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Das Deutsche Schwarzbunte Niederungsrind (DSN) ist eine milchbetonte Zweinutzungsrasse, die auf der Roten Liste der gefährdeten einheimischen Nutztierrassen steht. Sie wurde aufgrund ihrer geringeren Milchleistung durch Holstein-Rinder ersetzt. Ziel dieses Projekts war es, züchterisch nutzbare Marker zu identifizieren, die zur Verbesserung der Rasse DSN geeignet sind, um so zur besonders tiergerechten und nachhaltigen Produktion tierischer Erzeugnisse beizutragen. Mit der Einrichtung einer umfassenden Gewebe-, DNA- und Daten-Bank konnte die genomische Information nahezu der gesamten DSN-Population gesammelt werden. Damit ist die Grundlage für eine geeignete Lernstichprobe gelegt. Die genomischen Informationen haben gezeigt, dass die Inzucht in DSN geringer und die Diversität höher als in Holsteins ist, was auf eine sehr gute Zuchtarbeit schließen lässt. In gesamtgenomischen Analysen wurden genetische Marker zur Milchproduktion, zu Gesundheits- und Fruchtbarkeitsparametern bei DSN-Kühen und Wachstums- und Fleischleistung bei DSN-Schlachtbullen identifiziert. Genetische Marker für Milchproduktion und Fleischansatz sind entscheidend, um die Selektion auf höhere Milchleistung bei Erhaltung des Zweinutzungstyps effizient zu gestalten. Die identifizierten Marker können unterstützend bei der Auswahl von Zuchtbullen aus potentiellen Jungbullen, gezielten Anpaarungsentscheidungen zur Verbesserung der Leistung der Nachkommen und zur Vorhersage der Leistung junger Tiere genutzt werden. Gleichzeitig liegt ein Fokus darauf, Inzucht zu minimieren und die genetische Diversität in dieser kleinen Rasse zu erhalten. Zusammenfassend ist dieses Projekt ein bedeutender Schritt in Richtung einer verbesserten Zuchtauswahl und einer effizienteren Zucht auf genetischer Grundlage, um das Leistungspotential besser zu nutzen und die Robustheit und Diversität zu erhalten. Die identifizierten Marker sind wertvolle Werkzeuge, um die Zuchtentscheidung in der kleinen DSN-Population zu unterstützen.

The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the world. We analyze target enriched sequencing data of 5 Mb of the Y chromosome from 76 domestic males, together with 89 whole genome sequenced domestic males and five Przewalski's horses from previous studies. The resulting phylogeny comprises 153 HTs defined by 2966 variants and offers unprecedented resolution into the history of horse paternal lineages. It reveals the presence of a remarkable number of previously unknown haplogroups in Mongolian horses and insular populations. Phylogenetic placement of HTs retrieved from 163 archaeological specimens further indicates that most of the present-day Y-chromosomal variation evolved after the domestication process that started around 4200 years ago in the Western Eurasian steppes. Our comprehensive phylogeny significantly reduces ascertainment bias and constitutes a robust evolutionary framework for analyzing horse population dynamics and diversity.

In der aktuellen Studie erweiterten wir unsere frühere GWAS (Korkuć et al., 2021) unter Verwendung einer größeren Population von 2.160 DSN-Kühen und einer gesättigten SNP-Dichte von 11,7 Millionen Sequenzvarianten (Korkuć et al., 2023). Wir erwarteten eine höhere Signifikanz und eine verfeinerte Auflösung der zuvor assoziierten Loci und vor allem die Identifizierung zusätzlicher Loci.

German Black Pied (DSN) is considered an ancestral population of the Holstein breed. The goal of the current study was to fine-map genomic loci for milk production traits and to provide sequence variants for selection. We studied genome-wide associations for milk-production traits in 2160 DSN cows. Using 11.7 million variants from whole-genome sequencing of 304 representative DSN cattle, we identified 1980 associated variants (-log10(p)> 7.1) in 13 genomic loci on 9 chromosomes. The highest significance was found for the MGST1 region affecting milk fat content (-log10(p) = 11.93, MAF = 0.23, substitution effect of the minor allele (ßMA) = -0.151%). Different from Holstein, DGAT1 was fixed (0.97) for the alanine protein variant for high milk and protein yield. A key gene affecting protein content was CSN1S1 (-log10(p) = 8.47, MAF = 049, ßMA = -0.055%) and the GNG2 region (-log10(p) = 10.48, MAF = 0.34, ßMA = 0.054%). Additionally, we suggest the importance of FGF12 for protein and fat yield, HTR3C for milk yield, TLE4 for milk and protein yield, and TNKS for milk and fat yield. Selection for favored alleles can improve milk yield and composition. With respect to maintaining the dual-purpose type of DSN, unfavored linkage to genes affecting muscularity has to be investigated carefully, before the milk-associated variants can be applied for selection in the small population.

