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New Advances and Insights in Animal Genetics and Breeding

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A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Zoology".

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 22723

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Prof. Dr. Mingxing Chu

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Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Interests: animal genetics; animal molecular genetics; sheep and goat genetics and breeding
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Dr. Ran Di

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Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Interests: sheep; goats; reproductive traits; molecular mechanism; genetic markers; diversity
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Dr. Yufang Liu

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Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Interests: animal genetics; molecular mechanism; non-coding RNA; animal morphological traits
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Domestic animals provide people with essential resources, including meat, eggs, milk, fur, etc. Numerous studies, including pan-genomic, genomic, transcriptomic, proteomic, epigenomic, metabolomic and phenomic studies, have been used to illustrate biological processes, phenotypic formations, and evolutionary events in domestic animals. This Special Issue focuses on the latest advances and insights in animal genetics and breeding. Research on all farm animals will be welcome, including ruminants (cattle, sheep, and goats), pigs, horses, poultry, and fish. Research on aspects of animal genetics, breeding and reproduction, as well as other topics, will be considered. These topics could include molecular genetics, biodiversity, life cycles, and functional gene and regulatory mechanisms in complex traits. We hope that this Special Issue will provide a better understanding of animal genetics, development, and evolution, as well as offering some new approaches in animal breeding and enhancing the productivity of farm animals.

The aim of this Special Issue of Biology is to collate the latest advances and insights from the research fields of genetics, regulatory mechanisms, and breeding methods of domestic animals. We strive for this Special Issue to provide a better understanding of the genetic mechanisms underlying complex traits and provide new approaches to improve the farming of domestic animals. We welcome the submission of multiple article types, such as original research articles, reviews, methods, etc.

Prof. Dr. Mingxing Chu
Dr. Ran Di
Dr. Yufang Liu
Guest Editors

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Keywords

animal genetics
animal multi-omics
sheep and goat genetics and breeding
reproductive traits
molecular mechanism
genetic markers
diversity
non-coding RNA
animal morphological traits

Published Papers (10 papers)

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Research

19 pages, 1633 KiB

Open AccessArticle

Genetic Markers Associated with Milk Production and Thermotolerance in Holstein Dairy Cows Managed in a Heat-Stressed Environment

by Ricardo Zamorano-Algandar, Juan F. Medrano, Milton G. Thomas, R. Mark Enns, Scott E. Speidel, Miguel A. Sánchez-Castro, Guillermo Luna-Nevárez, José C. Leyva-Corona and Pablo Luna-Nevárez

Biology 2023, 12(5), 679; https://doi.org/10.3390/biology12050679 - 4 May 2023

Cited by 4 | Viewed by 3005

Abstract

Dairy production in Holstein cows in a semiarid environment is challenging due to heat stress. Under such conditions, genetic selection for heat tolerance appears to be a useful strategy. The objective was to validate molecular markers associated with milk production and thermotolerance traits in Holstein cows managed in a hot and humid environment. Lactating cows (n = 300) exposed to a heat stress environment were genotyped using a medium-density array including 53,218 SNPs. A genome-wide association study (GWAS) detected six SNPs associated with total milk yield (MY305) that surpassed multiple testing (p < 1.14 × 10⁻⁶). These SNPs were further validated in 216 Holstein cows from two independent populations that were genotyped using the TaqMan bi-allelic discrimination method and qPCR. In these cows, only the SNPs rs8193046, rs43410971, and rs382039214, within the genes TLR4, GRM8, and SMAD3, respectively, were associated (p < 0.05) with MY305, rectal temperature (RT), and respiratory rate. Interestingly, these variables improved as the number of favorable genotypes of the SNPs increased from 0 to 3. In addition, a regression analysis detected RT as a significant predictor (R² = 0.362) for MY305 in cows with >1 favorable genotype, suggesting this close relationship was influenced by genetic markers. In conclusion, SNPs in the genes TLR4, GRM8, and SMAD3 appear to be involved in the molecular mechanism that regulates milk production in cows under heat-stressed conditions. These SNPs are proposed as thermotolerance genetic markers for a selection program to improve the milk performance of lactating Holstein cows managed in a semiarid environment. Full article

(This article belongs to the Special Issue New Advances and Insights in Animal Genetics and Breeding)

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14 pages, 10494 KiB

Open AccessArticle

Hair Follicle Transcriptome Analysis Reveals Differentially Expressed Genes That Regulate Wool Fiber Diameter in Angora Rabbits

by Dongwei Huang, Haisheng Ding, Yuanlang Wang, Guanglong Cheng, Xiaofei Wang, Taishan Leng and Huiling Zhao

