Our results balance the trade-offs between conserving breeds as insurance against future uncertainties and current sustainable utilization.
Following this, the MVT core set method suggests conserving breeds that show a large difference in the respective population mean of a hypothetical quantitative trait.
Under the assumption that LD is conserved across breeds, reference populations from different breeds can be combined to increase the size of the reference population.
However, GWAS across breeds will be less likely to detect SNP that are in LD with QTL in only one breed and will be more likely to detect SNP in LD with QTL across both breeds, provided LD phase is conserved across breeds e.g. [ 40, 41].
In fact, multi-breed imputation is expected to improve imputation accuracy only when 50K haplotypes are conserved across breeds, which is quite unlikely given the history of the breeds and their estimated divergence time, even for the most closely related breeds.
de Roos et al. [ 7, 8] reported that the phase of LD between adjacent markers on the 50 K Bovine SNP chip frequently differed among B. taurus cattle breeds, which means that the power of association studies based on the 50 K chip will be reduced when using multiple breeds because the LD between SNPs and QTL is unlikely to be conserved across breeds.
The sharp decrease in imputation accuracies when an external breed was used as reference population also supports that haplotypes are less conserved across breeds.
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.
In Bos taurus cattle populations, LD phase is conserved across breeds among SNP alleles at short distances (5 to 30 kb) [ 11].
Although QTL regions are not well conserved between breeds within the same species nor between different species, it is well documented that syntenic regions are highly conserved between species [ 71].
