Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in Lolium perenne

<p>Abstract</p> <p>Background</p> <p>Association analysis is an alternative way for QTL mapping in ryegrass. So far, knowledge on nucleotide diversity and linkage disequilibrium in ryegrass is lacking, which is essential for the efficiency of association analyses.</p> <p>Results</p> <p>11 expressed disease resistance candidate (R) genes including 6 nucleotide binding site and leucine rich repeat (NBS-LRR) like genes and 5 non-NBS-LRR genes were analyzed for nucleotide diversity. For each of the genes about 1 kb genomic fragments were isolated from 20 heterozygous genotypes in ryegrass. The number of haplotypes per gene ranged from 9 to 27. On average, one single nucleotide polymorphism (SNP) was present per 33 bp between two randomly sampled sequences for the 11 genes. NBS-LRR like gene fragments showed a high degree of nucleotide diversity, with one SNP every 22 bp between two randomly sampled sequences. NBS-LRR like gene fragments showed very high non-synonymous mutation rates, leading to altered amino acid sequences. Particularly LRR regions showed very high diversity with on average one SNP every 10 bp between two sequences. In contrast, non-NBS LRR resistance candidate genes showed a lower degree of nucleotide diversity, with one SNP every 112 bp. 78% of haplotypes occurred at low frequency (<5%) within the collection of 20 genotypes. Low intragenic LD was detected for most R genes, and rapid LD decay within 500 bp was detected.</p> <p>Conclusion</p> <p>Substantial LD decay was found within a distance of 500 bp for most resistance candidate genes in this study. Hence, LD based association analysis is feasible and promising for QTL fine mapping of resistance traits in ryegrass.</p

Polymorphisms in O-methyltransferase genes are associated with stover cell wall digestibility in European maize (Zea mays L.)

<p>Abstract</p> <p>Background</p> <p>OMT (O-methyltransferase) genes are involved in lignin biosynthesis, which relates to stover cell wall digestibility. Reduced lignin content is an important determinant of both forage quality and ethanol conversion efficiency of maize stover.</p> <p>Results</p> <p>Variation in genomic sequences coding for <it>COMT, CCoAOMT1</it>, and <it>CCoAOMT2 </it>was analyzed in relation to stover cell wall digestibility for a panel of 40 European forage maize inbred lines, and re-analyzed for a panel of 34 lines from a published French study. Different methodologies for association analysis were performed and compared. Across association methodologies, a total number of 25, 12, 1, 6 <it>COMT </it>polymorphic sites were significantly associated with DNDF, OMD, NDF, and WSC, respectively. Association analysis for <it>CCoAOMT1 </it>and <it>CCoAOMT2 </it>identified substantially fewer polymorphic sites (3 and 2, respectively) associated with the investigated traits. Our re-analysis on the 34 lines from a published French dataset identified 14 polymorphic sites significantly associated with cell wall digestibility, two of them were consistent with our study. Promising polymorphisms putatively causally associated with variability of cell wall digestibility were inferred from the total number of significantly associated SNPs/Indels.</p> <p>Conclusions</p> <p>Several polymorphic sites for three O-methyltransferase loci were associated with stover cell wall digestibility. All three tested genes seem to be involved in controlling DNDF, in particular <it>COMT</it>. Thus, considerable variation among <it>Bm3 </it>wildtype alleles can be exploited for improving cell-wall digestibility. Target sites for functional markers were identified enabling development of efficient marker-based selection strategies.</p

Plots of squared correlations of allele frequencies (r) against distance between pairs of polymorphic sites in three genes: a) EST28, b) EST13, and c) EST1

<p><b>Copyright information:</b></p><p>Taken from "Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in "</p><p>http://www.biomedcentral.com/1471-2229/7/43</p><p>BMC Plant Biology 2007;7():43-43.</p><p>Published online 4 Aug 2007</p><p>PMCID:PMC1978496.</p><p></p> Curves show nonlinear regression of ron weighted distance

Surgical hand antisepsis with alcohol-based hand rub : comparison of effectiveness after 1.5 and 3 minutes of application

