************************************************ CONTENTS ************************************************

1. 	README.txt - This file.

2. 	Mayer_et_al_genotypes_DHlines_600k_raw.txt.gz -
	Genotype calls for 941 DH lines derived from 3 European maize landraces in text format.
	The file includes the unfiltered set of 616,201 markers.
	DNA was processed on the Affymetrix GeneTitan® platform with the Axiom® Maize Genotyping Array 
	following manufacturer’s protocol. Raw hybridization intensity data processing, clustering, genotype 
	calling, inclusion of inbreeding level information, off-target variant calling, and variant 
	categorization according to genotype cluster metrics were performed according to the Axiom® 
	Genotyping Solution Data Analysis Guide as described in Unterseer et al. 2014. A threshold 
	of 0.90 for the variant call frequency instead of the default value (0.97) was applied. 
	Information on SNP IDs, genome positions, probe sets, and alleles are available at NCBI GEO as 
	platform GPL18778 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18778);
	please be aware that allele information is based on B73 RefGen_v2 which was used for the array development,
	thus the given alleles in the file might now partly be according to the reverse strand for B73 RefGen_v4.
	The columns of this file contain:
	1: 	marker name
	2: 	chromosome (based on B73 RefGen_v4, unmapped markers are indicated by the value '0')
	3: 	position in bp (based on B73 RefGen_v4)
	4: 	Quality class of the genotype calling (see Unterseer et al. 2014)
	5-945:	Genotype calls of DH lines, the abbreviation of the respective landrace to which lines belong
		are included in the name (KE = Kemater Landmais Gelb, LL = Lalin, PE = Petkuser ferdinand Rot)
	
3. 	Mayer_et_al_genotypes_DHlines_600k_filteredImputed.txt.gz -
	Filtered and imputed genotype calls (as genotype scores 0 and 2) of 941 DH lines derived from 3 European
	maize landraces in text format. The file includes the filtered set of 501,124 markers. Filtering steps
	and imputation are described in Hölker et al. 2019 and Mayer et al. 2020.
	The columns of this file contain:
	1: 	marker name
	2: 	chromosome (based on B73 RefGen_v4, unmapped markers are indicated by the value '0')
	3: 	position in bp (based on B73 RefGen_v4)
	4: 	Allele corresponding to genotype score '0'	
	5: 	Allele corresponding to genotype score '2'
	6-946:	Genotype scores of DH lines, the abbreviation of the respective landrace to which lines belong
		are included in the name (KE = Kemater Landmais Gelb, LL = Lalin, PE = Petkuser Ferdinand Rot)	

4. 	Mayer_et_al_phenotypes_rawData.txt.gz -
	Plot based data of phenotypic values of 899 DH lines derived from 3 European maize landraces 
	and 14 breeding lines in text format. The columns of this file contain:
	1: 	Plot number
	2: 	Replication number
	3: 	Block number
	4: 	Genotype	
	5: 	Lattice number
	6:	Location
	7:	Year
	8:	Environment (combination of year and location)
	9-17:	Phenotypic values for the 9 traits analyzed in Mayer et al. 2020

5. 	Mayer_et_al_phenotypes_BLUEs_perEnvironment.txt.gz -
	Adjusted means for each DH line and check within each environment. The columns of this file contain:
	1: 	Genotype
	2:	Environment (combination of year and location)
	3-11:	Phenotypic values (adjusted means) for the 9 traits analyzed in Mayer et al. 2020

6. 	Mayer_et_al_phenotypes_BLUEs_acrossAllEnvironments.txt.gz -
	Adjusted means for each DH line and check across all 11 environments. The columns of this file contain:
	1: 	Genotype
	2-10:	Phenotypic values (adjusted means) for the 9 traits analyzed in Mayer et al. 2020

7. 	Mayer_et_al_phenotypes_BLUEs_acrossSixLocations2017.txt.gz -
	Adjusted means for each DH line and check across the six locations in 2017. The columns of this file contain:
	1: 	Genotype
	2-10:	Phenotypic values (adjusted means) for the 9 traits analyzed in Mayer et al. 2020	


*********************************************** REFERENCES **************************************************

Mayer et al. 2020:
Title: 		Discovery of beneficial haplotypes for complex traits in maize landraces
Authors:	Mayer, M.; Hölker, A.C.; González-Segovia, E.; Bauer, E.; Presterl, T.; Ouzunova, M.;
			Melchinger, A.E.; Schön, C.-C.
Year:		2020
Journal:	When the data was uploaded, the manuscript was accepted for publication by Nature Communications


Hölker et al. 2019:
Title: 		European maize landraces made accessible for plant breeding and genome-based studies
Authors:	Hölker, A.C.; Mayer, M.; Presterl, T.; Bolduan, T.; Bauer, E.; Ordas, B.; Brauner, P.C.;
			Ouzunova, M.; Melchinger, A.E.; Schön, C.-C.
Year:		2019
Journal:	Theoretical and Applied Genetics 132, 3333–3345
Doi:		10.1007/s00122-019-03428-8


Unterseer et al. 2014:
Title: 		A powerful tool for genome analysis in maize: development and evaluation 
			of the high density 600 k SNP genotyping array.
Authors:	Unterseer, S.; Bauer, E.; Haberer, G.; Seidel, M.; Knaak, C.; Ouzunova, M.; 
			Meitinger, T.; Strom, T.M.; Fries. R.; Pausch, H.; Bertani, C.; Davassi, A.; 
			Mayer, K.F.X.; Schön, C.-C.
Year:		2014
Journal:	BMC Genomics 15:823
Doi: 		10.1186/1471-2164-15-823


************************************************* CONTACT ******************************************************


Manfred Mayer

Technical University of Munich
TUM School of Life Sciences Weihenstephan
Plant Breeding

Liesel-Beckmann-Str. 2
85354 Freising
Germany

e-mail:	manfred.mayer@tum.de
http://www.plantbreeding.wzw.tum.de/


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