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Part 1: Document Description
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Citation |
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Title: |
Replication Data for: Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions |
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Identification Number: |
doi:10.7910/DVN/JR4X4C |
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Distributor: |
Harvard Dataverse |
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Date of Distribution: |
2019-06-27 |
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Version: |
1 |
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Bibliographic Citation: |
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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Citation |
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Title: |
Replication Data for: Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions |
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Identification Number: |
doi:10.7910/DVN/JR4X4C |
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Authoring Entity: |
Diaz, Santiago (International Center for Tropical Agriculture - CIAT) |
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Ariza-Suarez, Daniel (International Center for Tropical Agriculture - CIAT) |
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Izquierdo, Paulo (International Center for Tropical Agriculture - CIAT, Michigan State University - MSU) |
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Lobaton, Juan David (International Center for Tropical Agriculture - CIAT, University of New England) |
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de la Hoz, Juan (International Center for Tropical Agriculture - CIAT, University of California) |
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Acevedo, Fernando (International Center for Tropical Agriculture - CIAT, Universidad Nacional de Colombia) |
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Duitama, Jorge (International Center for Tropical Agriculture - CIAT, Universidad de los Andes) |
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Guerrero, Alberto (International Center for Tropical Agriculture - CIAT) |
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Cajiao, Cesar (International Center for Tropical Agriculture - CIAT) |
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Mayor, Victor (International Center for Tropical Agriculture - CIAT, Progeny Breeding) |
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Beebe, Stephen (International Center for Tropical Agriculture - CIAT) |
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Raatz, Bodo (International Center for Tropical Agriculture - CIAT) |
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Producer: |
International Center for Tropical Agriculture |
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Grant Number: |
OPP1114827 |
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Grant Number: |
Prime award number AID‐0AA‐A‐13‐00077, sub award number 4943-CIDT-AID-0077 |
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Distributor: |
Harvard Dataverse |
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Distributor: |
International Center for Tropical Agriculture |
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Access Authority: |
CIAT Data and Research Methods |
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Depositor: |
Barboza Candelo, Juliette |
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Date of Deposit: |
2019-06-26 |
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Holdings Information: |
https://doi.org/10.7910/DVN/JR4X4C |
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Study Scope |
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Keywords: |
Agricultural Sciences, 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 |
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Topic Classification: |
Inbred lines, Drought, Plant breeding, Genetic maps, Quantitative trait loci, Phaseolus vulgaris |
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Abstract: |
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. |
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Country: |
Colombia |
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Geographic Coverage: |
CIAT-HQ, Valle del Cauca, Palmira |
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Kind of Data: |
Trial Data |
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Kind of Data: |
Models |
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Kind of Data: |
Breeding Data |
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Kind of Data: |
