Überprüfung der Einsatzmöglichkeiten des mechanischen Schnitts in der ökologischen Apfelproduktion-Insbesondere im Hinblick auf die Schaderreger- und Schädlingspopulationen

In den vergangenen Jahren wurden im konventionellen Obstanbau vermehrt Versuche zum mechanischen Schnitt an Apfelbäumen durchgeführt. Durch den mechanischen Schnitt können Arbeitszeit und die damit verbundenen Lohnkosten eingespart werden. In ökologisch bewirtschafteten Apfelanlagen wurde der mechanische Schnitt jedoch bisher kaum angewendet, so dass keine Erfahrungen im Hinblick auf das Wuchs- und Ertragsverhalten bzw. Schädlingsaufkommen sowie Fruchtqualität vorliegen. Ein Hauptgrund für die zurzeit zögerliche Herangehensweise an dieses neue Verfahren im ökologischen Anbau ist trotz enormer Zeit- und Kostenersparnis, die zu erwartenden unerwünschten Nebenwirkungen auf die Schädlingspopulation, insbesondere der Blutlaus (Eriosoma lanigerum). Eine durch mechanischen Schnitt entstandene Fruchtwand bietet außerdem Vorteile für weitere Mechanisierungsmaßnahmen, wie z. B. die mechanische Ausdünnung mit dem Darwin-Fadengerät. Daher wurden in dem vorliegenden Projekt die Auswirkungen des mechanischen Schnitts und der mechanischen Ausdünnung in ökologisch bewirtschafteten Anlagen ermittelt. Am Versuchsstandort DLR Rheinpfalz, Standort KoGa Klein-Altendorf und in Praxisanlagen im Raum Grafschaft wurden Freilandversuche an den Sorten ’Jonagold’ (Öko- Versuchsparzelle DLR Rheinpfalz), ’Elstar’, ’Topaz’, ’Gala’, ’Pinova’ und ‘Natyra‘ (Praxisbetrieb) durchgeführt. In allen aufgeführten Sorten wurden die gleichen sechs Versuchsvarianten in Exaktversuchen mit vier Wiederholungen geprüft: 1. Praxisüblicher Handschnitt (Winter) 2. Praxisüblicher Handschnitt (Winter) + Darwin Fadengerät 3. Mechanischer Schnitt Edward Mähbalken (Grüne bis Rote Knospe) 4. Mechanischer Schnitt Edward Mähbalken + Darwin Fadengerät 5. Mechanischer Schnitt ERO Kreissägeblatt (Grüne bis Rote Knospe) 6. Mechanischer Schnitt ERO Kreissägeblatt + Darwin Fadengerät Zur Ermittlung des Ertragsverhaltens, der Fruchtqualität, des Schädlingsaufkommens sowie der Wirkung des Darwin Fadengerätes wurden jährlich die Anzahl der Blütenbüschel, die Schnittzeit, der Fruchtansatz, der Ertrag zur Ernte sowie der Anteil vermarktungsfähiger Fruchtgrößen, und das Aufkommen von Schaderregern und Schädlingen ermittelt. Generell konnte in keinem Versuchsjahr ein höherer Schädlings- und Krankheitsdruck in den mechanisch geschnittenen Varianten festgestellt werden; auch gab es keine Unterschiede zwischen Mähbalken und Kreissägeblatt. Allein die Sorte ‘Jonagold‘ wies einen Befall mit Blutlaus auf, welcher jedoch aus einem Befall vor Versuchsbeginn stammte. Durch den mechanischen Schnitt wurde dieser Befall nicht verstärkt. Bei allen untersuchten Sorten konnte die benötigte Handschnittzeit durch den mechanischen Schnitt deutlich bis zu fast 60 % reduziert werden. Eine zusätzliche mechanische Ausdünnung mittels Darwin Fadengerät kann zusätzlich die Zeit für die Handausdünnung reduzieren und einer Alternanz der Bäume entgegenwirken. Beim Ertrag konnten keine signifikanten Unterschiede zwischen Hand- und mechanischem Schnitt ermittelt werden

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Sex differences in oncogenic mutational processes

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Peer reviewe

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts