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Functional Genomics and Breeding of Animals
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Functional Genomics and Breeding of Animals

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (25 March 2025) | Viewed by 10803

Special Issue Editor

Dr. Tingxian Deng

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Guest Editor
Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
Interests: livestock genomes and transcriptomes; population genetics; whole-genome sequencing; genome-wide association studies; animal biodiversity
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Animal breeding is entering the big data era. With the rapid development of high-throughput sequencing technology, the generation of multi-omics data in livestock has been accelerated, leading to the arrival of a new era of "animal breeding big data". This not only provides new opportunities and challenges for animal breeding, but also provides new possibilities for the genetic analysis of economically important traits in animals. Understanding the economically important traits of animals can be used for management interventions in breeding programs and agricultural innovations.

Large-scale molecular markers and precise phenotypic data provide an important basis for the GWAS application and QTL mapping. Population genetics is a subfield of genetics that deals with genetic differences within and between populations, helping to explain the genetic background of the studied population and provide some key information on the application of GWAS. In addition, omic studies will facilitate and accelerate the breeding process and provide applications for genetic improvement, such as GS and MAS.

This Special Issue, "Functional Genomics and Breeding of Animals", will cover a range of research topics and review articles on the latest developments in genomics, transcriptomics, population genetics, and other multi-omics that can strengthen breeding strategies and advance the breeding process of livestock species.

Dr. Tingxian Deng
Guest Editor

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Keywords

  • animal breeding
  • genetic marker
  • RNA-seq
  • genome
  • population genetics
  • economical important traits
  • omics

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Published Papers (9 papers)

