Arqus Openness Position Paper

The Openness Position Paper published by the Arqus European University Alliance emphasises that Arqus institutions, in line with the policies, roadmaps and strategies of the EU and a wide range of stakeholders, are striving jointly to make further progress towards realising Open Science. The Position Paper identifies and acknowledges aims and values of Open Science and relates them to values, principles, and standards shared by the Arqus Alliance, followed by a vision for a future with Open Science. In the interest of a nuanced picture, the Position Paper discusses not only desired effects, but also possible areas of tension related to Open Science. It presents a wide range of specific aims and recommendations for each of the eleven elements of Open Science defined by the Arqus Openness Task Force: Governance Publications (including Open Access) Data (including research data management, FAIR and Open Data) Infrastructures (including support staff, Open Science software and tools, repositories, Open Labs) Methods (including source code, preregistration, materials, workflows, protocols, lab notes) Awareness and training (including education of early-stage researchers) Evaluation (including Open Metrics, research assessment, Open Peer Review, rewards and incentives) Communication (including multilingualism) Citizen Science Open Education Open Innovation The Position Paper concludes with an annex that highlights the progress already made in the implementation and support of Open Science practices at Arqus institutions.Cofunded by the Erasmus+Programme of the European Unio

A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome

SNP genotyping arrays have been useful for many applications that require a large number of molecular markers such as high-density genetic mapping, genome-wide association studies (GWAS), and genomic selection. We report the establishment of a large maize SNP array and its use for diversity analysis and high density linkage mapping. The markers, taken from more than 800,000 SNPs, were selected to be preferentially located in genes and evenly distributed across the genome. The array was tested with a set of maize germplasm including North American and European inbred lines, parent/F1 combinations, and distantly related teosinte material. A total of 49,585 markers, including 33,417 within 17,520 different genes and 16,168 outside genes, were of good quality for genotyping, with an average failure rate of 4% and rates up to 8% in specific germplasm. To demonstrate this array's use in genetic mapping and for the independent validation of the B73 sequence assembly, two intermated maize recombinant inbred line populations – IBM (B73×Mo17) and LHRF (F2×F252) – were genotyped to establish two high density linkage maps with 20,913 and 14,524 markers respectively. 172 mapped markers were absent in the current B73 assembly and their placement can be used for future improvements of the B73 reference sequence. Colinearity of the genetic and physical maps was mostly conserved with some exceptions that suggest errors in the B73 assembly. Five major regions containing non-colinearities were identified on chromosomes 2, 3, 6, 7 and 9, and are supported by both independent genetic maps. Four additional non-colinear regions were found on the LHRF map only; they may be due to a lower density of IBM markers in those regions or to true structural rearrangements between lines. Given the array's high quality, it will be a valuable resource for maize genetics and many aspects of maize breeding

Arqus Openness Position Paper

The Openness Position Paper published by the Arqus European University Alliance emphasises that Arqus institutions, in line with the policies, roadmaps and strategies of the EU and a wide range of stakeholders, are striving jointly to make further progress towards realising Open Science. The Position Paper identifies and acknowledges aims and values of Open Science and relates them to values, principles, and standards shared by the Arqus Alliance, followed by a vision for a future with Open Science. In the interest of a nuanced picture, the Position Paper discusses not only desired effects, but also possible areas of tension related to Open Science. It presents a wide range of specific aims and recommendations for each of the eleven elements of Open Science defined by the Arqus Openness Task Force: Governance Publications (including Open Access) Data (including research data management, FAIR and Open Data) Infrastructures (including support staff, Open Science software and tools, repositories, Open Labs) Methods (including source code, preregistration, materials, workflows, protocols, lab notes) Awareness and training (including education of early-stage researchers) Evaluation (including Open Metrics, research assessment, Open Peer Review, rewards and incentives) Communication (including multilingualism) Citizen Science Open Education Open Innovation The Position Paper concludes with an annex that highlights the progress already made in the implementation and support of Open Science practices at Arqus institutions

CC: Intraspecific variation of recombination rate in maize. Genome Biol

Abstract Background: In sexually reproducing organisms, meiotic crossovers ensure the proper segregation of chromosomes and contribute to genetic diversity by shuffling allelic combinations. Such genetic reassortment is exploited in breeding to combine favorable alleles, and in genetic research to identify genetic factors underlying traits of interest via linkage or association-based approaches. Crossover numbers and distributions along chromosomes vary between species, but little is known about their intraspecies variation

Intraspecific variation of recombination rate in maize

Abstract Background In sexually reproducing organisms, meiotic crossovers ensure the proper segregation of chromosomes and contribute to genetic diversity by shuffling allelic combinations. Such genetic reassortment is exploited in breeding to combine favorable alleles, and in genetic research to identify genetic factors underlying traits of interest via linkage or association-based approaches. Crossover numbers and distributions along chromosomes vary between species, but little is known about their intraspecies variation. Results Here, we report on the variation of recombination rates between 22 European maize inbred lines that belong to the Dent and Flint gene pools. We genotype 23 doubled-haploid populations derived from crosses between these lines with a 50 k-SNP array and construct high-density genetic maps, showing good correspondence with the maize B73 genome sequence assembly. By aligning each genetic map to the B73 sequence, we obtain the recombination rates along chromosomes specific to each population. We identify significant differences in recombination rates at the genome-wide, chromosome, and intrachromosomal levels between populations, as well as significant variation for genome-wide recombination rates among maize lines. Crossover interference analysis using a two-pathway modeling framework reveals a negative association between recombination rate and interference strength. Conclusions To our knowledge, the present work provides the most comprehensive study on intraspecific variation of recombination rates and crossover interference strength in eukaryotes. Differences found in recombination rates will allow for selection of high or low recombining lines in crossing programs. Our methodology should pave the way for precise identification of genes controlling recombination rates in maize and other organisms.Results have been achieved in the framework of the Transnational (Germany, France, Spain) Cooperation within the PLANT-KBBE Initiative Cornfed, additionally supported by the project AMAIZING. The work was financed by grants from Agence Nationale de la Recherche ('ANR') to AC, MF, MM, and PF, grants from the Ministry of Science and Innovation (Ministerio de Ciencia e Innovación ('MICINN')) to JMG and PR, and grants from the Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung, 'BMBF') to TA, AEM, MO, and CCS.Peer Reviewe

ASAS Recommendations for Requesting and Reporting Imaging in Patients with Suspected Axial Spondyloarthritis

Diekhoff T, Eshed I, Giraudo C, et al. ASAS Recommendations for Requesting and Reporting Imaging in Patients with Suspected Axial Spondyloarthritis. In: American College of Reumatology, ed. ABSTRACT SUPPLEMENT ACR Convergence 2022, November 10–14, 2022, Philadelphia, PA. Arthritis & Rheumatology. Vol 74. Hoboken: Wiley; 2022: 788-790