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Genetics and Genomics of Livestock Health, Fertility and Product Quality:...
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Genetics and Genomics of Livestock Health, Fertility and Product Quality: 2nd Edition

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

Deadline for manuscript submissions: 10 June 2025 | Viewed by 8809

Special Issue Editor

Prof. Dr. Michael E. Davis

E-Mail Website
Guest Editor
Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA
Interests: beef; dairy; genetics; genetic engineering; animal breeding; biostatistics; animal genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The global population is expected to approach 10 billion by the year 2050, while the economic status of people in developing countries will continue to improve. As a result, it is anticipated that the worldwide demand for animal products will increase by 70% by 2050. Increasing animal production will require a deep understanding of animal biology using genetics and genomics to feed the world’s growing population. Furthermore, consumers desire high-quality products for consumption. At the same time, farmers need to combat diseases in the face of increased antimicrobial resistance and pressure from consumers and regulators to minimize the use of antibiotics. Genetics and genomics will play key roles in increasing the efficiency of production systems. Genetic selection and innovations must target animal production, product quality, reproduction, health, and welfare such that a high-quality, safe, healthful, and affordable food supply is available to everyone around the world.

Considering the success of our previous Special Issue, we are pleased to launch “Genetics and Genomics of Livestock Health, Fertility and Product Quality: 2nd Edition”. Genetics and genomics papers that address these important topics are welcome.

Prof. Dr. Michael E. Davis
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

  • animal
  • genetics
  • genomics
  • production
  • product quality
  • reproduction
  • fertility
  • health
  • welfare

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Related Special Issue

Published Papers (6 papers)