OBJECTIVE: Research has shown 1.5 minutes of surgical hand antisepsis with alcohol-based hand rub to be at least as effective under experimental conditions as the 3-minute reference disinfection recommended by European Norm 12791. The aim of the present study was to validate the effectiveness of 1.5 minutes of surgical hand antisepsis in a clinical setting by comparing the effectiveness of 1.5- and 3-minute applications of alcohol-based hand rub (45% vol/vol 2-propanol, 30% vol/vol 1-propanol, and 0.2% mecetronium ethylsulphate). DESIGN: Prospective crossover trial in which each surgeon served as his or her own control, with individual randomization to the 1.5- or the 3-minute group during the first part of the trial. SETTING: Basel University Hospital, Switzerland. PARTICIPANTS: Thirty-two surgeons with different levels of postdoctoral training. METHODS: We measured the bactericidal effectiveness of 1.5 minutes and 3 minutes of surgical hand antisepsis with alcohol-based hand rub by assessing the mean (+/-SD) log10 number of colony-forming units before the application of hand rub (baseline), after the application of hand rub (immediate effect), and after surgery (sustained effect) so as to follow European Norm 12791 as closely as possible. RESULTS: The immediate mean (+/-SD) log10 reduction in colony-forming units (cfu) was 2.26 +/- 1.13 log10 cfu for the 1.5-minute group and 3.01 +/- 1.06 log10 cfu for the 3-minute group (P = .204). Similarly, there was no statistically significant difference between the 2 groups with respect to the sustained effect; the mean (+/-SD) log10 increase in bacterial density during surgery was 1.08 +/- 1.13 log10 cfu for the 1.5-minute group and 0.95 +/- 1.27 log10 cfu for the 3-minute group (P = .708). No adverse effects were recorded. CONCLUSION: In this clinical trial, surgical hand antisepsis with alcohol-based hand rub resulted in a similar bacterial reduction, regardless of whether it was applied for 3 or 1.5 minutes, which confirms experimental data generated with healthy volunteers

Polymorphisms in O-methyltransferase genes are associated with stover cell wall digestibility in European maize (Zea maysL.)

Background OMT (O-methyltransferase) genes are involved in lignin biosynthesis, which relates to stover cell wall digestibility. Reduced lignin content is an important determinant of both forage quality and ethanol conversion efficiency of maize stover. Results Variation in genomic sequences coding for COMT, CCoAOMT1, and CCoAOMT2 was analyzed in relation to stover cell wall digestibility for a panel of 40 European forage maize inbred lines, and re-analyzed for a panel of 34 lines from a published French study. Different methodologies for association analysis were performed and compared. Across association methodologies, a total number of 25, 12, 1, 6 COMT polymorphic sites were significantly associated with DNDF, OMD, NDF, and WSC, respectively. Association analysis for CCoAOMT1 and CCoAOMT2 identified substantially fewer polymorphic sites (3 and 2, respectively) associated with the investigated traits. Our re-analysis on the 34 lines from a published French dataset identified 14 polymorphic sites significantly associated with cell wall digestibility, two of them were consistent with our study. Promising polymorphisms putatively causally associated with variability of cell wall digestibility were inferred from the total number of significantly associated SNPs/Indels. Conclusions Several polymorphic sites for three O-methyltransferase loci were associated with stover cell wall digestibility. All three tested genes seem to be involved in controlling DNDF, in particular COMT. Thus, considerable variation among Bm3 wildtype alleles can be exploited for improving cell-wall digestibility. Target sites for functional markers were identified enabling development of efficient marker-based selection strategies.This article is published as Brenner, Everton A., Imad Zein, Yongsheng Chen, Jeppe R. Andersen, Gerhard Wenzel, Milena Ouzunova, Joachim Eder et al. "Polymorphisms in O-methyltransferase genes are associated with stover cell wall digestibility in European maize (Zea mays L.)." BMC plant biology 10, no. 1 (2010): 27. doi: 10.1186/1471-2229-10-27. Posted with permission.</p