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https://www.readbyqxmd.com/read/28315831/evaluating-methods-of-updating-training-data-in-long-term-genomewide-selection
#1
Jeffrey L Neyhart, Tyler Tiede, Aaron J Lorenz, Kevin P Smith
Genomewide selection is hailed for its ability to facilitate greater genetic gains per unit time. Over breeding cycles, the requisite linkage disequilibrium (LD) between quantitative trait loci (QTL) and markers is expected to change as a result of recombination, selection, and drift, leading to a decay in prediction accuracy. Previous research has identified the need to update the training population using data that may capture new LD generated over breeding cycles, however optimal methods of updating have not been explored...
March 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28301509/genome-wide-association-mapping-in-winter-barley-for-grain-yield-and-culm-cell-wall-polymer-content-using-the-high-throughput-compp-technique
#2
Andrea Bellucci, Alessandro Tondelli, Jonatan U Fangel, Anna Maria Torp, Xin Xu, William G T Willats, Andrew Flavell, Luigi Cattivelli, Søren K Rasmussen
A collection of 112 winter barley varieties (Hordeum vulgare L.) was grown in the field for two years (2008/09 and 2009/10) in northern Italy and grain and straw yields recorded. In the first year of the trial, a severe attack of barley yellow mosaic virus (BaYMV) strongly influenced final performances with an average reduction of ~ 50% for grain and straw harvested in comparison to the second year. The genetic determination (GD) for grain yield was 0.49 and 0.70, for the two years respectively, and for straw yield GD was low in 2009 (0...
2017: PloS One
https://www.readbyqxmd.com/read/28301146/effect-of-whole-grain-qingke-tibetan-hordeum-vulgare-l-zangqing-320-on-the-serum-lipid-levels-and-intestinal-microbiota-of-rats-under-high-fat-diet
#3
Xuejuan Xia, Guannan Li, Yongbo Ding, Tingyuan Ren, Jiong Zheng, Jianquan Kan
This study investigated the hypolipidemic effect of whole grain Qingke (WGQ) and its influence on intestinal microbiota. Changes in the serum lipid, intestinal environment, and microbiota of Sprague-Dawley rats fed high-fat diets supplemented with different doses of WGQ were determined. Results showed that high doses of WGQ significantly decreased (P < 0.05) the Lee's index, serum total cholesterol, low-density lipoprotein cholesterol, and non-high-density lipoprotein cholesterol levels whereas increased the body weight of the rats...
March 16, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28261319/non-destructive-determination-of-floral-staging-in-cereals-using-x-ray-micro-computed-tomography-%C3%A2%C2%B5ct
#4
Saoirse R Tracy, José Fernández Gómez, Craig J Sturrock, Zoe A Wilson, Alison C Ferguson
BACKGROUND: Accurate floral staging is required to aid research into pollen and flower development, in particular male development. Pollen development is highly sensitive to stress and is critical for crop yields. Research into male development under environmental change is important to help target increased yields. This is hindered in monocots as the flower develops internally in the pseudostem. Floral staging studies therefore typically rely on destructive analysis, such as removal from the plant, fixation, staining and sectioning...
