Research

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12 pages, 460 KiB

Open AccessArticle

Association of Variants in Innate Immune Genes TLR4 and TLR5 with Reproductive and Milk Production Traits in Czech Simmental Cattle

by Karel Novák, Terezie Valčíková, Kalifa Samaké and Marek Bjelka

Genes 2024, 15(1), 24; https://doi.org/10.3390/genes15010024 - 23 Dec 2023

Viewed by 802

Abstract

Bovine genes TLR4 and TLR5, which encode antibacterial toll-like receptors, were screened for polymorphisms in Czech Red Pied (Czech Simmental) cattle to identify variants associated with reproduction, udder health, and milk production traits. Variants were discovered by hybrid resequencing of 164 bulls [...] Read more.

Bovine genes TLR4 and TLR5, which encode antibacterial toll-like receptors, were screened for polymorphisms in Czech Red Pied (Czech Simmental) cattle to identify variants associated with reproduction, udder health, and milk production traits. Variants were discovered by hybrid resequencing of 164 bulls using HiSeq X-Ten and PacBio technologies and then individually genotyped. Nominal p-values < 0.05 for associations were detected in 18 combinations between 14 polymorphisms and 15 traits using one-way analysis of variance (ANOVA). The TLR4 variants g.610C>T (rs43578094) and g.10310T>G (rs8193072) in reference AC000135.1 were strictly associated with the index of early reproductive disorders and maternal calving ease, respectively, at false discovery rate (FDR) < 0.05. A highly permissive false discovery rate cutoff of 0.6 separated seventeen combinations in both genes comprising eight positives. In the case of the TLR4 variant g.9422T>C (rs8193060), indications were obtained for the association with as many as four reproductive traits: incidence of cystic ovaries, early reproductive disorders, calving ease, and production longevity. The permissive FDR interpretation for the TLR5 data indicated associations with cyst incidence and early reproduction disorders with maternal calving ease. Moreover, three TLR5 polymorphisms correlated with milk production traits. The discrepancy of the observed associations with the predicted impacts of the SNPs on protein function points to the role of haplotypes. Nevertheless, this question should be resolved on a larger scale. The observed associations are endorsed by independent evidence from the published functional roles in other species and by the published QTL mapping data. Full article

(This article belongs to the Special Issue Genetics and Genomics of Cattle)

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11 pages, 311 KiB

Open AccessArticle

Improving Breeding Value Reliability with Genomic Data in Breeding Groups of Charolais

by Michaela Brzáková, Zdeňka Veselá, Jan Vařeka and Jiří Bauer

Genes 2023, 14(12), 2139; https://doi.org/10.3390/genes14122139 - 27 Nov 2023

Viewed by 702

Abstract

The aim of this study was to assess the impact of incorporating genomic data using the single-step genomic best linear unbiased prediction (ssGBLUP) method compared to the best linear unbiased prediction (BLUP) method on the reliability of breeding values for age at first [...] Read more.

The aim of this study was to assess the impact of incorporating genomic data using the single-step genomic best linear unbiased prediction (ssGBLUP) method compared to the best linear unbiased prediction (BLUP) method on the reliability of breeding values for age at first calving, calving interval, and productive longevity at 78 months in Charolais cattle. The study included 48,590 purebred Charolais individuals classified into four subgroups based on genotyping and performance records. The results showed that considering genotypes significantly improved genomic estimated breeding values (GEBV) reliability across all categories except nongenotyped individuals. For young genotyped individuals, the increase in reliability was up to 27% for both sexes. The highest average reliability was achieved for genotyped proven bulls and cows with performance records, and the inclusion of genomic data further improved the reliability by up to 22% and 21% for cows and bulls, respectively. The gain in reliability was observed mainly during the first three calvings, and then the differences decreased. The imported individuals showed lower estimated breeding values (EBV) and GEBV reliabilities than the domestic population, probably due to the weak genetic connection with the domestic population. However, when the progeny of imported heifers were sired by domestic bulls, the reliability increased by up to 24%. For nongenotyped individuals, only a slight increase in reliability was observed; however, the number of genotyped individuals in the population was still relatively small. Full article

(This article belongs to the Special Issue Genetics and Genomics of Cattle)

