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Systematic Analysis and Application of Omics Data in Animal Breeding

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Bioinformatics".

Deadline for manuscript submissions: closed (15 September 2023) | Viewed by 15550

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Prof. Dr. Fuping Zhao

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Guest Editor

Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Interests: genomic prediction; pig breeding and genetics; genomic mating; selection signature detection

Prof. Dr. Zhe Zhang

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College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Interests: genomic selection; pig breeding and genetics; genome-wide association study

Dr. Lingzhao Fang

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Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH8 9YL, UK
Interests: bioinformatics; machine learning; functional genomics; meta-analysis

Dr. Ruidong Xiang

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Guest Editor

Faculty of Veterinary & Agricultural Science, The University of Melbourne, Melbourne, VIC 3052, Australia
Interests: statistical genomics; functional genomics; genomic prediction

Special Issue Information

Dear Colleagues,

I hope that you are all doing well.

Over the past decade, the application of genome-wide association studies and genomic selection in animals was mainly based on SNP chip data. Advances in next-generation sequencing technology and the reduction of sequencing costs have led to a surge in omics data including genomics, transcriptomics, epigenomics, metabolomics, proteomics, microbiomics etc. These rich omics data have provided unprecedented opportunities to systematically elucidate the biological mechanisms of economically important traits from multiple layers in the animals. Meanwhile, integrating omics data and genomic knowledge can improve the accuracy of genomic prediction. However, it is a major challenge not only in systematically analyzing these data and formulating new hypotheses but also effectively utilizing them for animal genetic improvement and conservation.

This Special Issue aims to collect high-quality original research articles, mini-reviews, and full-length reviews to address emerging challenges, focusing on “Systematic analysis and application of omics data in animal breeding”. Our topic welcomes but is not necessarily limited to progress in the knowledge of the aforementioned issues. Contributions by experts in the field in the form of research papers and critical reviews are called for.

We look forward to your submissions.

Prof. Dr. Fuping Zhao
Prof. Dr. Zhe Zhang
Dr. Lingzhao Fang
Dr. Ruidong Xiang
Guest Editors

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Keywords

omics data
genomic prediction
pig genome
quantitative genetics
population genetics

Published Papers (10 papers)

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Research

13 pages, 2871 KiB

Open AccessArticle

Impacts of Population Size and Domestication Process on Genetic Diversity and Genetic Load in Genus Ovis

by Dongfeng Wang, Hosein Salehian-Dehkordi, Langda Suo and Fenghua Lv

Genes 2023, 14(10), 1977; https://doi.org/10.3390/genes14101977 - 23 Oct 2023

Viewed by 1026

Abstract

In theoretical biology, a prevailing hypothesis posits a profound interconnection between effective population size (N_e), genetic diversity, inbreeding, and genetic load. The domestication and improvement processes are believed to be pivotal in diminishing genetic diversity while elevating levels of inbreeding and increasing genetic load. In this study, we performed a whole genome analysis to quantity genetic diversity, inbreeding, and genetic load across seven wild Ovis species and five domesticated sheep breeds. Our research demonstrates that the genetic load and diversity of species in the genus Ovis have no discernible impact on recent N_e, and three species within the subgenus Pachyceros tend to carry a higher genetic load and lower genetic diversity patterns. The results coincide with these species’ dramatic decline in population sizes within the subgenus Pachyceros ~80–250 thousand years ago. European mouflon presented with the lowest N_e, lower genetic diversity, and higher individual inbreeding coefficient but a lower genetic load (missense and LoF). This suggests that the small N_e of European mouflon could reduce harmful mutations compared to other species within the genus Ovis. We showed lower genetic diversity in domesticated sheep than in Asiatic mouflon, but counterintuitive patterns of genetic load, i.e., lower weak genetic load (missense mutation) and no significant difference in strong genetic load (LoF mutation) between domestic sheep and Asiatic mouflon. These findings reveal that the “cost of domestication” during domestication and improvement processes reduced genetic diversity and purified weak genetic load more efficiently than wild species. Full article

(This article belongs to the Special Issue Systematic Analysis and Application of Omics Data in Animal Breeding)

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18 pages, 6011 KiB

Open AccessArticle

Blood Transcriptomic Analyses Reveal Functional Pathways Associated with Thermotolerance in Pregnant Ewes Exposed to Environmental Heat Stress

by Rosa I. Luna-Ramirez, Sean W. Limesand, Ravi Goyal, Alexander L. Pendleton, Gonzalo Rincón, Xi Zeng, Guillermo Luna-Nevárez, Javier R. Reyna-Granados and Pablo Luna-Nevárez

