Brief description
| The dataset includes the genotypes of 2018 Brassica napus varieties, developed using the B. napus 60K single nucleotide polymorphism (SNP) array (see 10.1007/s00122-016-2849-1 for details). In addition, lesion lengths and area under the disease progress curve in response to infection with Sclerotinia sclerotiorum and flowering times are provided. |
Full description
| File list: File 1: tpg220088-supp-0002-MatS2.xlsx Availability: Available in the supplementary material of doi.org/10.1002/tpg2.20088. Description: Meta-data table describing the biological features, geographical origins and data sources for the 218 varieties in this data set. The sheet 'TableS1' provides the meta-data and the sheet 'Key' provides descriptions of the terms used in TableS1. Column key: ECOTYPE = ecotype based on likely vernalisation requirement. COUNTRY_OF_ORIGIN = the country in which the variety was first developed. ECOTYPE_AND_COUNTRY_INFO_SOURCE = the source of the information used to derive ecotype and country descriptions. ORIGINAL_DATA_TYPE = the origin of the genotype data. DATA_SOURCE = the source of the genotype data. DATA_SRA_ACCESSION = where applicable, the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) accession for genome data. NATIONAL_DATA_CENTER_ACCESSION = where applicable, the accession for data from the National Genomics Data Center (NGDC) of China. File 2: tpg220088-supp-0003-MatS3.xlsx Availability: Available in the supplementary material of doi.org/10.1002/tpg2.20088. Description: The genotypes of the 218 B. napus varieties tested based on the B. napus 60K single nucleotide polymorphism (SNP) array (see doi.org/10.1007/s00122-016-2849-1 for details). Genotypes are in numerical format, where 0 = homozygous reference, 1 = heterozygous, 2 = homozygous alternate and NA = missing data. Rows are B. napus 60K SNP array IDs and columns are variety numbers matching varieties in File 1 'tpg220088-supp-0002-MatS2.xlsx'. Methodology: Genotypes are derived from three sources. Genotype data for 99 lines from the 'associative expression and systems analysis of complex traits in oilseed rape / canola' (ASSYST) population were provided by professor Rod Snowdon of the University of Giessen, Germany; these data are described in doi.org/10.1007/s00122-011-1676-7. Genotype data for 10 varieties were derived from the supplementary material of doi.org/10.1111/1755-0998.12379. Genotype data for 3 varieties were derived from the supplementary material of doi.org/10.1071/CP17161. Genotype data for 19 varieties were developed using whole genome sequencing data from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) and National Genomics Data Center (NGDC) of China under the accessions listed in File 1 'tpg220088-supp-0002-MatS2'. Genotype data for the remaining 87 varieties were generated by the University of Western Australia using the B. napus 60K SNP array using standard procedures. All genotype data were filtered using the R package 'snpReady' version 0.9.6 (doi.org/10.1007/s11032-018-0844-8), removing those with a call rate of < 0.5 and minor allele frequency of < 0.01. Also using snpReady, missing SNPs were imputed using the Wright method. The data in File 2 'tpg220088-supp-0003-MatS3.xlsx' are the SNP data before filtering and imputation. File 3: 2019-phenotypes_reformatted.txt Availability: Not publicly available. Contact the Centre for Crop and Disease Management for access. Description: Table containing data for the 218 varieties, including lesion lengths at 1, 2 and 3 weeks post-inoculation of B. napus stems with agar plugs carrying S. sclerotiorum mycelium, and flowering time. The first column of the table is the numerical variety ID, which is also present in the genotype data in File 2 'tpg220088-supp-0003-MatS3.xlsx'. Descriptions of the data recorded in each column are given in File 3 '2019-phenotypes_reformatted_key.txt'. Methodology: Plants were grown in a temperature-controlled glasshouse in 5 L pots containing UWA plant biology mix and irrigated twice daily with drip irrigation for 1-2 minutes. Each pot received 2 g of fertilizer. Plants were inoculated at 30-50 % flowering with 5 mm potato dextrose agar plugs containing mycelium of the S. sclerotiorum isolate CU8.24 (described in doi.org/10.1080/07060661.2018.1516699). See doi.org/10.1002/tpg2.20088 for further methodological details. The lesion length data, and their relationship to the genotype data, are also summarised in doi.org/10.1002/tpg2.20088, where the genotype data are also available for download. All phenotype data are currently stored at Curtin University. File 4: 2019-phenotypes_reformatted_key.txt Availability: Not publicly available. Contact the Centre for Crop and Disease Management for access. Description: A file containing descriptions of the information contained in each column of File 3 '2019-phenotypes_reformatted.txt'. |
Issued: 2021
Data time period: 2019 to 2019
Spatial Coverage And Location
text: A single glasshouse in UWA, and the UWA and Curtin molecular biology laboratories.
Subjects
Agricultural, Veterinary and Food Sciences |
Agriculture, Land and Farm Management |
Biological Sciences |
Brassica napus |
Crop and Pasture Improvement (Incl. Selection and Breeding) |
Crop and Pasture Production |
Disease resistance |
Genome-wide association |
Genomic prediction |
Genomic selection |
Genotype |
Germplasm Management |
Plant Biology |
Plant Pathology |
Sclerotinia sclerotiorum |
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Identifiers
- DOI : 10.25917/4BB4-AV90
- global : 265ff03c-f494-49cc-8ef3-1c9e626cc661
