Special Issue "Advances in Cattle Breeding, Genetics and Genomics"

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 31 December 2021.

Special Issue Editor

Prof. Ikhide G. Imumorin
E-Mail
Guest Editor
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
Interests: cattle genetics; gene families; genomic imprinting; epigenetics; mammals

Special Issue Information

Dear Colleagues,

This special issue of Animals (IF: 2.323, ISSN 2076-2615) is directed at cutting edge research in cattle breeding, genetics and genomics with focus on application of modern molecular and mathematical methods for genetic improvement of bovine species for food, fiber and other useful products. Papers in the areas of quantitative and population genetics, genetic/genomic evaluation, genomics/proteomics and application of molecular methods to health, nutrition, production, nutrition are welcome.

Prof. Ikhide G. Imumorin
Guest Editor

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Keywords

  • cattle
  • breeding
  • genomics
  • genetics
  • nutrigenomics
  • cattle health
  • reproduction

Published Papers (15 papers)

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Research

Article
GPS Coordinates for Modelling Correlated Herd Effects in Genomic Prediction Models Applied to Hanwoo Beef Cattle
Animals 2021, 11(7), 2050; https://doi.org/10.3390/ani11072050 - 09 Jul 2021
Viewed by 910
Abstract
It is widely known that the environment influences phenotypic expression and that its effects must be accounted for in genetic evaluation programs. The most used method to account for environmental effects is to add herd and contemporary group to the model. Although generally [...] Read more.
It is widely known that the environment influences phenotypic expression and that its effects must be accounted for in genetic evaluation programs. The most used method to account for environmental effects is to add herd and contemporary group to the model. Although generally informative, the herd effect treats different farms as independent units. However, if two farms are located physically close to each other, they potentially share correlated environmental factors. We introduce a method to model herd effects that uses the physical distances between farms based on the Global Positioning System (GPS) coordinates as a proxy for the correlation matrix of these effects that aims to account for similarities and differences between farms due to environmental factors. A population of Hanwoo Korean cattle was used to evaluate the impact of modelling herd effects as correlated, in comparison to assuming the farms as completely independent units, on the variance components and genomic prediction. The main result was an increase in the reliabilities of the predicted genomic breeding values compared to reliabilities obtained with traditional models (across four traits evaluated, reliabilities of prediction presented increases that ranged from 0.05 ± 0.01 to 0.33 ± 0.03), suggesting that these models may overestimate heritabilities. Although little to no significant gain was obtained in phenotypic prediction, the increased reliability of the predicted genomic breeding values is of practical relevance for genetic evaluation programs. Full article
(This article belongs to the Special Issue Advances in Cattle Breeding, Genetics and Genomics)
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Article
Conservation of Imprinting and Methylation of MKRN3, MAGEL2 and NDN Genes in Cattle
Animals 2021, 11(7), 1985; https://doi.org/10.3390/ani11071985 - 02 Jul 2021
Viewed by 953
Abstract
Genomic imprinting is the epigenetic mechanism of transcriptional regulation that involves differential DNA methylation modification. Comparative analysis of imprinted genes between species can help us to investigate the biological significance and regulatory mechanisms of genomic imprinting. MKRN3, MAGEL2 and NDN are three [...] Read more.
