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| author | root | 2012-05-08 18:39:56 -0500 |
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diff --git a/web/dbdoc/SXMPublish.html b/web/dbdoc/SXMPublish.html new file mode 100755 index 00000000..55e8a160 --- /dev/null +++ b/web/dbdoc/SXMPublish.html @@ -0,0 +1,441 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> +<HTML><HEAD><TITLE>Barley SM Phenotype Database</TITLE> +<META http-equiv=Content-Type content="text/html; charset=iso-8859-1"> +<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'> +<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'> +<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT> + + +<style type="text/css"> +<!-- +p.MsoNormal { +margin-top:0in; +margin-right:0in; +margin-bottom:10.0pt; +margin-left:0in; +line-height:115%; +font-size:11.0pt; +font-family:"Calibri","sans-serif"; +} +p.MsoListParagraphCxSpFirst { +margin-top:0in; +margin-right:0in; +margin-bottom:.0001pt; +margin-left:.5in; +line-height:115%; +font-size:11.0pt; +font-family:"Calibri","sans-serif"; +} +p.MsoListParagraphCxSpMiddle { +margin-top:0in; +margin-right:0in; +margin-bottom:.0001pt; +margin-left:.5in; +line-height:115%; +font-size:11.0pt; +font-family:"Calibri","sans-serif"; +} +p.MsoListParagraphCxSpLast { +margin-top:0in; +margin-right:0in; +margin-bottom:10.0pt; +margin-left:.5in; +line-height:115%; +font-size:11.0pt; +font-family:"Calibri","sans-serif"; +} +span.Heading2Char { +font-family:"Times New Roman","serif"; +font-weight:bold; +} +.style2 { +font-size: small; +font-style: italic; +} +--> +</style> +</HEAD> +<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff> +<TABLE cellSpacing=5 cellPadding=4 width="100%" border=0> +<TBODY> +<TR> +<script language="JavaScript" src="/javascript/header.js"></script> +</TR> +<TR> +<TD bgColor=#eeeeee class="solidBorder"> +<Table width= "94%" cellSpacing=0 cellPadding=5><TR> +<!-- Body Start from Here --> +<TD valign="top" height="200" width="100%" bgcolor="#eeeeee"> +<P class="title"><I>Barley</I> Phenotype Database <A HREF="/webqtl/main.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A></P> + + +<class="subtitle"> +Steptoe x Morex (SxM):</A><br> +<Blockquote> <strong>North American Barley Genome Project (NABGP) dataset</strong><br> +Hayes, P. M., B. H. Liu, S. J. Knapp, F. Chen, B. Jones, T. Blake, J. Franckowiak, D Rasmusson, M. Sorrells, S. E. Ullrich, D. Wesenberg and A. Kleinhofs. 1993. Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor. Appl. Genet. 87: 392-401. The data set is available at the <a href="http://wheat.pw.usda.gov/ggpages/SxM/phenotypes.html">http://wheat.pw.usda.gov/ggpages/SxM/phenotypes.html</a> <p>It comprises the following agronomic and malting quality traits:<br> +* Grain yield (MT/ha)<br> +* Lodging (%)<br> +* Height (cm)<br> +* Heading date (days after January 1)<br> +* Grain protein (%)<br> +* Alpha amylase (20 Deg units)<br> +* Diastatic power (Deg)<br> +* Malt extract (%)<br> +Agronomic and malting quality traits were measured in 16 and 9 environments, respectively. The phenotype data files are coded for each environment as follows:<br> +Environment # Location Year Cooperator<br> +1 Crookston, Minnesota 1992 D. Rasmusson (rasmu002@maroon.tc.umn.edu)<br> +2 Ithaca, New York 1992 M. Sorrells (mes12@cornell.edu)<br> +3 Guelph, Ontario 1992 D. Falk (dfalk@crop.uoguelph.ca)<br> +4 Pullman, Washington 1992 S. Ullrich (ullrich@wsu.edu)<br> +5 Brandon, Manitoba 1992 W. Legge (legge@mbrsbr.agr.ca)<br> +6 Outlook, Saskatchewan 1992 R. Irvine<br> +7 Goodale, Saskatchewan 1992 B. Rossnagel (rossnagel@sask.uask.ca)<br> +8 Saskatoon, Saskatchewan 1992 B. Rossnagel (rossnagel@sask.uask.ca)<br> +9 Tetonia, Idaho D. Wesenberg (fax: 208-397-4165) 1992 <br> +10 Bozeman, Montana (irrigated) 1992 T. Blake (blake@hordeum.oscs.montana.edu)<br> +11 Bozeman, Montana (dryland) 1992 T. Blake (blake@hordeum.oscs.montana.edu)<br> +12 Aberdeen, Idaho 1991 D. Wesenberg (fax: 208-397-4165)<br> +13 Klamath Falls, Oregon 1991 P. Hayes (hayesp@css.orst.edu)<br> +14 Pullman, Washington 1991 S. Ullrich (ullrich@wsu.edu)<br> +15 Bozeman, Montana (irrigated) 1991 T. Blake (blake@hordeum.oscs.montana.edu)<br> +16 Bozeman, Montana (dryland) 1991 T. Blake (blake@hordeum.oscs.montana.edu)</p> +<p><strong>Other data sets</strong><br> +ENSAT-INP: Ecole Nationale Supérieure Agronomique de Toulouse, Institut National Polytechnique (ENSAT-INP), France<br> +UM: University of Minnesota, USA<br> +JLU: Justus Liebig University, Germany<br> +UW: University of Wageningen, Netherlands<br> +SCRI: Scottish Crop Research Institute, UK<br> +WSU: Washington State University, USA</p> +<p><strong>α-amylase (NABGP) </strong><br> +(see description of the NABGP dataset)</p> +<p><strong>Diastatic power (NABGP) </strong><br> +(see description of the NABGP dataset)</p> +<p><strong>Disease resistance, bacterial streak, Xanthomonas campestris (ENSAT-INP)</strong><br> +El Attari H., Rebai A., Hayes P. M.; Barrault G.; Dechamp-Guillaume G.; Sarrafi A. Potential of doubled-haploid lines and localization of quantitative trait loci (QTL) for partial resistance to bacterial leaf streak (Xanthomonas campestris pv. hordei) in barley. Theoretical and Applied Genetics 1998, vol. 96, no1, pp. 95-100.