12 pages, 1681 KiB

Open AccessArticle

Identification of Hub Genes and Target miRNAs Crucial for Milk Production in Holstein Friesian Dairy Cattle

by Zahra Roudbari, Morteza Mokhtari, Abdolvahab Ebrahimpour Gorji, Tomasz Sadkowski, Ayeh Sadat Sadr and Masoud Shirali

Genes 2023, 14(11), 2105; https://doi.org/10.3390/genes14112105 - 20 Nov 2023

Viewed by 1103

Abstract

Dairy milk production is a quantitative trait that is controlled by many biological and environmental factors. This study employs a network-driven systems approach and clustering algorithm to uncover deeper insights into its genetic associations. We analyzed the GSE33680 dataset from the GEO database [...] Read more.

Dairy milk production is a quantitative trait that is controlled by many biological and environmental factors. This study employs a network-driven systems approach and clustering algorithm to uncover deeper insights into its genetic associations. We analyzed the GSE33680 dataset from the GEO database to understand the biological importance of milk production through gene expression and modules. In this study, we employed CytoNCA and ClusterONE plugins within Cytoscape for network analysis. Moreover, miRWalk software was utilized to detect miRNAs, and DAVID was employed to identify gene ontology and pathways. The results revealed 140 up-regulated genes and 312 down-regulated genes. In addition, we have identified 91 influential genes and 47 miRNAs that are closely associated with milk production. Through our examination of the network connecting these genes, we have found significant involvement in important biological processes such as calcium ion transit across cell membranes, the BMP signaling pathway, and the regulation of MAPK cascade. The conclusive network analysis further reveals that GAPDH, KDR, CSF1, PYGM, RET, PPP2CA, GUSB, and PRKCA are closely linked to key pathways essential for governing milk production. Various mechanisms can control these genes, making them valuable for breeding programs aiming to enhance selection indexes. Full article

(This article belongs to the Special Issue Genetics and Genomics of Cattle)

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15 pages, 2219 KiB

Open AccessArticle

Inferring Causalities of Environmental and Genetic Factors for Differential Somatic Cell Count and Mastitis Pathogens in Dairy Cows Using Structural Equation Modelling

by Patricia Wagner, Kerstin Brügemann, Tong Yin, Petra Engel and Sven König

Genes 2023, 14(11), 2102; https://doi.org/10.3390/genes14112102 - 19 Nov 2023

Viewed by 935

Abstract

The aim of this study was to establish and evaluate a structural equation model to infer causal relationships among environmental and genetic factors on udder health. For this purpose, 537 Holstein Friesian cows were genotyped, and milk samples were analyzed for novel traits [...] Read more.

The aim of this study was to establish and evaluate a structural equation model to infer causal relationships among environmental and genetic factors on udder health. For this purpose, 537 Holstein Friesian cows were genotyped, and milk samples were analyzed for novel traits including differential somatic cell counts and specific mastitis pathogens. In the structural model, four latent variables (intramammary infection (IMI), production, time and genetics) were defined, which were explained using manifest measurable variables. The measurable variables included udder pathogens and somatic differential cell counts, milk composition, as well as significant SNP markers from previous genome-wide associations for major and minor pathogens. The housing system effect (i.e., compost-bedded pack barns versus cubicle barns) indicated a small influence on IMI with a path coefficient of −0.05. However, housing system significantly affected production (0.37), with ongoing causal effects on IMI (0.17). Thus, indirect associations between housing and udder health could be inferred via structural equation modeling. Furthermore, genotype by environment interactions on IMI can be represented, i.e., the detection of specific latent variables such as significant SNP markers only for specific housing systems. For the latent variable genetics, especially one SNP is of primary interest. This SNP is located in the EVA1A gene, which plays a fundamental role in the MAPK1 signaling pathway. Other identified genes (e.g., CTNNA3 and CHL1) support results from previous studies, and this gene also contributes to mechanisms of the MAPK1 signaling pathway. Full article

(This article belongs to the Special Issue Genetics and Genomics of Cattle)

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15 pages, 2273 KiB

Open AccessArticle

Selective Sweeps in Cattle Genomes in Response to the Influence of Urbanization and Environmental Contamination

by Silpa Mullakkalparambil Velayudhan, Shahin Alam, Tong Yin, Kerstin Brügemann, Andreas Buerkert, Veerasamy Sejian, Raghavendra Bhatta, Eva Schlecht and Sven König

Genes 2023, 14(11), 2083; https://doi.org/10.3390/genes14112083 - 15 Nov 2023

Viewed by 1145

Abstract

A genomic study was conducted to identify the effects of urbanization and environmental contaminants with heavy metals on selection footprints in dairy cattle populations reared in the megacity of Bengaluru, South India. Dairy cattle reared along the rural–urban interface of Bengaluru with/without access [...] Read more.

