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Animals
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Integrative Omics Technologies and Machine Learning Approaches in Animal Production
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Integrative Omics Technologies and Machine Learning Approaches in Animal Production

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

Deadline for manuscript submissions: 27 November 2024 | Viewed by 16309

Special Issue Editor

Dr. Sunday Peters

E-Mail Website
Guest Editor
Department of Animal Science, Berry College, Mount Berry, GA, USA
Interests: quantitative genetics; molecular genetics; statistical genetics; genomics; metabolomics; proteomics; metatranscriptomics; transcriptomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Advances in molecular biology have revolutionized research in livestock production. The application of genomics, transcriptomics, metatranscriptomics, proteomics, nutrigenomics, metagenomics, and metabolomics has not only provided the opportunity to decipher the genomic architecture underlying traits of interest but also enhanced our understanding of the molecular basis of growth, reproduction, and carcass merit, as well as the role of selection and nutrition and of other environmental factors. There is also a growing interest in the use of semi- and non-parametric methods for genomic prediction, because the conventional approach of using linear regression models has been said to ignore gene–gene interactions and higher order non-linearities. In this context, machine learning approaches provide interesting alternatives for marker-based genomic selection and omics approaches.

This Special Issue invites manuscripts that apply omics technologies and those that utilize any machine learning approach in livestock production.

Dr. Sunday Peters
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Genomics
  • Transcriptomics
  • Metatranscriptomics
  • Nutrigenomics
  • Proteomics
  • Metabolomics
  • Metagenomics
  • Artificial Neural Network
  • Machine Learning

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Published Papers (7 papers)

