Genome-Wide Association Study Using Whole-Genome Sequence Data for Fertility, Health Indicator, and Endoparasite Infection Traits in German Black Pied Cattle

Wolf, Manuel J.; Yin, Tongming; Neumann, Guilherme B.; Korkuć, Paula; Brockmann, Gudrun A.; König, Sven; May, Katharina

doi:10.3390/genes12081163

Cited by 10 publications

(6 citation statements)

References 80 publications

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“…We also detected several genomic regions with significant selection signals on BTA11 (11:31.25–38.71 Mb) and BTA13 (13:25.80–44.95 Mb). In gene annotation study of these regions, several candidate genes have been found related to reproductive system function in cattle, including Follicle Stimulating Hormone Receptor ( FSHR ) ( Widmer et al, 2021 ), KIAA1217 ( Mohammadi et al, 2020 ), Rho GTPase Activating Protein 21 ( ARHGAP21 ) ( Wolf et al, 2021 ), Myosin IIIA ( MY O 3A ) ( Mohammadi et al, 2020 ), and Glutamate Decarboxylase 2 ( GAD2 ) ( Mohammadi et al, 2020 ). Fertility is an essential element in beef cattle production because it directly relates to producing the offspring necessary to offset costs in production systems ( Thundathil et al, 2016 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Selection Signatures and Human-Mediated Introgression Events in Bos taurus indicus-influenced Composite Beef Cattle

Vahedi

Ardestani²,

Afshari³

et al. 2022

Front. Genet.

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Genetic introgression from interbreeding hybridization of European Bos taurus taurus (EBT) and Indian Bos taurus indicus (IBI) cattle breeds have been widely used to combine the climatic resilience of the IBI cattle and the higher productivity of EBT when forming new composite beef cattle (CB) populations. The subsequent breeding strategies have shifted their initial genomic compositions. To uncover population structure, signatures of selection, and potential introgression events in CB populations, high-density genotypes [containing 492,954 single nucleotide polymorphisms (SNPs) after the quality control] of 486 individuals from 15 cattle breeds, including EBT, IBI, and CB populations, along with two Bos grunniens genotypes as outgroup were used in this study. Then, in-depth population genetics analyses were performed for three CB breeds of Beefmaster, Brangus, and Santa Gertrudis. Neighbor-joining, principal components, and admixture analyses confirmed the historical introgression of EBT and IBI haplotypes into CB breeds. The fdM statistics revealed that only 12.9% of CB populations’ genetic components are of IBI origin. The results of signatures of selection analysis indicated different patterns of selection signals in the three CB breeds with primary pressure on pathways involved in protein processing and stress response in Beefmaster, cell proliferation regulation and immune response in Brangus, and amino acids and glucose metabolisms in Santa Gertrudis. An average of >90% of genomic regions underlying selection signatures were of EBT origin in the studied CB populations. Investigating the CB breeds’ genome allows the estimation of EBT and IBI ancestral proportions and the locations within the genome where either taurine or indicine origin alleles are under selective pressure. Such findings highlight various opportunities to control the selection process more efficiently and explore complementarity at the genomic level in CB populations.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Selection Signatures and Human-Mediated Introgression Events in Bos taurus indicus-influenced Composite Beef Cattle

Vahedi

Ardestani²,

Afshari³

et al. 2022

Front. Genet.

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“…Out of the significant SNPs, 14 were located near 12 known genes, including AKAP8, CLHC1, MEGF10, SATB2, GATA6, SPATA6, COL12A1, EPS8, LUZP2, RAMAC, IL12A and ANKRD55. On chromosome 7, the rs42228650 SNP was close to MEGF10, a gene that was found to be associated with SCS in dairy cows in a previous investigation [48] and was considered as a candidate gene associated with residuals for fecal egg counts of gastrointestinal nematodes in German Black Pied cattle in a recent study [54]. On the same chromosome, two significant SNPs (AX-106741653 and AX-115114947) in the RB breed were located close to the AKAP8 gene, which was associated with somatic cell count in seven different populations of dairy cows in a complex study that used the combined approach of examining previous results from differential gene expression analysis and GWAS studies to identify the key pathways and candidate genes that potentially confer genetic resistance to mastitis in dairy cows [48].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Studies for Milk Somatic Cell Score in Romanian Dairy Cattle

Ilie

Mizeranschi

Míhali

et al. 2021

Genes

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Mastitis is one of the most frequently encountered diseases in dairy cattle, negatively affecting animal welfare and milk production. For this reason, contributions to understanding its genomic architecture are of great interest. Genome-wide association studies (GWAS) have identified multiple loci associated with somatic cell score (SCS) and mastitis in cattle. However, most of the studies have been conducted in different parts of the world on various breeds, and none of the investigations have studied the genetic architecture of mastitis in Romanian dairy cattle breeds up to this point in time. In this study, we report the first GWAS for SCS in dairy cattle breeds from Romania. For GWAS, we used an Axiom Bovine v3 SNP-chip (>63,000 Single Nucleotide Polymorphism -SNPs) and 33,330 records from 690 cows belonging to Romanian Spotted (RS) and Romanian Brown (RB) cattle. The results found one SNP significantly associated with SCS in the RS breed and 40 suggestive SNPs with −log10 (p) from 4 to 4.9 for RS and from 4 to 5.4 in RB. From these, 14 markers were located near 12 known genes (AKAP8, CLHC1, MEGF10, SATB2, GATA6, SPATA6, COL12A1, EPS8, LUZP2, RAMAC, IL12A and ANKRD55) in RB cattle, 3 markers were close to ZDHHC19, DAPK1 and MMP7 genes, while one SNP overlapped the HERC3 gene in RS cattle. Four genes (HERC3, LUZP2, AKAP8 and MEGF10) associated with SCS in this study were previously reported in different studies. The most significant SNP (rs110749552) associated with SCS was located within the HERC3 gene. In both breeds, the SNPs and position of association signals were distinct among the three parities, denoting that mastitis is controlled by different genes that are dependent according to parity. The current results contribute to an expansion in the body of knowledge regarding the proportion of genetic variability explained by SNPs for SCS in dairy cattle.

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“…Not all those traits, however, are yet fully described in DSN and genetic variants affecting those traits are unknown. So far, studies on milk production ( Korkuć et al, 2021 ), mastitis resistance ( Meier et al, 2020 ), endoparasites infection resistance ( May et al, 2019 ), and fertility traits ( Wolf et al, 2021 ) identified some candidate variants and genes affecting those traits. To improve the identification of DSN-typical DNA variants underlying the phenotypic variance, a customized SNP chip was designed for DSN ( Neumann et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2023

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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.

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Genome-Wide Association Study Using Whole-Genome Sequence Data for Fertility, Health Indicator, and Endoparasite Infection Traits in German Black Pied Cattle

Cited by 10 publications

References 80 publications

Genome-Wide Selection Signatures and Human-Mediated Introgression Events in Bos taurus indicus-influenced Composite Beef Cattle

Genome-Wide Selection Signatures and Human-Mediated Introgression Events in Bos taurus indicus-influenced Composite Beef Cattle

Genome-Wide Association Studies for Milk Somatic Cell Score in Romanian Dairy Cattle

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

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