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Research

20 pages, 4525 KiB  
Article
Genome-Wide Runs of Homozygosity Reveal Inbreeding Levels and Trait-Associated Candidate Genes in Diverse Sheep Breeds
by Rui Ma, Jiaxin Liu, Xiao Ma and Ji Yang
Genes 2025, 16(3), 316; https://doi.org/10.3390/genes16030316 - 7 Mar 2025
Viewed by 639
Abstract
Background: Quantifying and controlling the inbreeding level in livestock populations is crucial for the long-term sustainability of animal husbandry. However, the extent of inbreeding has not been fully understood in sheep populations on a global scale. Methods: Here, we analyzed high-depth genomes of [...] Read more.
Background: Quantifying and controlling the inbreeding level in livestock populations is crucial for the long-term sustainability of animal husbandry. However, the extent of inbreeding has not been fully understood in sheep populations on a global scale. Methods: Here, we analyzed high-depth genomes of 210 sheep from 20 worldwide breeds to identify the pattern and distribution of genome-wide runs of homozygosity (ROH) and detect candidate selected genes in ROH islands for agronomic and phenotypic traits. Results: Leveraging whole-genome sequencing data, we found a large number of short ROH (e.g., <1.0 Mb) in all breeds and observed the overall higher values of ROH statistics and inbreeding coefficient in European breeds than in Asian breeds and Dorper sheep. We identified some well-known candidate genes (e.g., CAMK4, HOXA gene family, ALOX12, FGF11, and MTOR) and 40 novel genes (e.g., KLHL1, FGFRL1, WDR62, GDF6, KHDRBS2, and PAX1) that are functionally associated with fecundity, body size, and wool-related traits in sheep. Based on the candidate genes, we revealed different genetic bases for the fecundity traits of European and Asian sheep. Conclusions: This study improves the resolution of ROH detection and provides new insights into genomic inbreeding and trait architecture in sheep as well as useful markers for future breeding practice. Full article
(This article belongs to the Special Issue Functional Genomics and Breeding of Animals)
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13 pages, 2579 KiB  
Article
Analysis of Transcriptome Differences Between Subcutaneous and Intramuscular Adipose Tissue of Tibetan Pigs
by Xinming Li, Qiuyan Huang, Fanming Meng, Chun Hong, Baohong Li, Yecheng Yang, Zixiao Qu, Junda Wu, Fei Li, Haiyun Xin, Bin Hu, Jie Wu, Chuanhuo Hu, Xiangxing Zhu, Dongsheng Tang, Zongliang Du and Sutian Wang
Genes 2025, 16(3), 246; https://doi.org/10.3390/genes16030246 - 20 Feb 2025
Viewed by 593
Abstract
Background/Objectives: Fat deposition traits in pigs directly influence pork flavor, tenderness, and juiciness and are closely linked to overall pork quality. The Tibetan pig, an indigenous breed in China, not only possesses a high intramuscular fat content but also exhibits a unique [...] Read more.
Background/Objectives: Fat deposition traits in pigs directly influence pork flavor, tenderness, and juiciness and are closely linked to overall pork quality. The Tibetan pig, an indigenous breed in China, not only possesses a high intramuscular fat content but also exhibits a unique fat metabolism pattern due to long-term adaptation to harsh environments. This makes it an excellent genetic and physiological model for investigating fat deposition characteristics. Adipose tissue from different body regions displays varying morphologies, cytokines, and adipokines. This study aimed to examine adipose tissue deposition characteristics in different parts of Tibetan pigs and provide additional data to explore the underlying mechanisms of differential fat deposition. Methods: Our research identified significant differences in the morphology and gene expression patterns between subcutaneous fat (abdominal fat [AF] and back fat [BF]) and intramuscular fat (IMF) in Tibetan pigs. Results: Histological observations revealed that subcutaneous fat cells were significantly larger in area and diameter compared to IMF cells. The transcriptomic analysis further identified differentially expressed genes (DEGs) between subcutaneous fat and IMF, with a total of 65 DEGs in BF vs. IMF and 347 DEGs in AF vs. IMF, including 25 DEGs common to both comparisons. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these genes were significantly associated with lipid metabolism-related signaling pathways, such as the Wnt, mTOR, and PI3K-Akt signaling pathways. Several DEGs, including DDAH1, ADRA1B, SLCO3A1, and THBS3, may be linked to the differences in fat deposition in different parts of Tibetan pigs, thereby affecting meat quality and nutritional value. Conclusions: These findings provide new insights into the unique fat distribution and deposition characteristics of Tibetan pigs and establish a foundation for breeding strategies aimed at improving pork quality. Full article
(This article belongs to the Special Issue Functional Genomics and Breeding of Animals)
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20 pages, 10153 KiB  
Article
Characterization of the Complete Mitogenome of the Ring-Necked Pheasant Phasianus colchicus (Galliformes: Phasianidae) and Systematic Implications for Phasianinae Phylogenetics
by Qinggang Mei, Yiming Deng, Dongmei Zhao, Daoyu Jiang, Yaqing Liao, Xiangmei Yu, Peng Liu and Lichun Jiang
Genes 2024, 15(12), 1569; https://doi.org/10.3390/genes15121569 - 4 Dec 2024
Viewed by 972
Abstract
Background: Phasianidae mitogenomes exhibit significant structural variations critical for understanding evolution and subspecies divergence. However, annotations of these features in some pheasant species remain limited. This study aimed to enhance understanding of Phasianidae mitogenomes and their evolutionary patterns. Methods: A comparative analysis of [...] Read more.
