Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing

Abstract

German Black Pied cattle (Deutsches Schwarzbuntes Niederungsrind, DSN) are an endangered dual-purpose cattle breed originating from the North Sea region. The population comprises about 2,500 cattle and is considered one of the ancestral populations of the modern Holstein breed. The current study aimed at defining the breeds closest related to DSN cattle, characterizing their genomic diversity and inbreeding. In addition, the detection of selection signatures between DSN and Holstein was a goal. Relationship analyses using fixation index (FST), phylogenetic, and admixture analyses were performed between DSN and 68 other breeds from the 1000 Bull Genomes Project. Nucleotide diversity, observed heterozygosity, and expected heterozygosity were calculated as metrics for genomic diversity. Inbreeding was measured as excess of homozygosity (FHom) and genomic inbreeding (FRoH) through runs of homozygosity (RoHs). Region-wide FST and cross-population-extended haplotype homozygosity (XP-EHH) between DSN and Holstein were used to detect selection signatures between the two breeds, and RoH islands were used to detect selection signatures within DSN and Holstein. DSN showed a close genetic relationship with breeds from the Netherlands, Belgium, Northern Germany, and Scandinavia, such as Dutch Friesian Red, Dutch Improved Red, Belgian Red White Campine, Red White Dual Purpose, Modern Angler, Modern Danish Red, and Holstein. The nucleotide diversity in DSN (0.151%) was higher than in Holstein (0.147%) and other breeds, e.g., Norwegian Red (0.149%), Red White Dual Purpose (0.149%), Swedish Red (0.149%), Hereford (0.145%), Angus (0.143%), and Jersey (0.136%). The FHom and FRoH values in DSN were among the lowest. Regions with high FST between DSN and Holstein, significant XP-EHH regions, and RoH islands detected in both breeds harbor candidate genes that were previously reported for milk, meat, fertility, production, and health traits, including one QTL detected in DSN for endoparasite infection resistance. The selection signatures between DSN and Holstein provide evidence of regions responsible for the dual-purpose properties of DSN and the milk type of Holstein. Despite the small population size, DSN has a high level of diversity and low inbreeding. FST supports its relatedness to breeds from the same geographic origin and provides information on potential gene pools that could be used to maintain diversity in DSN.

Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German Black Pied cattle

“…We investigated the unmapped reads resulting from whole-genome sequencing using paired-end 150 bp reads of 302 DSN cattle that could not be aligned to the Bos taurus reference genome ARS-UCD1.2. The DSN breed is a small dual-purpose cattle population of 2 500 herdbook cows [ 13 ] that is considered a founder population of the high milk-yielding Holstein cattle [ 14 ]. DSN has been reported as a robust breed well adapted to pasture conditions.…”

Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds

“…The average estimate of inbreeding measured by homozygosity (F ROH ) showed higher values (0.12 and 0.11) for the breeds under intensive selection of important traits (Egyptian Nubian and Boer, respectively), compared to low values (0.05 and 0.03) for breeds that are not managed under specific breeding programs (Damascus and Barki, respectively) [ 53 ]. This shows that maintaining the local breeds with low population size is possible through adopting a breeding scheme that aim at less intensive selection for production traits [ 54 ], allowing a higher diversity in their genomes.…”

Late History of Cattle Breeds in Central Europe in Light of Genetic and Archaeogenetic Sources—Overview, Thoughts, and Perspectives

“…On the other hand, the collecting of genomic information for historical breeds, after the initial delay due to their low economic impact, is progressing at a high speed. For example, the genome of more than 300 animals have been sequenced in the German Black Pied breed, an endangered historical breed [94]. Its initial farming dates back to the 18th century in the North Sea region of Germany and the Netherlands (as Dutch Friesian).…”