</p> +<p>Two experiments were undertaken in a randomized complete block design with three replicates, in a controlled growth chamber. Twenty seeds per replicate were planted in plastic containers (60 x 40 x 8 cm) containing moistened vermiculite. At the two-leaf stage seedlings were inoculated with an Iranian strain of the pathogen.</p> +<p><strong>Disease resistance, head blight, Fusarium graminearum (UM) or FHB data set </strong><br> +Prom, L. K., B. J. Steffenson, B. Salas, T. G. Fetch Jr., and H. H. Casper. 1997. Barley accessions resistant to Fusarium head blight and the accumulation of deoxyvalenol. Cereal Res. Comm. 25:807-808.</p> +<p>Prom, L.K., Horsley, R.D., Steffenson, B.J., and Schwarz, P.B. 1999. Development of Fusarium head blight and accumulation of deoxynivalenol in barley sampled at different growth stages. J. Am. Soc. Brew. Chem. 57:60-63.</p> +<p>Steffenson, B. J. 2003. Fusarium head blight of barley: Impact, epidemics, management, and strategies for identifying and utilizing genetic resistance. Pages 241-295: In: K. J. Leonard and W.R. Bushnell, eds. 2003. Fusarium Head Blight of Wheat and Barley. APS Press. St. Paul. 512 pp.</p> +<p>Tacke, B. K., and H. H. Casper. 1996. Determination of deoxyvalenol in wheat, barley, and malt by column cleanup and gas chromatography with electron capture detection. J. Assoc. Off. Anal. Chem. 79:472-475.</p> +<p><strong>FHB and DON assays </strong><br> +Parents and DH progeny from the Steptoe/Morex were assessed for FHB severity (in %) and DON accumulation (in ppm) at three different environments in 1994 and 1995: Fargo, ND in both 1994 and 1995 and Langdon, ND in 1995. A randomized complete block design was used in the three environments and included a single replicate. Progeny and parents were planted in short rows (10-20 seeds) spaced 0.33 cm apart in two adjacent rows. Planting, maintenance of plots, and inoculation protocols were as described by (Prom et al. 1997). Disease assessments were made when the parents and DH progeny were at the mid-dough stage of development (growth stage 84-86) (Zadoks et al. 1974). The percent severity of FHB was determined by counting the number of infected kernels (those with greater than one-fourth of their surface area showing disease symptoms) and dividing that quantity by the total number of kernels in that spike multiplied by 100 (Prom et al. 1997). These assessments were made on 10-20 randomly selected spikes per plot as described by Prom et al. (1997). When the plants were mature, all spikes from each plot were harvested, dried, and threshed. DON assays were made using the method developed by Tacke and Casper (Tacke and Casper 1996). For this assay, a random six-gram sample of seed was used from each parent and DH line (Prom et al. 1999). </p> +<p><em>File names in the dataset:</em><br> +DON94F.TXT final<br> +amount of vomitoxin in samples vom ppm</p> +<p>DONP195F.TXT final<br> +DON levels in ppm planting date 1 (Fargo 1995)</p> +<p>DONP295F.TXT final<br> +DON levels in ppm planting date 2 (Fargo 1995)</p> +<p>DONP295L.TXT final<br> +DON levels in ppm planting date 2 (Langdon 1995)</p> +<p>DON94F.TXT final<br> +amount of vomitoxin vom ppm</p> +<p>FGINC04.94<br> +incidence of Fusarium graminearum isolated from seed in all severity classes.</p> +<p>FGINC14.94<br> +incidence of Fusarium graminearum isolated from seeds with a severity rating of 1, 2, 3, or 4.</p> +<p>FGINC24.94<br> +incidence of Fusarium graminearum isolated from seeds with a severity rating of 2, 3, or 4.</p> +<p>FGINC34.94<br> +incidence of Fusarium graminearum isolated from seeds with a severity rating of 3 or 4.</p> +<p>FHB1494F.TXT<br> +incidence of Fusarium head blight (visual rating) with a severity rating of 1, 2, 3, or 4.</p> +<p>FHB1494F.TXT final<br> +incidence of Fusarium head blight (visual rating) with a severity rating of 1, 2, 3, or 4.</p> +<p>FHB2494F.TXT<br> +no heading</p> +<p>FHB2494F.TXT final<br> +no heading</p> +<p>FHB3494F.TXT<br> +incidence of Fusarium head blight (visual rating) when severity categories 3 or 4 only are considered blighted.</p> +<p>FHB3494F.TXT final<br> +incidence of Fusarium head blight (visual rating) when severity categories 3 or 4 only are considered blighted.</p> +<p>FHBINC14.94<br> +incidence of Fusarium head blight (visual rating) with a severity rating of 1, 2, 3, or 4.</p> +<p>FHBINC34.94<br> +incidence of Fusarium head blight (visual rating) when severity categories 3 or 4 only are considered blighted.</p> +<p>FHBSE94F.TXT<br> +severity of Fusarium head blight </p> +<p>FHBSE94F.TXT final<br> +severity of Fusarium head blight </p> +<p>FHBSEV.94<br> +severity of Fusarium head blight </p> +<p>FPPLTT95.TXT final<br> +Fusarium Poae Isolations from seed 1995 (Fargo PD1, Fargo PD2, and Langdon PD2)</p> +<p>FSPD195F.TXT final<br> +Percentage of FHB infection in S/M lines from the first planting date at Fargo 1995</p> +<p>FSPD295F.TXT final<br> +Percentage of FHB infection in S/M lines from the second planting date at Fargo 1995</p> +<p>FSPD295L.TXT final<br> +Percentage of FHB infection in S/M lines from the second planting date at Langdon 1995</p> +<p>GRSTG94F.TXT<br> +developmental stages of the Steptoe/Morex population<br> +The first column is the SM line, <br> +the second is Zadok's Growth Stage, <br> +the third estimated days to mid-milk and<br> +the 4th days to heading (St. Paul).