2017: Plant Methods
https://www.readbyqxmd.com/read/28261253/heterogeneity-of-powdery-mildew-resistance-revealed-in-accessions-of-the-icarda-wild-barley-collection
#5
Antonin Dreiseitl
The primary genepool of barley comprises two subspecies - wild barley (Hordeum vulgare subsp. spontaneum) and cultivated barley H. vulgare. subsp. vulgare. The former originated 5.5 million years ago in southwest Asia and is the immediate ancestor of cultivated barley, which arose around 10,000 years ago. In this study, the specific resistance of a set of 146 wild barley accessions, maintained by the International Center for Agriculture Research in the Dry Areas (ICARDA), to 32 isolates of barley powdery mildew caused by Blumeria graminis f...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28261241/analysis-of-plant-pan-genomes-and-transcriptomes-with-get_homologues-est-a-clustering-solution-for-sequences-of-the-same-species
#6
Bruno Contreras-Moreira, Carlos P Cantalapiedra, María J García-Pereira, Sean P Gordon, John P Vogel, Ernesto Igartua, Ana M Casas, Pablo Vinuesa
The pan-genome of a species is defined as the union of all the genes and non-coding sequences found in all its individuals. However, constructing a pan-genome for plants with large genomes is daunting both in sequencing cost and the scale of the required computational analysis. A more affordable alternative is to focus on the genic repertoire by using transcriptomic data. Here, the software GET_HOMOLOGUES-EST was benchmarked with genomic and RNA-seq data of 19 Arabidopsis thaliana ecotypes and then applied to the analysis of transcripts from 16 Hordeum vulgare genotypes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28245065/deletion-bias-in-dna-double-strand-break-repair-differentially-contributes-to-plant-genome-shrinkage
#7
Giang T H Vu, Hieu X Cao, Bernd Reiss, Ingo Schubert
In order to prevent genome instability, cells need to be protected by a number of repair mechanisms, including DNA double-strand break (DSB) repair. The extent to which DSB repair, biased towards deletions or insertions, contributes to evolutionary diversification of genome size is still under debate. We analyzed mutation spectra in Arabidopsis thaliana and in barley (Hordeum vulgare) by PacBio sequencing of three DSB-targeted loci each, uncovering repair via gene conversion, single strand annealing (SSA) or nonhomologous end-joining (NHEJ)...
February 28, 2017: New Phytologist
https://www.readbyqxmd.com/read/28239779/variation-in-barley-1%C3%A2-%C3%A2-3-1%C3%A2-%C3%A2-%C3%A2-4-%C3%AE-glucan-endohydrolases-reveals-novel-allozymes-with-increased-thermostability
#8
Juanita C Lauer, Suong Cu, Rachel A Burton, Jason K Eglinton
Novel barley (1 → 3, 1 → 4)-β-glucan endohydrolases with increased thermostability. Rapid and reliable degradation of (1 → 3, 1 → 4)-β-glucan to produce low viscosity wort is an essential requirement for malting barley. The (1 → 3, 1 → 4)-β-glucan endohyrolases are responsible for the primary hydrolysis of cell wall β-glucan. The variation in β-glucanase genes HvGlb1 and HvGlb2 that encode EI and EII, respectively, were examined in elite and exotic germplasm. Six EI and 14 EII allozymes were identified, and significant variation was found in β-glucanase from Hordeum vulgare ssp...
February 26, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28224917/regulation-of-the-wheat-map-kinase-phosphatase-1-by-14-3-3-proteins
#9
Mouna Ghorbel, Valérie Cotelle, Chantal Ebel, Ikram Zaidi, Mélanie Ormancey, Jean-Philippe Galaud, Moez Hanin
Plant MAP kinase phosphatases (MKPs) are major regulators of MAPK signaling pathways and play crucial roles in controlling growth, development and stress responses. The presence of several functional domains in plant MKPs such as a dual specificity phosphatase catalytic domain, gelsolin, calmodulin-binding and serine-rich domains, suggests that MKPs can interact with distinct cellular partners, others than MAPKs. In this report, we identified a canonical mode I 14-3-3-binding motif (574KLPSLP579) located at the carboxy-terminal region of the wheat MKP, TMKP1...
April 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28214728/lipid-signalling-mediated-by-pld-pa-modulates-proline-and-h2o2-levels-in-barley-seedlings-exposed-to-short-and-long-term-chilling-stress
#10
Micaela Peppino Margutti, Matias Reyna, María Verónica Meringer, Graciela E Racagni, Ana Laura Villasuso
Phospholipase D (PLD) hydrolyses phospholipids to yield phosphatidic acid (PA) and a head group, and is involved in responses to a variety of environmental stresses, including chilling and freezing stress. Barley responses to chilling stress (induced by incubating seedlings at 4 °C) are dynamic and the duration of stress, either short (0-180 min) or long-term (24-36 h) had a significant impact on the response. We investigated the roles of PLD/PA in responses of barley (Hordeum vulgare) seedlings to short and long-term chilling stress, based on regulation of proline and reactive oxygen species (ROS) levels...