Genes 2023, 14(8), 1590; https://doi.org/10.3390/genes14081590 - 6 Aug 2023

Cited by 1 | Viewed by 1176

Abstract

Environmental heat stress triggers a series of compensatory mechanisms in sheep that are dependent on their genetic regulation of thermotolerance. Our objective was to identify genes and regulatory pathways associated with thermotolerance in ewes exposed to heat stress. We performed next-generation RNA sequencing on blood collected from 16 pregnant ewes, which were grouped as tolerant and non-tolerant to heat stress according to a physiological indicator. Additional samples were collected to measure complete blood count. A total of 358 differentially expressed genes were identified after applying selection criteria. Gene expression analysis detected 46 GO terms and 52 KEGG functional pathways. The top-three signaling pathways were p53, RIG-I-like receptor and FoxO, which suggested gene participation in biological processes such as apoptosis, cell signaling and immune response to external stressors. Network analysis revealed ATM, ISG15, IRF7, MDM4, DHX58 and TGFβR1 as over-expressed genes with high regulatory potential. A co-expression network involving the immune-related genes ISG15, IRF7 and DXH58 was detected in lymphocytes and monocytes, which was consistent with hematological findings. In conclusion, transcriptomic analysis revealed a non-viral immune mechanism involving apoptosis, which is induced by external stressors and appears to play an important role in the molecular regulation of heat stress tolerance in ewes. Full article

(This article belongs to the Special Issue Systematic Analysis and Application of Omics Data in Animal Breeding)

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11 pages, 3298 KiB

Open AccessArticle

Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data

by Yige Chen, Xudong Wu, Jinglin Wang, Yinhui Hou, Ying Liu, Bo Wang, Xiaojing Hu, Xianrui Zheng, Xiaodong Zhang, Yueyun Ding and Zongjun Yin

Genes 2022, 13(12), 2310; https://doi.org/10.3390/genes13122310 - 8 Dec 2022

Cited by 1 | Viewed by 1615

Abstract

As a distinguished Chinese indigenous pig breed that exhibits disease resistance and high meat quality, the Anqing six-end-white (AQ) pig represents a valuable germplasm resource for improving the quality of the pig breeding industry. In this study, 24 AQ pigs that were distantly blood-related and 6 Asian Wild Boar (AWB) were selected for 10× deep-genome resequencing. The signatures of the selection were analyzed to explore the genetic basis of their germplasm characteristics and to identify excellent germplasm-related functional genes based on NGS data. A total of 49,289,052 SNPs and 6,186,123 indels were detected across the genome in 30 pigs. Most of the genetic variations were synonym mutations and existed in the intergenic region. We identified 275 selected regions (top 1%) harboring 85 genes by applying a crossover approach based on genetic differentiation (F_ST) and polymorphism levels (π ratio). Some genes were found to be positively selected in AQ pigs’ breeding. The SMPD4 and DDX18 genes were involved in the immune response to pseudorabies virus (PRV) and porcine reproductive and respiratory syndrome virus (PRRSV). The BCL6 and P2RX6 genes were involved in biological regulation of immune T cells and phagocytes. The SLC7A4 and SPACA4 genes were related to reproductive performance. The MSTN and HIF1A genes were related to fat deposition and muscle development. Moreover, 138 overlapping regions were detected in selected regions and ROH islands of AQ pigs. Additionally, we found that the QTLs with the most overlapping regions were related to back fat thickness, meat color, pH value, fatty acid content, immune cells, parasitic immunity, and bacterial immunity. Based on functional enrichment analysis and QTLs mapping, we conducted further research on the molecular genetic basis of germplasm traits (disease resistance and excellent meat quality). These results are a reliable resource for conserving germplasm resources and exploiting molecular markers of AQ pigs. Full article

(This article belongs to the Special Issue Systematic Analysis and Application of Omics Data in Animal Breeding)

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13 pages, 1774 KiB

Open AccessFeature PaperArticle

Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs

by Wei Zhang, Mei Zhou, Linqing Liu, Shiguang Su, Lin Dong, Xinxin Meng, Xueting Li and Chonglong Wang

