Two sterility alleles inherited in the F2 generation as recessive alleles in two nonlinked loci were mapped using the single marker regression option in Windows QTL Cartographer version 2.5 [ 27].
We used the single marker analysis function of NEO (LEO.NB.SingleMarker) score, which is the log10 probability of this model divided by the log10 probability of the next best fitting alternative model [ 34].
To scan phenotypes against the genome-wide SNP genotype data for association between trait and SNP, we used the single-marker mixed model [ 12] (Methods).
PLINK was used in the single marker GWAS, and INTERSNP was used to perform the two-marker GWIS, focusing only on SNPs with p ≤ 0.01 for the GWAS analysis.
To correct for multiple testing, Bonferroni correction for the number of studied SNPs (n = 10) was used in the single marker analysis and permutation (10 000 permutations) was used in the sliding window analyses.
Strict replication criteria were used in the single-marker analyses (Konig 2011).
We used the single nucleotide polymorphism rs10065172C/T as a marker of this polymorphic allele and genotyped 370 African American and 177 Caucasian tuberculosis (TB) cases and 180 African American and 110 Caucasian controls.
In the OSNA assay, which used the CK19 single marker, it was reported that in an examination of 346 ALNs from 32 patients, sensitivity was 96.3%, specificity was 94.7% and the concordance rate was 94.8% (Visser et al, 2008).
Young bulls were selected using strategies based on 1) the single marker with greatest contrast (BEST1), 2) the sum of n greatest contrasts (BESTn), 3) the best n contrasts, limited to one per chromosome (LIMn), 4) the sum of all contrasts exceeding a given threshold n (THRESn), and 5) the sum of contrasts exceeding a threshold, but limited to one per chromosome (LIMT).
The low expression group was used as a reference in the single marker analyses.