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Research

20 pages, 5882 KiB  
Article
Effect of Different Dietary Iron Contents on Liver Transcriptome Characteristics in Wujin Pigs
by Lin Gao, Xiaokun Xing, Rongfu Guo, Qihua Li, Yan Xu, Hongbin Pan, Peng Ji, Ping Wang, Chuntang Yu, Jintao Li and Qingcong An
Animals 2024, 14(16), 2399; https://doi.org/10.3390/ani14162399 - 19 Aug 2024
Viewed by 907
Abstract
Iron is an important trace element that affects the growth and development of animals and regulates oxygen transport, hematopoiesis, and hypoxia adaptations. Wujin pig has unique hypoxic adaptability and iron homeostasis; however, the specific regulatory mechanisms have rarely been reported. This study randomly [...] Read more.
Iron is an important trace element that affects the growth and development of animals and regulates oxygen transport, hematopoiesis, and hypoxia adaptations. Wujin pig has unique hypoxic adaptability and iron homeostasis; however, the specific regulatory mechanisms have rarely been reported. This study randomly divided 18 healthy Wujin piglets into three groups: the control group, supplemented with 100 mg/kg iron (as iron glycinate); the low-iron group, no iron supplementation; and the high-iron group, supplemented with 200 mg/kg iron (as iron glycinate). The pre-feeding period was 5 days, and the formal period was 30 days. Serum was collected from empty stomachs before slaughter and at slaughter to detect changes in the serum iron metabolism parameters. Gene expression in the liver was analyzed via transcriptome analysis to determine the effects of low- and high-iron diets on transcriptome levels. Correlation analysis was performed for apparent serum parameters, and transcriptome sequencing was performed using weighted gene co-expression network analysis to reveal the key pathways underlying hypoxia regulation and iron metabolism. The main results are as follows. (1) Except for the hypoxia-inducible factor 1 (HIF-1) content (between the low- and high-iron groups), significant differences were not observed among the serum iron metabolic parameters. The serum HIF-1 content of the low-iron group was significantly higher than that of the high-iron group (p < 0.05). (2) Sequencing analysis of the liver transcriptome revealed 155 differentially expressed genes (DEGs) between the low-iron and control groups, 229 DEGs between the high-iron and control groups, and 279 DEGs between the low- and high-iron groups. Bioinformatics analysis showed that the HIF-1 and transforming growth factor-beta (TGF-β) signaling pathways were the key pathways for hypoxia regulation and iron metabolism. Four genes were selected for qPCR validation, and the results were consistent with the transcriptome sequencing data. In summary, the serum iron metabolism parameter results showed that under the influence of low- and high-iron diets, Wujin piglets maintain a steady state of physiological and biochemical indices via complex metabolic regulation of the body, which reflects their stress resistance and adaptability. The transcriptome results revealed the effects of low-iron and high-iron diets on the gene expression level in the liver and showed that the HIF-1 and TGF-β signaling pathways were key for regulating hypoxia adaptability and iron metabolism homeostasis under low-iron and high-iron diets. Moreover, HIF-1α and HEPC were the key genes. The findings provide a theoretical foundation for exploring the regulatory pathways and characteristics of iron metabolism in Wujin pigs. Full article
(This article belongs to the Special Issue Genetics and Genomics of Livestock Health, Fertility and Product Quality: 2nd Edition)
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18 pages, 1096 KiB  
Article
Udder, Claw, and Reproductive Health in Genomic Selection of the Czech Holstein
by Zuzana Krupová, Eva Kašná, Ludmila Zavadilová, Emil Krupa, Jiří Bauer and Marie Wolfová
Animals 2024, 14(6), 864; https://doi.org/10.3390/ani14060864 - 11 Mar 2024
Cited by 1 | Viewed by 1093
Abstract
The aim of this study was to construct an enhanced selection index using the genomic and economic parameters of new health disorders and current production and functional traits. Genomic evaluation for the incidence of clinical mastitis (CM), three claw disease traits, retained placenta [...] Read more.
The aim of this study was to construct an enhanced selection index using the genomic and economic parameters of new health disorders and current production and functional traits. Genomic evaluation for the incidence of clinical mastitis (CM), three claw disease traits, retained placenta (RET), metritis (MET), and cystic ovaries (CYS) was performed using linear animal models based on producer-recorded data. Good correlations among the health disorders were found, and their heritability estimates did not exceed 7%. Economic weights (EWs) for the health disorders were EUR −132.10 for CM, EUR −128.87 for overall claw diseases, EUR −52.10 for RET, EUR −80.48 for MET, and EUR −16.16 for CYS. These EWs indicate changes in the present value of the annual profit per cow when increasing the incidence of the traits by one case per cow year. Selection using the enhanced index resulted in favourable responses for most of the new health disorders (e.g., −0.001 and −0.006 cases of RET and MET per cow year, respectively), and also in the current breeding objective traits (+49 kg of milk, −0.02% of calf losses). An index contribution of 7% for the new health disorders was assessed as acceptable for the breeders. Full article
