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  • 1
    Online Resource
    Online Resource
    Whole-Genome Sequencing Data Reveal New Loci Affecting Milk Production in German Black Pied Cattle (DSN) (2023)
    Berlin : Humboldt-Universität zu Berlin
    Details
    UID:
    edochu_18452_26923
    Format: 1 Online-Ressource (18 Seiten)
    Content: 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.
    Content: Peer Reviewed
    In: Basel : MDPI, 14,3
    Language: English
    DOI: 10.3390/genes14030581
    DOI: 10.18452/26251
    URN: urn:nbn:de:kobv:11-110-18452/26923-7
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  • 2
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    Online Resource
    Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN) (2021)
    Berlin : Humboldt-Universität zu Berlin
    Details
    UID:
    edochu_18452_25217
    Format: 1 Online-Ressource (13 Seiten)
    Content: Background: German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd size of around 2500 animals. The ability to track sequence variants specific to DSN could help to support the conservation of DSN’s genetic diversity and to provide avenues for genetic improvement. Results: Whole-genome sequencing data of 304 DSN cattle were used to design a customized DSN200k SNP chip harboring 182,154 variants (173,569 SNPs and 8585 indels) based on ten selection categories. We included variants of interest to DSN such as DSN unique variants and variants from previous association studies in DSN, but also variants of general interest such as variants with predicted consequences of high, moderate, or low impact on the transcripts and SNPs from the Illumina BovineSNP50 BeadChip. Further, the selection of variants based on haplotype blocks ensured that the whole-genome was uniformly covered with an average variant distance of 14.4 kb on autosomes. Using 300 DSN and 162 animals from other cattle breeds including Holstein, endangered local cattle populations, and also a Bos indicus breed, performance of the SNP chip was evaluated. Altogether, 171,978 (94.31%) of the variants were successfully called in at least one of the analyzed breeds. In DSN, the number of successfully called variants was 166,563 (91.44%) while 156,684 (86.02%) were segregating at a minor allele frequency 〉 1%. The concordance rate between technical replicates was 99.83 ± 0.19%. Conclusion: The DSN200k SNP chip was proved useful for DSN and other Bos taurus as well as one Bos indicus breed. It is suitable for genetic diversity management and marker-assisted selection of DSN animals. Moreover, variants that were segregating in other breeds can be used for the design of breed-specific customized SNP chips. This will be of great value in the application of conservation programs for endangered local populations in the future.
    Content: Peer Reviewed
    Note: This article was supported by the German Research Foundation (DFG) and the Open Access Publication Fund of Humboldt-Universität zu Berlin.
    In: London : BioMed Central, 22
    Language: English
    DOI: 10.18452/24547
    DOI: 10.1186/s12864-021-08237-2
    URN: urn:nbn:de:kobv:11-110-18452/25217-5
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  • 3
    Online Resource
    Online Resource
    Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses (2022)
    Berlin : Humboldt-Universität zu Berlin
    Details
    UID:
    edochu_18452_27108
    Format: 1 Online-Ressource (25 Seiten)
    Content: The Y chromosome is a valuable genetic marker for studying the origin and influence of paternal lineages in populations. In this study, we conducted Y-chromosomal lineage-tracing in Arabian horses. First, we resolved a Y haplotype phylogeny based on the next generation sequencing data of 157 males from several breeds. Y-chromosomal haplotypes specific for Arabian horses were inferred by genotyping a collection of 145 males representing most Arabian sire lines that are active around the globe. These lines formed three discrete haplogroups, and the same haplogroups were detected in Arabian populations native to the Middle East. The Arabian haplotypes were clearly distinct from the ones detected in Akhal Tekes, Turkoman horses, and the progeny of two Thoroughbred foundation sires. However, a haplotype introduced into the English Thoroughbred by the stallion Byerley Turk (1680), was shared among Arabians, Turkomans, and Akhal Tekes, which opens a discussion about the historic connections between Oriental horse types. Furthermore, we genetically traced Arabian sire line breeding in the Western World over the past 200 years. This confirmed a strong selection for relatively few male lineages and uncovered incongruences to written pedigree records. Overall, we demonstrate how fine-scaled Y-analysis contributes to a better understanding of the historical development of horse breeds.