February 10, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28213323/growth-inhibition-and-efficiency-of-the-antioxidant-system-in-spring-barley-and-common-radish-grown-on-soil-polluted-ionic-liquids-with-iodide-anions
#11
Robert Biczak, Martyna Śnioszek, Arkadiusz Telesiński, Barbara Pawłowska
Ionic liquids (ILs) constitute a huge group of substances that are increasingly common in the commercial use. This situation may lead to the contamination of the soil environment which being the basic of plants vegetation. This paper presents the effect of four ILs with I(-) anion on the growth and development of spring barley (Hordeum vulgare) and common radish (Raphanus sativus L. subvar. radicula Pers) and changes in metabolism of the plants. Seedlings of spring barley and common radish cultivated on soil with increasing ILs concentration exhibited typical phytotoxicity symptoms...
February 14, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28212860/comparative-structure-function-characterization-of-the-saposin-like-domains-from-potato-barley-cardoon-and-arabidopsis-aspartic-proteases
#12
Brian C Bryksa, Douglas A Grahame, Rickey Y Yada
The present study characterized the aspartic protease saposin-like domains of four plant species, Solanum tuberosum (potato), Hordeum vulgare L. (barley), Cynara cardunculus L. (cardoon; artichoke thistle) and Arabidopsis thaliana, in terms of bilayer disruption and fusion, and structure pH-dependence. Comparison of the recombinant saposin-like domains revealed that each induced leakage of bilayer vesicles composed of a simple phospholipid mixture with relative rates Arabidopsis>barley>cardoon>potato...
February 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28204911/selection-of-transformation-efficient-barley-genotypes-based-on-tfa-transformation-amenability-haplotype-and-higher-resolution-mapping-of-the-tfa-loci
#13
Hiroshi Hisano, Brigid Meints, Matthew J Moscou, Luis Cistue, Begoña Echávarri, Kazuhiro Sato, Patrick M Hayes
The genetic substitution of transformation amenability alleles from 'Golden Promise' can facilitate the development of transformation-efficient lines from recalcitrant barley cultivars. Barley (Hordeum vulgare) cv. 'Golden Promise' is one of the most useful and well-studied cultivars for genetic manipulation. In a previous report, we identified several transformation amenability (TFA) loci responsible for Agrobacterium-mediated transformation using the F2 generation of immature embryos, derived from 'Haruna Nijo' × 'Golden Promise,' as explants...
February 15, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28192204/analysis-of-plant-udp-arabinopyranose-mutase-uam-role-of-divalent-metals-and-structure-prediction
#14
Jijin R A Kuttiyatveetil, David A R Sanders
UDP-arabinopyranose mutase (UAM) is a plant enzyme which interconverts UDP-arabinopyranose (UDP-Arap; a six-membered sugar) to UDP-arabinofuranose (UDP-Araf; a five-membered sugar). Plant mutases belong to a small gene family called Reversibly Glycosylated Proteins (RGPs). So far, UAM has been identified in Oryza sativa (Rice), Arabidopsis thaliana and Hordeum vulgare (Barley). The enzyme requires divalent metal ions for catalytic activity. Here, the divalent metal ion dependency of UAMs from O. sativa (rice) and A...
February 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28177826/phylogenetic-analysis-of-two-single-copy-nuclear-genes-revealed-origin-and-complex-relationships-of-hordeum-polyploids-in-triticeae-poaceae
#15
Qianni Hu, Genlou Sun
Two single copy nuclear genes, the second largest subunit of RNA polymerase II (RPB2) and thioredoxin-like gene (HTL), were used to explore the phylogeny and origin of polyploid species in Hordeum. Our results were partly in accord with previous studies, but disclosed additional complexity. Both RPB2 and HTL trees confirmed the presence of Xa genome in H. capense and H. secalinum, and that H. depressum originated from H. californicum together with other American diploids, either H. intercedens or H. pusillum...