Biology 2023, 12(3), 445; https://doi.org/10.3390/biology12030445 - 14 Mar 2023

Cited by 4 | Viewed by 1969

Abstract

Wool fiber diameter (WFD) is an important index of wool traits and the main determinant of wool quality and value. However, the genetic determinants of fiber diameter have not yet been fully elucidated. Here, coarse and fine wool of Wan strain Angora rabbits and their hair follicle traits were characterized. The results indicated significant differences in the diameters of wool fibers and their hair follicles. The RNA sequencing (RNA-Seq) technique was used to identify differences in gene expression in hair follicles between coarse and fine wool. In total, 2574 differentially expressed genes (DEGs) were found between the two hair follicle groups. Transcription factors, keratin-associated protein (KAP) and keratin (KRT) families, and ECM-related genes may control the structure of fine fibers in rabbits. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that skin development, epidermal cell and keratinocyte differentiation, epithelium development, and Notch and ribosome signaling pathways were significantly enriched, respectively. GSEA further filtered six important pathways and related core genes. PPI analysis also mined functional DEGs associated with hair structure, including LEF1, FZD3, SMAD3, ITGB6, and BMP4. Our findings provide valuable information for researching the molecular mechanisms regulating wool fiber and could facilitate enhanced selection of super-fine wool rabbits through gene-assisted selection in the future. Full article

(This article belongs to the Special Issue New Advances and Insights in Animal Genetics and Breeding)

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12 pages, 2714 KiB

Open AccessArticle

Epigenetic Regulation of miR-25 and Lnc107153 on Expression of Seasonal Estrus Key Gene CHGA in Sheep

by Ran Di, Yekai Fan, Xiaoyun He, Qiuyue Liu, Xiangyu Wang, Yiming Gong, Joram Mwashigadi Mwacharo, Caihong Wei, Yufang Liu and Mingxing Chu

Biology 2023, 12(2), 250; https://doi.org/10.3390/biology12020250 - 4 Feb 2023

Cited by 2 | Viewed by 1404

Abstract

Pituitary pars tuberalis (PT) plays an important role as the transmission center in the seasonal reproduction of animals. It helps convert external photoperiod signals into intrinsic seasonal reproduction signals. In sheep PT, specific expression patterns of several genes (including short photoperiod-induced gene CHGA and long photoperiod genes EYA3 and TSHβ) under different photoperiods are crucial characteristics during this signal transduction. Recent studies have revealed the role of epigenetics in regulating the expression of seasonal reproductive key genes. Therefore, we explored whether microRNAs and LncRNAs regulated the expressions of the above key genes. Firstly, the expression of miR-25 and CHGA showed a significant negative correlation in sheep PT. Results of the dual luciferase reporter assay and miR-25 overexpression indicated that miR-25 could inhibit the expression of CHGA by specifically binding to its 3′UTR region in pituitary cells. Then, expression negative correlation and dual luciferase reporter analyses were used to screen and identify the candidate LncRNA (Lnc107153) targeted by miR-25. Finally, the results of fluorescence in situ hybridization and Lnc107153 overexpression suggested that Lnc107153 and miR-25 were involved in the epigenetic regulation of CHGA expression. However, the expressions of EYA3 and TSHβ were not regulated by miRNAs. These results will provide new insights into the epigenetic regulatory network of key genes in sheep seasonal reproduction. Full article

(This article belongs to the Special Issue New Advances and Insights in Animal Genetics and Breeding)

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19 pages, 2785 KiB

Open AccessArticle

Integrated Proteotranscriptomics of the Hypothalamus Reveals Altered Regulation Associated with the FecB Mutation in the BMPR1B Gene That Affects Prolificacy in Small Tail Han Sheep

by Xiangyu Wang, Xiaofei Guo, Xiaoyun He, Ran Di, Xiaosheng Zhang, Jinlong Zhang and Mingxing Chu