A genomic study was conducted to identify the effects of urbanization and environmental contaminants with heavy metals on selection footprints in dairy cattle populations reared in the megacity of Bengaluru, South India. Dairy cattle reared along the rural–urban interface of Bengaluru with/without access to roughage from public lakeshores were selected. The genotyped animals were subjected to the cross-population–extended haplotype homozygosity (XP-EHH) methodology to infer selection sweeps caused by urbanization (rural, mixed, and urban) and environmental contamination with cadmium and lead. We postulated that social-ecological challenges contribute to mechanisms of natural selection. A number of selection sweeps were identified when comparing the genomes of cattle located in rural, mixed, or urban regions. The largest effects were identified on BTA21, displaying pronounced peaks for selection sweeps for all three urbanization levels (urban_vs_rural, urban_vs_mixed and rural_vs_mixed). Selection sweeps are located in chromosomal segments in close proximity to the genes lrand rab interactor 3 (RIN3), solute carrier family 24 member 4 (SLC24A4), tetraspanin 3 (TSPAN3), and proline-serine-threonine phosphatase interacting protein 1 (PSTPIP1). Functional enrichment analyses of the selection sweeps for all three comparisons revealed a number of gene ontology (GO) and KEGG terms, which were associated with reproduction, metabolism, and cell signaling-related functional mechanisms. Likewise, a number of the chromosomal segments under selection were observed when creating cattle groups according to cadmium and lead contaminations. Stronger and more intense positive selection sweeps were observed for the cadmium contaminated group, i.e., signals of selection on BTA 16 and BTA19 in close proximity to genes regulating the somatotropic axis (growth factor receptor bound protein 2 (GRB2) and cell ion exchange (chloride voltage-gated channel 6 (CLCN6)). A few novel, so far uncharacterized genes, mostly with effects on immune physiology, were identified. The lead contaminated group revealed sweeps which were annotated with genes involved in carcass traits (TNNC2, SLC12A5, and GABRA4), milk yield (HTR1D, SLCO3A1, TEK, and OPCML), reproduction (GABRA4), hypoxia/stress response (OPRD1 and KDR), cell adhesion (PCDHGC3), inflammatory response (ADORA2A), and immune defense mechanism (ALCAM). Thus, the findings from this study provide a deeper insight into the genomic regions under selection under the effects of urbanization and environmental contamination. Full article

(This article belongs to the Special Issue Genetics and Genomics of Cattle)

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14 pages, 7885 KiB

Open AccessArticle

Discovering Genomic Regions Associated with Reproductive Traits and Frame Score in Mexican Simmental and Simbrah Cattle Using Individual SNP and Haplotype Markers

by René Calderón-Chagoya, Vicente Eliezer Vega-Murillo, Adriana García-Ruiz, Ángel Ríos-Utrera, Guillermo Martínez-Velázquez and Moisés Montaño-Bermúdez

Genes 2023, 14(11), 2004; https://doi.org/10.3390/genes14112004 - 27 Oct 2023

Viewed by 892

Abstract

Reproductive efficiency stands as a critical determinant of profitability within beef production systems. The incorporation of molecular markers can expedite advancements in reproductive performance. While the use of SNPs in association analysis is prevalent, approaches centered on haplotypes can offer a more comprehensive [...] Read more.

