Open AccessGenomic analyses suggest adaptive differentiation of northern European native cattle breeds
Author(s) -
Stronen Astrid V.,
Pertoldi Cino,
Iacolina Laura,
Kadarmideen Haja N.,
Kristensen Torsten N.
Publication year - 2019
Publication title -
evolutionary applications
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.776
H-Index - 68
ISSN - 1752-4571
DOI - 10.1111/eva.12783
Subject(s) - biology , genetic diversity , inbreeding , population , evolutionary biology , effective population size , outcrossing , genetic variation , population genomics , nucleotide diversity , genetic drift , breed , population bottleneck , runs of homozygosity , genetics , genomics , single nucleotide polymorphism , ecology , allele , microsatellite , haplotype , genotype , genome , demography , sociology , pollen , gene
Native domestic breeds represent important cultural heritage and genetic diversity relevant for production traits, environmental adaptation and food security. However, risks associated with low effective population size, such as inbreeding and genetic drift, have elevated concerns over whether unique within‐breed lineages should be kept separate or managed as one population. As a conservation genomic case study of the genetic diversity represented by native breeds, we examined native and commercial cattle ( Bos taurus ) breeds including the threatened Danish Jutland cattle. We examined population structure and genetic diversity within breeds and lineages genotyped across 770K single nucleotide polymorphism loci to determine (a) the amount and distribution of genetic diversity in native breeds, and (b) the role of genetic drift versus selection. We further investigated the presence of outlier loci to detect (c) signatures of environmental selection in native versus commercial breeds, and (d) native breed adaptation to various landscapes. Moreover, we included older cryopreserved samples to determine (e) whether cryopreservation allows (re)introduction of original genetic diversity. We investigated a final set of 195 individuals and 677K autosomal loci for genetic diversity within and among breeds, examined population structure with principal component analyses and a maximum‐likelihood approach and searched for outlier loci suggesting artificial or natural selection. Our findings demonstrate the potential of genomics for identifying the uniqueness of native domestic breeds, and for maintaining their genetic diversity and long‐term evolutionary potential through conservation plans balancing inbreeding with carefully designed outcrossing. One promising opportunity is the use of cryopreserved samples, which can provide important genetic diversity for populations with few individuals, while helping to preserve their traditional genetic characteristics. Outlier tests for native versus commercial breeds identified genes associated with climate adaptation, immunity and metabolism, and native breeds may carry genetic variation important for animal health and robustness in a changing climate.