Retelling the recent evolution of genetic diversity for Guzerá: Inferences from LD decay, runs of homozygosity and Ne over the generations

Genetic diversity is the one of the most important issues in conservation studies of livestock breeds or endangered species. In the present study, we tested the feasibility of describing the recent evolution in genetic diversity through genome-wide SNP genotyping and estimates of linkage disequilibrium decay patterns, effective population size, inbreeding coefficient based on runs of homozygosity and population structure. We choose the bovine indicine breed Guzerá because it has suffered recent bottlenecks which have been registered historically. A sample of 1036 females was genotyped using Illumina BovineSNP50. A resampling strategy was applied to correct for sampling biases caused by the population structure in herds, and by the extensive use of some sires for artificial reproduction. A subsample of 210 animals and 32,806 markers with MAF>0.01 was used. Very low linkage disequilibrium was detected for distances greater than 120 Kb between two markers. Furthermore, three points of decrease in effective population size between generations were detected, which coincide with the historically registered bottlenecks. The inbreeding coefficient, based on runs of homozygosity, confirmed a strong contribution of the last 20-30 generations to current inbreeding. In the population structure analysis, the most probable number of sub-populations is 2, reflecting selection purpose (beef or dual-purpose). Taken together, these results allow a retelling of the recent evolution of this breed. The strategy described here will be useful for other breeds or even species for which a careful historical registry is not available for conservation proposals.