Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe

Abstract

Background: Local cattle breeds need special attention, as they are valuable reservoirs of genetic diversity. Appropriate breeding decisions and adequate genomic management of numerically smaller populations are required for their conservation. At this point, the analysis of dense genome-wide marker arrays provides encompassing insights into the genomic constitution of livestock populations. We have analyzed the genetic characterization of ten cattle breeds originating from Germany, The Netherlands and Denmark belonging to the group of red dairy breeds in Northern Europe. The results are intended to provide initial evidence on whether joint genomic breeding strategies of these populations will be successful.

Results: Traditional Danish Red and Groningen White-Headed were the most genetically differentiated breeds and their populations showed the highest levels of inbreeding. In contrast, close genetic relationships and shared ancestry were observed for the populations of German Red and White Dual-Purpose, Dutch Meuse-Rhine-Yssel, and Dutch Deep Red breeds, reflecting their common histories. A considerable amount of gene flow from Red Holstein to German Angler and to German Red and White Dual-Purpose was revealed, which is consistent with frequent crossbreeding to improve productivity of these local breeds. In Red Holstein, marked genomic signatures of selection were reported on chromosome 18, suggesting directed selection for important breeding goal traits. Furthermore, tests for signatures of selection between Red Holstein, Red and White Dual-Purpose, and Meuse-Rhine-Yssel uncovered signals for all investigated pairs of populations. The corresponding genomic regions, which were putatively under different selection pressures, harboured various genes which are associated with traits such as milk and beef production, mastitis and female fertility.

Conclusions: This study provides comprehensive knowledge on the genetic constitution and genomic connectedness of divergent red cattle populations in Northern Europe. The results will help to design and optimize breeding strategies. A joint genomic evaluation including some of the breeds studied here seems feasible.

Fig. 1

Boxplots showing the level of genomic inbreeding (F_ROH>4 Mb) per breed. Red dots indicate the mean values. ANG German Angler, DBE Dutch Belted, DFR Dutch Friesian Red, DR Deep Red, GWH Groningen White-Headed, IR Improved Red, MRY Meuse-Rhine-Yssel, RDM70 Traditional Danish Red, RDN Red and White Dual-Purpose, RH Red Holstein

Fig. 2

Genetic relatedness among the cattle breeds from Germany, The Netherlands and Denmark using principal component analysis (a PC1 vs. PC2; b PC2 vs. PC3; c PC2 vs. PC4). ANG German Angler, DBE Dutch Belted, DFR Dutch Friesian Red, DR Deep Red, GWH Groningen White-Headed, IR Improved Red, MRY Meuse-Rhine-Yssel, RDM70 Traditional Danish Red, RDN Red and White Dual-Purpose, RH Red Holstein

Fig. 3

Unsupervised model-based clustering results of 393 individuals using 19,717 SNPs. Presented are K values from 2 to 8. ANG German Angler, DBE Dutch Belted, DFR Dutch Friesian Red, DR Deep Red, GWH Groningen White-Headed, IR Improved Red, MRY Meuse-Rhine-Yssel, RDM70 Traditional Danish Red, RDN Red and White Dual-Purpose, RH Red Holstein

Fig. 4

Phylogenetic tree of 22 cattle breeds with five migration events constructed using the TreeMix software. ANG German Angler, AYR Finnish Ayrshire, BRV Braunvieh, BSW Brown Swiss, DBE Dutch Belted, DFR Dutch Friesian Red, DR Deep Red, GNS Guernsey, GWH Groningen White-Headed, HOL Holstein Friesian, IR Improved Red, JER Jersey, MON Montbéliarde, MRY Meuse-Rhine-Yssel, NDA N’Dama, NRC Norwegian Red Cattle, PRP French Red Pied Lowland, RDM70 Traditional Danish Red, RDN Red and White Dual-Purpose, RH Red Holstein, SHO Shorthorn, SIM Simmental Cattle

Fig. 5

Genome-wide distribution of standardized |iHS| values averaged in windows of 500 kb per chromosome for the populations Red Holstein (a), Red and White Dual-Purpose (b) and Meuse-Rhine-Yssel (c). Dashed lines indicate the cut-off values representing 0.5% of windows with highest standardized |iHS|

Fig. 6

Genome-wide distribution of standardized |XPEHH| values averaged in windows of 500 kb per chromosome for the comparison of Red Holstein and Red and White Dual-Purpose (a), Red Holstein and Meuse-Rhine-Yssel (b) and Red and White Dual-Purpose and Meuse-Rhine-Yssel (c). Dashed lines indicate the cut-off values representing windows with 0.5% highest |XPEHH| scores