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.

Genetic diversity in Iranian indigenous sheep vis-à-vis selected exogenous sheep breeds and wild mouflon.

The heterogeneity of climate and different agro-ecological conditions in Iran have resulted in development of 27 indigenous sheep breeds. Wild Asiatic mouflon (Ovis orientalis) is believed to be the ancestor of Iranian sheep. Evaluation of genetic diversity and population structure within and among domestic breeds has important implications for animal breeding programs and genetic resources management. Based on 50K SNP genotype data, we studied the genetic diversity of five indigenous Iranian sheep breeds: Afshari (n = 37), Moghani (n = 34), Qezel (n = 35), Zel (n = 46) and Lori-Bakhtiari (n = 46), and Asiatic mouflon (n = 8) sampled from Iran. Furthermore, genetic diversity and the breed admixture of Iranian sheep were assessed on a larger geographic scale using a reference panel comprising: three indigenous Afghan breeds - Arabi (n = 15), Balouchi (n = 15) and Gadik (n = 15); three indigenous breeds from Turkey and Cyprus - Cyprus Fat Tail (n = 30), Karakas (n = 18) and Norduz (n = 20); and three commercial European breeds - Suffolk (n = 19), Comisana (n = 24) and Engadine Red Sheep (n = 24). The results revealed that the investigated breeds are divided into five genetically distinct clusters according to their geographic origin. Afshari was closest to the local mouflon population and showed signs of mouflon admixture. Qezel was identified as a hybrid sheep breed. Much evidence supported the Afghan breeds being identical. Inbreeding values, which were estimated based on ROHs, were highest for Suffolk (FROH  = 0.0544) and lowest for Balouchi (FROH  = 0.0078). In conclusion, analysis of selected breeds from neighboring countries along with Asiatic mouflon gave a deeper insight into the evolutionary history and origin of Iranian sheep with important implications for future breed management.

Oral transmission as a route of infection for viral haemorrhagic septicaemia virus in rainbow trout, Oncorhynchus mykiss (Walbaum).

Surveys among wild marine fish have revealed occurrence of viral haemorrhagic septicaemia virus (VHSV) infections in a high number of diverse fish species. In marine aquaculture of rainbow trout, preying on invading wild fish might thus be a risk factor for introduction and adaptation of VHSV and subsequent disease outbreaks. Our objective was to determine whether an oral transmission route for VHSV in rainbow trout exists. Juvenile trout were infected through oral, waterborne and cohabitation transmission routes, using a recombinant virus strain harbouring Renilla luciferase as reporter gene. Viral replication in stomach and kidney tissue was detected through bioluminescence activity of luciferase and qRT-PCR. Replication was detected in both tissues, irrespective of transmission route. Replication patterns, however, differed among transmission routes. In trout infected through oral transmission, replication was detected in the stomach prior to kidney tissue. In trout infected through waterborne or cohabitation transmission, replication was detected in kidney prior to stomach or in both tissues simultaneously. We demonstrate the existence of an oral transmission route for VHSV in rainbow trout. This implies that preying on invading infected wild fish is a risk factor for introduction of VHSV into marine cultures of rainbow trout.