Genomic Data |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Disclaimer: |
Whilst utmost care has been taken by CIAT and data authors while collecting and compiling the data, the data is however offered "as is" with no express or implied warranty. In no event shall the data authors, CIAT, or relevant funding agencies be liable for any actual, incidental or consequential damages arising from use of the data. <BR/><BR/> By using the CIAT Dataverse, the user expressly acknowledges that the Data may contain some nonconformities, defects, or errors. No warranty is given that the data will meet the user's needs or expectations or that all nonconformities, defects, or errors can or will be corrected. <BR/><BR/> The user should always verify actual data; therefore the user bears all responsibility in determining whether the data is fit for the user’s intended use. The user of the data should use the related publications as a baseline for their analysis whenever possible. Doing so will be an added safeguard against misinterpretation of the data. Related publications are listed in the metadata section of the Dataverse study. |
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Notes: |
<P><a rel="license" href="http://creativecommons.org/licenses/by/4.0/" target="_blank"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br /> These data and documents are licensed under a <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank"> Creative Commons Attribution 4.0 International license.</a> You may copy, distribute and transmit the data as long as you acknowledge the source through proper <a href="http://best-practices.dataverse.org/data-citation/" target="_blank">data citation</a>.</P> <Strong>Disclaimer</Strong> <P> Whilst utmost care has been taken by CIAT and data authors while collecting and compiling the data, the data is however offered "as is" with no express or implied warranty. In no event shall the data authors, CIAT, or relevant funding agencies be liable for any actual, incidental or consequential damages arising from use of the data. <BR/><BR/> By using the CIAT Dataverse, the user expressly acknowledges that the Data may contain some nonconformities, defects, or errors. No warranty is given that the data will meet the user's needs or expectations or that all nonconformities, defects, or errors can or will be corrected. <BR/><BR/> The user should always verify actual data; therefore the user bears all responsibility in determining whether the data is fit for the user’s intended use. The user of the data should use the related publications as a baseline for their analysis whenever possible. Doing so will be an added safeguard against misinterpretation of the data. Related publications are listed in the metadata section of the Dataverse study. </P> |
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Other Study Description Materials |
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Related Publications |
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Citation |
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Title: |
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. |
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Identification Number: |
10.5061/dryad.46pk7 |
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Bibliographic Citation: |
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. |
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Citation |
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Title: |
Perea, Claudia, Juan Fernando De La Hoz, Daniel Felipe Cruz, Juan David Lobaton, Paulo Izquierdo, Juan Camilo Quintero, Bodo Raatz, and Jorge Duitama. 2016. “Bioinformatic Analysis of Genotype by Sequencing (GBS) Data with NGSEP.” BMC Genomics 17 (S5): 498. |
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Identification Number: |
10.1186/s12864-016-2827-7 |
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Bibliographic Citation: |
Perea, Claudia, Juan Fernando De La Hoz, Daniel Felipe Cruz, Juan David Lobaton, Paulo Izquierdo, Juan Camilo Quintero, Bodo Raatz, and Jorge Duitama. 2016. “Bioinformatic Analysis of Genotype by Sequencing (GBS) Data with NGSEP.” BMC Genomics 17 (S5): 498. |
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File Description--f3457163 |
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File: 01. MAGIC_raw_data.tab |
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Notes: |
UNF:6:EAo3yU0k/iG2JYskX8lgjQ== |
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Raw phenotypic data from the three trials |
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File Description--f3457162 |
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File: 03. MAGIC_model_data.tab |
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Notes: |