</p> +<p>GRSTG94F.TXT final<br> +developmental stages of the Steptoe/Morex population<br> +The first column is the SM line, <br> +the second is Zadok's Growth Stage, <br> +the third estimated days to mid-milk and<br> +the 4th days to heading (St. Paul).</p> +<p>GRTHSTGE.94<br> +developmental stages of the Steptoe/Morex population<br> +The first column is the SM line, <br> +the second is Zadok's Growth Stage, <br> +the third estimated days to mid-milk and the 4th days to heading (St. Paul).</p> +<p>GZP0494F.TXT<br> +incidence of Fusarium graminearum isolated from seed in all severity classes.</p> +<p>GZP0494F.TXT final<br> +incidence of Fusarium graminearum isolated from seed in all severity classes.</p> +<p>GZP1494F.TXT<br> +incidence of Fusarium graminearum isolated from seeds with a severity rating of 1, 2, 3, or 4.</p> +<p>GZP1494F.TXT final<br> +incidence of Fusarium graminearum isolated from seeds with a severity rating of 1, 2, 3, or 4.</p> +<p>GZP2494F.TXT<br> +incidence of Fusarium graminearum isolated from seeds with a severity rating of 2, 3, or 4.</p> +<p>GZP2494F.TXT final<br> +incidence of Fusarium graminearum isolated from seeds with a severity rating of 2, 3, or 4.<br> +ND94 </p> +<p>GZP3494F.TXT<br> +incidence of Fusarium graminearum isolated from seeds with a severity rating of 3 or 4.</p> +<p>GZP3494F.TXT final<br> +incidence of Fusarium graminearum isolated from seeds with a severity rating of 3 or 4.</p> +<p>GZPLT95.TXT final<br> +no heading</p> + +<p>HDPD295L.TXT final<br> +1995 LANGDON - number of days until heading (planted June 9)</p> +<p>SEVPD1F95.TXT<br> +Percentage of FHB infection in S/M lines from the first planting date at Fargo 1995</p> +<p>SEVPD2F95.TXT<br> +Percentage of FHB infection in S/M lines<br> +from the second planting date at Fargo 1995</p> +<p>SEVPD2L95.TXT<br> +Percentage of FHB infection in S/M lines from the second planting date at Langdon 1995</p> +<p>SMDNSITY.95 (Converted)<br> +head density ratings (field 1995)spikelets/cm </p> +<p>SMFHB1.95F<br> +1st planting date Fargo</p> +<p>SMFHB2.95F<br> +2nd planting date Fargo</p> +<p>SMFHB2.95L<br> +2nd planting date Langdon</p> +<p>SPDEN95F.TXT final<br> +spikelet density ratings (Fargo 1995) </p> +<p>SPDEN95L.TXT final<br> +spikelet density ratings (Langdon 1995) spikelets/cm </p> +<p>SPIKELET DENSITY FARGO 95<br> +spikelet density ratings (Fargo 1995) spikelets/cm</p> +<p>SPIKELET DENSITY LANGDON 95<br> +spikelet density ratings (Langdon 1995) spikelets/cm</p> +<p>SPKDENF95.TXT<br> +spikelet density ratings (Fargo 1995) spikelets/cm</p> +<p>SPKDENL95.TXT<br> +spikelet density ratings (Langdon 1995) spikelets/cm</p> +<p>VOMPPM.94<br> +No headings<br> +</p> +<p><strong>Disease resistance, leaf scald, <em>Rhynchosporium secalis</em> (JLU) </strong><br> +Schweizer GF, Herz M, Mikolajewski S, Brenner M, Hartl L, Baumer M (2004) Genetic mapping of a novel scald resistance gene Rrs15CI8288 in barley. 9th International Barley Genetics Symposium, Brno, Czech Republic, 20-26 June 2004. Proceedings:258-265).</p> +<p>Jackson LF, Webster RK (1976) Race differentiation, distribution and frequency of Rhynchosporium secalis in California. Phytopathology 66:719-725.</p> +<p>Schweizer G, Baumer M, Daniel G, Rugel H, Röder MS (1995) RFLP-markers linked to scald (Rhynchosporium secalis) resistance gene Rh2 in barley. Theor Appl Genet 90:920-924.</p> +<p><span class="style2">Disease resistance assay R. secalis </span><br> +<br> +General description<br> +Disease severity was assessed at seedling stage in a greenhouse chamber. Therefore, the plants were sown and grown at a temperature of 16-18°C in 9x9 cm plastic pots whereas each line was represented by four individuals. The plants were inoculated at the three-leaves stage, approximately 20 days after sowing. The parents as well as some differential genotypes (resistant: Atlas; susceptible: Alexis, Hendrix, Steffi) were included as internal controls. <br> +The single-spore isolate 271 (Straßmoos, Bavaria) of R. secalis, provided by Dr. Sachs, BBA Kleinmachnow, was grown for approximately 20 days on Lima bean agar (Difco, Detroit, USA) in Petri-dishes at 16°C in the dark. The spores were harvested after addition of water by gently rubbing of the mycel with a glass rod. The advanced spore suspension was decanted, filtrated and adjusted to 2-300.000 spores/ml. One inoculum preparation was used for the inoculation of all seedlings. by covering the inoculated plants with black plastic hoods for 48 hours high humidity and darkness were maintained to provide optimal infection conditions. 10-14 days after infection plants were assessed visually for scald symptoms on the lamina of the second leaf approximately according to the scale described by Jackson & Webster (1976). The third leaf was later consult to verify the infection. The final score of scald severity per DH line was achieved by averaging the scoring results of the four included plants.