Genomic imprinting is the epigenetic mechanism of transcriptional regulation that involves differential DNA methylation modification. Comparative analysis of imprinted genes between species can help us to investigate the biological significance and regulatory mechanisms of genomic imprinting. MKRN3, MAGEL2 and NDN are three maternally imprinted genes identified in the human PWS/AS imprinted locus. This study aimed to assess the allelic expression of MKRN3, MAGEL2 and NDN and to examine the differentially methylated regions (DMRs) of bovine PWS/AS imprinted domains. An expressed single-nucleotide polymorphism (SNP)-based approach was used to investigate the allelic expression of MKRN3, MAGEL2 and NDN genes in bovine adult tissues and placenta. Consistent with the expression in humans and mice, we found that the MKRN3, MAGEL2 and NDN genes exhibit monoallelic expression in bovine somatic tissues and the paternal allele expressed in the bovine placenta. Three DMRs, PWS-IC, MKRN3 and NDN DMR, were identified in the bovine PWS/AS imprinted region by analysis of the DNA methylation status in bovine tissues using the bisulfite sequencing method and were located in the promoter and exon 1 of the SNRPN gene, NDN promoter and 5’ untranslated region (5’UTR) of MKRN3 gene, respectively. The PWS-IC DMR is a primary DMR inherited from the male or female gamete, but NDN and MKRN3 DMR are secondary DMRs that occurred after fertilization by examining the methylation status in gametes. Full article
(This article belongs to the Special Issue Advances in Cattle Breeding, Genetics and Genomics)
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Article
Genome-Wide Association Study on Reproduction-Related Body-Shape Traits of Chinese Holstein Cows
Animals 2021, 11(7), 1927; https://doi.org/10.3390/ani11071927 - 28 Jun 2021
Viewed by 391
Abstract
Reproduction is an important production activity for dairy cows, and their reproductive performance can directly affect the level of farmers’ income. To better understand the genomic regions and biological pathways of reproduction-related traits of dairy cows, in the present study, three body shape [...] Read more.
Reproduction is an important production activity for dairy cows, and their reproductive performance can directly affect the level of farmers’ income. To better understand the genomic regions and biological pathways of reproduction-related traits of dairy cows, in the present study, three body shape traits—Loin Strength (LS), Rump Angle (RA), and Pin Width (PW)—were selected as indicators of the reproductive ability of cows, and we conducted genome-wide association analyses on them. The heritability of these three traits was medium, ranging from 0.20 to 0.38. A total of 11 significant single-nucleotide polymorphisms (SNPs) were detected associated with these three traits. Bioinformatics analysis was performed on genes close to the significant SNPs (within 200 Kb) of LS, RA, and PW, and we found that these genes were totally enriched in 20 gene ontology terms and six KEGG signaling pathways. Finally, the five genes CDH12, TARP, PCDH9, DTHD1, and ARAP2 were selected as candidate genes that might affect LS. The six genes LOC781835, FSTL4, ATG4C, SH3BP4, DMP1, and DSPP were selected as candidate genes that might affect RA. The five genes USP6NL, CNTN3, LOC101907665, UPF2, and ECHDC3 were selected as candidate genes that might affect the PW of Chinese Holstein cows. Our results could provide useful biological information for the improvement of body shape traits and contribute to the genomic selection of Chinese Holstein cows. Full article
(This article belongs to the Special Issue Advances in Cattle Breeding, Genetics and Genomics)
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Article
Detection of Genomic Regions with Pleiotropic Effects for Growth and Carcass Quality Traits in the Rubia Gallega Cattle Breed
Animals 2021, 11(6), 1682; https://doi.org/10.3390/ani11061682 - 04 Jun 2021
Viewed by 1285
Abstract
The breeding scheme in the Rubia Gallega cattle population is based upon traits measured in farms and slaughterhouses. In recent years, genomic evaluation has been implemented by using a ssGBLUP (single-step Genomic Best Linear Unbiased Prediction). This procedure can reparameterized to perform ssGWAS [...] Read more.