January 11, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28168328/patterns-of-evolutionary-trajectories-and-domestication-history-within-the-genus-hordeum-assessed-by-remap-markers
#16
Georgi Bonchev, Roman Dusinský, Pavol Hauptvogel, Miroslav Švec
The patterns of genetic diversity related to the taxonomy and domestication history of 85 accessions representing the main four species of the genus Hordeum were examined by retrotransposon-microsatellite amplified polymorphism (REMAP) markers based on the retrotransposon BARE-1. A substantial level of genetic polymorphisms at among- and within-species level was observed showing that this retrotransposon family and its adjacent genomic regions has been a target for genome dynamics during the evolution and domestication of barley...
February 6, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28167022/differences-in-nutritional-quality-between-wild-and-domesticated-forms-of-barley-and-emmer-wheat
#17
REVIEW
Kim Henrik Hebelstrup
Grasses such as wheat and barley constitute some of the main crops currently cultivated worldwide. Cultivation of wild cereals such as Hordeum spontaneum (wild barley) and Triticum diccocoides (wild emmer) started in southwest Asia. Despite the many studies on the origins of agriculture and plant domestication, surprisingly few studies have discussed the importance of the nutritional quality of barley and emmer wheat in their evolution. A comparison of domesticated forms of these cereals with their wild progenitors suggests an evolution towards bigger grains with higher glycemic loads in the form of higher relative starch content with lower relative protein, fiber and mineral contents...
March 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28160617/reinforcing-plant-evolutionary-genomics-using-ancient-dna
#18
REVIEW
Rafal M Gutaker, Hernán A Burbano
Improved understanding of ancient DNA (aDNA) biochemical properties coupled with application of next generation sequencing (NGS) methods enabled sequencing and authenticating genomes of historical samples. This advancement ignited a revolution in plant evolutionary genomics by allowing direct observations of past molecular diversity. Analyses of genomes sequenced from temporally distributed samples of Gossypium sp., Phytophthora infestans and Arabidopsis thaliana improved our understanding of the evolutionary rates and time scales at which genome remodeling takes place...
February 1, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28150529/free-asparagine-and-sugars-profile-of-cereal-species-the-potential-of-cereals-for-acrylamide-formation-in-foods
#19
Slađana Žilić, Dejan Dodig, Zorica Basić, Jelena Vančetović, Primož Titan, Nenad Đurić, Nataša Tolimir
Cereals based food is one of the major source of Maillard reaction products in the diet. Free amino acids and reducing sugars are considered to be the main precursors in the formation of these heat-induced compounds. In order to determine genetic resources with reduced potential for acrylamide formation, the content of sugars, as well as free asparagine were analyzed in a total of 30 cultivars of 10 varieties belonging to eight species (Triticum aestivum var. lutescens, T. aestivum var. alba, T. aestivum var...
February 2, 2017: Food Additives & Contaminants. Part A, Chemistry, Analysis, Control, Exposure & Risk Assessment
https://www.readbyqxmd.com/read/28145604/comparison-of-the-effect-of-ionic-liquids-containing-hexafluorophosphate-and-trifluoroacetate-anions-on-the-inhibition-of-growth-and-oxidative-stress-in-spring-barley-and-common-radish
#20
Robert Biczak, Barbara Pawłowska, Joanna Feder-Kubis, Arkadiusz Telesiński
Ionic liquids (ILs) are a group of chemical compounds, with chemical properties, which are of great interest to various fields of science and industry. However, commercial use of these substances raises concern as they may threaten the natural ecosystems. This study used two types of (-)-menthol-containing chiral imidazolium ionic liquids (CILs): 1-[(1R,2S,5R)-(-)-menthoxymethyl]-3-methylimidazolium hexafluorophoshate [Im-Men][PF6 ] and 1-[(1R,2S,5R)-(-)-menthoxymethyl]-3-methylimidazolium trifluoroacetate [Im-Men][CF3 CO2 ]...
February 1, 2017: Environmental Toxicology and Chemistry
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