Data from: Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines

Spindel J, Begum H, Akdemir D, Virk P, Collard B, Redoña E, Atlin G, Jannink J, McCouch SR

Date Published: February 24, 2015

DOI: http://dx.doi.org/10.5061/dryad.7369p

 

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Title MET_GBS_data_crfilt_.75_allchrom.hmp.txt
Downloaded 161 times
Description Post-imputation GBS data for the IRRI breeding population used in Spindel et al., 2015 and Begum and Spindel et al., 2015 (with additional filtering, see papers for details). GBS dataset contains all SNPs with call rates >= .75 and all individuals with missing data < .6
Download MET_crfilt_.75_allchrom.hmp.txt.zip (8.460 Mb)
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Title MET_crfilt_.90_outliers_removed_for_RRBlup
Downloaded 37 times
Description Post-imputation GBS dataset used specifically for GS cross-validation in Spindel et al., 2015. Dataset contains all markers with call rates >= .9 and lines that were included in the GS analysis (i.e., sub-population outliers are removed from this dataset). The data are formatted for use with the R rrBLUP package.
Download MET_crfilt_.90_outliers_removed_for_RRBlu...ed.csv (112.6 Mb)
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Title binned_subsets_2_14
Downloaded 86 times
Description contains the evenly distributed genotype subsets used in Spindel et al., 2015
Download binned_subsets_2_14.zip (20.12 Mb)
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Title random_subsets
Downloaded 85 times
Description contains the randomly distributed genotype subsets used in Spindel et al., 2015
Download random_subsets_from_.75_crFilt.zip (15.47 Mb)
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Title RYT_plotdata_by_GHID_corrected_PUBLIC_ACCESS
Downloaded 97 times
Description contains the raw phenotype data for genotyped individuals for 2009-2012, dry and wet seasons, used in Spindel et al., 2015.
Download RYT_plotdata_by_GHID_corrected_PUBLIC_ACCESS.zip (95.92 Kb)
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When using this data, please cite the original publication:

Spindel J, Begum H, Akdemir D, Virk P, Collard B, Redoña E, Atlin G, Jannink J, McCouch SR (2015) Genomic Selection and Association Mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines. PLOS Genetics 11(2): e1004982. http://dx.doi.org/10.1371/journal.pgen.1004982

Additionally, please cite the Dryad data package:

Spindel J, Begum H, Akdemir D, Virk P, Collard B, Redoña E, Atlin G, Jannink J, McCouch SR (2015) Data from: Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.7369p
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