Hintergrund: Die Berlin Fat Mouse Inzuchtlinie (BFMI) ist ein Modell für Adipositas und das metabolische Syndrom. Diese Studie zielte darauf ab, genetische Varianten zu identifizieren, die mit dem gestörten Glukosestoffwechsel assoziiert sind, indem die fettleibigen Linien BFMI861-S1 und BFMI861-S2 verwendet wurden, die genetisch eng verwandt sind, sich aber in mehreren Merkmalen unterscheiden. BFMI861-S1 ist insulinresistent und speichert ektopisches Fett in der Leber, während BFMI861-S2 insulinsensitiv ist. Methoden: Die QTL-Analyse wurde in zwei fortgeschrittenen Intercross-Linien (AIL) in der Generation durchgeführt. Eine AIL wurde aus der Kreuzung BFMI861-S1 x BFMI861-S2 und die zweite AIL aus der Kreuzung BFMI861-S1 x BFMI861-B6N erhalten. Für beide AILs wurden Phänotypen über 25 bzw. 20 Wochen gesammelt. Zur Priorisierung von positionellen Kandidatengenen wurden Gesamtgenomsequenzierung und Genexpressionsdaten der Elternlinien verwendet. Ergebnisse: Für den AIL BFMI861-S1 x BFMI861-S2 wurden überlappende QTL für das Gonadenfettgewebegewicht und die Blutglukosekonzentration auf Chromosom (Chr) 3 (95,8–100,1 Mb) und für das Gonadenfettgewebegewicht, Lebergewicht und Blut nachgewiesen Glukosekonzentration auf Chr 17 (9,5–26,1 Mb). Für die AIL BFMI861-S1 x BFMI861-B6N zeigte ein hochsignifikanter QTL auf Chromosom (Chr) 1 (157–168 Mb) einen Zusammenhang mit dem Lebergewicht. Ein QTL für das Körpergewicht nach 20 Wochen wurde auf Chr 3 (34,1 – 40 Mb) gefunden, der sich mit einem QTL für das scAT-Gewicht überlappte. In einem multiplen QTL-Mapping-Ansatz wurde ein zusätzliches QTL, das das Körpergewicht bei 16 Wochen beeinflusste, auf Chr 6 (9,5–26,1 Mb) identifiziert. Schlussfolgerungen: Die QTL-Kartierung zusammen mit einem detaillierten Priorisierungsansatz ermöglichte es uns, Kandidatengene zu identifizieren, die mit Merkmalen des metabolischen Syndroms in beiden AILs assoziiert sind., Background: The Berlin Fat Mouse Inbred line (BFMI) is a model for obesity and the metabolic syndrome. This study aimed to identify genetic variants associated with the impaired glucose metabolism using the obese lines BFMI861-S1 and BFMI861-S2, which are genetically closely related, but differ in several traits. BFMI861-S1 is insulin resistant and stores ectopic fat in the liver, whereas BFMI861-S2 is insulin sensitive. Methods: QTL-analysis was performed in two advanced intercross lines (AIL) in generation. One AIL obtained from the cross BFMI861-S1 x BFMI861-S2 and the second AIL from the cross BFMI861-S1 x BFMI861-B6N. For both AILs phenotypes were collected over 25 and 20 weeks, respectively. For prioritization of positional candidate genes whole genome sequencing and gene expression data of the parental lines were used. Results: For the AIL BFMI861-S1 x BFMI861-S2 overlapping QTL for gonadal adipose tissue weight and blood glucose concentration were detected on chromosome (Chr) 3 (95.8-100.1 Mb), and for gonadal adipose tissue weight, liver weight, and blood glucose concentration on Chr 17 (9.5-26.1 Mb). For the AIL BFMI861-S1 x BFMI861-B6N one highly significant QTL on chromosome (Chr) 1 (157–168 Mb) showed an association with liver weight. A QTL for body weight at 20 weeks was found on Chr 3 (34.1 – 40 Mb) overlapping with a QTL for scAT weight. In a multiple QTL mapping approach, an additional QTL affecting body weight at 16 weeks was identified on Chr 6 (9.5-26.1 Mb). Conclusions: QTL mapping together with a detailed prioritization approach allowed us to identify candidate genes associated with traits of the metabolic syndrome in both AILs.

This article was supported by the German Research Foundation (DFG) and the Open Access Publication Fund of Humboldt-Universität zu Berlin., Banning antibiotic growth promotors and other antimicrobials in poultry production due to the increasing antimicrobial resistance leads to increased feeding of potential alternatives such as probiotics. However, the modes of action of those feed additives are not entirely understood. They could act even with a direct effect on the immune system. A previously established animal-related in vitro system using primary cultured peripheral blood mononuclear cells (PBMCs) was applied to investigate the effects of immune-modulating feed additives. Here, the immunomodulation of different preparations of two probiotic Bacillus strains, B. subtilis DSM 32315 (BS), and B. amyloliquefaciens CECT 5940 (BA) was evaluated. The count of T-helper cells and activated T-helper cells increased after treatment in a ratio of 1:3 (PBMCs: Bacillus) with vital BS (CD4+: p < 0.05; CD4+CD25+: p < 0.01). Furthermore, vital BS enhanced the proliferation and activation of cytotoxic T cells (CD8+: p < 0.05; CD8+CD25+: p < 0.05). Cell-free probiotic culture supernatants of BS increased the count of activated T-helper cells (CD4+CD25+: p < 0.1). UV-inactivated BS increased the proportion of cytotoxic T cells significantly (CD8+: p < 0.01). Our results point towards a possible involvement of secreted factors of BS in T-helper cell activation and proliferation, whereas it stimulates cytotoxic T cells presumably through surface contact. We could not observe any effect on B cells after treatment with different preparations of BS. After treatment with vital BA in a ratio of 1:3 (PBMCs:Bacillus), the count of T-helper cells and activated T-helper cells increased (CD4+: p < 0.01; CD4+CD25+: p < 0.05). Cell-free probiotic culture supernatants of BA as well as UV-inactivated BA had no effect on T cell proliferation and activation. Furthermore, we found no effect of BA preparations on B cells. Overall, we demonstrate that the two different Bacillus strains enhanced T cell activation and proliferation, which p, Federal Ministry of Education and Research, Peer Reviewed

This article was supported by the German Research Foundation (DFG) and the Open Access Publication Fund of Humboldt-Universität zu Berlin., 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 endoparas