Genes 2022, 13(11), 2026; https://doi.org/10.3390/genes13112026 - 3 Nov 2022

Cited by 2 | Viewed by 1714

Abstract

Single nucleotide polymorphism was widely used to perform genetic and evolution research in pigs. However, little is known about the effect of copy number variation (CNV) on characteristics in pigs. This study performed a genome-wide comparison of CNVs between Wannan black pigs (WBP) and Asian wild boars (AWB), using whole genome resequencing data. By using Manta, we detected in total 28,720 CNVs that covered approximately 1.98% of the pig genome length. We identified 288 selected CNVs (top 1%) by performing Fst statistics. Functional enrichment analyses for genes located in selected CNVs were found to be muscle related (NDN, TMOD4, SFRP1, and SMYD3), reproduction related (GJA1, CYP26B1, WNT5A, SRD5A2, PTPN11, SPEF2, and CCNB1), residual feed intake (RFI) related (MAP3K5), and ear size related (WIF1). This study provides essential information on selected CNVs in Wannan black pigs for further research on the genetic basis of the complex phenotypic and provides essential information for direction in the protection and utilization of Wannan black pig. Full article

(This article belongs to the Special Issue Systematic Analysis and Application of Omics Data in Animal Breeding)

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7 pages, 558 KiB

Open AccessArticle

Genomic Variant in NK-Lysin Gene Is Associated with T Lymphocyte Subpopulations in Pigs

by Shifeng Tong, Ningkun Shi, Kaichen Zheng, Zongjun Yin, Xiaodong Zhang and Yang Liu

Genes 2022, 13(11), 1985; https://doi.org/10.3390/genes13111985 - 31 Oct 2022

Cited by 1 | Viewed by 1161

Abstract

As an antimicrobial peptide, NK-lysin (NKL) plays an important role in the innate immune system of organisms. In this study, 300 piglets (68 Landrace pigs, 158 Large White pigs and 74 Songliao Black pigs) were used to further explore the function of NLK gene in porcine immune system. The quantitative real-time PCR analysis detected the NKL gene’s expression, and the result demonstrated that NKL mRNA was expressed in lung, spleen, stomach, kidney, liver and heart, and the expression level decreased sequentially. A single-nucleotide polymorphism (SNP, g.59070355 G > A) in intron 3 of the NKL gene was detected by PCR amplification and sequencing. The results of the Chi-square (χ2) test showed that the genotype of the SNP was consistent with the Hardy-Weinberg equilibrium. What’s more, association analysis results showed the SNP in NKL gene was significantly associated with T lymphocyte subpopulations. Different genotypes had significant effects on the proportion of CD4⁻CD8⁻, CD4⁻CD8⁺, CD4⁺CD8⁺, CD8⁺, CD4⁺/CD8⁺ in peripheral blood (p < 0.05). These results further suggested that NKL could be recognized as a promising immune gene for swine disease resistance breeding. Full article

(This article belongs to the Special Issue Systematic Analysis and Application of Omics Data in Animal Breeding)

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13 pages, 489 KiB

Open AccessArticle

Evaluation of the Maturity and Gene Expression of Sheep Oocytes and Embryos Cultured in Media Supplemented with Marjoram (Origanum vulgare) Extract

by Mashael M. Alotaibi, Ahmad R. Alhimaidi, Muath Q. Al-Ghadi, Aiman A. Ammari and Nawal M. Al-Malahi

Genes 2022, 13(10), 1844; https://doi.org/10.3390/genes13101844 - 12 Oct 2022

Cited by 1 | Viewed by 1511

Abstract

This study aimed to evaluate the effects of marjoram extract on oocyte maturation and gene expression in sheep oocytes and embryos. The first experiment studied the effect of the extract as an antioxidant to improve the in vitro maturation media used for sheep oocytes; the oocytes were matured in a TCM199 medium supplemented with 1 or 10 µg/mL of marjoram extract or the control, 0 µg, for 24 hr. Then, the maturation was estimated, and the gene expression was measured by using qPCR. The second experiment studied the effect of the extract on the development of sheep embryos produced in vitro; the fertilized oocytes were cultured in a SOF medium supplemented with 1 or 10 µg/mL of marjoram extract or the control, 0 µg, for 7 days. Then, the gene expression was measured using qPCR. The results showed that the marjoram extract did not improve nuclear maturation or the blastocyst rate. There was a significant increase in the level of GDF-9 gene expression in mature oocytes in the treatment groups. An increase in the expression of BCL-2 and EGR-1 genes was observed for the blastocysts in the 10 µg/mL group. We concluded that the marjoram extract did not improve nuclear maturation, but it did affect the expression of some genes in sheep oocytes and embryos. Full article