Biology 2023, 12(1), 72; https://doi.org/10.3390/biology12010072 - 30 Dec 2022

Cited by 3 | Viewed by 1820

Abstract

The litter size and ovulation rate are different among ewes of different FecB genotypes in Small Tail Han sheep. These variants in reproductive phenotypes may be regulated by hormones released by the hypothalamic–pituitary–ovarian axis. However, there have been few reports on the hypothalamus regarding regulating an increase in ovulation in sheep with FecB mutation at different estrous stages. Thus, we examined the abundance of hypothalamus tissue protein profiles of six FecB mutant homozygous (BB) and six wild-type (WW) ewes at the luteal and follicular phases. We determined this abundance by tandem mass tag-based quantitative analysis and parallel reaction monitoring methods. Furthermore, an integrated proteotranscriptomic analysis was performed by the Data Integration Analysis for Biomarker discovery using the latent variable approaches for Omics studies (DIABLO) framework to examine biological processes and pathway alterations by the FecB mutant. The abundance of 154 proteins was different between the two estrous stages. Growth hormone and prolactin were particularly enriched in the neuroactive ligand–receptor interactions, the prolactin signaling pathway, and the PI3K-Akt signaling pathway which are related to hypothalamic function and reproduction. We combined proteome and transcriptome data from different estrous stages and genotypes. There is a high correlation (Pearson correlation coefficient = 0.99) between the two datasets in the first two components. We applied the traditional single-omic multivariate approach to obtain differentially abundant proteins and differentially expressed genes. The major fertility related biomarkers were selected using the two approaches mentioned above. Several key pathways (GABAergic synapse, neuroactive ligand–receptor interaction, estrogen and MAPK signaling pathways) were enriched, which are central to gonadotrophin-releasing hormone (GnRH) secretion and reproduction. A higher level of gamma-aminobutyric acid type A receptor subunit alpha1 (GABRA1) and gamma-aminobutyric acid type A receptor subunit beta2 (GABRB2) expression was observed in BB ewes as compared to WW ewes. This finding suggested that a greater production of GnRH during follicular development in BB ewes may explain the higher mature follicle number in mutant ewes. FKBP prolyl isomerase 1A (FKBP1A), which was a major feature factor in the proteome selected by DIABLO, was an important switch for activating the transforming growth factor beta (TGFβ) pathway, and its expression was higher in the WW ewes than in the BB ewes. We suggest that BB sheep maintain TGFβ pathway activity by reducing FKBP1A protein abundance. This innovative data integration in the hypothalamus may provide fresh insight into the mechanisms by which the FecB mutation affects sheep fertility, while providing novel biomarkers related to reproductive endocrinology in sheep breeding. Full article

(This article belongs to the Special Issue New Advances and Insights in Animal Genetics and Breeding)

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14 pages, 2476 KiB

Open AccessArticle

Effect of Sox18 on the Induction Ability of Dermal Papilla Cells in Hu Sheep

by Tingyan Hu, Xiaoyang Lv, Tesfaye Getachew, Joram M. Mwacharo, Aynalem Haile, Kai Quan, Yutao Li, Shanhe Wang and Wei Sun

Biology 2023, 12(1), 65; https://doi.org/10.3390/biology12010065 - 30 Dec 2022

Cited by 1 | Viewed by 1588

Abstract

Sox18 is a developmental gene that encodes transcription factors. It has been indicated as be a key gene affecting the growth and development of hair follicles, in which dermal papilla cells (DPCs) have been demonstrated to play an important role through their ability to induce the formation of hair follicles. Pre-laboratory studies have found that Sox18 is differentially expressed in the dermal papilla cells of different pattern types of Hu sheep. We speculated that Sox18 plays an important role in the dermal papilla cells of Hu sheep. In our study, we analyzed the effect of Sox18 on the induction ability of DPCs in order to elucidate the function and molecular mechanism of Sox18 in the DPCs of Hu sheep. We first identified the expression of Sox18 in the DPCs of Hu sheep by immunofluorescence staining. We then used alkaline phosphatase staining, cell morphology observations and RT-PCR to detect the effect of Sox18 on the induction of DPCs after overexpression of or interference with Sox18. We also used RT-PCR, WB and immunofluorescence staining to detect the effect of Sox18 on the Wnt/β-catenin signal pathway in DPCs. We found that Sox18 was specifically expressed in the DPCs of Hu sheep, and that Sox18 could enhance the alkaline phosphatase activity in the DPCs of Hu sheep and accelerate cell agglutination. The results of RT-PCR revealed that Sox18 promoted the mRNA expression of Versican, HHIP and FGFRI, and inhibited the mRNA expression of BMP4 and WIF1. Further studies showed that Sox18 promoted the expression of β-catenin and activated the Wnt/β-catenin signal pathway in DPCs. When the Wnt/β-catenin signal pathway of DPCs was activated, the induction ability of DPCs was enhanced. Overall, we believe that Sox18 could enhance the induction ability of DPCs in Hu sheep and regulate the induction ability of DPCs through the Wnt/β-catenin signal pathway. Full article

(This article belongs to the Special Issue New Advances and Insights in Animal Genetics and Breeding)