The breeding scheme in the Rubia Gallega cattle population is based upon traits measured in farms and slaughterhouses. In recent years, genomic evaluation has been implemented by using a ssGBLUP (single-step Genomic Best Linear Unbiased Prediction). This procedure can reparameterized to perform ssGWAS (single-step Genome Wide Association Studies) by backsolving the SNP (single nucleotide polymorphisms) effects. Therefore, the objective of this study was to identify genomic regions associated with the genetic variability in growth and carcass quality traits. We implemented a ssGBLUP by using a database that included records for Birth Weight (BW-327,350 records-), Weaning Weight (WW-83,818-), Cold Carcass Weight (CCW-91,621-), Fatness (FAT-91,475-) and Conformation (CON-91,609-). The pedigree included 464,373 individuals, 2449 of which were genotyped. After a process of filtering, we ended up using 43,211 SNP markers. We used the GBLUP and SNPBLUP model equivalences to obtain the effects of the SNPs and then calculated the percentage of variance explained by the regions of the genome between 1 Mb. We identified 7 regions of the genome for CCW; 8 regions for BW, WW, FAT and 9 regions for CON, which explained the percentage of variance above 0.5%. Furthermore, a number of the genome regions had pleiotropic effects, located at: BTA1 (131–132 Mb), BTA2 (1–11 Mb), BTA3 (32–33 Mb), BTA6 (36–38 Mb), BTA16 (24–26 Mb), and BTA 21 (56–57 Mb). These regions contain, amongst others, the following candidate genes: NCK1, MSTN, KCNA3, LCORL, NCAPG, and RIN3. Full article
(This article belongs to the Special Issue Advances in Cattle Breeding, Genetics and Genomics)
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Article
Long Intergenic Non-Coding RNAs in the Mammary Parenchyma and Fat Pad of Pre-Weaning Heifer Calves: Identification and Functional Analysis
Animals 2021, 11(5), 1268; https://doi.org/10.3390/ani11051268 - 28 Apr 2021
Viewed by 371
Abstract
Enhanced plane of nutrition at pre-weaning stage can promote the development of mammary gland especially heifer calves. Although several genes are involved in this process, long intergenic non-coding RNAs (lincRNAs) are regarded as key regulators in the regulated network and are still largely [...] Read more.
Enhanced plane of nutrition at pre-weaning stage can promote the development of mammary gland especially heifer calves. Although several genes are involved in this process, long intergenic non-coding RNAs (lincRNAs) are regarded as key regulators in the regulated network and are still largely unknown. We identified and characterized 534 putative lincRNAs based on the published RNA-seq data, including heifer calves in two groups: fed enhanced milk replacer (EH, 1.13 kg/day, including 28% crude protein, 25% fat) group and fed restricted milk replacer (R, 0.45 kg/day, including 20% crude protein, 20% fat) group. Sub-samples from the mammary parenchyma (PAR) and mammary fat pad (MFP) were harvested from heifer calves. According to the information of these lincRNAs’ quantitative trait loci (QTLs), the neighboring and co-expression genes were used to predict their function. By comparing EH vs R, 79 lincRNAs (61 upregulated, 18 downregulated) and 86 lincRNAs (54 upregulated, 32 downregulated) were differentially expressed in MFP and PAR, respectively. In MFP, some differentially expressed lincRNAs (DELs) are involved in lipid metabolism pathways, while, in PAR, among of DELs are involved in cell proliferation pathways. Taken together, this study explored the potential regulatory mechanism of lincRNAs in the mammary gland development of calves under different planes of nutrition. Full article
(This article belongs to the Special Issue Advances in Cattle Breeding, Genetics and Genomics)
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Article
Impact of Censored or Penalized Data in the Genetic Evaluation of Two Longevity Indicator Traits Using Random Regression Models in North American Angus Cattle
Animals 2021, 11(3), 800; https://doi.org/10.3390/ani11030800 - 12 Mar 2021
Viewed by 545
Abstract
This study aimed to evaluate the impact of different proportions (i.e., 20%, 40%, 60% and 80%) of censored (CEN) or penalized (PEN) data in the prediction of breeding values (EBVs), genetic parameters, and computational efficiency for two longevity indicators (i.e., traditional and functional [...] Read more.