<br> +<br>Detailed description<br> +The Steptoe/Morex DH mapping population and reference cultivars were tested for reaction to Rhynchosporium secalis according to Schweizer et al. 1995 with some modifications. The single-spore isolate “271” (Straßmoos, LfL-Bavaria, Germany) of R. secalis, provided by Dr. Sachs was grown for approximately 20 days on 2.3% (w/v) Lima bean agar (Difco Laboratories) in Petri-dishes at 16°C in the dark. For inoculation a conidial suspension was prepared by rinsing the plates with water and filtering the mycel through gauze. The spore concentration was adjusted to 200.000 spores/ml-1. One inoculum preparation was used for all seedlings in a given experiment.<br> +Seedlings at the 2- to 3-leaf stage (3 weeks after sowing) were sprayed uniformly with inoculum (approximately 0.25 ml per plant) and left for 20 min to dry. Inoculated plants were then lightly sprayed with water and kept for 48h in a dark moist chamber at 18°C. DH lines (four independent plants/DH line) were assessed 10-14 days after inoculation visually for scald symptoms on the lamina of the second leaf (the third leaf was used as further control) according to the scale described by Jackson & Webster (1976). Differential genotypes ´Atlas´ (res) and ´Steffi´ (susc) and the parents Steptoe and Morex were used as reference cultivars. </p> +<p><strong>Disease resistance, net blotch, <em>Pyrenophora teres</em> (UM) </strong><br> +Steffenson, B.J., Hayes, P.M., and Kleinhofs, A. 1996. Genetics of seedling and adult plant resistance to net blotch (Pyrenophora teres f. teres) and spot blotch (Cochliobolus sativus) in barley. Theor. Appl. Genet. 92:552-558.</p> +<p>Burleigh JR, Loubane, M (1984) Plot size effects on disease progress and yield of wheat infected by Mycosphaerella graminicola and barley infected by Pyrenophora teres. Phytopathology 74:545--549 <br> +<br> +Fetch, T.G., Jr., and Steffenson, B.J. 1999. Rating scales for assessing infection responses of barley infected with Cochliobolus sativus. Plant Dis. 83:213-217.</p> +<p>James WC (1971) A manual of disease assessment keys for plant diseases. Can Dep Agric Publ 1458</p> +<p>Tekauz, A (1985) A numerical scale to classify reactions of barley to Pyrenophora teres. Can J Plant Pathol 7:181—183</p> +<p>Fetch, T. G., Jr., and Steffenson, B. J. 1999. Rating scales for assessing infection responses of<br> +barley infected with Cochliobolus sativus. Plant Dis. 83:213-217.</p> +<p><em>Seedling evaluations</em><br> +For seedling evaluations, four to six seeds of parents and DH lines were sown in plastic cones (3.8 cm diameter and 21 cm length) filled with a peat moss:perlite (3:1) potting mix and grown at 22-26C in a greenhouse. Fertilization was provided at planting with water soluble (15-0-15, N-P-K) and controlled release (14-14-14, N-P-K) formulations. When the second leaves of plants were fully expanded (14 days after planting), inoculations were made with conidial suspensions of the individual pathogens using an atomizer pressured by an air pump at 414 kPa. Inoculations with isolate ND89-19 of P. t. f. teres and ND85F of C. sativus were made using a concentration of 5,000 and 8,000 conidia/ml, respectively. The volume of the inoculum suspension applied to each plant was approximately 0.15 ml. To facilitate even distribution and adherence of conidia, 10 ul of Tween® 20 (polyoxyethylene-20-sorbitan monolaurate) was added for every 100 ml of the inoculum suspension. Plants were allowed to dry slightly after inoculation before being placed in chambers maintained near saturation by periodic mistings from ultrasonic humidifiers. After a 16 hour infection period in complete darkness, the plants were allowed to dry slowly for approximately four hours before being returned to the greenhouse. Assessments of the infection response (IR) were made 9--11 days post-inoculation using the rating scale of Tekauz (1985) for net blotch and Fetch and Steffenson (1999) for spot blotch. The experiment was conducted in a randomized complete block design with two replicates and was repeated twice.</p> +<p><em>Adult plant evaluations</em><br> +Parents and DH lines were also evaluated to the net and spot blotch pathogens in the field at Langdon and Fargo, North Dakota, respectively. The host entries were sown in hill plots (8--15 seeds/hill) spaced 0.3 m apart in paired rows. Susceptible barley genotypes (cultivar Hector for net blotch and line ND 5883 for spot blotch) were planted around the paired rows of hill plots to increase disease development in the nurseries. When most of the DH lines were at the mid-tillering stage of development, the susceptible spreader plants were inoculated with barley straw infected with either isolate ND89-19 of P. t. f. teres or ND85F of C. sativus. This infected barley straw was taken from the previous season's crop at the respective locations. Assessments of disease severity (percentage of leaf area affected by disease) were made at the mid-dough stage of development using standard disease area diagrams (Burleigh and Loubane [1984] for net blotch and James [1971] for spot blotch). The experimental design was a randomized complete block with three replications. Evaluations for net blotch reaction were made in 1991 only and for spot blotch both in 1991 and 1992. </p> +<p><strong>Disease resistance, leaf rust, <em>Puccinia hordei</em> (UW) </strong><br> +Marcel TC, Varshney RK, Barbieri M, Jafary H, de Kock MJ, Graner A, Niks RE: A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues. Theor.Appl.Genet. 