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11 pages, 1896 KiB

Open AccessArticle

Comprehensive Transcriptome Analysis of Different Skin Colors to Evaluate Genes Related to the Production of Pigment in Celestial Goldfish

by Rongni Li, Yansheng Sun, Ran Cui and Xin Zhang

Biology 2023, 12(1), 7; https://doi.org/10.3390/biology12010007 - 21 Dec 2022

Cited by 2 | Viewed by 1614

Abstract

Skin color is an important phenotypic feature of vertebrate fitness under natural conditions. Celestial goldfish, a common goldfish breed in China, mainly shows three kinds of skin colors including white, yellow and brown. However, the molecular genetic basis of this phenotype is still unclear. In this study, high-throughput sequencing was carried out on the back skin tissues of celestial goldfish with different skin colors. About 58.46 Gb of original data were generated, filtered and blasted, and 74,297 mRNAs were obtained according to the reference transcriptome. A total of 4653 differentially expressed genes were screened out among the brown, yellow and white groups, and the expression of melanogenesis related genes in brown goldfish was significantly higher than the other two groups. There are 19 common differentially expressed genes among three groups, of which eight genes are related to pigment production, including tyrp1a, slc2a11b, mlana, gch2, loc113060382, loc113079820, loc113068772 and loc113059134. RT-qPCR verified that the expression patterns of randomly selected differentially expressed transcripts were highly consistent with those obtained by RNA sequencing. GO and KEGG annotation revealed that these differentially expressed genes were mostly enriched in pathways of the production of pigment, including melanogenesis, tyrosine metabolism, Wnt signaling pathway, MAPK signaling pathway etc. These results indicated that the external characteristics of goldfish are consistent with the analysis results at transcriptome level. The results of this study will lay a foundation for further study on the expression characteristics and gene network analysis of pigment related genes. Full article

(This article belongs to the Special Issue New Advances and Insights in Animal Genetics and Breeding)

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11 pages, 3379 KiB

Open AccessArticle

m6A Methylation Analysis Reveals Networks and Key Genes Underlying the Coarse and Fine Wool Traits in a Full-sib Merino Family

by Guoying Hua, Xue Yang, Yuhao Ma, Tun Li, Jiankui Wang and Xuemei Deng

Biology 2022, 11(11), 1637; https://doi.org/10.3390/biology11111637 - 9 Nov 2022

Cited by 3 | Viewed by 1559

Abstract

In our study, a set of lambs with coarse wool type all over their bodies were discovered within a full-sib family during an embryo transfer experiment of merino fine wool sheep. The difference between coarse and fine wool traits were studied from the perspective of RNA modification-N6-methyladenosine. A total of 31,153 peaks were collected, including 15,968 peaks in coarse skin samples and 15,185 peaks in fine skin samples. In addition, 7208 genes were differentially m6A methylated, including 4167 upregulated and 3041 downregulated in coarse skin samples. Four key genes (EDAR, FGF5, TCHH, KRT2) were obtained by comprehensive analysis of the MeRIP-seq and RNA sequence, which are closely related to primary wool follicle morphogenesis and development. The PI3K/AKT pathway was enriched through different m6A-related genes. These results provided new insights to understand the role of epigenetics in wool sheep domestication and breeding. Full article

(This article belongs to the Special Issue New Advances and Insights in Animal Genetics and Breeding)

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26 pages, 1839 KiB

Open AccessArticle

Genetic Characterization and Alternative Preservation Ways of Locally Adapted Sheep Breeds: Cases of Private and Public Sheep Sectors in Tunisia and Italy

by Yousra Ben Sassi-Zaidy, Aziza Mohamed-Brahmi, Rafik Aloulou, Faouzia Charfi-Cheikhrouha, Filippo Cendron, Nicola Tormen and Martino Cassandro

Biology 2022, 11(11), 1623; https://doi.org/10.3390/biology11111623 - 6 Nov 2022

Cited by 2 | Viewed by 1820

Abstract

Non-commercialized sheep breeds known as local or native breeds are well adapted to their environmental constraints and constitute precious genetic resources that need prioritization for genetic diversity characterization and preservation. The aim of the present study was to assess the genetic diversity level and the related preservation decisions of very old and traditional native Mediterranean sheep breeds from Tunisia and Italy using 17 microsatellite markers. In total, 975 sheep were sampled from five Tunisian, one Center Italian, and four Venetian native breeds. Both private and publicly available farms were considered for each breed for breeding strategies’ comparison purposes. The microsatellite set used was highly informative (PIC = 0.80 ± 0.08), with a total of 383 alleles. Moderate genetic differentiation was revealed between the native sheep of the two Mediterranean sides (global overall loci F_ST = 0.081). The genetic diversity level was higher in the case of the Tunisian native breeds compared to the Italian ones, as evidenced by higher mean allelic richness, higher expected and observed heterozygosities, and lower inbreeding levels. Priority for conservation suggestions was carried out for each private or public breed population based on the contribution of each population to the diversity of the whole data. The four Venetian breeds, already undergoing conservation, the Tunisian dairy breed, and the very ancient Maghrebian breed, would be favored for conservation. In conclusion, our results highlighted the importance of the analyzed Mediterranean native sheep breeds as valuable inherited genetic reservoirs and supported previous conservation decisions made for the threatened breeds. Full article

