Because of the extensive between-breed linkage disequilibrium (LD) in the F2 resource populations, standard association test, marker-assisted association test and F-drop test were performed to analyze the association between the candidate genes and the ear size in the current F2 resource population as described in Zhao et al.[ 30].
Sutter, N. B., Eberle, M., H. G., P., Kruglyak, L. & E. A., O. Extensive and breed specific linkage disequilibrium in Canis familiaris.
Between breeds however, linkage disequilibrium phase among SNP is only conserved at 5-10 kb, for Bos taurus breeds at least [ 7].
Sutter, N. B. et al. Extensive and breed-specific linkage disequilibrium in Canis familiaris.
Within a single breed or line, linkage disequilibrium (LD) between QTL (quantitative trait loci) and SNPs may extend across a relatively large distance, and therefore a QTL is expected to be in LD with several surrounding SNPs.
The effect of the B allele at this lead-SNP was in the same direction (increasing or decreasing) for the associated traits across different breeds, indicating that linkage phase between this lead-SNP and the causal mutation is conserved across breeds (Additional files 1, 2, 3, 4, 7, 8, 10 and 12) suggesting that the SNP is very close to the causal mutation.
This approach takes advantage of the allelic nature of traits between breeds and the extended regions of linkage disequilibrium within breeds as well as the power of strong artificial selection for breed-defining traits [24].
However in crossbred populations, 1) effects of SNPs may be breed specific, and 2) linkage disequilibrium may not be restricted to markers that are tightly linked to the QTL.
This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds.
The first approach is based on the calculation of correlation coefficients r for the same pair of SNPs in two different breeds as measures of linkage disequilibrium (LD) [ 23].
The current study was designed to address this point by examining the concordance between a genomic diversity dataset comprising genome-wide SNP data from two cattle breeds and a set of linkage mapping results from a study in an F2/Backcross population bred from founders of these same breeds.