This study aimed to evaluate the impact of different proportions (i.e., 20%, 40%, 60% and 80%) of censored (CEN) or penalized (PEN) data in the prediction of breeding values (EBVs), genetic parameters, and computational efficiency for two longevity indicators (i.e., traditional and functional longevity; TL and FL, respectively). In addition, three different criteria were proposed for PEN: (1) assuming that all cows with censored records were culled one year after their last reported calving; (2) assuming that cows with censored records older than nine years were culled one year after their last reported calving, while censored (missing) records were kept for cows younger than nine years; and (3) assuming that cows with censored records older than nine years were culled one year after their last reported calving, while cows younger than nine years were culled two years after their last reported calving. All analyses were performed using random regression models based on fourth order Legendre orthogonal polynomials. The proportion of commonly selected animals and EBV correlations were calculated between the complete dataset (i.e., without censored or penalized data; COM) and all simulated proportions of CEN or PEN. The computational efficiency was evaluated based on the total computing time taken by each scenario to complete 150,000 Bayesian iterations. In summary, increasing the CEN proportion significantly (p-value < 0.05 by paired t-tests) decreased the heritability estimates for both TL and FL. When compared to CEN, PEN tended to yield heritabilities closer to COM, especially for FL. Moreover, similar heritability patterns were observed for all three penalization criteria. High proportions of commonly selected animals and EBV correlations were found between COM and CEN with 20% censored data (for both TL and FL), and COM and all levels of PEN (for FL). The proportions of commonly selected animals and EBV correlations were lower for PEN than CEN for TL, which suggests that the criteria used for PEN are not adequate for TL. Analyses using COM and CEN took longer to finish than PEN analyses. In addition, increasing the amount of censored records also tended to increase the computational time. A high proportion (>20%) of censored data has a negative impact in the genetic evaluation of longevity. The penalization criteria proposed in this study are useful for genetic evaluations of FL, but they are not recommended when analyzing TL. Full article
(This article belongs to the Special Issue Advances in Cattle Breeding, Genetics and Genomics)
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Article
Identification of Genomic Regions for Carcass Quality Traits within the American Simmental Association Carcass Merit Program
Animals 2021, 11(2), 471; https://doi.org/10.3390/ani11020471 - 10 Feb 2021
Viewed by 509
Abstract
USDA quality and yield grade are primary driving forces for carcass value in the United States. Carcass improvements can be achieved by making selection decisions based on the results of genetic evaluations in the form of expected progeny differences (EPD), real-time ultrasound imaging, [...] Read more.
USDA quality and yield grade are primary driving forces for carcass value in the United States. Carcass improvements can be achieved by making selection decisions based on the results of genetic evaluations in the form of expected progeny differences (EPD), real-time ultrasound imaging, and physical evaluation of candidate breeding animals. In an effort to advance their ability to accurately predict the breeding value of potential sires for carcass traits, the American Simmental Association launched the Carcass Merit Program as a means to collect progeny sire group carcass information. All records were extracted from the American Simmental Association database. Progeny data were organized by sire family and progeny performance phenotypes were constructed. Sire genotypes were filtered, and a multi-locus mixed linear model was used to perform an association analysis on the genotype data, while correcting for cryptic relatedness and pedigree structure. Three chromosomes were found to have genome-wide significance and this conservative approach identified putative QTL in those regions. Three hundred ninety-three novel regions were identified across all traits, as well as 290 novel positional candidate genes. Correlations between carcass characteristics and maternal traits were less unfavorable than those previously reported. Full article
(This article belongs to the Special Issue Advances in Cattle Breeding, Genetics and Genomics)
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Article
Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle
Animals 2021, 11(1), 192; https://doi.org/10.3390/ani11010192 - 15 Jan 2021
Viewed by 741
Abstract
The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, [...] Read more.
The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock. Full article
(This article belongs to the Special Issue Advances in Cattle Breeding, Genetics and Genomics)
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Article
Using Random Regression Models to Genetically Evaluate Functional Longevity Traits in North American Angus Cattle
Animals 2020, 10(12), 2410; https://doi.org/10.3390/ani10122410 - 16 Dec 2020
Cited by 2 | Viewed by 692
Abstract
This study aimed to propose novel longevity indicators by comparing genetic parameters for traditional (TL; i.e., the cow’s lifespan after the first calving) and functional (FL; i.e., how long the cow stayed in the herd while also calving; assuming no missing (FLa) or [...] Read more.
