, 97.1, 88.5, and 90.3% at the levels of 0.2, 1, 5, 10, and 20 μg/g (ppm), respectively. The recoveries from a single kernel were between 93.0 and 95.9%. The precision (coefficient of variance) of the method was in the range 0.8−12.3%. The method detection limit (MDL) and the method quantification limit (MQL) were 18.5 and 55.6 ng/g (ppb), respectively. The ergosterol analysis method developed can be used to handle 80 samples daily by one person, making it suitable for screening cereal cultivars for resistance to fungal infection. The ability for detecting low levels of ergosterol in a single kernel provides a tool to investigate early fungal invasion and to study mechanisms of resistance to fungal diseases.Item Applications of Genomewide Selection in a New Plant Breeding Program(2019-07) Neyhart, JeffreyNewly established breeding programs must undergo population improvement and determine superior germplasm for deployment in diverse growing environments. More rapid progress towards these goals may be made by incorporating genomewide selection, or the use of genomewide molecular markers to predict the merit of unphenotyped individuals. Within the context of a new two-row barley (Hordeum vulgare L.) breeding program, my objectives were to i) investigate various methods of updating training population data and their impact on long-term genomewide recurrent selection, ii) assess genomewide prediction accuracy with informed subsetting of data across diverse environments, and iii) validate genomewide predictions of the mean, genetic variance, and superior progeny mean of potential breeding crossses. My first study relied on simulations to examine the impact on prediction accuracy and response to selection when updating the training population each cycle with lines selected based on predictions (best, worst, both best and worst), model criteria (PEVmean and CDmean), random sampling, or no selections. In the short-term, we found that updating with the best or both best and worst predicted lines resulted in high prediction accuracy and genetic gain; in the long-term, all methods (besides not updating) performed similarly. In an actual breeding program, a breeder may want phenotypic data on lines predicted to be the best and our results suggest that this method may be effective for long-term genomewide selection and practical for a breeder. In my second study, a 183-line training population and 50-line offspring validation population were phenotyped in 29 location-year environments for grain yield, heading date, and plant height. Environmental relationships were measured using phenotypic data, geographic distance, or environmental covariables. When adding data from increasingly distant environments to a training set, we observed diminishing gains in prediction accuracy; in some cases, accuracy declined with additional data. Clustering environments led to a small, but non-significant gain in prediction accuracy compared to simply using data from all environments. Our results suggest that informative environmental subsets may improve genomewide selection within a single population, but not when predicting a new generation under realistic breeding circumstances. Finally, my third study used genomewide marker effects from the same training population above to predict the mean (μ), genetic variance (VG), and superior progeny mean (μSP ; mean of the best 10% of lines) of 330,078 possible crosses for Fusarium head blight (FHB) severity, heading date, and plant height. Twenty-seven of these crosses were developed as validation populations. Predictions of μ and μSP were moderate to high in accuracy (rMP = 0.46 – 0.69), while predictions of VG were less accurate (rMP = 0.01 – 0.48). Predictive ability was likely a function of trait heritability, as rMP estimates for heading date (the most heritable) were highest and rMP estimates for FHB severity (the least heritable) were lowest. Accurate predictions of VG and μ are feasible, but, like any implementation of genomewide selection, reliable phenotypic data is critical.Item Evaluating genomewide marker-based breeding methods in traditional and wild relative-derived barley populations(2016-04) Tiede, TylerThe genetic improvement of plants for human use is the primary goal of plant breeding. Through repeated processes of population development and selection, breeders have produced highly productive plants that are adapted to a vast array of environments and cultivation practices. The challenges that drove plant breeders in the past, such as increasing production, novel or increasingly prevalent abiotic and biotic stresses, and evolving end-user demands persist today and are compounded with unprecedented population growth. Genomic selection (GS), a genomewide marker-based selection method, has been shown to be an efficient and effective breeding tool. Its general applicability to plant breeding and principles guiding its use have been established by simulation and empirical cross-validation studies. More recently, studies have demonstrated genetic gains over multiple cycles of selection in a variety of crop species. In the first chapter we provide additional evidence for the effectiveness of GS in an actual breeding program by demonstrating significant gains of 164.74 kg ha-1 and -1.41 ppm for grain yield and DON, respectively, two unfavorably correlated quantitative traits, across three cycles of selection in a spring six-row barley breeding population. With its general effectiveness established, the next step is to increase the accuracy