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Part 1: Document Description
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Citation |
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Title: |
Replication Data for: Genomic prediction of agronomic traits in common bean under environmental stress |
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Identification Number: |
doi:10.7910/DVN/XCD67U |
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Distributor: |
Harvard Dataverse |
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Date of Distribution: |
2020-03-24 |
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Version: |
1 |
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Bibliographic Citation: |
Keller, Beat; Ariza-Suarez, Daniel; De la Hoz, Juan; Aparicio, Johan Steven; Portilla Benavides, Ana Elisabeth; Buendia, Hector Fabio; Mayor, Victor Manuel; Studer, Bruno; Raatz, Bodo, 2020, "Replication Data for: Genomic prediction of agronomic traits in common bean under environmental stress", https://doi.org/10.7910/DVN/XCD67U, Harvard Dataverse, V1, UNF:6:2ucpalum7jucY0dQs56Z3A== [fileUNF] |
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Citation |
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Title: |
Replication Data for: Genomic prediction of agronomic traits in common bean under environmental stress |
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Identification Number: |
doi:10.7910/DVN/XCD67U |
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Authoring Entity: |
Keller, Beat (Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich) |
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Ariza-Suarez, Daniel (International Center for Tropical Agriculture - CIAT) |
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De la Hoz, Juan (University of California) |
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Aparicio, Johan Steven (International Center for Tropical Agriculture - CIAT) |
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Portilla Benavides, Ana Elisabeth (International Center for Tropical Agriculture - CIAT) |
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Buendia, Hector Fabio (International Center for Tropical Agriculture - CIAT) |
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Mayor, Victor Manuel (Progeny Breeding, Madrid, Colombia) |
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Studer, Bruno (Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich) |
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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: |
OPP1198373 |
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Distributor: |
Harvard Dataverse |
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Distributor: |
International Center for Tropical Agriculture |
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Access Authority: |
Alliance Data Management |
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Depositor: |
Cruz Arias, Paola Andrea |
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Date of Deposit: |
2020-03-11 |
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Holdings Information: |
https://doi.org/10.7910/DVN/XCD67U |
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Study Scope |
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Keywords: |
Agricultural Sciences, Earth and Environmental Sciences, Genomic selection, genotype x environment interactions, common bean (Phaseolus vulgaris L.), genome-wide association studies (GWAS), plant breeding, drought, phosphorus, Agrobiodiversity, Latin America and the Caribbean, Crops for Health |
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Topic Classification: |
Inbred lines, Drought stress, Heritability, Abiotic stress, Plant breeding, Breeding lines, Genotype environment interaction, Phaseolus vulgaris |
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Abstract: |
These datasets contain phenotypic and genotypic data of a panel of elite Andean breeding lines of common bean (Phaseolus vulgaris L.) from CIAT. This population has been tested in twelve yield trials carried out in Palmira and Darien (Colombia) between 2013 and 2018 to assess its performance under irrigated, drought and variable soil P conditions. These trials were laid out in the field with an alpha-lattice experimental design using two to three replicates, and a non-replicated trial in 2016. Meteorological data for these trials is also provided. Different agronomic traits were evaluated including Days to Flowering (DF), Days to Physiological Maturity (DPM), 100 seed weight (100SdW) and Yield (Yd). The agronomic performance of the population was modeled using linear mixed models with spatial correction. From these models, best linear unbiased estimators (BLUEs) and their corresponding standard errors (SE) were obtained. This population was genotyped by sequencing (GBS) using the ApeKI-based restriction digestion. The genotypic data is presented in a variant call format (VCF) file of 5,820 SNPs and 481 lines. The genotypic matrix was imputed using Beagle (v4.1). These datasets were used to test genomic prediction models on the panel in order to assess their prediction ability under different scenarios and parameter settings. |
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Kind of Data: |
Trial data |
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Kind of Data: |
Models |
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Kind of Data: |
Observation data |
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Kind of Data: |
Breeding data |
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Kind of Data: |