2007, 114:487-500.</p> +<p><em>Disease evaluations at seedling plant stage</em><br> +The standard barley leaf rust isolate 1.2.1 (P. hordei Otth) was used to evaluate the level of partial resistance of the 150 DH lines of StMx at seedling stage in a greenhouse compartment. The disease experiments were conducted in six replications in time and within each replication one seedling of each DH line was inoculated. The seeds were sown in trays of 37 x 39 cm, each of them containing two rows of 10–15 seeds. In each tray one seed of each parental line, Steptoe and Morex and of the control lines, L94 and Vada, were sown. The inoculation was performed with about 200 spores per cm2. The latency period (LP) on each seedling was evaluated and the relative latency period (RLP50S) was calculated, relative to the LP on L94.</p> +<p><strong>Disease resistance, spot blotch, <em>Cochliobolus sativus</em> (UM)</strong><br> +See the net blotch description</p> +<p><strong>Disease resistance, stem rust, <em>Puccinia graminis</em> (UM)</strong><br> +Stakman EC, Stewart DM, Loegering WQ (1962) Identification of physiologic races of Puccinia graminis var. tritici. USDA Agricultural Research Service Bulletin 617.</p> +<p>Miller JD, J.W.Lambert (1965) Variability and inheritance of reaction of barley to race<br> +32 l5B of stem rust. Aqron J 47:373-377.</p> +<p>Druka, A., Potokina, E., Luo, Z., Bonar, N., Druka, I., Zhang, L., Marshall, D.F., Steffenson, B.J., Close, T.J., Wise, R.P., Kleinhofs, A., Williams, R.W., Kearsey, M.J. and Waugh, R. 2008. Exploiting regulatory variation to identify genes underlying quantitative resistance to the wheat stem rust pathogen Puccinia graminis f. sp. tritici in barley. Theoretical and Applied Genetics. 117(2):261-72</p> +<p><em>Stem rust infection phenotyping</em><br> +Each of the St/Mx DH lines was challenged with the stem rust fungus race Pgt-MCC in 5 replications over 2 years (1990 and 1991). Phenotypic scores were made 12 to 14 days after inoculation according to the infection type (IT) scale of Stakman et al. (1962) as modified by Miller and Lambert (Miller and Lambert 1965). Under the Stakman system, IT 0 indicates no visible infection; only a necrotic “fleck” (i.e. hypersensitive response) with no sporulation; IT 1 designates a minute uredinium (i.e. sporulating pustule) surrounded by necrosis; IT 2 designates a small uredinium often surrounded by chlorosis; IT 3 designates a moderate sized uredinium sometimes surrounded by chlorosis; and IT 4 designates a large uredinium. Since barley exhibits chlorosis in association with most ITs (excluding IT 0, and IT 1), Miller and Lambert modified the Stakman system and classified ITs 2, 3, and 4 on the basis of uredinium size alone. Barley often exhibits a mixture of different ITs on a single plant—the “mesothetic” reaction described by Stakman et al (1962). ITs on the St/Mx DH lines were recorded according to prevalence. In most cases, the one or two most common ITs comprised over 75% of the total observed and were used to assign the general binary classes of resistant and susceptible. ITs 0, 1 and 2 were<br> +3 considered indicative of host resistance (i.e. a low infection type), whereas IT 3 and 4<br> +4 were indicative of host susceptibility (a high infection type). The classic “diamond<br> +5 shaped” uredinium of IT 4 was not observed on plants in the St/Mx population.<br> +</p> +<p><strong>Emergence of the second leaf (SCRI) </strong><br> +Seeds of all 150 recombinant lines from the Steptoe x Morex DH population and the parents, Steptoe and Morex were planted in the 24 x 30 cm pots filled with the ‘Cereal Mix’ and placed on the automatically irrigated glasshouse benches (cubicle AO59). Three sterilized seeds per line were sown in each of four replicate pots. Placement of the pots was randomized across the glasshouse space. Temperature in the cubicle was set at 20° with 16-hr light/15° 8-hr dark periods. Intensity of the supplementary light was 400 µE m–1 sec–1. </p> +<p><strong>Single leaf frequency </strong><br> +After 20 days, seedlings were counted based on number of emerged visible leaves (either single or two). Frequency of the single leaf across all four replicates within the recombinant line was used for QTL mapping.</p> +<p><em>Ratio</em><br> +The lengths of the leaf blades were measured for the seedlings that have two visible leaves. Ratio of the length of both blades was used for QTL mapping.</p> +<p><strong>Endosperm modification (SCRI) </strong><br> +Jorgensen (1988) Carlsberg Res. Commun. 53:277</p> +<p>ImageJ is a public domain Java image processing program. <br> +Rasband, W.S., ImageJ, U. S. National Institutes of Health, Bethesda, Maryland, USA, http://rsb.info.nih.gov/ij/, 1997-2008.</p> +<p>Abramoff, M.D., Magelhaes, P.J., Ram, S.J. "Image Processing with ImageJ". Biophotonics International, volume 11, issue 7, pp. 36-42, 2004.</p> +<p>Druka, A., Muehlbauer, G., Druka, I., Caldo, R., Baumann, U., Rostoks, N., Schreiber, A., Wise, R., Close, T., Kleinhofs, A., Graner, A., Schulman, A., Langridge, P., Sato, K., Hayes, P., McNicol, J., Marshall, D., Waugh, R. 2006. An atlas of gene expression from seed to seed through barley development. Functional Integrative Genomics 6, 202-211.