Analysis of genetic diversity in Brown Swiss, Jersey and Holstein populations using genome-wide single nucleotide polymorphism markers

摘要

Background Studies of genetic diversity are essential in understanding the extent of differentiation between breeds, and in designing successful diversity conservation strategies. The objective of this study was to evaluate the level of genetic diversity within and between North American Brown Swiss (BS, n?=?900), Jersey (JE, n?=?2,922) and Holstein (HO, n?=?3,535) cattle, using genotyped bulls. GENEPOP and FSTAT software were used to evaluate the level of genetic diversity within each breed and between each pair of the three breeds based on genome-wide SNP markers (n?=?50,972). Results Hardy-Weinberg equilibrium (HWE) exact test within breeds showed a significant deviation from equilibrium within each population ( P st) indicated that the combination of BS and HO in an ideally amalgamated population had higher genetic diversity than the other pairs of breeds. Conclusion Results suggest that the three bull populations have substantially different gene pools. BS and HO show the largest gene differentiation and jointly the highest total expected gene diversity compared to when JE is considered. If the loss of genetic diversity within breeds worsens in the future, the use of crossbreeding might be an option to recover genetic diversity, especially for the breeds with small population size.