This study aimed to propose novel longevity indicators by comparing genetic parameters for traditional (TL; i.e., the cow’s lifespan after the first calving) and functional (FL; i.e., how long the cow stayed in the herd while also calving; assuming no missing (FLa) or missing (FLb) records for unknown calving) longevity, considering different culling reasons (natural death, structural problems, disease, fertility, performance, and miscellaneous). Longevity definitions were evaluated from 2 to 15 years of age, using single- and multiple-trait Bayesian random regression models (RRM). The RRM fitting heterogenous residual variance and fourth order Legendre polynomials were considered as the optimal models for the majority of longevity indicators. The average heritability estimates over ages for FLb (from 0.08 to 0.25) were always higher than those for FLa (from 0.07 to 0.19), and higher or equal to the ones estimated for TL (from 0.07 to 0.23), considering the different culling reasons. The average genetic correlations estimated between ages were low to moderate (~0.40), for all longevity definitions and culling reasons. However, removing the extreme ages (i.e., 2 and >12 years) increased the average correlation between ages (from ~0.40 to >0.70). The genetic correlations estimated between culling reasons were low (0.12 and 0.20 on average, considering all ages and ages between 3 and 12 years old, respectively), indicating that longevity based on different culling reasons should be considered as different traits in the genetic evaluations. Higher average genetic correlations (estimated from 3 to 12 years old) were observed between TL and FLb (0.73) in comparison to TL and FLa (0.64), or FLa and FLb (0.65). Consequently, a higher average proportion of commonly-selected sires, for the top 1% sires, was also observed between TL and FLb (91.74%), compared to TL and FLa (59.68%), or FLa and FLb (61.01%). Higher prediction accuracies for the expected daughter performances (calculated based on the pedigree information) were obtained for FLb in comparison to TL and FLa. Our findings indicate that FLb is preferred for the genetic evaluation of longevity. In addition, it is recommended including multiple longevity traits based on different groups of culling reasons in a selection sub-index, as they are genetically-different traits. Genetic selection based on breeding values at the age of four years is expected to result in greater selection responses for increased longevity in North American Angus cattle. Full article
(This article belongs to the Special Issue Advances in Cattle Breeding, Genetics and Genomics)
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Article
Bta-miR-376a Targeting KLF15 Interferes with Adipogenesis Signaling Pathway to Promote Differentiation of Qinchuan Beef Cattle Preadipocytes
Animals 2020, 10(12), 2362; https://doi.org/10.3390/ani10122362 - 10 Dec 2020
Cited by 4 | Viewed by 618
Abstract
Intramuscular fat (IMF) is a quality index associated with the taste and juiciness of meat. The deposition of IMF is affected by genetic and non-genetic factors, such as age, slaughter location, gender of the animal, and diet. Micro-ribonucleic acids (miRNA) are transcriptional regulators [...] Read more.
Intramuscular fat (IMF) is a quality index associated with the taste and juiciness of meat. The deposition of IMF is affected by genetic and non-genetic factors, such as age, slaughter location, gender of the animal, and diet. Micro-ribonucleic acids (miRNA) are transcriptional regulators involved in adipogenesis, but the specific role of miR-376a in regulation of bovine adipocytes remains unknown. Our findings indicated that miR-376a was a potential negative regulator of bovine adipocyte differentiation. A bta-miR-376a mimic inhibited mRNA and protein expression of the marker genes, CDK1, CDK2, PCNA, C/EBPα, FAS, and PPAR γ, and significantly reduced ratios (%) of S-phase cells, the number of cells stained with 5-ethynyl-2′-deoxyuridine, and adipocyte proliferation. Oil red O staining and triglyceride content analysis also confirmed that bta-miR-376a was involved in adipocyte differentiation. Luciferase activities confirmed that Krüppel-like transcription factor 15 (KLF15) was a direct target gene of bta-miR-376a, and that KLF15 was a key transcription factor in adipogenesis. Therefore, bta-miR-376a might be a target for increasing beef IMF. Full article
(This article belongs to the Special Issue Advances in Cattle Breeding, Genetics and Genomics)
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Article
Overexpression of PLIN1 Promotes Lipid Metabolism in Bovine Adipocytes
Animals 2020, 10(11), 1944; https://doi.org/10.3390/ani10111944 - 22 Oct 2020
Cited by 3 | Viewed by 846
Abstract
Perilipin 1 (PLIN1) is a protein encoded by the PLIN1 gene in eukaryotes. PLIN1 is a member of the PAT protein family, a family of proteins related to lipid droplet (LD) surface proteins. PLIN1 phosphorylation plays a vital role during fat metabolism of [...] Read more.
