Replication Data for: Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

Version 1.6
Diaz, Santiago; Ariza-Suarez, Daniel; Izquierdo, Paulo; Lobaton, Juan David; de la Hoz, Juan; Acevedo, Fernando; Duitama, Jorge; Guerrero, Alberto; Cajiao, Cesar; Mayor, Victor; Beebe, Stephen; Raatz, Bodo, 2019, "Replication Data for: Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions", https://doi.org/10.7910/DVN/JR4X4C, Harvard Dataverse, V1, UNF:6:9Mo09XULmZ19DQpPaR+Byw== [fileUNF]
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Description
These datasets contain phenotypic and genotypic data of a MAGIC (Multiparent Advanced Generation Inter-Crosses) population of common bean (Phaseolus vulgaris L.), developed by inter-crossing of eight Mesoamerican elite breeding lines. The main goal for this population is to be used for applications in breeding and breeding tool development, which will support efforts to develop climate resilient germplasm, as well as information for basic research questions aiming to uncover the genetic basis of important agronomic traits. The raw phenotypic data come from three different trials carried out in Palmira (Colombia). Two replicated trials were laid out in the field with an alpha-lattice experimental design in 2013 and 2014, and an additional non-replicated trial in 2016. Several agronomic traits were assessed, including Days to Flowering (DF), Days to Physiological Maturity (DPM), 100 seed weight (100SdW), Yield (Yd), Pod Harvest Index (PHI), Iron and Zinc content (SdFe and SdZn). The agronomic performance of the population was modeled using linear mixed models with spatial correction. From these models, best linear unbiased estimators / predictors were obtained (BLUEs/BLUPs). The genotypic datasets include a variant call format (VCF) file of 20,615 GBS variants genotyped for 629 RILs (recombinant inbred lines) and 8 founder. From this matrix, a large and dense genetic map was obtained. This map accounts for multiple recombination events from multiple founder lines using SNP data, conferring higher accuracy due to the large population size. It makes it suitable for analyzing the linkage and segregation patterns for genetic mapping in the species Phaseolus vulgaris.
Subject Agricultural Sciences
Keyword Genotyping-By-Sequencing (GBS), Genome-Wide Association Study (GWAS), Multiparent Advanced Generation Inter-Crosses (MAGIC), Quantitative Trait Loci (QTL), Whole Genome Sequencing (WGS), Beans, Latin America and the Caribbean, Agrobiodiversity - AGBIO, Common Bean Ontology
Related Publication Lobaton JD, Miller T, Gil J, Ariza D, De La Hoz JF, Soler A, Beebe S, Duitama J, Gepts P, Raatz B (2018) Data from: Resequencing of common bean identifies regions of inter-gene pool introgression and provides comprehensive resources for molecular breeding. Dryad Digital Repository.doi: 10.5061/dryad.46pk7
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02. MAGIC_raw_data_dictionary.xls
MS Excel Spreadsheet - 33.5 KB
Published Jun 27, 2019
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MD5: b01b07108d628edcc402305e31d3b418
Data dictionary for MAGIC_raw_data
Documentation
04. MAGIC_model_data_dictionary.xls
MS Excel Spreadsheet - 30.5 KB
Published Jun 27, 2019
38 Downloads
MD5: fa3798a447c0cd7bc4ce22a26e586dc2
Data dictionary for MAGIC_model_data
Documentation
07. MAGIC_genetic_map_dictionary.xls
MS Excel Spreadsheet - 26.0 KB
Published Jun 27, 2019
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MD5: 00246a84d05b03c2608609d71da53fd1
Data dictionary for MAGIC_genetic_map
Documentation
01. MAGIC_raw_data.tab
Tabular Data - 960.9 KB
Published Jun 27, 2019
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20 Variables, 6868 Observations UNF:6:EAo3yU0k/iG2JYskX8lgjQ==
Raw phenotypic data from the three trials
Data
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03. MAGIC_model_data.tab
Tabular Data - 141.6 KB
Published Jun 27, 2019
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10 Variables, 2502 Observations UNF:6:kA5bu7t39gt/SQi/GR/JGA==
Modeled phenotypic data from the two replicated trials using mixed linear models with spatial correction
Data
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05. MAGIC_Pvulgaris_GBS.vcf.gz
Gzip Archive - 56.4 MB
Published Jun 27, 2019
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MD5: 2ce4f7c1a438c44e3786a5a4558e0410
Genotypic matrix obtained from GBS data for 629 MAGIC RILs and 8 founder lines. The definition of each field in the matrix is contained within the file’s header, as specified in the VCF format (https://samtools.github.io/hts-specs/VCFv4.2.pdf). This file is gzip compressed.
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06. MAGIC_genetic_map.tab
Tabular Data - 251.7 KB
Published Jun 27, 2019
75 Downloads
4 Variables, 5739 Observations UNF:6:257kvPy9YjTfiBY58etD1A==
Genetic map for the MAGIC population using 5739 non-redundant SNP markers
Data
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