UNF:6:kA5bu7t39gt/SQi/GR/JGA== |
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Modeled phenotypic data from the two replicated trials using mixed linear models with spatial correction |
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File Description--f3457168 |
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File: 06. MAGIC_genetic_map.tab |
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Notes: |
UNF:6:257kvPy9YjTfiBY58etD1A== |
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Genetic map for the MAGIC population using 5739 non-redundant SNP markers |
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List of Variables: |
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Variables |
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f3457163 Location: |
Summary Statistics: Valid 6868.0; StDev 0.8806698239577355; Max. 2016.0; Min. 2013.0; Mean 2013.5468841001748; Variable Format: numeric Notes: UNF:6:Z82LxVglDtUnf/W8Wze9fA== |
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f3457163 Location: |
Summary Statistics: Valid 6868.0; Max. 8320.0; Mean 5322.413511939458; StDev 1523.3477914156394; Min. 2629.0; Variable Format: numeric Notes: UNF:6:bBqNO/OrBLPWZmMvw5Wcyw== |
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f3457163 Location: |
Variable Format: character Notes: UNF:6:WXbjz9V2eXevBUVE5IktSw== |
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f3457163 Location: |
Variable Format: character Notes: UNF:6:NSfD9V2vCVWlTmZC8NN3lA== |
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f3457163 Location: |
Variable Format: character Notes: UNF:6:+NamJ+eLj7bZN3a2LaWS3Q== |
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f3457163 Location: |
Summary Statistics: Mean 17.465517241379064; Min. 1.0; StDev 13.112700979879264; Max. 56.0; Valid 6264.0 Variable Format: numeric Notes: UNF:6:RLmc+5jraW9NsViys2HgJg== |
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f3457163 Location: |
Summary Statistics: Mean 80.12068965517119; Min. 1.0; StDev 65.35522355915155; Valid 6264.0; Max. 212.0 Variable Format: numeric Notes: UNF:6:afzc3K0MbJHkXyHUrpdfYA== |
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f3457163 Location: |
Summary Statistics: Mean 2.0; StDev 0.8165617624694359; Valid 6264.0; Min. 1.0; Max. 3.0; Variable Format: numeric Notes: UNF:6:vnhkJuKRJRto8cxnMVcMpQ== |
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f3457163 Location: |
Summary Statistics: Min. 1.0; Mean 28.12068965517191; StDev 21.501845416572447; Valid 6264.0; Max. 72.0 Variable Format: numeric Notes: UNF:6:t5I+v94yLjETcFIdTHrzXg== |
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f3457163 Location: |
Summary Statistics: Max. 45.0; Mean 35.89940828402365; StDev 2.3622554411956176; Min. 28.0; Valid 6253.0 Variable Format: numeric Notes: UNF:6:HdvbUabonb4h4GHTxA5tLw== |
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f3457163 Location: |
Summary Statistics: Mean 61.87178257394081; Min. 54.0; StDev 2.9992315832943923; Valid 6255.0; Max. 72.0 Variable Format: numeric Notes: UNF:6:FJPNkWwH8c6ZSv/LmE8XNw== |
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f3457163 Location: |
Summary Statistics: Mean 21.185044207219462; StDev 4.141212806820155; Max. 39.67906977; Valid 6247.0; Min. 2.0 Variable Format: numeric Notes: UNF:6:eoOnssfyPwy8387137Clzw== |
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f3457163 Location: |
Summary Statistics: Valid 6228.0; StDev 92.1380001078773; Mean 160.81678612716757; Max. 662.256; Min. 4.536; Variable Format: numeric Notes: UNF:6:qTeGKsxtndqC6JEK+Ztc9w== |
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f3457163 Location: |
Summary Statistics: Mean 11.944217118997916; Max. 17.3; Valid 6227.0; StDev 2.1049580258973046; Min. 0.02; Variable Format: numeric Notes: UNF:6:sZAKMYz6okD97SYPc0V51g== |
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f3457163 Location: |
Summary Statistics: Valid 6234.0; StDev 0.30439553862048263; Min. 0.06; Max. 4.2; Mean 1.7128893166506278; Variable Format: numeric Notes: UNF:6:WQP0kZEnh/fAEnKfOLrMqw== |
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f3457163 Location: |
Summary Statistics: StDev 9.219691066501781; Min. 1.0; Max. 87.0; Mean 29.262035099017847; Valid 6211.0 Variable Format: numeric Notes: UNF:6:yZwxGT905+dNKvGylFLxSQ== |
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f3457163 Location: |
Summary Statistics: Max. 21000.3907; Valid 6209.0; Min. 25.78604651; Mean 996.3627842893417; StDev 641.4299817540993; Variable Format: numeric Notes: UNF:6:FZZQ/Gjszp0BffPRW83Csg== |
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f3457163 Location: |
Summary Statistics: Valid 4318.0; StDev 5.509731183380519; Mean 72.56101669559055; Min. 33.28938695; Max. 86.79509632; Variable Format: numeric Notes: UNF:6:COmeSwoU+e4uvGCdtNyGLg== |