</p> +<p>Plant material was generated essentially as described previously (Druka et al 2006) but with some modifications specific to these studies. To obtain embryo-derived tissue from the germinating grain, 30–50 sterilized seeds per line of the trial set were germinated on a petri plate between three layers of wet 3-mm filter paper in the dark, for 16 hr at 17° and 8 hr at 12°, for 96 hr total. 6-10 similarly looking or ‘average’ seeds were cut in half longitudally, and stained with calcuflor. </p> +<p><em>Calcufluor staining</em><br> +1) 30 sec - 1min 0.1% calcufluor (H2O);<br> +2) 10 sec 70% EtOH;<br> +3) Dry shortly;<br> +4) 30-60 sec 0.1% fast green H2O;<br> +5) blot off residual stain, put under the UV microscope at 400 nm to take photographs.<br> +Photographs were taken by using Leica DM IL Inverted contrasting microscope Leica Microsystems. Image analysis was by using ImageJ software.</p> +<p><strong>Fermentability (SCRI) </strong><br> +Fermentability is the proportion of fermentable material in a malt extract. It is measured using a standard yeast strain following 48 hrs fermentation according to the IoB Recommended Methods for Analysis (1992) buut modified for small aliquots as described by Swanson & Thomas (1996)</p> +<p><strong>Fermentable malt extract (SCRI) </strong><br> +Fermentable malt extract is the total amount of fermentable material in a sample of barley grain and is the product of hot water extract and ferementability</p> +<p><strong>Flecking of leaves (SCRI) </strong><br> +Leaf flecking is a visual score of the degree of flag and flag leaf-1 coverage by dark brown leasions that are not attributable to known foliar pathogens or pests. It is scored on a 1-8 scale with 1 = 0 and 9=100% coverage</p> +<p><strong>Germination (WSU) </strong><br> +See Dormancy and Pre-harvest sprouting </p> +<p><strong>Grain length F0-F9 (SCRI) </strong><br> +Number of seeds from a sample of approx 100 cleaned grain that have passed over a 2.5mm sieve and are between 2.5 and 3 mm in width as determined by MARVIN 4.0 analysis of a digital image (www.gta-sensorik.com)</p> +<p><strong>Grain length, average (SCRI) </strong><br> +Grain length is the average length of a sample of approx 100 cleaned sseds that have passed over a 2.5mm sieve. Seed length is determined by analysis of digital images using the Marvin 4.0 system (www.gta-sensorik.com).</p> +<p><strong>Grain nitrogen (SCRI) </strong><br> +Grain nitrogen is the estimated % nitrogen content of a sample of cleaned grain that has passed over a 2.5mm sieve. It was measured by a FOSS 1251 Near Infra Red Transmittance grain analyser (www.foss.dk)</p> +<p><strong>Grain protein (NABGP) </strong><br> +(see description of the NABGP dataset).</p> +<p><strong>Grain shape (width/length) (SCRI) </strong><br> +Grain shape is the average grain width divided by the average grain length.</p> +<p><strong>Grain surface area (SCRI) </strong><br> +Grain surface area is the average area 2D area of a sample of approx 100 leaned barley grain that have passed over a 2.5mm sieve. Surface area is determined by analysis of digital images using the Marvin 4.0 system (www.gta-sensorik.com).</p> +<p><strong>Grain width (average) (SCRI) </strong><br> +Grain width is the average width of a sample of approx 100 cleaned seeds that have passed over a 2.5mm sieve. Seed width is determined by analysis of digital images using the Marvin 4.0 system (www.gta-sensorik.com).</p> +<p><strong>Grain width F0-F9 (SCRI) </strong><br> +Number of seeds from a sample of approx 100 cleaned grain that have passed over a 2.5mm sieve and are between 2.5 and 3 mm in width as determined by MARVIN 4.0 analysis of a digital image (www.gta-sensorik.com).</p> +<p><strong>Head length (SCRI) </strong><br> +Length (cm) of ear from collar to base of awn of last spikelet measured on a random sample from a field grown barley plot.</p> +<p><strong>Heading date - glasshouse (SCRI) </strong><br> +Seeds of all 150 recombinant lines from the Steptoe x Morex DH population and the parents, Steptoe and Morex were planted in the 24 x 30 cm pots filled with the ‘Cereal Mix’ and placed on the automatically irrigated glasshouse benches (cubicle AO59). Three sterilized seeds per line were sown in each of four replicate pots. Placement of the pots was randomized across the glasshouse space. Temperature in the cubicle was set at 20° with 16-hr light/15° 8-hr dark periods. Intensity of the supplementary light was 400 µE m–1 sec–1. </p> +<p>Heading date was measured as number of days to anthesis. Anthesis was determined by observing the colour and the response of anthers to the mechanical disturbance. Anthers should be yellow and a slight mechanical disturbance should cause shedding of the pollen meaning that anthesis is about to happen.</p> +<p><strong>Heading date (NABGP) </strong><br> +(see description of the NABGP dataset)</p> +<p><strong>Heading date (SCRI) </strong><br> +Days after May31st on which 50% of the plot first reached DGS53</p> +<p><strong>Heading date (UM) </strong><br> +Steffenson, B. J. 2003. Fusarium head blight of barley: Impact, epidemics, management, and strategies for identifying and utilizing genetic resistance. Pages 241-295: In: K. J. Leonard and W.R. Bushnell, eds. 2003. Fusarium Head Blight of Wheat and Barley. APS Press. St. Paul. 512 pp.