Relationship of Icelandic cattle with Northern and Western European cattle breeds, admixture and population structure

Opportunities of Genomics for the Use of Semen Cryo-Conserved in Gene Banks

Shortly after the introduction of cryo-conserved semen in the main farm animal species, gene banks were founded. Safeguarding farm animal genetic diversity for future use was and is the main objective. A sampling of sires was based on their pedigree and phenotypic information. Nowadays, DNA information from cryo-conserved sires and from animals in the living populations has become available. The combination of their DNA information can be used to realize three opportunities: 1) to make the gene bank a more complete archive of genetic diversity, 2) to determine the history of the genetic diversity from the living populations, and 3) to improve the performance and genetic diversity of living populations. These three opportunities for the use of gene bank sires in the genomic era are outlined in this study, and relevant recent literature is summarized to illustrate the great value of a gene bank as an archive of genetic diversity.

Genetic Differentiation among Livestock Breeds—Values for Fst

Simple Summary

The degree of relationship among livestock breeds can be quantified by the F_st statistic, which measures the extent of genetic differentiation between them. An F_st value of 0.1 has often been taken as indicating that two breeds are indeed genetically distinct, but this concept has not been evaluated critically. Here, F_st values have been collated for the six major livestock species: cattle, sheep, goats, pigs, horses, and chickens. These values are remarkably variable both within and between species, demonstrating that F_st > 0.1 is not a reliable criterion for breed distinctiveness. However, the large body of F_st data accumulated in the last 20–30 years represents an untapped database that could contribute to the development of interdisciplinary research involving livestock breeds.

Abstract

(1) Background: The F_st statistic is widely used to characterize between-breed relationships. F_st = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding F_st values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed F_st were as follows, cattle: microsatellite 0.06–0.12, SNP 0.08–0.15; sheep: microsatellite 0.06–0.10, SNP 0.06–0.17; horses: microsatellite 0.04–0.11, SNP 0.08–0.12; goats: microsatellite 0.04–0.14, SNP 0.08–0.16; pigs: microsatellite 0.06–0.27, SNP 0.15–0.22; chickens: microsatellite 0.05–0.28, SNP 0.08–0.26. (4) Conclusions: (1) Large amounts of F_st data are available for a substantial proportion of the world’s livestock breeds, (2) the value for between-breed F_st of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated F_st data may have value for interdisciplinary research.

Genomic inbreeding and selection signatures in the local dairy breed Icelandic Cattle

Icelandic Cattle is the only dairy cattle breed native to Iceland. It currently numbers ca. 26 000 breeding females. We used 50k genotypes of over 8000 Icelandic Cattle to estimate genomic and pedigree-based inbreeding and to detect selection signatures using the integrated haplotype score. We used 47 Icelandic bulls genotyped with a 770k SNP chip to estimate LD decay for comparison with other Nordic dairy cattle breeds. We detected ROHs on the autosomes and computed ROH-based autosomal inbreeding coefficients. Average inbreeding coefficients according to pedigree and ROHs were 0.0621 and 0.101. Effective population sizes for the years 2009-2017 according to pedigree, ROHs, genomic relationship matrix, excess of homozygosity and individual increase in inbreeding were 81, 65, 60, 58 and 92 respectively. We identified three regions and six candidate genes that showed a signature of selection according to the integrated haplotype score (P < 0.05) on chromosomes 1, 16 and 23. The LD structure of Icelandic Cattle is shaped by a long period of isolation and a small founder population. The estimate of LD at distances closer than 0.3 Mb is lower in Icelandic Cattle than in Danish Jersey, but is higher than in Danish Holstein and Red Nordic Dairy Cattle breeds. Our findings show that inbreeding rates in Icelandic Cattle currently are sustainable according to FAO guidelines, and our results do not indicate severe historical inbreeding.

Comparison of bovine milk oligosaccharides in native North European cattle breeds

Milk oligosaccharides are of high interest due to their bioactive properties. This study is the first to characterise milk oligosaccharides from native North European cattle breeds, as represented by 80 milk samples collected from eight native breeds originated from Norway (Norwegian Doela cattle and Norwegian Telemark cattle), Sweden (Swedish Mountain cattle), Denmark (Danish Red anno 1970), Iceland (Icelandic cattle), Lithuania (native Lithuanian Black and White) and Finland (Western Finncattle and Eastern Finncattle). Using high-performance liquid-chromatography chip/quadrupole time-of-flight mass-spectrometry, 18 unique monosaccharide compositions and a multitude of isomers were identified. No N-glycolylneuraminic acid was identified among these breeds. Western Finncattle milk was most abundant in neutral, acidic and fucosylated oligosaccharides. Further, Eastern Finncattle milk was significantly higher in acidic oligosaccharides and Icelandic cattle milk significantly higher in fucosylated oligosaccharides, compared to the mean. This study highlights specific native breeds of particular interest for future exploitation of milk oligosaccharides and breeding strategies.