Title of the dataset:
Metadata from publication "Genetic Mapping of the Root Mycobiota in rice and its Role in Drought Tolerance"

Creators:
Andreo-Jimenez, Beatriz
te Beest, Dennis E.
Kruijer, Willem
Vannier, Nathan 
Kadam, Niteen N. 


Contributors:
Jagadish, S. V. Krishna 
van der Linden, Gerard
Ruyter-Spira, Carolien
Vandenkoornhuyse, Philippe 
Bouwmeester, Harro J.
Melandri, Giovanni


Related publication:
Andreo-Jimenez et al. 2023

Description:
Microbial and genomic data from root samples from rice plants grown under flooded and drought conditions, to unravel the genetic factors involved in the rice-microbe interaction, 
and whether genetics play a role in rice drought tolerance. Root mycobiota was characterized (18S SSU rRNA) in 296 rice accessions (Oryza sativa L. subsp. indica) under control and drought conditions.
Genome wide association mapping (GWAS) resulted in the identification of ten significant single nucleotide polymorphisms (SNPs) associated with root-associated fungi. 

Keywords:
drought, fungi, root mycobiota, GWAS, Oryza sativa (rice), roots


Spatial coverage:
Experiment was done in one location (IRRI, Philipines): 14°11'N, 121°15'E; elevation 21 m above sea level.

Temporal coverage:
Experiment was done once (2013)

This dataset contains the following files:

Control.OTU_0001.pdf (QQ-Plot for GWAS on OTU_0001 under control)
Drought.OTU_0002.pdf (QQ-Plot for GWAS on OTU_0002 under drought)
Drought.OTU_0007.pdf (QQ-Plot for GWAS on OTU_0007 under drought)
Drought.OTU_0011.pdf (QQ-Plot for GWAS on OTU_0011 under drought)
Drought.OTU_0015.pdf (QQ-Plot for GWAS on OTU_0015 under drought)
Drought.OTU_0019.pdf (QQ-Plot for GWAS on OTU_0019 under drought)
genotypes_in_our_study.txt (list of rice accessions names used in the study)
LD_selection_20220301.R (scripts used for the LD calculation and candidate genes selection)
rice_90k.RData (Genomic information of the rice panel used in the study: kinship values, SNPs)
scorecontrol.pdf (QQ-Plot for GWAS on RDA mycobiota scores in control)
scoredrought.pdf (QQ-Plot for GWAS on RDA mycobiota scores in drought)
SNPs_75K_windows_multi_gwas_LOD4_topSNPs.txt (list of SNPs found in the study to be related to rice roots and drought adaptation)
supplementary_information_file2.csv: It contains the sequence clusters counts obtained after the de-noising and taxa affiliation steps.
supplementary_information_file3.csv: It contains the sequence clusters taxonomical affiliations, their 18S SSU sequences and taxonomy.
supplementary_information_file4.xlsx: It contains genotypes metadata: genotypes names and their yield in both treatments, control and drought.
				      A diagram with the experimental set up is also included.



Methods, materials and software:
Statistical analyses were run in R Studio.


This dataset is published under the CC BY (Attribution) license.
This licence lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation.

