Notice
This record is in review state, the data has not yet been validated.
Replication data for: Association genetics and genomic prediction for resistance to the pea root rot complex in a diverse collection of Pisum sativum L.
Abstract
This repository contains genotypic and phenotypic data from a collection of 254 genotypes of pea (Pisum sativum L.). These data was used to identify genomic regions in the pea genome associated with root rot resistance.
Contributors
Contact person: Studer, Bruno
Contact person: Ariza-Suarez, Daniel
![cc](/themes/Mirage2//images/orcid_icon.png)
Data collector: Wille, Lukas
Producer: Ariza-Suarez, Daniel
![cc](/themes/Mirage2//images/orcid_icon.png)
Project leader: Gfeller, Valentin
Project leader: Messmer, Monika M.
Project leader: Studer, Bruno
Project member: Hohmann, Pierre
Project member: Schneider, Michael
Project member: Horton, Matthew W.
Software
Base calling was performed using RTA software (v3). The bcl2fastq2 software (v2.20) was then used to demultiplex libraries and generate FASTQ reads.Sequence demultiplexing of individual samples was performed with Stacks (v2.60; https://doi.org/10.1111/mec.12354), allowing up to one mismatch in the adapter sequence. Adapter tails were clipped with HTStream (v1.3.3; https://github.com/s4hts/HTStream). Using Bowtie (v2.4.4; https://doi.org/10.1038/nmeth.1923), the processed reads were mapped to the reference genomes of P. sativum cv. ‘Caméor’ (https://doi.org/10.1038/s41588-019-0480-1) and ‘Zhongwang 6’ (https://doi.org/10.1038/s41588-022-01172-2). The mapped reads were used for single nucleotide polymorphism (SNP) calling using NGSEP (v4.1.0; https://doi.org/10.1111/1755-0998.13737). The variant call format (VCF) matrix was filtered for genotype calls with a quality score above 30, minor allele frequency above 0.02, and a maximum observed heterozygosity rate of 0.05 per SNP marker. Finally, variants in less than 22% genotyped samples were removed to reduce the proportion of missing data in the genotypic matrix to approximately 30%. The predicted effect of these sequence variants on the gene models of the reference genomes was annotated with snpEff (v5.0e; https://doi.org/10.4161/fly.19695).Date collected
2021-01Date created
2022-03/2022-10Subject
pea root rot complex (PRRC); genome wide association studies (GWAS); Genomic prediction; Pisum sativumOrganisational unit
03969 - Studer, Bruno / Studer, Bruno
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