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Replication data for: Association genetics and genomic prediction for resistance to the pea root rot complex in a diverse collection of Pisum sativum L.

dc.contributor.author
Ariza-Suarez, Daniel
dc.contributor.author
Hohmann, Pierre
dc.contributor.author
Wille, Lukas
dc.contributor.author
Gfeller, Valentin
dc.contributor.author
Schneider, Michael
dc.contributor.author
Horton, Matthew W.
dc.contributor.author
Messmer, Monika M.
dc.contributor.author
Studer, Bruno
dc.contributor.contactPerson
Studer, Bruno
dc.contributor.contactPerson
Ariza-Suarez, Daniel
dc.contributor.dataCollector
Wille, Lukas
dc.contributor.producer
Ariza-Suarez, Daniel
dc.contributor.projectLeader
Gfeller, Valentin
dc.contributor.projectLeader
Messmer, Monika M.
dc.contributor.projectLeader
Studer, Bruno
dc.contributor.projectMember
Hohmann, Pierre
dc.contributor.projectMember
Schneider, Michael
dc.contributor.projectMember
Horton, Matthew W.
dc.date.accessioned
2024-07-03T07:59:36Z
dc.date.available
2024-07-03T07:59:36Z
dc.date.created
2022-03/2022-10
en_US
dc.date.issued
2024-07
dc.identifier.uri
http://hdl.handle.net/20.500.11850/681298
dc.description.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.
en_US
dc.language.iso
en
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.subject
pea root rot complex (PRRC)
en_US
dc.subject
genome wide association studies (GWAS)
en_US
dc.subject
Genomic prediction
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dc.subject
Pisum sativum
en_US
dc.title
Replication data for: Association genetics and genomic prediction for resistance to the pea root rot complex in a diverse collection of Pisum sativum L.
en_US
dc.title.alternative
Identification of a resistance QTL against a pea root rot complex in a diverse population of Pisum sativum L.
en_US
dc.type
Dataset
dc.rights.license
Creative Commons Attribution 4.0 International
ethz.date.collected
2021-01
en_US
ethz.code.ddc
DDC - DDC::6 - Technology, medicine and applied sciences::630 - Agriculture
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science::02703 - Institut für Agrarwissenschaften / Institute of Agricultural Sciences::03969 - Studer, Bruno / Studer, Bruno
en_US
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science::02703 - Institut für Agrarwissenschaften / Institute of Agricultural Sciences::03969 - Studer, Bruno / Studer, Bruno
en_US
ethz.relation.cites
10.3929/ethz-b-000452341
ethz.date.deposited
2024-07-03T07:59:37Z
ethz.source
FORM
ethz.eth
yes
en_US
ethz.doipreview
Yes
en_US
ethz.description.methods
This data was derived from plant material reported by Wille et al. (2020; https://doi.org/10.3389/fpls.2020.542153). Briefly, a panel of 254 pea genotypes was assembled and tested for root rot resistance. The panel contained full-leaf and semi-leaf-less genotypes comprising 177 genebank accessions from the USDA-ARS GRIN Pea Core Collection, 47 advanced breeding lines from a private organic breeding organization (Getreidezüchtung Peter Kunz, Switzerland) and 34 registered cultivars from Europe. The population was genotyped-by-sequencing (GBS) following the protocol proposed by Poland et al. (2012; https://doi.org/10.1371/journal.pone.0032253) using a combination of PstI and MspI as restriction enzymes. GBS libraries were prepared at the plateforme d’analyses génomiques of the Institut de Biologie Intégrative et des Systèmes (IBIS, Université Laval, Québec, Canada) with the following modifications: a BluePippin (Sage Scientific, Beverly, MA) was used to size the libraries before PCR amplification (elution set between 50 and 65 min, on a 2% gel). Libraries were normalized, pooled, and then denatured in 0.02N NaOH and neutralized using HT1 buffer. Plate barcoding was used to enable sequencing on a shared Illumina NovaSeq S4 lane. Sequencing was performed at the Centre d’expertise et de services Genome Québec in Canada. The pool was loaded at 225pM on an Illumina NovaSeq S4 lane using the Xp protocol according to the manufacturer’s recommendations. The run was performed for 2x150 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level.
en_US
ethz.description.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).
en_US
ethz.rosetta.exportRequired
true
ethz.COinS
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