(This article belongs to the Special Issue Systematic Analysis and Application of Omics Data in Animal Breeding)

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12 pages, 1435 KiB

Open AccessArticle

Model Comparison of Heritability Enrichment Analysis in Livestock Population

by Xiaodian Cai, Jinyan Teng, Duanyang Ren, Hao Zhang, Jiaqi Li and Zhe Zhang

Genes 2022, 13(9), 1644; https://doi.org/10.3390/genes13091644 - 13 Sep 2022

Viewed by 1433

Abstract

Heritability enrichment analysis is an important means of exploring the genetic architecture of complex traits in human genetics. Heritability enrichment is typically defined as the proportion of an SNP subset explained heritability, divided by the proportion of SNPs. Heritability enrichment enables better study of underlying complex traits, such as functional variant/gene subsets, biological networks and metabolic pathways detected through integrating explosively increased omics data. This would be beneficial for genomic prediction of disease risk in humans and genetic values estimation of important economical traits in livestock and plant species. However, in livestock, factors affecting the heritability enrichment estimation of complex traits have not been examined. Previous studies on humans reported that the frequencies, effect sizes, and levels of linkage disequilibrium (LD) of underlying causal variants (CVs) would affect the heritability enrichment estimation. Therefore, the distribution of heritability across the genome should be fully considered to obtain the unbiased estimation of heritability enrichment. To explore the performance of different heritability enrichment models in livestock populations, we used the VanRaden, GCTA and α models, assuming different α values, and the LDAK model, considering LD weight. We simulated three types of phenotypes, with CVs from various minor allele frequency (MAF) ranges: genome-wide (0.005 ≤ MAF ≤ 0.5), common (0.05 ≤ MAF ≤ 0.5), and uncommon (0.01 ≤ MAF < 0.05). The performances of the models with two different subsets (one of which contained known CVs and the other consisting of randomly selected markers) were compared to verify the accuracy of heritability enrichment estimation of functional variant sets. Our results showed that models with known CV subsets provided more robust enrichment estimation. Models with different α values tended to provide stable and accurate estimates for common and genome-wide CVs (relative deviation 0.5–2.2%), while tending to underestimate the enrichment of uncommon CVs. As the α value increased, enrichments from 15.73% higher than true value (i.e., 3.00) to 48.93% lower than true value for uncommon CVs were observed. In addition, the long-range LD windows (e.g., 5000 kb) led to large bias of the enrichment estimations for both common and uncommon CVs. Overall, heritability enrichment estimations were sensitive for the α value assumption and LD weight consideration of different models. Accuracy would be greatly improved by using a suitable model. This study would be helpful in understanding the genetic architecture of complex traits and provides a reference for genetic analysis in the livestock population. Full article

(This article belongs to the Special Issue Systematic Analysis and Application of Omics Data in Animal Breeding)

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10 pages, 1234 KiB

Open AccessArticle

Expression and Genetic Effects of GLI Pathogenesis-Related 1 Gene on Backfat Thickness in Pigs

by Xin Liu, Hanmei Li, Longchao Zhang, Ligang Wang and Lixian Wang

Genes 2022, 13(8), 1448; https://doi.org/10.3390/genes13081448 - 14 Aug 2022

Cited by 1 | Viewed by 1283

Abstract

Backfat thickness (BFT) is an important carcass composition trait and regarded as a breeding focus. Our initial transcriptome analysis of pig BFT identified GLI pathogenesis-related 1 (GLIPR1) as one of the promising candidate genes. This study was conducted to identify the expression profiles, polymorphisms, and genetic effects of the GLIPR1 gene on BFT in pigs. The expression of the GLIPR1 gene existed in every detected tissue, and there was a significantly higher expression in spleen and adipose tissue than others (p < 0.05). At the different ages of pig, the expression of the GLIPR1 gene was low at an early age, increased with growth, and reached the highest level at 180 days. Genetic polymorphism analysis was detected in 553 individuals of the Large White × Minzhu F2 population. Four SNPs in the promoter significantly associated with 6–7 rib BFT (p < 0.05) were predicted to alter the transcription factor binding sites (TFBS), and the mutations of g.38758089 T>G and g.38758114 G>C were predicted to change the TFs associated with the regulation of adipogenesis. Haplotypes were formed by the detected SNPs, and one block showed a strong association with BFT (p < 0.05). In summary, our results indicate that the expression profiles and genetic variants of GLIPR1 affected the BFT of pigs. To our knowledge, this study is the first to demonstrate the biological function and genetic effects of the GLIPR1 gene on the BFT of pig and provide genetic markers to optimize breeding for BFT in pigs. Full article