Reproductive efficiency stands as a critical determinant of profitability within beef production systems. The incorporation of molecular markers can expedite advancements in reproductive performance. While the use of SNPs in association analysis is prevalent, approaches centered on haplotypes can offer a more comprehensive insight. The study used registered Simmental and Simbrah cattle genotyped with the GGP Bovine 150 k panel. Phenotypes included scrotal circumference (SC), heifer fertility (HF), stayability (STAY), and frame score (FS). After quality control, 105,129 autosomal SNPs from 967 animals were used. Haplotype blocks were defined based on linkage disequilibrium. Comparison between haplotypes and SNPs for reproductive traits and FS was conducted using Bayesian and frequentist models. 23, 13, 7, and 2 SNPs exhibited associations with FS, SC, HF, and STAY, respectively. In addition, seven, eight, seven, and one haplotypes displayed associations with FS, SC, HF, and STAY, respectively. Within these delineated genomic segments, potential candidate genes were associated. Full article

(This article belongs to the Special Issue Genetics and Genomics of Cattle)

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27 pages, 2431 KiB

Open AccessArticle

Genetic Distinctness and Diversity of American Aberdeen Cattle Compared to Common Beef Breeds in the United States

by Nayan Bhowmik, Travis Seaborn, Kris A. Ringwall, Carl R. Dahlen, Kendall C. Swanson and Lauren L. Hulsman Hanna

Genes 2023, 14(10), 1842; https://doi.org/10.3390/genes14101842 - 22 Sep 2023

Viewed by 1232

Abstract

American Aberdeen (AD) cattle in the USA descend from an Aberdeen Angus herd originally brought to the Trangie Agricultural Research Centre, New South Wales, AUS. Although put under specific selection pressure for yearling growth rate, AD remain genomically uncharacterized. The objective was to [...] Read more.

American Aberdeen (AD) cattle in the USA descend from an Aberdeen Angus herd originally brought to the Trangie Agricultural Research Centre, New South Wales, AUS. Although put under specific selection pressure for yearling growth rate, AD remain genomically uncharacterized. The objective was to characterize the genetic diversity and structure of purebred and crossbred AD cattle relative to seven common USA beef breeds using available whole-genome SNP data. A total of 1140 animals consisting of 404 purebred (n = 8 types) and 736 admixed individuals (n = 10 types) was used. Genetic diversity metrics, an analysis of molecular variance, and a discriminant analysis of principal components were employed. When linkage disequilibrium was not accounted for, markers influenced basic diversity parameter estimates, especially for AD cattle. Even so, intrapopulation and interpopulation estimates separate AD cattle from other purebred types (e.g., Latter’s pairwise F_ST ranged from 0.1129 to 0.2209), where AD cattle were less heterozygous and had lower allelic richness than other purebred types. The admixed AD-influenced cattle were intermediate to other admixed types for similar parameters. The diversity metrics separation and differences support strong artificial selection pressures during and after AD breed development, shaping the evolution of the breed and making them genomically distinct from similar breeds. Full article

(This article belongs to the Special Issue Genetics and Genomics of Cattle)

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15 pages, 850 KiB

Open AccessArticle

Advanced Skeletal Ossification Is Associated with Genetic Variants in Chronologically Young Beef Heifers

by Katie A. Shira, Brenda M. Murdoch, Kimberly M. Davenport, Gabrielle M. Becker, Shangqian Xie, Antonetta M. Colacchio, Phillip D. Bass, Michael J. Colle and Gordon K. Murdoch

Genes 2023, 14(8), 1629; https://doi.org/10.3390/genes14081629 - 15 Aug 2023

Viewed by 977

Abstract

Osteogenesis is a developmental process critical for structural support and the establishment of a dynamic reservoir for calcium and phosphorus. Changes in livestock breeding over the past 100 years have resulted in earlier bone development and increased physical size of cattle. Advanced skeletal [...] Read more.

Osteogenesis is a developmental process critical for structural support and the establishment of a dynamic reservoir for calcium and phosphorus. Changes in livestock breeding over the past 100 years have resulted in earlier bone development and increased physical size of cattle. Advanced skeletal maturity is now commonly observed at harvest, with heifers displaying more mature bone than is expected at 30 months of age (MOA). We surmise that selection for growth traits and earlier reproductive maturity resulted in co-selection for accelerated skeletal ossification. This study examines the relationship of single nucleotide polymorphisms (SNPs) in 793 beef heifers under 30 MOA with USDA-graded skeletal maturity phenotypes (A-, B-, C- skeletal maturity). Further, the estrogen content of FDA-approved hormonal implants provided to heifers prior to harvest was evaluated in association with the identified SNPs and maturities. Association tests were performed, and the impact of the implants were evaluated as covariates against genotypes using a logistic regression model. SNPs from the ESR1, ALPL, PPARGC1B, SORCS1 genes, and SNPs near KLF14, ANKRD61, USP42, H1C1, OVCA2, microRNA mir-29a were determined to be associated with the advanced skeletal ossification phenotype in heifers. Higher dosage estrogen implants increased skeletal maturity in heifers with certain SNP genotypes. Full article