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Research

18 pages, 3067 KiB  
Article
Genomic Prediction Accuracies for Growth and Carcass Traits in a Brangus Heifer Population
by Sunday O. Peters, Kadir Kızılkaya, Mahmut Sinecen, Burcu Mestav, Aranganoor K. Thiruvenkadan and Milton G. Thomas
Animals 2023, 13(7), 1272; https://doi.org/10.3390/ani13071272 - 6 Apr 2023
Viewed by 1748
Abstract
The predictive abilities and accuracies of genomic best linear unbiased prediction (GBLUP) and the Bayesian (BayesA, BayesB, BayesC and Lasso) genomic selection (GS) methods for economically important growth (birth, weaning, and yearling weights) and carcass (depth of rib fat, apercent intramuscular fat and [...] Read more.
The predictive abilities and accuracies of genomic best linear unbiased prediction (GBLUP) and the Bayesian (BayesA, BayesB, BayesC and Lasso) genomic selection (GS) methods for economically important growth (birth, weaning, and yearling weights) and carcass (depth of rib fat, apercent intramuscular fat and longissimus muscle area) traits were characterized by estimating the linkage disequilibrium (LD) structure in Brangus heifers using single nucleotide polymorphisms (SNP) markers. Sharp declines in LD were observed as distance among SNP markers increased. The application of the GBLUP and the Bayesian methods to obtain the GEBV for growth and carcass traits within k-means and random clusters showed that k-means and random clustering had quite similar heritability estimates, but the Bayesian methods resulted in the lower estimates of heritability between 0.06 and 0.21 for growth and carcass traits compared with those between 0.21 and 0.35 from the GBLUP methodologies. Although the prediction ability of the GBLUP and the Bayesian methods were quite similar for growth and carcass traits, the Bayesian methods overestimated the accuracies of GEBV because of the lower estimates of heritability of growth and carcass traits. However, GBLUP resulted in accuracy of GEBV for growth and carcass traits that parallels previous reports. Full article
(This article belongs to the Special Issue Integrative Omics Technologies and Machine Learning Approaches in Animal Production)
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15 pages, 2788 KiB  
Article
Differential Expression of Innate and Adaptive Immune Genes during Acute Physical Exercise in American Quarter Horses
by Judith Wilson, Marcos De Donato, Brooke Appelbaum, Carly Turner Garcia and Sunday Peters
Animals 2023, 13(2), 308; https://doi.org/10.3390/ani13020308 - 16 Jan 2023
Cited by 5 | Viewed by 2074
Abstract
Overtraining syndrome (OTS) is the reduction in performance due to excess training and lack of proper recovery, which can lead to a chronic deprivation of energy and reduction in the repair of damage that can accumulate over time. Here, the effect of acute, [...] Read more.
Overtraining syndrome (OTS) is the reduction in performance due to excess training and lack of proper recovery, which can lead to a chronic deprivation of energy and reduction in the repair of damage that can accumulate over time. Here, the effect of acute, intense physical exercise on the expression of innate and adaptive immune genes in 12 racing-bred American Quarter Horses, after resting for 3 days and immediately after intense exercise for 1.8 miles were compared. The expression of 84 genes related to innate and adaptive immune responses was analyzed. Significant variation among individuals and between sexes was observed. The analysis showed that five genes were differentially expressed in both females and males, three only in females, and two in males. The upregulated genes were IL13 (male only), CCR4 (female only), TLR6, TLR9 (female only), NFKBIA, CXCR3, and TLR4, while the downregulated genes were IL6 (female only), CD4 (male only), and MYD88. The three main pathways containing genes that were affected by acute, intense physical exercise were Th1 and Th2 cell differentiation, and the NF-kappa B and chemokine signaling pathways, suggesting the activation of the proinflammatory responses as a result of the stress from the acute exercise. Gene expression could be used to assess indications of OTS. Full article
(This article belongs to the Special Issue Integrative Omics Technologies and Machine Learning Approaches in Animal Production)
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16 pages, 2980 KiB  
Article
Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications
by Hengwu Ding, De Bi, Shiyun Han, Ran Yi, Sijia Zhang, Yuanxin Ye, Jinming Gao, Jianke Yang and Xianzhao Kan
Animals 2023, 13(1), 96; https://doi.org/10.3390/ani13010096 - 27 Dec 2022
Cited by 6 | Viewed by 2106
Abstract
The superfamily Certhioidea currently comprises five families. Due to the rapid diversification, the phylogeny of Certhioidea is still controversial. The advent of next generation sequencing provides a unique opportunity for a mitogenome-wide study. Here, we first provided six new complete mitogenomes of Certhioidea [...] Read more.