    Content: Peer Reviewed
    In: Basel : MDPI, 13,2
    Language: English
    DOI: 10.3390/genes13020229
    DOI: 10.18452/26428
    URN: urn:nbn:de:kobv:11-110-18452/27108-1
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  • 4
    Online Resource
    Online Resource
    Capture Sequencing to Explore and Map Rare Casein Variants in Goats (2021)
    Berlin : Humboldt-Universität zu Berlin
    Details
    UID:
    edochu_18452_23562
    Format: 1 Online-Ressource (13 Seiten)
    Content: Genetic variations in the four casein genes CSN1S1, CSN2, CSN1S2, and CSN3 have obtained substantial attention since they affect the milk protein yield, milk composition, cheese processing properties, and digestibility as well as tolerance in human nutrition. Furthermore, milk protein variants are used for breed characterization, biodiversity, and phylogenetic studies. The current study aimed at the identification of casein protein variants in five domestic goat breeds from Sudan (Nubian, Desert, Nilotic, Taggar, and Saanen) and three wild goat species [Capra aegagrus aegagrus (Bezoar ibex), Capra nubiana (Nubian ibex), and Capra ibex (Alpine ibex)]. High-density capture sequencing of 33 goats identified in total 22 non-synonymous and 13 synonymous single nucleotide polymorphisms (SNPs), of which nine non-synonymous and seven synonymous SNPs are new. In the CSN1S1 gene, the new non-synonymous SNP ss7213522403 segregated in Alpine ibex. In the CSN2 gene, the new non-synonymous SNPs ss7213522526, ss7213522558, and ss7213522487 were found exclusively in Nubian and Alpine ibex. In the CSN1S2 gene, the new non-synonymous SNPs ss7213522477, ss7213522549, and ss7213522575 were found in Nubian ibex only. In the CSN3 gene, the non-synonymous SNPs ss7213522604 and ss7213522610 were found in Alpine ibex. The identified DNA sequence variants led to the detection of nine new casein protein variants. New variants were detected for alpha S1 casein in Saanen goats (CSN1S1∗C1), Bezoar ibex (CSN1S1∗J), and Alpine ibex (CSN1S1∗K), for beta and kappa caseins in Alpine ibex (CSN2∗F and CSN3∗X), and for alpha S2 casein in all domesticated and wild goats (CSN1S2∗H), in Nubian and Desert goats (CSN1S2∗I), or in Nubian ibex only (CSN1S2∗J and CSN1S2∗K). The results show that most novel SNPs and protein variants occur in the critically endangered Nubian ibex. This highlights the importance of the preservation of this endangered breed. Furthermore, we suggest validating and further characterizing the new casein protein variants.
    Content: Peer Reviewed
    Note: This article was supported by the German Research Foundation (DFG) and the Open Access Publication Fund of Humboldt-Universität zu Berlin.
    In: Lausanne : Frontiers Media, 12
    Language: English
    DOI: 10.3389/fgene.2021.620253
    DOI: 10.18452/22900
    URN: urn:nbn:de:kobv:11-110-18452/23562-1
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  • 5
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    Online Resource
    An Agouti-Signaling-Protein Mutation is Strongly Associated with Melanism in European Roe Deer (Capreolus capreolus) (2020)
    Berlin : Humboldt-Universität zu Berlin
    Details
    UID:
    edochu_18452_22296
    Format: 1 Online-Ressource (8 Seiten)
    Content: Although the European roe deer (Capreolus capreolus) population of North-West Germany has a remarkable number of melanistic specimens between 10% and 25%, the underlying genetic mutation-causing melanism is still unknown. We used a gene targeting approach focusing on MC1R and ASIP as important genes of coat coloration. Overall, 1384 bp of MC1R and 2039 bp of ASIP were sequenced in 24 specimens and several SNPs were detected. But only the ASIP-SNP c.33G〉T completely segregated both phenotypes leading to the amino acid substitution p.Leu11Phe. The SNP was further evaluated in additional 471 samples. Generally, all black specimens (n = 33) were homozygous TT, whereas chestnut individuals were either homozygote GG (n = 436) or heterozygote GT (n = 26). Considering the fact that all melanistic animals shared two mutated alleles of the strongly associated SNP, we concluded that melanism is inherited in a recessive mode in European roe deer.
    Content: Peer Reviewed
    In: Basel : MDPI, 11,6
    Language: English
    DOI: 10.18452/21569
    DOI: 10.3390/genes11060647
    URN: urn:nbn:de:kobv:11-110-18452/22296-2
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  • 6
    Book
    Book
    Die Farben der Pferde : Genetik - Klassifizierung - Charakteristik (2009)
    Brunsbek : Cadmos
    Details
    UID:
    kobvindex_ZLB15125526
    Format: 271 Seiten , zahlr. Ill., graph. Darst.
    ISBN: 9783861274605
    Language: German
    Keywords: Pferderasse ; Farbe ; Vererbung
    URL: http://d-nb.info/991547926/04
    Author information: Reißmann, Monika
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  • 7
    Online Resource
    Online Resource
    Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German Black Pied cattle (2023)
    Berlin : Humboldt-Universität zu Berlin
    Details
    UID:
    edochu_18452_29027
    Format: 1 Online-Ressource (7 Seiten)
    Content: When resequencing animal genomes, some short reads cannot be mapped to the reference genome and are usually discarded. In this study, unmapped reads from 302 German Black Pied cattle were analyzed to identify potential pathogenic DNA. These unmapped reads were assembled and blasted against NCBI’s database to identify bacterial and viral sequences. The results provided evidence for the presence of pathogens. We found sequences of Bovine parvovirus 3 and Mycoplasma species. These findings emphasize the information content of unmapped reads for gaining insight into bacterial and viral infections, which is important for veterinarians and epidemiologists.
    Content: Peer Reviewed
    Note: The article processing charge was funded by the Open Access Publication Fund of Humboldt-Universität zu Berlin.
