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

(5 citation statements)

References 79 publications

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“…Within this context, selection can contribute to reducing infestation levels and economic losses caused by parasitism and to mitigating the environmental impact resulting from the inappropriate use of chemical products for parasite control (Passafaro et al 2015; Cardoso et al 2015; Biegelmeyer et al 2017; Ribeiro et al 2021).In general, the genetic and phenotypic correlations involving a sexual precocity trait and a resistance trait were not signi cant, suggesting that selection aimed at improving male and female sexual precocity will not result in unfavorable correlated responses in parasite resistance. Our results support the ndings of Wolf et al(Wolf et al 2021) who did not identify overlaps of genes related to indicator traits of fertility and those related to infection with endoparasites in German Black Pied cattle. On the other hand,Prayaga et al (2009) observed that selection aimed at improving traits related to heifer puberty can cause changes in the resistance of animals to parasites.…”

supporting

confidence: 92%

Genetic and phenotypic parameters for sexual precocity and parasite resistance traits in Nellore cattle

Moraes

Gouveia

Ribeiro

et al. 2023

Preprint

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Indicator traits of sexual precocity are widely used as selection criteria for the genetic improvement of beef cattle; however, the impact of selection for these traits on resistance to endo- and ectoparasites is unknown. Therefore, this study aimed to estimate the genetic and phenotypic parameters for indicator traits of sexual precocity and parasite resistance in Nellore cattle. The sexual precocity traits evaluated were probability of first calving (PFC) and scrotal circumference at 12 and 18 months of age (SC12 and SC18). The resistance-related traits included tick (TC), gastrointestinal nematode egg (NEC), and Eimeria spp. oocyst (EOC) counts. (Co)variance components were estimated by Bayesian inference using multitrait animal models. The mean heritabilities for PFC, SC12, SC18, TC, NEC and EOC were 0.23, 0.38, 0.42, 0.14, 0.16, 0.06, respectively, and suggest that selection will change the mean values of these traits over time. The genetic and phenotypic correlations for most pairs formed by a precocity and a resistance trait were not different from zero, suggesting that selection for sexual precocity traits will not result in changes in resistance traits. Thus, selection for indicator traits of sexual precocity does not elicit unfavorable correlated responses in resistance to endo- and ectoparasites and joint selection aimed at improving these traits can be performed using multitrait selection methods, when necessary.

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supporting

confidence: 92%

Genetic and phenotypic parameters for sexual precocity and parasite resistance traits in Nellore cattle

Moraes

Gouveia

Ribeiro

et al. 2023

Preprint

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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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“…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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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 79 publications

Genetic and phenotypic parameters for sexual precocity and parasite resistance traits in Nellore cattle

Genetic and phenotypic parameters for sexual precocity and parasite resistance traits in Nellore 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

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