The superfamily Certhioidea currently comprises five families. Due to the rapid diversification, the phylogeny of Certhioidea is still controversial. The advent of next generation sequencing provides a unique opportunity for a mitogenome-wide study. Here, we first provided six new complete mitogenomes of Certhioidea (Certhia americana, C. familiaris, Salpornis spilonota, Cantorchilus leucotis, Pheugopedius coraya, and Pheugopedius genibarbis). We further paid attention to the genomic characteristics, codon usages, evolutionary rates, and phylogeny of the Certhioidea mitogenomes. All mitogenomes we analyzed displayed typical ancestral avian gene order with 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and one control region (CR). Our study indicated the strand-biased compositional asymmetry might shape codon usage preferences in mitochondrial genes. In addition, natural selection might be the main factor in shaping the codon usages of genes. Additionally, evolutionary rate analyses indicated all mitochondrial genes were under purifying selection. Moreover, MT-ATP8 and MT-CO1 were the most rapidly evolving gene and conserved genes, respectively. According to our mitophylogenetic analyses, the monophylies of Troglodytidae and Sittidae were strongly supported. Importantly, we suggest that Salpornis should be separated from Certhiidae and put into Salpornithidae to maintain the monophyly of Certhiidae. Our findings are useful for further evolutionary studies within Certhioidea. Full article
(This article belongs to the Special Issue Integrative Omics Technologies and Machine Learning Approaches in Animal Production)
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18 pages, 5031 KiB  
Article
An Integrated Bioinformatics Approach to Identify Network-Derived Hub Genes in Starving Zebrafish
by Amin Mortazavi, Mostafa Ghaderi-Zefrehei, Mustafa Muhaghegh Dolatabady, Mahdi Golshan, Sajad Nazari, Ayeh Sadat Sadr, Saeid Kadkhodaei, Ikhide G. Imumorin, Sunday O. Peters and Jacqueline Smith
Animals 2022, 12(19), 2724; https://doi.org/10.3390/ani12192724 - 10 Oct 2022
Cited by 1 | Viewed by 2524
Abstract
The present study was aimed at identifying causative hub genes within modules formed by co-expression and protein–protein interaction (PPI) networks, followed by Bayesian network (BN) construction in the liver transcriptome of starved zebrafish. To this end, the GSE11107 and GSE112272 datasets from the [...] Read more.
The present study was aimed at identifying causative hub genes within modules formed by co-expression and protein–protein interaction (PPI) networks, followed by Bayesian network (BN) construction in the liver transcriptome of starved zebrafish. To this end, the GSE11107 and GSE112272 datasets from the GEO databases were downloaded and meta-analyzed using the MetaDE package, an add-on R package. Differentially expressed genes (DEGs) were identified based upon expression intensity N(µ = 0.2, σ2 = 0.4). Reconstruction of BNs was performed by the bnlearn R package on genes within modules using STRINGdb and CEMiTool. ndufs5 (shared among PPI, BN and COEX), rps26, rpl10, sdhc (shared between PPI and BN), ndufa6, ndufa10, ndufb8 (shared between PPI and COEX), skp1, atp5h, ndufb10, rpl5b, zgc:193613, zgc:123327, zgc:123178, wu:fc58f10, zgc:111986, wu:fc37b12, taldo1, wu:fb62f08, zgc:64133 and acp5a (shared between COEX and BN) were identified as causative hub genes affecting gene expression in the liver of starving zebrafish. Future work will shed light on using integrative analyses of miRNA and DNA microarrays simultaneously, and performing in silico and experimental validation of these hub-causative (CST) genes affecting starvation in zebrafish. Full article
(This article belongs to the Special Issue Integrative Omics Technologies and Machine Learning Approaches in Animal Production)
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10 pages, 1549 KiB  
Article
Assessment of Mutation Drift Equilibrium and the Occurrence of a Recent Genetic Bottleneck in South Indian Zebu Cattle
by Vandana Manomohan, Saravanan Ramasamy, Rudolf Pichler, Murali Nagarajan, Sivakumar Karuppusamy, Sudhakar Krovvidi, Raja K. Nachiappan, Sunday O. Peters and Kathiravan Periasamy
Animals 2022, 12(14), 1838; https://doi.org/10.3390/ani12141838 - 19 Jul 2022
Viewed by 1653
Abstract
During the last few decades, the effective population size of indigenous zebu cattle breeds has declined drastically, resulting in the classification of some of them into the vulnerable, endangered, or critically endangered category. Drastic reductions in the effective size of a population may [...] Read more.
During the last few decades, the effective population size of indigenous zebu cattle breeds has declined drastically, resulting in the classification of some of them into the vulnerable, endangered, or critically endangered category. Drastic reductions in the effective size of a population may result in genetic bottlenecks and can affect within-breed genetic variability and its viability. The present study was undertaken with the objective of evaluating South Indian zebu cattle populations for mutation drift equilibrium and to detect the occurrence of recent genetic bottleneck events. A total of 293 cattle from eight indigenous breeds were genotyped at 27 FAO/ISAG-recommended microsatellite marker loci. Three different statistical tests, viz., the sign test, standardized differences test, and Wilcoxon sign rank test