(This article belongs to the Special Issue Genetics and Genomics of Livestock Health, Fertility and Product Quality: 2nd Edition)
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13 pages, 3240 KiB  
Article
Identification and Analysis of Genes Related to Testicular Size in 14-Day-Old Piglets
by Yunjiao Zhao, Liangzhi Zhang, Lei Wang, Jianbo Zhang, Wenjuan Shen, Yuhong Ma, Chengxiang Ding and Guofang Wu
Animals 2024, 14(1), 172; https://doi.org/10.3390/ani14010172 - 4 Jan 2024
Cited by 2 | Viewed by 1665
Abstract
The RNA-Seq technology was used to screen the key genes that affect the early development of the testes of Duroc × Landrace × Yorkshire piglets, to determine the regulatory pathway and provide reference for subsequent reproductive performance research, breeding, and other production practices. [...] Read more.
The RNA-Seq technology was used to screen the key genes that affect the early development of the testes of Duroc × Landrace × Yorkshire piglets, to determine the regulatory pathway and provide reference for subsequent reproductive performance research, breeding, and other production practices. This study selected 14-day-old Duroc × Landrace × Yorkshire piglets as the trial animals. Testes from piglets with similar weights and no pathological changes were divided into small testis (ST) and large testis (LT) groups, and the RNA-Seq screening of differentially expressed genes (DEGs) was performed to find candidate genes and regulatory pathways related to early testicular development. The results show that 570 DEGs were found in the ST and LT groups, with 281 upregulated and 289 downregulated. The DEGs were mainly enriched on 47 gene ontology (GO) functional items. The Kyoto encyclopedia of genes and genotypes (KEGG) enrichment analysis found that there were 44 significantly enriched KEGG signal pathways, and the regulation of testicular development mainly focused on the arachidonic acid metabolism, Wnt signaling pathway and GnRH secretion pathways. The PTGES, SFRP1, SPP1, PLA2G4E, KCNJ5, PTGS2, and HCN1 genes were found to be as closely related to the testicular development of these Duroc × Landrace × Yorkshire piglets, and the differential gene expression was consistent with the real-time quantitative reverse transcription PCR (real-time qRT-PCR) validation results. This study was validated by high-throughput sequencing analysis and real-time qRT-PCR, and showed that the PTGES, SFRP1, SPP1, PLA2G4E, KCNJ5, PTGS2, and HCN1 genes may be involved in the regulation of germ cell development, spermatogenesis and semen traits. These should be further studied as candidate genes for early testicular development and reproductive trait regulation in boars. Full article
(This article belongs to the Special Issue Genetics and Genomics of Livestock Health, Fertility and Product Quality: 2nd Edition)
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14 pages, 11984 KiB  
Article
Integrated 4D Analysis of Intramuscular Fat Deposition: Quantitative Proteomic and Transcriptomic Studies in Wannanhua Pig Longissimus Dorsi Muscle
by Xiaojin Li, Fei Xie, Ruidong Li, Lei Li, Man Ren, Mengmeng Jin, Ju Zhou, Chonglong Wang and Shenghe Li
Animals 2024, 14(1), 167; https://doi.org/10.3390/ani14010167 - 4 Jan 2024
Cited by 2 | Viewed by 1489
Abstract
Wannanhua (WH) is a pig breed indigenous to Anhui Province, China. This breed has a high intramuscular fat (IMF) content, making it an ideal model for investigating lipid deposition mechanisms in pigs. IMF content is one of the main indicators of meat quality [...] Read more.
Wannanhua (WH) is a pig breed indigenous to Anhui Province, China. This breed has a high intramuscular fat (IMF) content, making it an ideal model for investigating lipid deposition mechanisms in pigs. IMF content is one of the main indicators of meat quality in pigs and is regulated by multiple genes and metabolic pathways. Building upon our prior transcriptomic investigation, the present study focused on the longissimus dorsi muscle tissue of Wannanhua (WH) pigs in the rapid fat-deposition stages (120 and 240 days of age). Employing 4D label-free quantitative proteomic analysis, we identified 106 differentially expressed proteins (DEPs). Parallel reaction monitoring (PRM) technology was used to verify the DEPs, and the results showed that the 4D label-free results were reliable and valid. Functional enrichment and protein–protein interaction analyses showed that the DEPs were mainly involved in the skeletal-muscle-associated structural proteins, mitochondria, energy metabolism, and fatty acid metabolism. By integrating transcriptomic data, we identified seven candidate genes including ACADL, ACADM, ANKRD2, MYOZ2, TNNI1, UCHL1, and ART3 that play a regulatory role in fat deposition and muscle development. These findings establish a theoretical foundation for future analyses of lipid deposition traits, contributing to potential enhancements in pig meat quality during breeding and advancing the selection process for Chinese indigenous breeds. Full article