of GS and thereby increase genetic gains. For this, we first showed that updating the training population (TP) with phenotyped lines from recent breeding cycles, specifically selected lines, had an overall positive effect on prediction accuracy. Additionally, we investigated four recently-proposed algorithms that seek to optimize the composition of a TP. Overall the optimization algorithms improved prediction accuracy when compared to a randomly selected TP subset of the same size, but which algorithm performed best was dependent on the trait being predicted and other factors discussed within. This retrospective investigation highlighted the importance of maintaining and optimizing the TP when using GS in real breeding situations to maximize prediction accuracy, thereby maximizing gain from selection and resource utilization. Furthermore, genetic gains depend on genetic variation. Exotic germplasm can be exploited to introduce genetic variability into elite breeding populations to drive genetic gains and address new or changing breeding targets. Wide crosses between elite and exotic germplasm have been widely used to identify large-effect QTL and breed for improved disease or insect resistance. The utility of exotic germplasm to improve quantitative traits, which includes many important agronomic traits, has not been tested as widely. In the second chapter we select parents from an advanced backcross population constructed from 25 wild barley (Hordeum vulgare L. spp spontaneum) accessions crossed to the common high-yielding malting barley cultivar, Rasmusson. We extended the genomic selection framework to identify parent combinations that, with ideal recombination, should produce progeny with large numbers of exotic introgressions with favorable effects. We compared the marker-based crossing strategy to the traditional methods of crossing the topmost performing parents or the most genetically diverse parents. After one round of marker-based progeny selection from these crosses we identified breeding lines, harboring exotic introgressions, which consistently yielded higher than Rasmusson across five trial locations. While none of these lines were statistically better than Rasmusson, there is compelling evidence that the introgression of wild alleles contributed to increased yield. The three parent selection strategies were not significantly different for their ability to identify superior progeny.Item Forever Green Cookbook(Minnesota Institute for Sustainable Agriculture, 2021) Dooley, BethForever Green Cookbook Primary tabs These days, knowing where our food comes from and how it’s grown is more important than ever. Along with taste and nutrition, we want to be sure that it’s good for the land and wildlife, that it provides our farmers with a sustainable livelihood, and that good food is accessible to everyone. Such is the work of the Forever Green Initiative (FGI); a University of Minnesota and United States Department of Agriculture (USDA) Agricultural Research Service Program; which engages teams of experts in genomics, breeding, agronomics, soil health, and commercialization. Since its outset, FGI has placed equal importance on working hand in hand with the farmers, rural communities, food businesses, policy makers, and consumers who insist that healthy food, healthy rural communities, and a healthy environment are not mutually exclusive. Many of them are familiar pantry staples – grains, flour, oils, nuts, fruit, and vegetables. Today, these are all being grown in ways that connect recent advances in agricultural methods with ancient knowledge. Here are delicious ingredients for conscientious cooks. After all, “eating is an agricultural act.” – Wendell Berry.Item Herbicide and Nonherbicide Injury Symptoms on Spring Wheat and Barley(St. Paul, MN: University of Minnesota Extension Service, 1998) Cavanaugh, Kevin J.; Durgan, Beverly R.; Zollinger, Richard K.; Selberg, Wayne A.Covers the topic of wheat and barely injury in two parts: herbicide injury symptoms and nonherbicide injury symptoms.Item Identification and chromosomal location of major genes for resistance to Pyrenophora teres in a doubled-haploid barley population(Genome, 2006) Steffenson, Brian; Friesen, T.L.; Faris, J.D.; Lai, Z.Net blotch, caused by Pyrenophora teres, is one of the most economically important diseases of barley worldwide. Here, we used a barley doubled-haploid population derived from the lines SM89010 and Q21861 to identify major quantitative trait loci (QTLs) associated with seedling resistance to P. teres f. teres (net-type net blotch (NTNB)) and P. teres f. maculata (spot-type net blotch (STNB)). A map consisting of simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers was used to identify chromosome locations of resistance loci. Major QTLs for NTNB and STNB resistance were located on chromosomes 6H and 4H, respectively. The 6H locus (NTNB) accounted for as much as 89% of the disease variation, whereas the 4H locus (STNB resistance) accounted for 64%. The markers closely linked to the resistance gene loci will be useful for marker-assisted selection.Key words: disease resistance, Drechslera teres, molecular markers.Item Implementing Association Mapping and Genomic Selection to Advance Breeding for Complex Traits in Barley(2016-07) Falcon, CelesteTo efficiently respond to challenges presented by global climate change, plant breeders can implement methods that utilize genome-wide marker data to discover and deploy useful genes. We investigated the use of genome-wide