Perilipin 1 (PLIN1) is a protein encoded by the PLIN1 gene in eukaryotes. PLIN1 is a member of the PAT protein family, a family of proteins related to lipid droplet (LD) surface proteins. PLIN1 phosphorylation plays a vital role during fat metabolism of adipose tissue lipolysis and fat storage in adipocytes. However, to further explore the regulation of the PLIN1 gene on the proliferation, differentiation and lipid metabolism of bovine adipocytes. In this study, the mRNA expression of PLIN1, at day six, was the highest during bovine adipocyte differentiation. Moreover, PLIN1 can promote the proliferation and differentiation of preadipocytes in cattle. On the sixth day, after transfection with, and overexpression of, the PLIN1 gene in bovine preadipocytes via adenovirus, cell samples were collected, and transcriptome sequencing was performed. A total of 1923 differentially expressed genes were detected. Through GO and KEGG pathway analysis, the differentially expressed genes were established to be mainly enriched in the AMPK, Wnt, and PPAR signaling pathways related to fat proliferation and differentiation. In conclusion, at the transcriptional level, PLIN1 plays an important role in regulating fat proliferation and metabolism. Additionally, the sequencing results screened new differentially expressed genes related to fat metabolism, providing theoretical support for molecular breeding of Qinchuan beef cattle. Full article
(This article belongs to the Special Issue Advances in Cattle Breeding, Genetics and Genomics)
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Article
Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle
Animals 2020, 10(10), 1836; https://doi.org/10.3390/ani10101836 - 09 Oct 2020
Cited by 2 | Viewed by 730
Abstract
In recent years, studies on the biological mechanisms underlying complex traits have been facilitated by innovations in high-throughput genotyping technology. We conducted a weighted single-step genome-wide association study (WssGWAS) to evaluate backfat thickness, carcass weight, eye muscle area, marbling score, and yearling weight [...] Read more.
In recent years, studies on the biological mechanisms underlying complex traits have been facilitated by innovations in high-throughput genotyping technology. We conducted a weighted single-step genome-wide association study (WssGWAS) to evaluate backfat thickness, carcass weight, eye muscle area, marbling score, and yearling weight in a cohort of 1540 Hanwoo beef cattle using BovineSNP50 BeadChip. The WssGWAS uncovered thirty-three genomic regions that explained more than 1% of the additive genetic variance, mostly located on chromosomes 6 and 14. Among the identified window regions, seven quantitative trait loci (QTL) had pleiotropic effects and twenty-six QTL were trait-specific. Significant pathways implicated in the measured traits through Gene Ontology (GO) term enrichment analysis included the following: lipid biosynthetic process, regulation of lipid metabolic process, transport or localization of lipid, regulation of growth, developmental growth, and multicellular organism growth. Integration of GWAS results of the studied traits with pathway and network analyses facilitated the exploration of the respective candidate genes involved in several biological functions, particularly lipid and growth metabolism. This study provides novel insight into the genetic bases underlying complex traits and could be useful in developing breeding schemes aimed at improving growth and carcass traits in Hanwoo beef cattle. Full article
(This article belongs to the Special Issue Advances in Cattle Breeding, Genetics and Genomics)
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Article
Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle
Animals 2020, 10(8), 1425; https://doi.org/10.3390/ani10081425 - 14 Aug 2020
Cited by 4 | Viewed by 1019
Abstract
Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms. Identifications of ROH leading to reduction in performance can provide valuable insight into the genetic architecture of complex traits. Here, we evaluated genome-wide patterns of [...] Read more.
Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms. Identifications of ROH leading to reduction in performance can provide valuable insight into the genetic architecture of complex traits. Here, we evaluated genome-wide patterns of homozygosity and their association with important traits in Chinese Wagyu beef cattle. We identified a total of 29,271 ROH segments from 462 animals. Within each animal, an average number of ROH was 63.36 while an average length was 62.19 Mb. To evaluate the enrichment of ROH across genomes, we initially identified 280 ROH regions by merging ROH events across all individuals. Of these, nine regions containing 154 candidate genes, were significantly associated with six traits (body height, chest circumference, fat coverage, backfat thickness, ribeye area, and carcass length; p < 0.01). Moreover, we found 26 consensus ROH regions with frequencies exceeding 10%, and several regions overlapped with QTLs, which are associated with body weight, calving ease, and stillbirth. Among them, we observed 41 candidate genes, including BCKDHB, MAB21L1, SLC2A13, FGFR3, FGFRL1, CPLX1, CTNNA1, CORT, CTNNBIP1, and NMNAT1, which have been previously reported to be related to body conformation, meat quality, susceptibility, and reproductive traits. In summary, we assessed genome-wide autozygosity patterns and inbreeding levels in Chinese Wagyu beef cattle. Our study identified many candidate regions and genes overlapped with ROH for several important traits, which could be unitized to assist the design of a selection mating strategy in beef cattle. Full article
(This article belongs to the Special Issue Advances in Cattle Breeding, Genetics and Genomics)
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Communication
Effect of Expressions and SNPs of Candidate Genes on Intramuscular Fat Content in Qinchuan Cattle
Animals 2020, 10(8), 1370; https://doi.org/10.3390/ani10081370 - 07 Aug 2020
Viewed by 749
Abstract
Marbling is characterized by the amount and distribution of intramuscular fat (IMF). The AKIRIN2, TTN, EDG1, and MYBPC1 genes are well-known marbling-related genes, which were first identified in Japanese Black beef cattle. The objectives of this study were to analyze [...] Read more.
Marbling is characterized by the amount and distribution of intramuscular fat (IMF). The AKIRIN2, TTN, EDG1, and MYBPC1 genes are well-known marbling-related genes, which were first identified in Japanese Black beef cattle. The objectives of this study were to analyze the correlation of the expression levels of these genes in the longissimus muscle (LM) with IMF content, and the associations between the single nucleotide polymorphisms (SNPs) in these genes and IMF content in Chinese Qinchuan cattle (n = 350). The association analyses showed that the g.42041062G>T SNP in the EDG1 gene was significantly associated with IMF content in Qinchuan (p < 0.05). Further, the expressions of the EDG1 and MYBPC1 were up-regulated (p < 0.05) in LM of Qinchuan cattle group with low IMF content. Down-regulations of the AKIRIN2 and TTN genes (p < 0.05 and p < 0.01, respectively) were observed in the Qinchuan cattle group with high IMF content. These results suggest possible effects of the expression levels of selected genes on IMF content in the LM, and the g.42041062G>T SNP in the EDG1 gene might be useful as a molecular marker for IMF content in Qinchuan. Full article
(This article belongs to the Special Issue Advances in Cattle Breeding, Genetics and Genomics)
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Article
Mir-193b Regulates the Differentiation, Proliferation, and Apoptosis of Bovine Adipose Cells by Targeting the ACSS2/AKT Axis
Animals 2020, 10(8), 1265; https://doi.org/10.3390/ani10081265 - 24 Jul 2020
Cited by 3 | Viewed by 755
Abstract
The precise functions and molecular mechanisms of microRNAs (miRNAs) in adipocytes are primarily unknown. Studies have demonstrated that miR-193b plays a pivotal role in the differentiation of preadipocytes. Herein, we evaluated the effects of bta-miR-193b on the growth and development of adipocytes, using [...] Read more.
The precise functions and molecular mechanisms of microRNAs (miRNAs) in adipocytes are primarily unknown. Studies have demonstrated that miR-193b plays a pivotal role in the differentiation of preadipocytes. Herein, we evaluated the effects of bta-miR-193b on the growth and development of adipocytes, using the EdU cell proliferation method, flow cytometry analysis, CCK-8 assay, RT-qPCR, Western blotting, and oil red O staining. We observed that the overexpression of bta-miR-193b significantly affected the differentiation, proliferation, and apoptosis of adipocytes. The results of the dual-fluorescent reporter vector experiments demonstrated that bta-miR-193b directly targeted Acyl-CoA synthetase short-chain family member 2 (ACSS2). Additionally, the effects of ACSS2 overexpression on the proliferation and apoptosis in adipose cells were the opposite of those induced by bta-miR-193b. We also demonstrated that ACSS2 can significantly promote the expression of AKT and pAKT proteins. Therefore, this study presents a novel mechanism by which bta-miR-193b regulates adipocyte development by targeting ACSS2. Full article
(This article belongs to the Special Issue Advances in Cattle Breeding, Genetics and Genomics)
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