(This article belongs to the Special Issue New Advances and Insights in Animal Genetics and Breeding)

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22 pages, 5790 KiB

Open AccessArticle

miR-381-3p Inhibits Intramuscular Fat Deposition through Targeting FABP3 by ceRNA Regulatory Network

by Yao Jiang, Jiali Liu, Huatao Liu, Wei Zhang, Xiaojin Li, Linqing Liu, Mei Zhou, Jieru Wang, Shiguang Su, Xiangdong Ding and Chonglong Wang

Biology 2022, 11(10), 1497; https://doi.org/10.3390/biology11101497 - 13 Oct 2022

Cited by 4 | Viewed by 1902

Abstract

Intramuscular fat (IMF) deposition is an important determinant of pork quality and a complex process facilitated by non-coding ceRNAs. In this study, 52 Berkshire × Anqing Sixwhite crossbred pigs were slaughtered to measure eight carcass and pork quality traits. Whole-transcriptome sequencing analysis was performed using longissimus dorsi samples of six low- and high-IMF samples; 34 ceRNA networks, based on 881, 394, 158 differentially expressed (DE) lncRNAs, miRNAs, and mRNAs, were constructed. Following weighted gene co-expression network analysis between the low and high IMF, only one ceRNA, lncRNA4789/miR-381-3p/FABP3, that showed similar DE trend in longissimus dorsi tissue was retained. Dual-luciferase reporter assays further indicated that FABP3 was a direct, functional target of miR-381-3p, where miR-381-3p overexpression inhibited the mRNA and protein expression of FABP3. In addition, overexpressed lncRNA4789 attenuated the effect of miR-381-3p on FABP3 by sponging miR-381-3p. Cell function verification experiment demonstrated that miR-381-3p suppressed IMF deposition by inhibiting preadipocyte cell differentiation and lipid droplet deposition via the suppression of FABP3 expression in the peroxisome proliferator-activated receptor signalling pathway, whereas lncRNA4789 rescued FABP3 expression by sponging miR-381-3p. Our study may aid in identifying novel molecular markers for its optimization in IMF which is of importance in breeding for improving pork quality. Full article

(This article belongs to the Special Issue New Advances and Insights in Animal Genetics and Breeding)

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18 pages, 4445 KiB

Open AccessArticle

N-Carbamylglutamate Improves Reproductive Performance and Alters Fecal Microbiota and Serum Metabolites of Primiparous Sows during Gestation after Fixed-Time Artificial Insemination

by Tao Feng, Linli Xiao, Jiahua Bai, Hongxiang Ding, Liyan Pang, Yuqing Song, Yusheng Qin, Xiaoling Xu, Jing Wang and Yan Liu

Biology 2022, 11(10), 1432; https://doi.org/10.3390/biology11101432 - 30 Sep 2022

Cited by 2 | Viewed by 1595

Abstract

N-carbamylglutamate (NCG) supplementation during gestation improves reproductive performance in sows after conventional artificial insemination. However, whether NCG can improve reproductive performance and change fecal microbiota and serum metabolite levels during pregnancy in sows after fixed-time artificial insemination (FTAI) remains unclear. Two hundred multiparous sows were assigned a diet from mating until farrowing: control (corn–soybean meal) or NCG supplementation (0.05% NCG). At days 30, 70, and 110 of gestation and after farrowing, maternal microbial diversity and serum metabolites were studied. Supplementation of NCG increased the number of piglets born alive and the litter weight (all p < 0.05) and altered the fetal microbial community during gestation. Some genera were particularly abundant at different time points during gestation and after farrowing, but none were commonly abundant across all four time points. Metabolic analysis revealed that NCG supplementation significantly increased the serum concentrations of NCG, ferulic acid, cinnamoylglycine, 3-phenyllactic acid, and gamma-glutamylglutamic acid in the NCG group compared with levels in the control group. Our results reveal that NCG supplementation during gestation improves reproductive performance in sows after FTAI, exerting both direct (increased serum NCG levels) and indirect effects (altered intestinal microbiome and serum metabolites) on sow reproduction and, ultimately, improving placental and fetal development. Full article

(This article belongs to the Special Issue New Advances and Insights in Animal Genetics and Breeding)

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