Genomic data |
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Kind of Data: |
Climate 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> |
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Other Study Description Materials |
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File Description--f3776452 |
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File: VEF_BLUE_data.tab |
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Notes: |
UNF:6:Sg+leovjjWAPaFgLab8jpw== |
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File Description--f3776451 |
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File: VEF_BLUE_data_dictionary.tab |
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Notes: |
UNF:6:wQ+6KynAuO0WqYMy6g6HiA== |
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File Description--f3776450 |
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File: VEF_meteoro.tab |
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Notes: |
UNF:6:4bf4NFXyGxbUk6gVAcZm6w== |
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File Description--f3776449 |
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File: VEF_meteoro_dictionary.tab |
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Notes: |
UNF:6:5La2CgFIHi4m+dxv/MQa/g== |
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File Description--f3776447 |
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File: VEF_raw_phenotypic_data.tab |
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Notes: |
UNF:6:MKlHwAoi9et46Y0+tGJdlw== |
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File Description--f3776448 |
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File: VEF_raw_phenotypic_data_dictionary.tab |
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Notes: |
UNF:6:8wWXj6JJ6UWI/iDyC4bKAQ== |
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List of Variables: |
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Variables |
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f3776452 Location: |
Variable Format: character Notes: UNF:6:SVeUyaE/LExF9yZ+0AUkiQ== |
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f3776452 Location: |
Variable Format: character Notes: UNF:6:fj2uVQyKwjJ1X9bKLrlhRQ== |
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f3776452 Location: |
Summary Statistics: Valid 2651.0; StDev 3.909604892940651; Max. 48.20193595; Min. 28.69928928; Mean 35.42198365964165; Variable Format: numeric Notes: UNF:6:TBUqe3oSSqtPko4s++9Uog== |
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f3776452 Location: |
Summary Statistics: Min. 0.126886794; Mean 0.7230178727385888; Valid 2651.0; Max. 1.651747083; StDev 0.3544446409557062; Variable Format: numeric Notes: UNF:6:fFl8WBGkZymgY8DwaK/HhA== |
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f3776452 Location: |
Summary Statistics: Valid 2029.0; Min. 57.07739915; Max. 86.24433461; Mean 68.92819322887136; StDev 8.751353847763049 Variable Format: numeric Notes: UNF:6:nQnsiTVp80UOMrLAxbXcIQ== |
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f3776452 Location: |
Summary Statistics: Mean 0.8523364483656974; Valid 2029.0; Min. 0.231791854; StDev 0.3276104747980823; Max. 1.475691534 Variable Format: numeric Notes: UNF:6:Rcg8GgYqundTg4/1gSWUww== |
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f3776452 Location: |
Summary Statistics: Max. 72.40591487; Mean 39.496376968878224; Min. 3.629959268; Valid 3334.0; StDev 11.104159333581137 Variable Format: numeric Notes: UNF:6:xUqyVNlsDMc9nuK7VNrPuw== |
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f3776452 Location: |
Summary Statistics: Max. 4.391980044; Mean 2.3024453634151163; Valid 3334.0; Min. 0.622351715; StDev 0.8769964198428404 Variable Format: numeric Notes: UNF:6:gaKkmnp8Eq3IU0Ss5TncIA== |
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f3776452 Location: |
Summary Statistics: Max. 3032.63816; Min. -245.3953338; Mean 1141.8092648584727; Valid 3550.0; StDev 515.7578450509146 Variable Format: numeric Notes: UNF:6:UK9jJQSAemEteCJ/mEFMng== |
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f3776452 Location: |
Summary Statistics: Mean 186.1204597158141; Max. 370.2708156; Min. 41.44652295; StDev 65.7198723308149; Valid 3550.0 Variable Format: numeric Notes: UNF:6:C3e2GpGxLuuudb3hDbBhIg== |
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f3776451 Location: |
Variable Format: character Notes: UNF:6:J9B026sbxcIgM0ko2AZ8PQ== |
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f3776451 Location: |
Variable Format: character Notes: UNF:6:Nog39MRuZqKLS+XpNJe/QQ== |
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f3776450 Location: |
Variable Format: character Notes: UNF:6:20dw+hsl/eFc/Oii+eVnLg== |
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f3776450 Location: |
Variable Format: character Notes: UNF:6:AVqAMrr5uDI7Xve5pt6r9w== |
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f3776450 Location: |
Summary Statistics: Min. 0.0; StDev 2.2698764330895846; Valid 984.0; Mean 30.16941056910569; Max. 37.1 Variable Format: numeric Notes: UNF:6:iQxjEyQo5pqXpb2VvPseLw== |
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f3776450 Location: |
Summary Statistics: Mean 19.329268292682926; StDev 1.428847209141321; Max. 24.0; Valid 984.0; Min. 0.0 Variable Format: numeric Notes: UNF:6:o/SpXW2l4fS8dcOLDVDD2A== |
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f3776450 Location: |
Summary Statistics: Mean 20.235234215885946; StDev 1.371763040423793; Min. 0.0; Valid 982.0; Max. 26.1 Variable Format: numeric Notes: UNF:6:GxjjHV6v98QN4nMfBP4LuA== |
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f3776450 Location: |