Background: Phasianidae mitogenomes exhibit significant structural variations critical for understanding evolution and subspecies divergence. However, annotations of these features in some pheasant species remain limited. This study aimed to enhance understanding of Phasianidae mitogenomes and their evolutionary patterns. Methods: A comparative analysis of complete mitogenomes from Phasianus colchicus, Phasianus versicolor, and 22 other accipitrids was conducted, examining codon usage, rRNA structures, selective pressures, phylogenetics, and structural variations. Results: The mitogenome of P. colchicus is 16,696 bp, comprising 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region, with a base composition of A: 30.61%, T: 25.26%, C: 30.85%, and G: 13.28%. Phylogenetic analysis revealed P. colchicus and P. versicolor are closely related, with the following relationship: ((Phasianus + Chrysolophus) + (Crossoptilon + Lophura)). Divergence timing aligns with the Tibetan Plateau uplift during the Tertiary Pliocene. Ka/Ks analysis suggests the CO I, CO II, CO III, ND1, ND4L, and ND6 genes in Phasianus underwent strong selective pressure for plateau adaptation. Conclusions: The study confirms Phasianus monophyly and its close relationship with Chrysolophus. Adaptation-related selective pressures on the CO I, CO II, CO III, ND1, ND4L, and ND6 genes highlight its role in plateau environments, offering valuable insights into pheasant phylogeny. Full article
(This article belongs to the Special Issue Functional Genomics and Breeding of Animals)
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16 pages, 5425 KiB  
Article
Integrative Transcriptomics and Proteomics Analysis Reveals THRSP’s Role in Lipid Metabolism
by Yujie Li, Ke Xu, Ao Zhou, Zhong Xu, Junjing Wu, Xianwen Peng, Shuqi Mei and Hongbo Chen
Genes 2024, 15(12), 1562; https://doi.org/10.3390/genes15121562 - 30 Nov 2024
Viewed by 1517
Abstract
Background/Objectives: Abnormalities in lipid metabolism and endoplasmic reticulum (ER) stress are strongly associated with the development of a multitude of pathological conditions, including nonalcoholic fatty liver disease (NAFLD), diabetes mellitus, and obesity. Previous studies have indicated a potential connection between thyroid hormone responsive [...] Read more.
Background/Objectives: Abnormalities in lipid metabolism and endoplasmic reticulum (ER) stress are strongly associated with the development of a multitude of pathological conditions, including nonalcoholic fatty liver disease (NAFLD), diabetes mellitus, and obesity. Previous studies have indicated a potential connection between thyroid hormone responsive (THRSP) and lipid metabolism and that ER stress may participate in the synthesis of key regulators of adipogenesis. However, the specific mechanisms remain to be investigated. Methods: In this study, we explored the roles of THRSP in lipid metabolism by interfering with THRSP gene expression in mouse mesenchymal stem cells, comparing the effects on adipogenesis between control and interfered groups, and by combining transcriptomic and proteomic analysis. Results: Our results showed that the number of lipid droplets was significantly reduced after interfering with THRSP, and the expression levels of key regulators of adipogenesis, such as LPL, FABP4, PLIN1, and CIDEC, were significantly downregulated. Both transcriptomic and proteomic results showed that the differential genes (proteins) were enriched in the processes of lipolytic regulation, ER stress, cholesterol metabolism, sphingolipid metabolism, PPAR signaling pathway, and glycerophospholipid metabolism. The ER stress marker gene, ATF6, was the most significantly downregulated transcription factor. In addition, RT-qPCR validation indicated that the expression levels of PPAR signaling pathway gene SCD1; key genes of lipid droplet generation including LIPE, DGAT1, and AGPAT2; and ER stress marker gene ATF6 were significantly downregulated. Conclusions: These suggest that THRSP is involved in regulating ER stress and the PPAR signaling pathway, which is closely related to lipid synthesis and metabolism. Interfering with the expression of THRSP may be helpful in ameliorating the occurrence of diseases related to abnormalities in lipid metabolism. Full article
(This article belongs to the Special Issue Functional Genomics and Breeding of Animals)
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21 pages, 9147 KiB  
Article
Exploration and Enrichment Analysis of the QTLome for Important Traits in Livestock Species
by Francisco J. Jahuey-Martínez, José A. Martínez-Quintana, Felipe A. Rodríguez-Almeida and Gaspar M. Parra-Bracamonte
Genes 2024, 15(12), 1513; https://doi.org/10.3390/genes15121513 - 26 Nov 2024
Cited by 1 | Viewed by 1296
Abstract
Background: Quantitative trait loci (QTL) are genomic regions that influence essential traits in livestock. Understanding QTL distribution and density across species’ genomes is crucial for animal genetics research. Objectives: This study explored the QTLome of cattle, pigs, sheep, and chickens by analyzing QTL [...] Read more.
