Developing a research strategy to better understand, observe, and simulate urban atmospheric processes at kilometer to subkilometer scales

A Met Office/Natural Environment Research Council Joint Weather and Climate Research Programme workshop brought together 50 key international scientists from the UK and international community to formulate the key requirements for an Urban Meteorological Research strategy. The workshop was jointly organised by University of Reading and the Met Office

RADtyping: An Integrated Package for Accurate <i>De Novo</i> Codominant and Dominant RAD Genotyping in Mapping Populations

<div><p>Genetic linkage maps are indispensable tools in genetic, genomic and breeding studies. As one of genotyping-by-sequencing methods, RAD-Seq (restriction-site associated DNA sequencing) has gained particular popularity for construction of high-density linkage maps. Current RAD analytical tools are being predominantly used for typing codominant markers. However, no genotyping algorithm has been developed for dominant markers (resulting from recognition site disruption). Given their abundance in eukaryotic genomes, utilization of dominant markers would greatly diminish the extensive sequencing effort required for large-scale marker development. In this study, we established, for the first time, a novel statistical framework for <i>de novo</i> dominant genotyping in mapping populations. An integrated package called RADtyping was developed by incorporating both <i>de novo</i> codominant and dominant genotyping algorithms. We demonstrated the superb performance of RADtyping in achieving remarkably high genotyping accuracy based on simulated and real mapping datasets. The RADtyping package is freely available at <a href="http://www2.ouc.edu.cn/mollusk/detailen.asp?id=727" target="_blank">http://www2.ouc.edu.cn/mollusk/ detailen.asp?id=727</a>.</p></div

Codominant and dominant SNPs confirmed by Sanger-based amplicon sequencing.

a<p>BsaXI restriction sites are highlighted in bold and SNP alleles are indicated in parentheses.</p

Consistency of dominant genotyping on replicate 2b-RAD libraries prepared from two parents and ten progeny.

<p>Note, average sequencing depths for two parents were 181× and 185× in rep1 and 190× and 235× in rep2, while for progeny, they were 37–46× in rep1 and 22–30× in rep2.</p

Sanger validation of 2b-RAD genotypes.

<p>Sanger validation of 2b-RAD genotypes.</p

An overview of the RADtyping approach for <i>de novo</i> codominant and dominant genotyping in a mapping population.

<p>Representative reference sites are obtained by assembling parental sequencing reads into “locus” clusters. These sites are further classified into parent-shared and parent-specific sites for subsequent codominant and dominant genotyping. Main principles of codominant and dominant genotyping algorithms are shown in flowcharts, and more details are described in the Methods section.</p

Summary of polymorphic markers obtained by 2b-RAD sequencing of a <i>C. farreri</i> mapping population.

a<p>Total marker no. refers to all polymorphic markers reported by RADtyping regardless of whether they follow Mendelian segregation in progeny.</p>b<p>For dominant markers, only those in accord with Mendelian segregation were scored to ensure the correct assignment of markers to different segregation patterns.</p>c<p>This segregation type was scored separately apart from the main pipeline.</p

Evaluation of the performance of RADtyping using a pseudo F₁ mapping population.

<p>The simulated population was created by a crossing of two <i>Arabidopsis</i> plants with predefined SNPs in their genomes and progeny were subject to <i>in silico</i> sequencing together with their parents at different sequencing depths with sequencing errors enabled. <i>De novo</i> codominant and dominant genotyping was evaluated in three key aspects: genotype coverage (a, b), removal of repetitive sites (b, e), and genotyping accuracy (c, f).</p