Summary Statistics: Mean 28.41291963377416; Valid 983.0; Max. 33.3; Min. 0.0; StDev 3.1881472699547033 Variable Format: numeric Notes: UNF:6:88b1eanvifzlvqCZKxX+BA== |
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f3776450 Location: |
Summary Statistics: Max. 27.8; Mean 23.329765545361877; StDev 2.616687196389824; Min. 0.0; Valid 981.0; Variable Format: numeric Notes: UNF:6:10/zcv8Ni4wDaM/IsUjYmw== |
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f3776450 Location: |
Summary Statistics: Max. 100.0; Min. 0.0; Mean 93.46028513238291; Valid 982.0; StDev 9.058083673551884 Variable Format: numeric Notes: UNF:6:t+RoGDQoJJmuy46NJ3sSOw== |
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f3776450 Location: |
Summary Statistics: Min. 0.0; Valid 983.0; StDev 21.902750967990613; Max. 666.0; Mean 63.877924720244145; Variable Format: numeric Notes: UNF:6:3D4vbC9ajHC+ojn0EEipbQ== |
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f3776450 Location: |
Summary Statistics: StDev 10.099005104276113; Valid 981.0; Mean 78.46585117227319; Min. 0.0; Max. 98.0 Variable Format: numeric Notes: UNF:6:5cA68ryGJalTG2Dbd/jW5Q== |
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f3776450 Location: |
Summary Statistics: StDev 11.763969106852938; Min. 0.0; Valid 982.0; Max. 256.0; Mean 58.35743380855397; Variable Format: numeric Notes: UNF:6:OZ1CIHQY+91jLJgXvrkIfw== |
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f3776450 Location: |
Summary Statistics: Max. 70.8; Mean 2.7966463414634153; Min. 0.0; StDev 8.139748305383973; Valid 984.0; Variable Format: numeric Notes: UNF:6:vd05QhtCC4mrRD5zxzF1zQ== |
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f3776450 Location: |
Summary Statistics: Valid 984.0; Max. 12.7; Mean 4.840853658536585; Min. 0.0; StDev 1.6472850387556697; Variable Format: numeric Notes: UNF:6:4+qZ5BHUwNaQLGaIEKVTmg== |
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f3776449 Location: |
Variable Format: character Notes: UNF:6:VSDKhxGBcfWIcZCL17t/lg== |
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f3776449 Location: |
Variable Format: character Notes: UNF:6:jA9JFWhyjV+druUpc2q3eA== |
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f3776447 Location: |
Variable Format: character Notes: UNF:6:50vGM5CyaL9FWTrBF+YoJA== |
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f3776447 Location: |
Variable Format: character Notes: UNF:6:+GWsI9XLvn8Uh5iJfRfs4A== |
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f3776447 Location: |
Variable Format: character Notes: UNF:6:uZ7YASSapYSQtJl9KSIeNA== |
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f3776447 Location: |
Variable Format: character Notes: UNF:6:L/oNjNMC5R81Jsi3+9QSGw== |
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f3776447 Location: |
Variable Format: character Notes: UNF:6:jE+sMGFigAQ6ay+YaJ4ijw== |
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f3776447 Location: |
Summary Statistics: Max. 90.0; Mean 26.25898918782975; Min. 1.0; Valid 11931.0; StDev 18.291047657983345 Variable Format: numeric Notes: UNF:6:GuMnoPm9JV9gx2O0dRUZeg== |
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f3776447 Location: |
Summary Statistics: Min. 1.0; Mean 24.958092364428964; StDev 20.392504429252394; Valid 11931.0; Max. 106.0; Variable Format: numeric Notes: UNF:6:fu4kTvGViHjFNW3Jbs/FZA== |
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f3776447 Location: |
Variable Format: character Notes: UNF:6:kua1TeRCDzNjtgs/wFL7cg== |
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f3776447 Location: |
Summary Statistics: Valid 9008.0; Max. 49.0; Min. 26.0; Mean 34.026976021314425; StDev 3.8308066929302167 Variable Format: numeric Notes: UNF:6:hm/nEQ0AURWpm+tL99qj6g== |
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f3776447 Location: |
Summary Statistics: StDev 7.582307263371765; Mean 65.38127563286673; Min. 51.0; Valid 7071.0; Max. 86.0; Variable Format: numeric Notes: UNF:6:o3LRs1yZAmm1XbdkosZ6HQ== |
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f3776447 Location: |
Summary Statistics: Mean 26.222278738555293; Max. 101.0; Min. 0.0; Valid 11796.0; StDev 13.15907156637495; Variable Format: numeric Notes: UNF:6:t0joD6wehPvp0sS2f3PaTQ== |
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f3776447 Location: |
Summary Statistics: StDev 1.8868605403655276; Max. 20.81; Min. 7.81; Mean 12.501291593328311; Valid 11931.0; Variable Format: numeric Notes: UNF:6:pSbL+fXKc0xrWsSqGkZyBA== |
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f3776447 Location: |
Summary Statistics: Min. 0.0; Max. 170.0; Valid 11002.0; Mean 36.91824764140743; StDev 11.833078296986141 Variable Format: numeric Notes: UNF:6:Mb5YtsP0isSwaZSUejwIkg== |
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f3776447 Location: |
Summary Statistics: Max. 1096.0; Mean 282.81467575577915; StDev 163.20687088515558; Valid 11809.0; Min. 3.0; Variable Format: numeric Notes: UNF:6:b7loifR6T9IeJTIhybSwIA== |
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f3776447 Location: |
Summary Statistics: Valid 11775.0; Max. 4505.915881; Min. 13.13639221; Mean 1203.3906544550566; StDev 612.6484079697418 Variable Format: numeric Notes: UNF:6:kFjv776NmerI8uycGfwgcA== |
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f3776448 Location: |
Variable Format: character Notes: UNF:6:5NY1X4HEpnAocebBUwvMPA== |
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f3776448 Location: |
Variable Format: character Notes: UNF:6:5/Xdi1rVsf5ykDhySXzM2Q== |
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Label: |
VEF_Pvulgaris_genotypic_data.vcf.gz |
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Notes: |
application/x-gzip |