Background: Quantitative trait loci (QTL) are genomic regions that influence essential traits in livestock. Understanding QTL distribution and density across species’ genomes is crucial for animal genetics research. Objectives: This study explored the QTLome of cattle, pigs, sheep, and chickens by analyzing QTL distribution and evaluating the correlation between QTL, gene density, and chromosome size with the aim to identify QTL-enriched genomic regions. Methods: Data from 211,715 QTL (1994–2021) were retrieved from the AnimalQTLdb and analyzed using R software v4.2.1. Unique QTL annotations were identified, and redundant or inconsistent data were removed. Statistical analyses included Pearson correlations and binomial, hypergeometric, and bootstrap-based enrichment tests. Results: QTL densities per Mbp were 10 for bovine, 4 for pig, 1 for sheep, and 3 for chicken genomes. Analysis of QTL distribution across chromosomes revealed uneven patterns, with certain regions enriched for QTL. Correlation analysis revealed a strong positive relationship between QTL and gene density/chromosome size across all species (p < 0.05). Enrichment analysis identified pleiotropic regions, where QTL affect multiple traits, often aligning with known candidate and major genes. Significant QTL-enriched windows (p < 0.05) were detected, with 699 (187), 355 (68), 50 (15), and 38 (17) genomic windows for cattle, pigs, sheep, and chickens, respectively, associated with overall traits (and specific phenotypic categories). Conclusions: This study provides critical insights into QTL distribution and its correlation with gene density, offering valuable data for advancing genetic research in livestock species. The identification of QTL-enriched regions also highlights key areas for future exploration in trait improvement programs. Full article
(This article belongs to the Special Issue Functional Genomics and Breeding of Animals)
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15 pages, 1935 KiB  
Article
Genomic Regions Associated with Spontaneous Abortion in Holstein Heifers
by Emaly M. Suarez, Victoria C. Kelson, Jennifer N. Kiser, Kimberly M. Davenport, Brenda M. Murdoch and Holly L. Neibergs
Genes 2024, 15(12), 1498; https://doi.org/10.3390/genes15121498 - 22 Nov 2024
Viewed by 1009
Abstract
Background/Objectives: The dairy industry relies on reproductive efficiency to maintain efficient milk production. Spontaneous abortion (SA), defined as pregnancy loss between gestation days 42 and 260, occurred in 4.5% of the artificially inseminated (AI) Holstein heifers and 31.6% of the embryo transfer (ET) [...] Read more.
Background/Objectives: The dairy industry relies on reproductive efficiency to maintain efficient milk production. Spontaneous abortion (SA), defined as pregnancy loss between gestation days 42 and 260, occurred in 4.5% of the artificially inseminated (AI) Holstein heifers and 31.6% of the embryo transfer (ET) recipient Holstein heifers that received in vitro-produced frozen embryos on a single dairy farm in Idaho. Methods: A genome-wide association analysis (GWAA) was performed to identify the associations (FDR p < 0.05) with SA in heifers that were bred by AI (1351 controls that delivered at term and 63 cases that aborted) that conceived following the first insemination, as well as in 59 controls and 273 cases of ET recipient heifers pregnant from the first ET. Results: There were 216 loci and 413 positional candidate genes associated (FDR p < 0.05) with SA in the heifers bred by AI in a recessive model and no loci associated with SA in the ET recipients. Conclusions: The identification of loci associated with SA in the heifers bred by AI may be used to reduce fetal loss through genomic selection. Full article
(This article belongs to the Special Issue Functional Genomics and Breeding of Animals)
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16 pages, 6930 KiB  
Article
Transcriptomic Analysis of Hippocampus abdominalis Larvae Under High Temperature Stress
by Wenjie Xiao, Baoying Guo, Jie Tan, Changlin Liu, Da Jiang, Hao Yu and Zhen Geng
Genes 2024, 15(10), 1345; https://doi.org/10.3390/genes15101345 - 21 Oct 2024
Viewed by 1181
Abstract
Objectives: Acute temperature stress was explored in Hippocampus abdominalis through a comprehensive RNA-seq analysis. Methods: RNA-seq was conducted on 20-day-old H. abdominalis after 24 h of temperature stress. Four experimental conditions were established: a control group (18 °C) and three temperature treatment groups [...] Read more.
Objectives: Acute temperature stress was explored in Hippocampus abdominalis through a comprehensive RNA-seq analysis. Methods: RNA-seq was conducted on 20-day-old H. abdominalis after 24 h of temperature stress. Four experimental conditions were established: a control group (18 °C) and three temperature treatment groups (21, 24, and 27 °C). Results: Seahorse larvae were found to be unaffected by 21 °C and 24 °C and were able to survive for short periods of time during 24 h of incubation, whereas mortality approached 50% at 27 °C. The sequencing process produced 75.63 Gb of high-quality clean data, with Q20 and Q30 base percentages surpassing 98% and 96%, respectively. A total of 141, 333, and 1598 differentially expressed genes were identified in the 21, 24, and 27 °C groups vs. a control comparison group, respectively. Notably, the number of up-regulated genes was consistently higher than that of down-regulated genes across all comparisons. Gene Ontology functional annotation revealed that differentially expressed genes were predominantly associated with metabolic processes, redox reactions, and biosynthetic functions. In-depth KEGG pathway enrichment analysis demonstrated that down-regulated genes were significantly enriched in pathways related to steroid biosynthesis, terpenoid backbone biosynthesis, spliceosome function, and DNA replication. Up-regulated genes were enriched in pathways associated with the FoxO signaling pathway and mitophagy (animal). The results indicated that temperature stress induced extensive changes in gene expression in H. abdominalis, involving crucial biological processes such as growth, biosynthesis, and energy metabolism. Conclusions: This study provided key molecular mechanisms in the response of H. abdominalis to temperature stress, offering a strong basis for future research aimed at understanding and mitigating the effects of environmental stressors on marine species. Full article