(This article belongs to the Special Issue Systematic Analysis and Application of Omics Data in Animal Breeding)

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15 pages, 1921 KiB

Open AccessArticle

A Comprehensive Analysis of the Myocardial Transcriptome in ZBED6-Knockout Bama Xiang Pigs

by Shengnan Wang, Wenjie Tian, Dengke Pan, Ling Liu, Cheng Xu, Yuehui Ma, Dandan Wang and Lin Jiang

Genes 2022, 13(8), 1382; https://doi.org/10.3390/genes13081382 - 1 Aug 2022

Cited by 2 | Viewed by 1797

Abstract

The ZBED6 gene is a transcription factor that regulates the expression of IGF2 and affects muscle growth and development. However, its effect on the growth and development of the heart is still unknown. Emerging evidence suggests that long noncoding RNAs (lncRNAs) can regulate genes at the epigenetic, transcriptional, and posttranscriptional levels and play an important role in the development of eukaryotes. To investigate the function of ZBED6 in the cardiac development of pigs, we constructed the expression profiles of mRNAs and lncRNAs in myocardial tissue obtained from Bama Xiang pigs in the ZBED6 knockout group (ZBED6-KO) and the wild-type group (ZBED6-WT). A total of 248 differentially expressed genes (DEGs) and 209 differentially expressed lncRNAs (DELs) were detected, and 105 potential cis target genes of DELs were identified. The functional annotation analysis based on the Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) databases revealed two GO items related to muscle development by the cis target genes of DELs. Moreover, IGF2 was the direct target gene of ZBED6 by ChIP-PCR experiment. Our results explored the mechanism and expression profile of mRNAs and lncRNAs of ZBED6 gene knockout on myocardium tissue development, mining the key candidate genes in that process like IGF2. Full article

(This article belongs to the Special Issue Systematic Analysis and Application of Omics Data in Animal Breeding)

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14 pages, 17020 KiB

Open AccessArticle

Spatiotemporal Regulation of Circular RNA Expression during Liver Development of Chinese Indigenous Ningxiang Pigs

by Wenwu Chen, Haiming Ma, Biao Li, Fang Yang, Yu Xiao, Yan Gong, Zhi Li, Ting Li, Qinghua Zeng, Kang Xu and Yehui Duan

Genes 2022, 13(5), 746; https://doi.org/10.3390/genes13050746 - 24 Apr 2022

Cited by 5 | Viewed by 1778

Abstract

Background: There have been many studies on the relationship between circRNAs and fat deposition. Although the liver is a central organ for fat metabolism, there are few reports on the relationship between circRNAs in the liver and fat deposition. Methods: In this study, we systematically analyzed circular RNAs in the liver of Ningxiang pigs, at four time points after birth (30 days, 90 days, 150 days and 210 days). Results: A total of 3705 circRNAs were coexpressed in four time periods were found, and KEGG analysis showed that the significantly upregulated pathways were mainly enriched in lipid metabolism and amino acid metabolism, while significantly downregulated pathways were mainly related to signal transduction, such as ECM–receptor interaction, MAPK signaling pathway, etc. Short time-series expression miner (STEM) analysis showed multiple model spectra that were significantly enriched over time in the liver. By constructing a competing endogenous RNA (ceRNA) regulatory network, 9187 pairs of networks related to the change in development time were screened. Conclusions: The expression profiles of circRNAs in Ningxiang pig liver were revealed at different development periods, and it was determined that there is differential coexpression. Through enrichment analysis of these circRNAs, it was revealed that host genes were involved in metabolism-related signaling pathways and fatty acid anabolism. Through STEM analysis, many circRNAs involved in fat metabolism, transport, and deposition pathways were screened, and the first circRNA–miRNA–mRNA regulation network map in Ningxiang pig liver was constructed. The highly expressed circRNAs related to fat deposition were verified and were consistent with RNA-Seq results. Full article

(This article belongs to the Special Issue Systematic Analysis and Application of Omics Data in Animal Breeding)

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