Abstract
The German White-headed Mutton (GWM) sheep is a monitoring population believed to have been improved through crosses with other breeds, e.g., Texel (TXL) and French Berrichone du Cher (BDC). The primary aim of the study was to analyse genetic diversity and breed composition of GWM sheep. Furthermore, different measures of computing inbreeding from the runs of homozygosity (ROH) were investigated. Data for GWM consisted of pedigree information on 19,000 animals and 40,753 quality filtered SNPs on 46 individuals. Additionally, publicly available genotype data on 209 individuals belonging to nine sheep breeds were included in the analysis. Due to evenness of SNPs spacing and proportionality of the number of SNPs in each autosome to autosome length, a high correlation (rp = 0.99) was found between genomic inbreeding coefficients computed based on the length of ROH (FROH_L) and those computed relative to the number of SNPs in ROH (FROH_N). Total inbreeding was partitioned into values for individual chromosomes revealing the highest levels of inbreeding on chromosomes 1, 2 and 3. Correlations between the ROH-based inbreeding measures and pedigree inbreeding reached 0.82. The observed heterozygosity estimate in GWM was high (0.39), however, the breed suffered low level of effective population size (~50) from a genomic viewpoint. Moreover, effective number of founders (186), and effective number of ancestors (144) implied disequilibrium of founder contribution and a genetic bottleneck in the breed. Multidimensional scaling and network visualisation analyses revealed close connectedness of GWM to BDC and German Texel (GTX). A model-based admixture analysis consistently indicated the flow of genes from other breeds, particularly BDC to GWM. Our analyses highlight the mixed genetic background of GWM sheep and furthermore, suggest a close monitoring of the breed to consolidate its genetic diversity while averting further reduction in the effective population size.
Highlights
Domestic sheep (Ovis aries) are important livestock species of most agricultural-based economies
The quality of pedigree information was higher in the reference subpopulation than in the entire pedigree data
The current study revealed varying degrees of genetic similarity between the breed of interest and other sheep breeds
Summary
Domestic sheep (Ovis aries) are important livestock species of most agricultural-based economies. They serve a variety of functions including the provision of products such as meat, milk, wool, skin and horn; by-products in the form of manure for fertilisation and dung for fuel or biogas production; and other benefits including landscape maintenance and dike protection, and a source of income and sociocultural prestige [1, 2]. The demand and supply of sheep and specific sheep products can have a profound influence on the breeding objective of sheep industry. In Germany, sheep breeders in the 1870s had to abandon the breeding of wool sheep in favour of mutton or dual-purpose sheep production [3]. A sharp rise in human population growth necessitated changes in policies to allow for an increase in food production in the country
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