(This article belongs to the Special Issue Functional Genomics and Breeding of Animals)
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16 pages, 2934 KiB  
Article
Hepatic Transcriptome Reveals Potential Key Genes Contributing to Differential Milk Production
by Chao Du, A La Teng Zhu La, Shengtao Gao, Wenshuo Gao, Lu Ma, Dengpan Bu and Wenju Zhang
Genes 2024, 15(9), 1229; https://doi.org/10.3390/genes15091229 - 20 Sep 2024
Cited by 1 | Viewed by 1092
Abstract
Background: Despite the widespread adoption of TMR or PMR and the formulas designed to sufficiently cover the cows’ requirements, individual dairy cows’ milk production varies significantly. The liver is one of the most important organs in cow lactation metabolism and plays an essential [...] Read more.
Background: Despite the widespread adoption of TMR or PMR and the formulas designed to sufficiently cover the cows’ requirements, individual dairy cows’ milk production varies significantly. The liver is one of the most important organs in cow lactation metabolism and plays an essential role in the initiation of lactation. Objectives: This study aimed to investigate the potential key genes in the liver contributing to the different milk production. Methods: We enrolled 64 cows and assigned them to high or low milk yield (MY) groups according to their first 3 weeks of milk production. We performed RNAseq for 35 liver samples with 18 from prepartum and 17 from postpartum cows. Results: The continuous milk yield observation showed a persistently higher milk yield in high MY cows than low MY cows in the first 3 weeks. High MY cows showed better feed conversion efficiency. We identified 795 differentially expressed genes (DGEs) in the liver of high MY cows compared with low MY cows, with up-regulated genes linked to morphogenesis and development pathways. Weighted gene co-expression network analysis (WGCNA) revealed four gene modules positively correlating with milk yield, and protein and lactose yield (p < 0.05). Using the intersected genes between the four gene modules and DEGs, we constructed the linear mixed-effects models and identified six hub genes positively associated and two hub genes negatively associated with milk yield (Coefficients > 0.25, p < 0.05). Random forest machine learning model training based on these eight hub genes could efficiently predict the milk yield (p < 0.001, R2 = 0.946). Interestingly, the expression patterns of these eight hub genes remained remarkably similar before and after parturition. Conclusions: The present study indicated the critical role of liver in milk production. Activated processes involved in morphogenesis and development in liver may contribute to the higher milk production. Eight hub genes identified in this study may provide genetic research materials for dairy cow breeding. Full article
(This article belongs to the Special Issue Functional Genomics and Breeding of Animals)
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19 pages, 2212 KiB  
Article
Genetic Foundations of Nellore Traits: A Gene Prioritization and Functional Analyses of Genome-Wide Association Study Results
by Adebisi R. Ogunbawo, Henrique A. Mulim, Gabriel S. Campos and Hinayah R. Oliveira
Genes 2024, 15(9), 1131; https://doi.org/10.3390/genes15091131 - 27 Aug 2024
Cited by 2 | Viewed by 1301
Abstract
The main goal of this study was to pinpoint functional candidate genes associated with multiple economically important traits in Nellore cattle. After quality control, 1830 genomic regions sourced from 52 scientific peer-reviewed publications were used in this study. From these, a total of [...] Read more.
The main goal of this study was to pinpoint functional candidate genes associated with multiple economically important traits in Nellore cattle. After quality control, 1830 genomic regions sourced from 52 scientific peer-reviewed publications were used in this study. From these, a total of 8569 positional candidate genes were annotated for reproduction, 11,195 for carcass, 5239 for growth, and 3483 for morphological traits, and used in an over-representation analysis. The significant genes (adjusted p-values < 0.05) identified in the over-representation analysis underwent prioritization analyses, and enrichment analysis of the prioritized over-represented candidate genes was performed. The prioritized candidate genes were GFRA4, RFWD3, SERTAD2, KIZ, REM2, and ANKRD34B for reproduction; RFWD3, TMEM120A, MIEF2, FOXRED2, DUSP29, CARHSP1, OBI1, JOSD1, NOP58, and LOXL1-AS1 for the carcass; ANKRD34B and JOSD1 for growth traits; and no genes were prioritized for morphological traits. The functional analysis pinpointed the following genes: KIZ (plays a crucial role in spindle organization, which is essential in forming a robust mitotic centrosome), DUSP29 (involved in muscle cell differentiation), and JOSD1 (involved in protein deubiquitination, thereby improving growth). The enrichment of the functional candidate genes identified in this study highlights that these genes play an important role in the expression of reproduction, carcass, and growth traits in Nellore cattle. Full article
(This article belongs to the Special Issue Functional Genomics and Breeding of Animals)
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