    In: London : BioMed Central, 2023, 54
    Language: English
    DOI: 10.18452/28387
    DOI: 10.1186/s13567-023-01227-0
    URN: urn:nbn:de:kobv:11-110-18452/29027-7
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  • 8
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    Online Resource
    Effects of DGAT1 on milk performance in Sudanese Butana × Holstein crossbred cattle (2022)
    Berlin : Humboldt-Universität zu Berlin
    Details
    UID:
    edochu_18452_28696
    Format: 1 Online-Ressource (6 Seiten)
    Content: The improvement of milk production of indigenous Sudanese cattle such as Bos indicus Butana and its cross with Holstein is a major goal of the Sudanese government to ensure sufficient healthy nutrition in the country. In this study, we investigated the K232A polymorphism of diacylglycerol acyltransferase (DGAT1), a well-known modulator of milk production in other breeds. We determined allele frequencies and the allele effects on milk production. Therefore, 93 purebred Butana and 203 Butana × Holstein crossbred cattle were genotyped using competitive allele-specific PCR assays. Association analysis was performed using a linear mixed model in R. In purebred Butana cattle, the lysine DGAT1 protein variant K232, which is found to be associated with higher fat and protein contents, as well as higher fat yield was highly frequent at 0.929, while its frequency in Butana × Holstein crossbred cattle was 0.394. Significant effects were found on milk yield (P = 7.6 × 10−20), fat yield (P = 2.2 × 10−17), protein yield (P = 2.0 × 10−19) and lactose yield (P = 4.0 × 10−18) in crossbred cattle. As expected, the protein variant K232 was disadvantageous since it was decreasing milk, protein, and lactose yields by 1.741 kg, 0.063 kg and 0.084 kg, respectively. No significant effects were found for milk fat, protein, and lactose contents. The high frequency of the lysine DGAT1 protein variant K232 in Butana cattle could contribute to their high milk fat content in combination with low milk yield. In Butana × Holstein crossbred cattle, the DGAT1 marker can be used for effective selection and thus genetic improvement of milk production.
    Content: Peer Reviewed
    In: Dordrecht [u.a.] : Springer Science + Business Media B.V., 54,2
    Language: English
    DOI: 10.18452/27892
    DOI: 10.1007/s11250-022-03141-7
    URN: urn:nbn:de:kobv:11-110-18452/28696-8
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  • 9
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    Online Resource
    Validation of somatic cell score-associated SNPs from Holstein cattle in Sudanese Butana and Butana × Holstein crossbred cattle (2022)
    Berlin : Humboldt-Universität zu Berlin
    Details
    UID:
    edochu_18452_29058
    Format: 1 Online-Ressource (6 Seiten)
    Content: The Bos indicus zebu cattle Butana is the most commonly used indigenous dairy cattle breed in Sudan. In the last years, high-yielding Holstein dairy cattle were introgressed into Butana cattle to improve their milk yield and simultaneously keep their good adaption to extreme environmental conditions. With the focus on the improvement of milk production, other problems arose such as an increased susceptibility to mastitis. Thus, genetic selection for mastitis resistance should be considered to maintain healthy and productive cows. In this study, we tested 10 single nucleotide polymorphisms (SNPs) which had been associated with somatic cell score (SCS) in Holstein cattle for association with SCS in 37 purebred Butana and 203 Butana × Holstein crossbred cattle from Sudan. Animals were genotyped by competitive allele-specific PCR assays and association analysis was performed using a linear mixed model. All 10 SNPs were segregating in the crossbred Butana × Holstein populations, but only 8 SNPs in Sudanese purebred Butana cattle. The SNP on chromosome 13 was suggestively associated with SCS in the Butana × Holstein crossbred population (rs109441194, 13:79,365,467, PBF = 0.054) and the SNP on chromosome 19 was significantly associated with SCS in both populations (rs41257403, 19:50,027,458, Butana: PBF = 0.003, Butana × Holstein: PBF = 6.2 × 10−16). The minor allele of both SNPs showed an increase in SCS. Therefore, selection against the disadvantageous minor allele could be used for genetic improvement of mastitis resistance in the studied populations. However, investigations in a bigger population and across the whole genome are needed to identify additional genomic loci.
    Content: Peer Reviewed
    In: Dordrecht : Springer Science + Business Media B.V, 54,1
    Language: English
    DOI: 10.18452/28427
    DOI: 10.1007/s11250-022-03048-3
    URN: urn:nbn:de:kobv:11-110-18452/29058-1
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  • 10
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    Online Resource
    Genome-wide association study of body morphological traits in Sudanese goats (2018)
    Show associated volumes
    Details
    UID:
    gbv_169118750X
    Format: Diagramme
    ISSN: 1365-2052
    In: Animal genetics, Oxford [u.a.] : Wiley-Blackwell, 1986, 49(2018), 5, Seite 478-482, 1365-2052
    In: volume:49
    In: year:2018
    In: number:5
    In: pages:478-482
    Language: English
    DOI: 10.1111/age.12686
    URL: https://doi.org/10.1111/age.12686
    Author information: Reyer, Henry 1983-
    Author information: Reißmann, Monika
    Author information: Wimmers, Klaus
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