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f3457163 Location: |
Summary Statistics: Valid 1410.0; Max. 93.9; StDev 8.325952412453361; Mean 57.12968085106383; Min. 33.3 Variable Format: numeric Notes: UNF:6:B1Tmi43GNgXO4yfkwYa+VQ== |
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f3457163 Location: |
Summary Statistics: Min. 16.7; Valid 1410.0; StDev 4.225714054743678; Max. 50.8; Mean 26.268297872340426; Variable Format: numeric Notes: UNF:6:btm6TrOlOn+zicH8USPhKw== |
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f3457162 Location: |
Variable Format: character Notes: UNF:6:empT0FooTeaGXXBCPyjO1w== |
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f3457162 Location: |
Variable Format: character Notes: UNF:6:uZ/g/VnPRst9gWrA3ZXDNA== |
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f3457162 Location: |
Summary Statistics: StDev 0.49988116849795566; Max. 2014.0; Min. 2013.0; Valid 2502.0; Mean 2013.4852118305355 Variable Format: numeric Notes: UNF:6:uy7lKogiQDToqP4N737KZQ== |
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f3457162 Location: |
Summary Statistics: Valid 2502.0; StDev 1.7784859112919975; Max. 42.94; Min. 27.5; Mean 35.79430855315747 Variable Format: numeric Notes: UNF:6:90uq/JvqH7GLGA1TPVNoUw== |
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f3457162 Location: |
Summary Statistics: Min. 55.27; StDev 2.516921835733642; Mean 61.36259792166267; Max. 71.16; Valid 2502.0 Variable Format: numeric Notes: UNF:6:SUaq1/G2Gefzsjsk04IZuw== |
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f3457162 Location: |
Summary Statistics: StDev 4.255355764825952; Max. 81.58; Min. 45.41; Mean 72.28604037267081; Valid 1288.0 Variable Format: numeric Notes: UNF:6:Dv6mgNNq1dIZZ3wlrZjQtw== |
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f3457162 Location: |
Summary Statistics: Max. 34.96; Valid 2502.0; StDev 3.4061562191861627; Mean 20.745387689848123; Min. 11.14 Variable Format: numeric Notes: UNF:6:SdzDmsVsW4eCH1bmMA5QzA== |
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f3457162 Location: |
Summary Statistics: StDev 424.7254372741068; Max. 2755.22; Valid 2502.0; Mean 1118.0041806554757; Min. 78.44; Variable Format: numeric Notes: UNF:6:vsVxZQTauO1ZMKS5S5o5fg== |
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f3457162 Location: |
Summary Statistics: Mean 60.22273102310231; Valid 1212.0; Min. 39.84; Max. 91.19; StDev 6.521859252487724 Variable Format: numeric Notes: UNF:6:XPmSVBcQRUi/p8j3UFIx1w== |
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f3457162 Location: |
Summary Statistics: Mean 29.001897689768978; Max. 43.46; StDev 2.7156300866269496; Valid 1212.0; Min. 20.67 Variable Format: numeric Notes: UNF:6:xX6x2TqGn0VuP00sbDMjWw== |
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f3457168 Location: |
Variable Format: character Notes: UNF:6:h48Sg8evIktcyutUvHnByA== |
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f3457168 Location: |
Variable Format: character Notes: UNF:6:AyYAzJ7rf6V0wX7W8UWXeQ== |
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f3457168 Location: |
Summary Statistics: Mean 40.63898937097055; Max. 97.82; Valid 5739.0; StDev 25.81186135625466; Min. 0.0 Variable Format: numeric Notes: UNF:6:YoT5eIeaUYf+X0eP5upCYg== |
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f3457168 Location: |
Summary Statistics: Valid 5739.0; Mean 2.5575507122843865E7; StDev 1.950945375741195E7; Max. 6.2969309E7; Min. 17920.0 Variable Format: numeric Notes: UNF:6:o9pwpugL/8ojtajIjE7Vfw== |
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Label: |
02. MAGIC_raw_data_dictionary.xls |
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Text: |
Data dictionary for MAGIC_raw_data |
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Notes: |
application/vnd.ms-excel |
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Label: |
04. MAGIC_model_data_dictionary.xls |
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Text: |
Data dictionary for MAGIC_model_data |
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Notes: |
application/vnd.ms-excel |
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Label: |
05. MAGIC_Pvulgaris_GBS.vcf.gz |
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Text: |
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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Notes: |
application/x-gzip |
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Label: |
07. MAGIC_genetic_map_dictionary.xls |
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Text: |
Data dictionary for MAGIC_genetic_map |
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Notes: |
application/vnd.ms-excel |