(This article belongs to the Special Issue Genetics and Genomics of Cattle)

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25 pages, 418 KiB

Open AccessArticle

Investigating the Genetic Background of Spastic Syndrome in North American Holstein Cattle Based on Heritability, Genome-Wide Association, and Functional Genomic Analyses

by Anna Neustaeter, Luiz F. Brito, W. J. Brad Hanna, John D. Baird and Flavio S. Schenkel

Genes 2023, 14(7), 1479; https://doi.org/10.3390/genes14071479 - 20 Jul 2023

Viewed by 1169

Abstract

Spastic syndrome is a chronic, progressive disorder of adult cattle characterized by episodes of sudden involuntary muscle contractions or spasms of the extensor and abductor muscles of one or both hind limbs. In this study, a case-control genome-wide association study (GWAS) was performed [...] Read more.

Spastic syndrome is a chronic, progressive disorder of adult cattle characterized by episodes of sudden involuntary muscle contractions or spasms of the extensor and abductor muscles of one or both hind limbs. In this study, a case-control genome-wide association study (GWAS) was performed on an adult Holstein cattle cohort. Based on the 50 K and high-density (HD) SNP panel GWAS, we identified 98 and 522 SNPs, respectively. The most significant genomic regions identified are located on BTA9 at approximately 87 megabase pairs (Mb) and BTA7 between 1 and 20 Mb. Functional analyses of significant SNPs identified genes associated with muscle contraction, neuron growth or regulation, and calcium or sodium ion movement. Two candidate genes (FIG4 and FYN) were identified. FIG4 is ubiquitously expressed in skeletal muscle and FYN is involved with processes such as forebrain development, neurogenesis, locomotion, neurogenesis, synapse development, neuron migration, and the positive regulation of neuron projection development. The CACNA1A gene, which codes for a calcium channel subunit protein in the calcium signaling pathway, seems the most compelling candidate gene, as many calcium ion channel disorders are non-degenerative, and produce spastic phenotypes. These results suggest that spastic syndrome is of polygenic inheritance, with important genomic areas of interest on BTA7 and BTA9. Full article

(This article belongs to the Special Issue Genetics and Genomics of Cattle)

Review

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31 pages, 1805 KiB

Open AccessReview

Genomic Selection for Dairy Cattle Behaviour Considering Novel Traits in a Changing Technical Production Environment

by Larissa Elisabeth Behren, Sven König and Katharina May

Genes 2023, 14(10), 1933; https://doi.org/10.3390/genes14101933 - 13 Oct 2023

Viewed by 2249

Abstract

Cow behaviour is a major factor influencing dairy herd profitability and is an indicator of animal welfare and disease. Behaviour is a complex network of behavioural patterns in response to environmental and social stimuli and human handling. Advances in agricultural technology have led [...] Read more.

Cow behaviour is a major factor influencing dairy herd profitability and is an indicator of animal welfare and disease. Behaviour is a complex network of behavioural patterns in response to environmental and social stimuli and human handling. Advances in agricultural technology have led to changes in dairy cow husbandry systems worldwide. Increasing herd sizes, less time availability to take care of the animals and modern technology such as automatic milking systems (AMSs) imply limited human–cow interactions. On the other hand, cow behaviour responses to the technical environment (cow–AMS interactions) simultaneously improve production efficiency and welfare and contribute to simplified “cow handling” and reduced labour time. Automatic milking systems generate objective behaviour traits linked to workability, milkability and health, which can be implemented into genomic selection tools. However, there is insufficient understanding of the genetic mechanisms influencing cow learning and social behaviour, in turn affecting herd management, productivity and welfare. Moreover, physiological and molecular biomarkers such as heart rate, neurotransmitters and hormones might be useful indicators and predictors of cow behaviour. This review gives an overview of published behaviour studies in dairy cows in the context of genetics and genomics and discusses possibilities for breeding approaches to achieve desired behaviour in a technical production environment. Full article

(This article belongs to the Special Issue Genetics and Genomics of Cattle)

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