Genomic analyses suggest adaptive differentiation of northern European native cattle breeds

Abstract

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.

Evolution and domestication of the Bovini species

“…2018), northern Europe (Stronen et al . 2019), north‐west Europe (Kelleher et al . 2017), north‐west and southern Europe (Upadhyay et al .…”

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

“…Our data agreed with the findings of Xu et al [15], who performed the genotyping of three commercial taurine breeds by using high-density DNA array and observed similar level of genetic variability (H E = 0.337-0.356). In contrast, Stronen et al [17] detected lower genetic variability in taurine breeds (H E = 0.226 and 0.298); this was probably because of the small population size of the studied native breeds. We observed slight excess of heterozygotes in both the Russian breeds ( U F IS = -0.022 and -0.013 for Kholmogor and Yaroslavl breeds, respectively), which agrees with the findings obtained using DNA chips of lower density [9,10].…”

“…Several studies have explored the genome diversity and adaptation of cattle breeds by using high-density DNA arrays [15][16][17]. However, the patterns of genetic variation within Russian cattle breeds have not yet been assessed using this powerful genetic tool.…”

Local adaptations of Mediterranean sheep and goats through an integrative approach

“…DPH6 belongs to the circadian rhythm-related GO categories. Moreover it was found under selection in northern European cattle (Stronen et al, 2019), in yaks (Lan et al, 2018), and associated with plateau conditions in Chinese sheep (Yang et al, 2016).…”