</p> +<p>Zadoks, J. C., T. T. Chang, and C. F. Konzak. 1974. A decimal code for the growth stages of cereals. Weed. Res. 14:415-421.</p> +<p><em>Morphological and agronomic trait assessment</em><br> +Various morphological (especially spike characters) and agronomic traits may affect the development of FHB on lines in the field (Steffenson 2003). To determine the possible contribution of such factors on FHB severity, assessments were made on heading date, plant height, spike, and the number of nodes per cm of rachis in the spike (kernel density). Heading date was defined as the number of days from planting to when 50% of the plants in a plot had emerged spikes. Plant height was the number of cm from the ground to the tip of the spike, excluding the awns. Spike angle was rated at maturity on a scale of 1 to 3 where spikes bending less than 45 degrees from vertical were scored as 1; those bending from 45-120 degrees from vertical were scored as 2, and those bending greater than 120 degrees from vertical were scored as 3. The number of nodes per cm of rachis was measured on four randomly selected spikes for each parent and DH line. </p> +<p><strong>Hot water extract (SCRI) </strong><br> +Amount of material extracted by hot water from a clean 25g sample of barley grain that has passed over a 2.5mm sieve following micro-malting under standard conditions of steeping and air rests. Hot water extract is measured by refractometry and expressed as Lintner degrees per kg. NB, this is equivalent to malt extract but the micro-malting protocol will be different.</p> +<p><strong>Lodging (NABGP) </strong><br> +(see description of the NABGP dataset)</p> +<p><strong>Lodging (SCRI) </strong><br> +Lodging is the proportion of the plot that is less than 45 degrees from horizontal. It is measured on a 1-9 scale with 1=0 and 9=100%.</p> +<p><strong>Malt extract (NABGP) </strong><br> +(see description of the NABGP dataset)</p> +<p><strong>Malt extract (SCRI) </strong><br> +See HWE</p> +<p><strong>Maturity (SCRI) </strong><br> +Maturity is a visual estimate of the relative physiological maturity of a plot with 1=early and 9=late.</p> +<p><strong>Milling energy (SCRI) </strong><br> +Milling energy is the amount of energy required to mill a weighed sample of clean grain that has passed over a 2.5mm sieve. It is expressed as Joules per 5g grain ane measured using the Comparamill.</p> +<p><strong>Moisture content in the grain (SCRI) </strong><br> +Estimate of moisture in sample by NIT after drying and storage!</p> +<p><strong>Necrotic spotting doughy stage (SCRI) </strong><br> +Spotting at the doughy stage is a visual score of the degree of flag and flag leaf-1 coverage by dark brown lesions that are considered to be due to infection by Ramularia collo-cygni. It is scored on a 1-9 scale with 1 = 0 and 9=100% covereage</p> +<p><strong>Normalised difference vegetation index (SCRI) </strong><br> +NDVI is ((ref660nm-ref770nm)/(ref660nm+ref770nm)) as measured by the Greenseeker (www.ntechindustries.com) at GS61</p> +<p><strong>Normalised difference vegetation index @GS43 (SCRI) </strong><br> +NDVI is ((ref660nm-ref770nm)/(ref660nm+ref770nm)) as measured by the Greenseeker (www.ntechindustries.com) at GS43</p> +<p><strong>Plant height (NABGP) </strong><br> +(see description of the NABGP dataset)</p> +<p><strong>Plant height (SCRI) </strong><br> +Height is the height(cm) of a plot from the ground to the collar at GS71+</p> +<p><strong>Dormancy and pre-harvest sprouting (WSU)</strong><br> +AOSA (1988) Association of Official Seed Analysis rules for testing seeds. J Seed Technol 12 (3).<br> +Ullrich, S.E., J.A. Clancy, I.A. del Blanco, H. Lee, V.A. Jitkov, F. Han, A. Kleinhofs, and K. Matsui. 2007. Genetic analysis of preharvest sprouting in a six-row barley cross. Molecular Breeding. Submitted.</p> +<p>Hayes, P. M., B. H. Liu, S. J. Knapp, F. Chen, B. Jones, T. Blake, J. Franckowiak, D Rasmusson, M. Sorrells, S. E. Ullrich, D. Wesenberg and A. Kleinhofs. 1993. Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor. Appl. Genet. 87: 392-401.</p> +<p>Han, F., and S.E. Ullrich. 1994. Mapping of quantitative trait loci for malting quality traits in barley. Barley Genetics Newsletter 23:84-97.</p> +<p>Ullrich, S. E., P. M. Hayes, W. E. Dyer, T. K. Blake, and J. A. Clancy. 1993. Quantitative trait locus analysis of seed dormancy in "Steptoe" barley. p. 136-145. In: M. K. Walker-Simmons and J. L. Reid (eds.) Preharvest sprouting in cereals 1992. Amer.Assoc. Cereal Chemist, St. Paul.</p> +<p>Oberthur, L., T.K. Blake, W.E. Dyer, and S.E. Ullrich. 1995. Genetic analysis of seed dormancy in barley (Hordeum vulgare L.). J. Quant. Trait Loci (on line), available: http://probe.nalusda.gov. 8000/other docs/jqtl/jqtl 1995-05/ dormancy.html.</p> +<p>Han, F., S.E. Ullrich, S. Chirat, S. Menteur, L. Jestin, A. Sarrafi, P.M. Hayes, B.L. Jones, T.K. Blake, D.M. Wesenberg, A. Kleinhofs, and A. Kilian. 1995. Mapping of b-glucan content and b-glucanase activity loci in barley grain and malt. Theor. Appl. Genet. 