1. Linkage disequilibrium (LD) extent in B1 population by chromosome Chromosomes I to XII Mariela Aponte Villadoma Elisa J. Mihovilovich Castro Merideth Bonierbale

2. Procedure n LD was measured using the raw genotypic data of 272 DArT markers with known map position n Linkage disequilibrium between DArT loci was quantified by the square correlation coefficient, ‘r 2 ’ (Weir, 1996) n Tassel v.2.0.1 was used to measure LD http://www.maizegenetics.net/bioinformatics http://www.maizegenetics.net/bioinformatics n 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)

3. 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.TASSEL: Software for association mapping of complex traits in diverse samples.

4. Chromosome I LD extent=13.5 cM r 2 values estimated on raw genotypic data as a function of distance (cM)

5. Chromosome II LD extent=15.9 cM r 2 values estimated on raw genotypic data as a function of distance (cM)

6. Chromosome III LD extent=23.3 cM Significant disequilibria are represented by filled diamonds r 2 values estimated on raw genotypic data as a function of distance (cM)

7. Chromosome IV LD extent=15.6 cM Significant disequilibria are represented by filled diamonds r 2 values estimated on raw genotypic data as a function of distance (cM)

8. Chromosome V LD extent=1.6 cM Significant disequilibria are represented by filled diamonds r 2 values estimated on raw genotypic data as a function of distance (cM)

9. Chromosome VI LD extent=28.3 cM r 2 values estimated on raw genotypic data as a function of distance (cM) Significant disequilibria are represented by filled diamonds

10. Chromosome VII LD extent=29.5 cM Significant disequilibria are represented by filled diamonds r 2 values estimated on raw genotypic data as a function of distance (cM)

11. Chromosome VIII LD extent=2.7 cM Significant disequilibria are represented by filled diamonds r 2 values estimated on raw genotypic data as a function of distance (cM)

12. Chromosome IX LD extent=10.9 cM Significant disequilibria are represented by filled diamonds r 2 values estimated on raw genotypic data as a function of distance (cM)

13. Chromosome X LD extent=1.03 cM Significant disequilibria are represented by filled diamonds r 2 values estimated on raw genotypic data as a function of distance (cM)

14. Chromosome XI LD extent=0.6 cM Significant disequilibria are represented by filled diamonds r 2 values estimated on raw genotypic data as a function of distance (cM)

15. Chromosome XII LD extent=15.4 cM Significant disequilibria are represented by filled diamonds r 2 values estimated on raw genotypic data as a function of distance (cM)