were performed using allele frequency data to detect loci with heterozygosity excess under the infinite alleles, stepwise, and two-phase mutation models. Under the infinite alleles model, the observed number of loci with heterozygosity excess (He > Heq) ranged between 10 and 19 among the investigated cattle breeds. However, the observed heterozygosity excess was not statistically significant (p > 0.05) in any of the studied breeds. Similarly, the standardized differences test and Wilcoxon sign rank test revealed no concrete evidence for the occurrence of a recent genetic bottleneck in South Indian zebu cattle breeds. The qualitative test for mode-shift distortion revealed a normal L-shaped distribution of allele frequencies, suggesting a lack of evidence for the loss of low-frequency alleles in all the investigated South Indian zebu cattle breeds. Full article
(This article belongs to the Special Issue Integrative Omics Technologies and Machine Learning Approaches in Animal Production)
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10 pages, 909 KiB  
Communication
Genomic Imprinting at the Porcine DIRAS3 Locus
by Jinsoo Ahn, In-Sul Hwang, Mi-Ryung Park, Seongsoo Hwang and Kichoon Lee
Animals 2021, 11(5), 1315; https://doi.org/10.3390/ani11051315 - 3 May 2021
Cited by 4 | Viewed by 2184
Abstract
The epigenetic mechanisms underlying genomic imprinting include DNA methylation and monoallelic expression of genes in close proximity. Although genes imprinted in humans and mice have been widely characterized, there is a lack of detailed and comprehensive studies in livestock species including pigs. The [...] Read more.
The epigenetic mechanisms underlying genomic imprinting include DNA methylation and monoallelic expression of genes in close proximity. Although genes imprinted in humans and mice have been widely characterized, there is a lack of detailed and comprehensive studies in livestock species including pigs. The purpose of this study was to investigate a detailed methylation status and parent-of-origin-specific gene expression within the genomic region containing an underexamined porcine DIRAS3 locus. Through whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) of porcine parthenogenetic embryos and analyses of public RNA-seq data from adult pigs, DNA methylation and monoallelic expression pattern were investigated. As a result, maternal hypermethylation at the DIRAS3 locus and hypothalamus-specific and monoallelic expression of the DIRAS3 gene were found in pigs. In conclusion, the findings from this study suggest that the presence of maternal hypermethylation, or imprints, might be maintained and related to monoallelic expression of DIRAS3 during pig development. Full article
(This article belongs to the Special Issue Integrative Omics Technologies and Machine Learning Approaches in Animal Production)
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9 pages, 918 KiB  
Article
Plasma Carboxyl-Metabolome Is Associated with Average Daily Gain Divergence in Beef Steers
by Ibukun Ogunade, Adeoye Oyebade, Bremansu Osa-Andrews and Sunday Peters
Animals 2021, 11(1), 67; https://doi.org/10.3390/ani11010067 - 1 Jan 2021
Cited by 3 | Viewed by 2454
Abstract
We applied an untargeted metabolomics technique to analyze the plasma carboxyl-metabolome of beef steers with divergent average daily gain (ADG). Forty-eight newly weaned Angus crossbred beef steers were fed the same total mixed ration ad libitum for 42 days. On day 42, the [...] Read more.
We applied an untargeted metabolomics technique to analyze the plasma carboxyl-metabolome of beef steers with divergent average daily gain (ADG). Forty-eight newly weaned Angus crossbred beef steers were fed the same total mixed ration ad libitum for 42 days. On day 42, the steers were divided into two groups of lowest (LF: n = 8) and highest ADG (HF: n = 8), and blood samples were obtained from the two groups for plasma preparation. Relative quantification of carboxylic-acid-containing metabolites in the plasma samples was determined using a metabolomics technique based on chemical isotope labeling liquid chromatography mass spectrometry. Metabolites that differed (fold change (FC) ≥ 1.2 or ≤ 0.83 and FDR ≤ 0.05) between LF and HF were identified using a volcano plot. Metabolite set enrichment analysis (MSEA) of the differential metabolites was done to determine the metabolic pathways or enzymes that were potentially altered. In total, 328 metabolites were identified. Volcano plot analysis revealed 43 differentially abundant metabolites; several short chain fatty acids and ketone bodies had greater abundance in HF steers. Conversely, several long chain fatty acids were greater in LF steers. Five enzymatic pathways, such as fatty acyl CoA elongation and fatty-acid CoA ligase were altered based on MSEA. This study demonstrated that beef steers with divergent ADG had altered plasma carboxyl-metabolome, which is possibly caused by altered abundances and/or activities of enzymes involved in fatty acid oxidation and biosynthesis in the liver. Full article
(This article belongs to the Special Issue Integrative Omics Technologies and Machine Learning Approaches in Animal Production)
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