91:921-927.</p> +<p>Clancy, J.A., F. Han, and S.E. Ullrich. 2003. Comparative mapping of b-amylase activity QTLs among three barley crosses. Crop Sci.43:1043-1052.</p> +<p>Ullrich, S.E., J.A. Clancy, I.A. del Blanco, H. Lee, V.A. Jitkov, F. Han, A. Kleinhofs, and K. Matsui. 2007. Genetic analysis of preharvest sprouting in a six-row barley cross. Molecular Breeding. Submitted.<br> +</p> +<p><em>Dormancy as measured by germination tests</em><br> +Dormancy defined as the failure of viable mature seed to germinate under favorable conditions was measured indirectly by measuring germination percentage, as there is no known direct test for dormancy. Two different after-ripening periods (0 and 14 days) were included in the study to measure the state of and change in dormancy over time. Genetic sub-traits for dormancy based on physiological activity/state could include the development of dormancy as seeds mature, the state of dormancy at maturity, and the dissipation of dormancy with time following maturity. The latter two situations were considered in this study. Germination percentage has also been used to measure susceptibility/resistance to preharvest sprouting (PHS) as well, but it is also a very indirect measure, which assumes that dormancy is the opposite of PHS, which may or may not be entirely true.</p> +<p>Seeds were harvested at physiological maturity (as determined when green color was lost from the spike). Heads were collected and stored in a -20°C freezer prior to germination tests of the seeds to arrest physiological activity. Germination tests were carried out after two different post-harvest after-ripening periods at room temperature; 0 d and 14 d for materials grown in field and glasshouse environments. For each after-ripening period, two replications of 100 seeds were germinated at 20°C on moist filter paper in a petri dish. Standard germination tests were performed (AOSA 1988). After 7 d the number of germinated seeds were counted and expressed as a percentage of the total.</p> +<p>Pre-harvest Sprouting (PHS) experiment in the greenhouse.<br> +Trait scores:<br> +0 = no visible roots<br> +1 = roots <or = 3/ no shoots<br> +2 = roots < or = 5/ shoots < or = 3<br> +3 = roots < or = 8/ shoots < or = 5<br> +4 = roots and shoots over 25% but < 50% of head<br> +5 roots and shoots over 50% of head</p> +<p><strong>Predicted spirit yield (SCRI) </strong><br> +PSY is fermentable extract multiplied vy a constant to give the yield of spirit(l) per tonne of malt (Dolan, 1982).</p> +<p><strong>Soluble nitrogen content of wort (SCRI) </strong><br> +Soluble nitrogen content is the amount of nirogen that has been solubilised in a hot water extract follwing micro-malting under standard conditions (see Hot Water Extract, HWE). It is measure by UV spectrophotometry (Haselmore & Gill, 1995).</p> +<p><strong>Spike density (UM)</strong><br> +Steffenson, B. J. 2003. Fusarium head blight of barley: Impact, epidemics, management, and strategies for identifying and utilizing genetic resistance. Pages 241-295: In: K. J. Leonard and W.R. Bushnell, eds. 2003. Fusarium Head Blight of Wheat and Barley. APS Press. St. Paul. 512 pp.</p> +<p>Zadoks, J. C., T. T. Chang, and C. F. Konzak. 1974. A decimal code for the growth stages of cereals. Weed. Res. 14:415-421.</p> +<p><em>Morphological and agronomic trait assessment</em><br> +Various morphological (especially spike characters) and agronomic traits may affect the development of Fusarium Head Blight (FHB) on lines in the field (Steffenson 2003). To determine the possible contribution of such factors on FHB severity, assessments were made on heading date, plant height, spike, and the number of nodes per cm of rachis in the spike (kernel density). Heading date was defined as the number of days from planting to when 50% of the plants in a plot had emerged spikes. Plant height was the number of cm from the ground to the tip of the spike, excluding the awns. Spike angle was rated at maturity on a scale of 1 to 3 where spikes bending less than 45 degrees from vertical were scored as 1; those bending from 45-120 degrees from vertical were scored as 2, and those bending greater than 120 degrees from vertical were scored as 3. The number of nodes per cm of rachis was measured on four randomly selected spikes for each parent and DH line. </p> +<p><strong>Thousand grain weight (SCRI) </strong><br> +Thousand grain weight is measured by counting and weighing a clean sample of grain that has passed over a 2.5 mm sieve using MARVIN 4.0 (www.gta-sensorik.com)</p> +<p><strong>Vegetation index (SCRI) </strong><br> +This is Infra Red Vegetation Index, IRVI (ref660nm/ref770nm) as measured by the Greenseeker (www.ntechindustries.com) at GS61.</p> +<p><strong>Vegetation index @ GS43 (SCRI) </strong><br> +This is Infra Red Vegetation Index, IRVI (ref660nm/ref770nm) as measured by the Greenseeker (www.ntechindustries.com) at GS43.</p> +<p><strong>Yield (MT/ha) (NABGP)</strong><br> +(see description of the NABGP dataset).<br> +</p> +<p> </p> +<p> </p> +</Blockquote> + + +<P class="subtitle"> About this file:</P> +<Blockquote> +<P> The file started, Dec 9, 2006 by AD. 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