Summary

This page contains links to the full 35k breeders’ array genotype data for the spring NIAB tetraploid x hexaploid wheat Nested Association Mapping population (NIAB_SW_TET_NAM). The data consists of 35,143 markers and 1,983 genotypes (including individuals and parents). There are 58 nested populations, each formed through backcrossing a different tetraploid donor with the recurrent parent Paragon. The genotyping array was the Breeders’ 35K Axiom® array (Affymetrix product ID 550524) and the genotyping was carried out at the University of Bristol, the DNA extraction and SNP calling was completed at NIAB. All work was funded by the Biotechnology and Biological Sciences Research Council (BBSRC) Cross-Institute Strategic Programme ‘Designing Future Wheat’ BB/P016855/1.

Data Download

The data can be downloaded here. The zip folder includes the following files:

  • full.markers.spring.thex.nam.v1.csv the dataset with NIAB codes.

  • pedigree.for.spring.thex.nam.csv a file with information on the pedigree of the 58 nested populations.

Information on data

The genotype QC in the axiom software was completed with QC thresholds of DQC = 0.8 and a QC call rate = 90%. An inbred penalty of 4 and a cr-cut off of 96 were used in the SNP calling. The data is in numeric format and was converted from the original axiom call codes format (AA, AB, BB and NoCall) using the following conversion:

"NoCall" = NA "AA" = 0 "AB" = 1 "BB" = 2

The marker calls for all 35,143 SNPs are included. The last 26 columns of the data contain SNP metrics outputted from the axiom software.

The data includes NAM individuals, tetraploid parents and a number of Paragon replicates in the following number:

Line Type Count
NAM individuals 1784
Tetraploid parents 186
Paragon replicates 11
Robigus replicates 2

The spring NIAB_SW_TET_NAM population contains 58 nested populations, backcrossed into Paragon and each with a different tetraploid donor. Each NAM individual’s name starts with a population code (e.g. THEX002_x_x_x). The below table shows the pedigree and information of genotypes in the data:

Population Code No. of Genotypes Founder of Population Recurrent Parent
THEX002 4 tios Paragon
THEX003 34 em27996 Paragon
THEX010 46 em14078 Paragon
THEX011 24 em14235 Paragon
THEX012 24 em16608 Paragon
THEX013 22 em17202 Paragon
THEX014 12 em18083 Paragon
THEX015 36 em18209 Paragon
THEX016 22 em18210 Paragon
THEX018 34 dic012a Paragon
THEX019 14 dic012b Paragon
THEX020 122 dic016a Paragon
THEX021 36 dic016b Paragon
THEX022 5 dic034 Paragon
THEX023 12 dic036 Paragon
THEX024 37 dic045 Paragon
THEX031 3 dic071 Paragon
THEX032 16 dic072 Paragon
THEX033 17 dic082 Paragon
THEX035 14 dic094 Paragon
THEX036 53 dic096 Paragon
THEX038 13 dic107 Paragon
THEX041 14 dic120 Paragon
THEX043 9 dic130 Paragon
THEX044 18 dic143 Paragon
THEX046 19 dic147 Paragon
THEX047 22 dic199 Paragon
THEX090 36 du030_1 Paragon
THEX092 57 du067_1 Paragon
THEX094 50 du088_2 Paragon
THEX096 74 ardente Paragon
THEX100 63 claudio Paragon
THEX101 44 croc1 Paragon
THEX102 38 cultur Paragon
THEX104 44 exceldur Paragon
THEX105 13 hoh501 Paragon
THEX106 47 hoh506 Paragon
THEX108 55 karim Paragon
THEX109 57 lloyd Paragon
THEX110 21 miradoux Paragon
THEX113 70 pescodou Paragon
THEX114 14 sculptur Paragon
THEX117 37 cudic24 Paragon
THEX145 27 acalou Paragon
THEX148 20 dic115 Paragon
THEX149 52 dic145 Paragon
THEX150 11 dic051 Paragon
THEX190 10 dic056 Paragon
THEX191 24 dic065 Paragon
THEX193 1 dic087 Paragon
THEX195 19 dic121 Paragon
THEX196 37 du057_1 Paragon
THEX197 18 dakter Paragon
THEX198 25 langdon Paragon
THEX212 63 cudic16 Paragon
THEX213 26 capelli Paragon
THEX214 28 hoh-501 Paragon
THEX224 21 biensur Paragon

Contact

For queries on the data and usage please contact:

  • fiona.leigh@niab.com, bethany.love@niab.com and tally.wright@niab.com