association mapping and genomic selection to improve two traits related to protecting natural resources: nitrogen use efficiency (NUE) and winter hardiness. In our first study, we identified quantitative trait loci (QTL) for improved NUE using phenotypic data and calculated stress indices in conjunction with genome-wide marker data for 250 six-row and 250 two-row barley breeding lines. We identified a QTL for grain protein concentration (GPC) on chromosome 6H that has been mapped previously in barley and is collinear with the well-characterized Gpc-B1 locus in wheat. Groups of lines defined by marker haplotypes at this locus exhibited significant differences in GPC but not in grain yield. Overall, our results indicated that potentially effective breeding strategies for NUE include selection based on stress indices, marker assisted selection for desirable alleles, and genomic selection to capture small effect loci. In a second study, we assessed the utility of genomic selection to initiate a breeding program for winter barley based on observed gains from selection, changes in phenotypic variation, and changes in marker allele frequencies. After conducting two cycles of genomic selection for a selection index that combined predictions for low temperature tolerance, malt extract, grain yield, heading date, and plant height, we assessed the selected sets of lines in field trials. Between cycles 0 and 2, genomic selection improved low temperature tolerance and malt extract while maintaining the other selection index traits. Phenotypic variance fluctuated but did not change significantly. Three markers previously shown to be linked to winter hardiness traits shifted in genotypic frequency over the cycles of selection. Based on all marker data, the population shifted toward similarity with the winter growth-type parent lines after two cycles of genomic selection. Overall, this study demonstrated that genomic selection is an effective method for improving trait values in a population at the initiation of a breeding program. Together, these studies support the use of marker-based breeding strategies to improve genetically complex traits that contribute to sustainable agricultural systems that will address climate change.Item Natural genetic variation and gene expression patterns underlying lateral shoot (tiller) development in barley (Hordeum vulgare L)(2018-12) Haaning, AllisonThe main shoot and other above-ground tissues develop from the shoot apical meristem (SAM), including axillary meristems (AXM) from which lateral branches develop. In barley, lateral branches called tillers contribute directly to grain yield and define shoot architecture. Two studies were completed to gain a better understanding of the genetic control of tiller development. One focused on characterizing natural phenotypic and genetic variation in tiller number throughout development in a large, diverse germplasm collection; and the second focused on identifying meristem-specific genes and characterizing gene expression patterns that varied by meristem type (SAM or AXM) and morphological stage. Results from the first study revealed that correlations between tiller development (tillering) and factors previously shown to influence tiller development, like photoperiod response and spike row-type, varied depending on environment and genetic background. Furthermore, no major trade-offs existed between tiller number and other traits, and natural genetic variation associated with tillering largely overlapped variation associated with days to heading and spike row-type. Results of the second study revealed a set of genes upregulated in most meristems compared to non-meristem tissues, many of which have been characterized in other species and are likely important for general meristem maintenance or function. Results also suggested that gene expression was primarily differentiated by genotype, meristem type, and morphological stage; however, expression profiles of SAM and AXM were very similar at later developmental stages. A small number of genes were only expressed in SAM or AXM, and clustering based on expression across all meristems revealed genes upregulated in AXM that may be important for tiller development, as some, like UNICULME4 and INTERMEDIUM-C (TEOSINTE BRANCHED 1 ortholog) have already been implicated in tiller development. Genes that were upregulated in ligules compared to leaves were also identified, and clustering of these genes revealed some that were expressed more highly in ligules and AXM that may, as in other species, have dual functions in leaf and tiller development.Item Phenotypic and genotypic data of barley Gen10 population to study a pericentromeric region on chromosome 6H(2021-06-01) Yin, Lu; Huang, Yadong; Sallam, Ahmad; Heinen, Shane; Li, Lin; Beaubien, Karen; Dill-Macky, Ruth; Dong, Yanhong; Steffenson, Brian; Smith, Kevin; Muehlbauer, Gary; smith376@umn.edu; Smith, Kevin; University of Minnesota Barley Breeding and Genetics (Smith Lab)The phenotypic and genotypic data of the Gen10 population used to study a genetic region on chromosome 6H of barley associated with multiple traits. Gen10 is a population of ~100 Chevron-derived recombinant near-isogenic lines that contained the Fusarisum head blight/kernel discoloration resistance locus from Chevron, a landrace, in the genetic background of Lacey, an elite malting barley variety.Item Puccinia coronata var. hordei var. nov. morphology and pathogenicity(Mycologia, 1999) Steffenson, Brian; Jin, Y.A new variety of Puccinia coronata causing