Linkage disequilibrium (LD) extent in B1 population by

chromosome Chromosomes I to XII

Mariela Aponte VilladomaElisa J. Mihovilovich CastroMerideth Bonierbale

Procedure

LD was measured using the raw genotypic data of 272 DArT markers with known map position

Linkage disequilibrium between DArT loci was quantified by the square correlation coefficient, ‘r2’ (Weir, 1996)

Tassel v.2.0.1 was used to measure LD http://www.maizegenetics.net/bioinformatics

One thousand permutations were performed to calculate the proportion of permuted genotype distributions that are less probable than the observed genotype distribution under the null hypothesis of independence (Weir, 1996)

References

Weir SB (1996) Genetic data analysis II. Sinauer Associates, Inc., Sunderland, pp 91-138

Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635.

Chromosome I LD extent=13.5 cMr2 values estimated on raw genotypic data as a function of distance (cM)

Chromosome II LD extent=15.9 cM r2 values estimated on raw genotypic data as a function of distance (cM)

Chromosome III LD extent=23.3 cM

Significant disequilibria are represented by filled diamonds

r2 values estimated on raw genotypic data as a function of distance (cM)

Chromosome IV LD extent=15.6 cM

Significant disequilibria are represented by filled diamonds

r2 values estimated on raw genotypic data as a function of distance (cM)

Chromosome V LD extent=1.6 cM

Significant disequilibria are represented by filled diamonds

r2 values estimated on raw genotypic data as a function of distance (cM)

Chromosome VI LD extent=28.3 cM

r2 values estimated on raw genotypic data as a function of distance (cM)

Significant disequilibria are represented by filled diamonds

Chromosome VII LD extent=29.5 cM

Significant disequilibria are represented by filled diamonds

r2 values estimated on raw genotypic data as a function of distance (cM)

Chromosome VIII LD extent=2.7 cM

Significant disequilibria are represented by filled diamonds

r2 values estimated on raw genotypic data as a function of distance (cM)

Chromosome IX LD extent=10.9 cM

Significant disequilibria are represented by filled diamonds

r2 values estimated on raw genotypic data as a function of distance (cM)

Chromosome X LD extent=1.03 cM

Significant disequilibria are represented by filled diamonds

r2 values estimated on raw genotypic data as a function of distance (cM)

Chromosome XI LD extent=0.6 cM

Significant disequilibria are represented by filled diamonds

r2 values estimated on raw genotypic data as a function of distance (cM)

Chromosome XII LD extent=15.4 cM

Significant disequilibria are represented by filled diamonds

r2 values estimated on raw genotypic data as a function of distance (cM)