(This article belongs to the Special Issue Genetics and Genomics of Livestock Health, Fertility and Product Quality: 2nd Edition)
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11 pages, 963 KiB  
Article
The Effect of Sow Maternal Behavior on the Growth of Piglets and a Genome-Wide Association Study
by Xin Liu, Hanmei Li, Ligang Wang, Longchao Zhang and Lixian Wang
Animals 2023, 13(24), 3753; https://doi.org/10.3390/ani13243753 - 5 Dec 2023
Cited by 1 | Viewed by 1569
Abstract
Sows’ maternal behavior is important for improving piglet survival and growth; thus, breeding for good mothering sows is necessary for pig production. However, there is little research on the genetic mechanism of maternal behavior. In this study, a comparative analysis of piglets’ growth [...] Read more.
Sows’ maternal behavior is important for improving piglet survival and growth; thus, breeding for good mothering sows is necessary for pig production. However, there is little research on the genetic mechanism of maternal behavior. In this study, a comparative analysis of piglets’ growth traits between good and bad maternal behavior groups and a genome-wide association study (GWAS) was performed to elucidate the impact of sows’ maternal behavior on piglet growth and identify candidate genes and markers of sow’s maternal behaviors. Comparing the growth traits of piglets between good and bad sows’ maternal behavior groups, the results showed that the growth traits of piglets from sows with good maternal behavior were better than those from sows with bad maternal behavior and especially for the multiparous sows group, this comparative difference was significant. For the intensive study of the genetic mechanisms of sows’ maternal behavior, a total of 452 sows were genotyped using the Illumina Porcine 50K SNP Chip, and 4 traits, including biting piglets (BP), crushing piglets (CP), trampling piglets (TP) and screaming test (ST), were examined. Using a GWAS, 20 single nucleotide polymorphisms (SNPs) were found to be associated with these traits. Within 1 Mb upstream and downstream of the significant SNPs screened, 138 genes were obtained. After pathway enrichment and gene annotation, HIP1, FZD9 and HTR7 were identified as important candidate genes affecting sows’ maternal behaviors. These findings preliminarily elucidate the genetic basis of sows’ maternal behavior traits and provide candidate genes and markers for molecular breeding in pigs. Full article
(This article belongs to the Special Issue Genetics and Genomics of Livestock Health, Fertility and Product Quality: 2nd Edition)
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12 pages, 3699 KiB  
Article
Effects of Copy Number Variations in the Plectin (PLEC) Gene on the Growth Traits and Meat Quality of Leizhou Black Goats
by Ke Wang, Yuelang Zhang, Xiaotao Han, Qun Wu, Hu Liu, Jiancheng Han and Hanlin Zhou
Animals 2023, 13(23), 3651; https://doi.org/10.3390/ani13233651 - 25 Nov 2023
Cited by 2 | Viewed by 1205
Abstract
The plectin (PLEC) gene is crucial in regulating muscle development and maintaining the cytoskeleton. An abnormal expression of PLEC can lead to muscle atrophy and muscular dystrophy. In a previous study, we found that Leizhou black goats exhibit abundant structural variations [...] Read more.
The plectin (PLEC) gene is crucial in regulating muscle development and maintaining the cytoskeleton. An abnormal expression of PLEC can lead to muscle atrophy and muscular dystrophy. In a previous study, we found that Leizhou black goats exhibit abundant structural variations in the PLEC gene. However, the genetic effects of these variations on growth traits and meat quality in goats are not fully understood. In this study, three PLEC copy number variations (CNVs) were identified in a population of 417 Leizhou black goats, using quantitative polymerase chain reaction (qPCR) technology. Population distribution analysis revealed a high abundance of various types of these three CNVs. PLEC mRNA was found to be highly expressed in muscle tissue and remained consistently high from 1 month to 24 months after birth. Specifically, the gain type of CNV-1 (chr14: 81056401-81064800) showed a significant association with PLEC mRNA expression in muscle tissue (p < 0.01). The sequence of CNV-1 in PLEC shares similarities with three domain superfamilies associated with muscle development and skin disease. Furthermore, there were significant differences in chest circumference, body weight, carcass weight, the cross-sectional area of the longissimus dorsi lumbar muscle, and shear stress between different types of CNV-1 (p < 0.05). Notably, goats with the CNV-1 gain type demonstrated better phenotypic values compared to those with loss and normal types. These findings suggest that PLEC CNV-1 could play a crucial role in the growth and muscle development of Leizhou black goats, making it a potential marker for assisted selection in goat breeding. Full article
(This article belongs to the Special Issue Genetics and Genomics of Livestock Health, Fertility and Product Quality: 2nd Edition)
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