a disease on barley and other gramineous species is described. The fungus is different from other reported forms of P coronata in both morphology and pathogenicity. Its most prominent characters are the elongated teliospore appendages with dichotomous branching and wide pathogenicity on species in the tribe Triticeae, particularly the genus Hordeum. The name of P coronata var. hordei is proposed for the rust fungus. The common name 'crown rust of barley' is proposed for the disease of barley caused by this rust fungus. Results of inoculation indicated that P coronata var. hordei is pathogenic on species of Aegilops, Agropyron, Elymus, Elytrigia, Leymus, Pascopyrum, Psathyrostachys, Secale, and Triticum in the tribe Triticeae, and some species of Brachypodium, Bromus, Festuca, and Lolium in the tribe Poeae, and Phalaris in the tribe Aveneae. In the northern Great Plains of the USA, the following native and introduced gramineous species were found naturally infected by P coronata var. hordei: Bromus tectorum, Elymus canadensis, E. trachycaulus, E. virginicus, Elytrigia intermedia, E. repens, Hordeum jubatum, H. vulgare, Leymus angustus, L. cinerius, L. dahuricus, L. racemosus, Pascopyrum smithii, Psathyrostachys juncea, and Secale cer- eale.Item Sample 360 video for the analysis of plant movement(2018-09-12) Susko, Alexander, Q; susko004@umn.edu; Susko, Alexander, Q; University of Minnesota Oat Breeding and Genetics LabViolent movement of cereal crop stems can lead to failure under high winds. Known as lodging, this phenomenon is particularly severe in cereal crops such as oat, barley, and wheat, and contributes to yield and economic losses. Quantifying the movement of cereal crops under field wind stress could aid in the breeding and selecting of lodging resistant cereals. We present a method to quantify the wave like movement of cereal crop rows in a high throughput fashion under field wind conditions. By analyzing pre-defined regions of hemispherical 4K resolution video, we obtain a time varying color signal of wind induced stem and canopy movement. Bandpass filtering is applied to the color signals to filter out changes in lighting due to sunlight changes, enabling comparisons across different lighting conditions. Peaks are then identified in the signal, and the distance in frames to the next peak as well as the absolute area under the curve between peaks is recorded. The distributions of distances to adjacent peaks (expressed as frequencies) are recorded and the area within a defined frequency bin is summed to get an approximation of the frequency and amount movement. We applied this method to analyze the wind induced movement of 16 cereal cultivars planted in a randomized complete block design on 5 different windy days. We detected significant differences in the mean frequency and amplitude within 0.2 Hz frequency bins among 16 cereal cultivars, with mean frequencies ranging between 1.24 and 1.53 Hz. This method quantifies the frequency and amplitude of movement in cereal varieties at high throughput in the field, and shows promise for characterizing the physiological basis for differences in cereal movement and lodging resistance.Item The Small Grains Field Guide(St. Paul, MN: University of Minnesota Extension Service, 2005) Wiersma, Jochum J.; Ransom, Joel K.This book is a guide for the production of wheat, barley, and oats in Minnesota and North Dakota. Contains 10 sections: Agronomic Management, Crop Growth and Staging, Fertility Management, Photographs, Pesticide Management, Weed Control, Disease and Pest Management, Harvest and Storage Management, Wheat Marketing, and Useful Internet Information Resources.Item SNP Genotyping Data for the Barley Population in "Registration of the S2MET Barley Mapping Population for Multi-Environment Genomewide Selection"(2019-07-25) Neyhart, Jeffrey L; Smith, Kevin P; smith376@umn.edu; Smith, Kevin, P; University of Minnesota Barley-Oat-Silphium Breeding and Genetics LabTwo barley populations were genotyped for use in studies of genomewide selection: a training population of 183 individuals and a selection candidate population of 1200 individuals.Item Variants from "The role of deleterious substitutions in crop genomes"(2016-07-26) Kono, Thomas J Y; Fu, Fengli; Mohammadi, Mohsen; Hoffman, Paul J; Liu, Chaochih; Stupar, Robert M; Smith, Kevin P; Tiffin, Peter; Fay, Justin C; Morrell, Peter L; konox006@umn.edu; Kono, Thomas J YSNP calls in protein coding regions were obtained from 15 barley and 8 soybean lines. Non synonymous SNPs were predicted to be deleterious or not using three approaches.Item Videos for Cereal Crops in a Wind Tunnel(2019-05-10) Susko, Alexander Q; susko004@umn.edu; Susko, Alexander; University of Minnesota Saint Anthony Falls Laboratory92 videos analyzed for "A wind tunnel analysis of cereal drag coefficients and stem bending". Scripts for analysis, including data obtained for the videos, is available online at https://github.com/Hortus/windtunnel_video_analysis.Item Wheat and Barley Drying(St. Paul, MN: University of Minnesota Extension Service, 1992) Wilcke, William F.; Hellevang, Kenneth J.This fact sheet gives recommendations for drying wheat or barley that has been harvested at high moisture content.Item Wheat and Barley Storage(St. Paul, MN: University of Minnesota Extension Service, 1992) Wilcke, William F.; Hellevang, Kenneth J.This fact sheet describes how to select and manage grain storage equipment to reduce losses to mold and insects, and reduce exposure to mold spores and pesticides.