Topic Editors

National Institute for Agricultural and Veterinary Research (INIAV), 2005-048 Santarém, Portugal
Prof. Dr. Pedro M. Aponte
Colegio de Ciencias Biológicas y Ambientales (COCIBA), Universidad San Francisco de Quito (USFQ), Quito 170157, Ecuador

Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection

Abstract submission deadline
20 January 2025
Manuscript submission deadline
20 March 2025
Viewed by
14640

Topic Information

Dear Colleagues,

The worldwide demand for animal-derived products will increase dramatically in the next 30 years due to global population growth. Therefore, a comprehensive understanding of animal breeding through reproduction performance and genomic selection will be of the utmost importance to satisfy the growing food demand. In view of this, combining assisted reproductive techniques (ARTs) and genetic/genomic molecular tools (GMTs) for animal selection will play a key role in improving and maximizing animal production systems' efficiency. This Topic aims to present original research and/or reviews related to ARTs and GMTs. All studies on factors affecting livestock performance with a particular focus on reproduction management, health control, longevity improvement, and welfare practices based on ART- and GMT-derived results are welcome. Furthermore, we encourage studies that contribute significantly to further advancing these fields and those based on ARTs, such as in vitro fertilization (IVF), intracytoplasmic sperm injection (ICSI), in vitro/in vivo embryo production (IVP), embryo transfer (ET), controlled ovarian hyperstimulation (superovulation), gamete sex determination, artificial insemination (AI), gamete cryopreservation, nuclear transfer/cloning, stem cells technologies (SCTs), etc. Moreover, contributions focused on complementary techniques for ARTs, including DNA isolation and analysis (DIA), polymerase chain reaction (PCR/rtPCR), DNA sequencing, recombinant plasmids, gene cloning, transgenesis, Southern blotting, single-nucleotide polymorphism (SNPs), genome-wide association studies (GWASs), etc., are welcome as well.

 Potential subtopics of interest include (but are not limited to) the following:

  • Research surrounding the reproductive basis of important fertility traits;
  • Application of ARTs to genetic resources for increasing reproductive/productive performance traits;
  • Studies on reproduction–nutrition interaction and efficient reproductive and production traits;
  • Research on genes implicated in reproductive and production traits;
  • Sequencing research surrounding breeding and genetics;
  • Studies on reproduction–health control interaction and efficient production traits;
  • Research on biodiversity protection programs, germplasm banking, and ex situ preservation;
  • Studies on reproduction–welfare practices and efficient production traits;
  • Interactions between reproduction–environment (climate) and impact on reproductive and production traits;
  • Research on reproduction–longevity interactions for increasing fertility and productivity traits.

We look forward to receiving your contributions.

Dr. Manuel García-Herreros
Prof. Dr. Pedro M. Aponte
Topic Editors

Participating Journals

Journal Name Impact Factor CiteScore Launched Year First Decision (median) APC
Agriculture
agriculture
3.6 3.6 2011 17.7 Days CHF 2600 Submit
Animals
animals
3.0 4.2 2011 18.1 Days CHF 2400 Submit
Dairy
dairy
- 2.4 2020 24.6 Days CHF 1200 Submit
Genes
genes
3.5 5.1 2010 16.5 Days CHF 2600 Submit
International Journal of Molecular Sciences
ijms
5.6 7.8 2000 16.3 Days CHF 2900 Submit
Veterinary Sciences
vetsci
2.4 2.3 2014 19.6 Days CHF 2600 Submit

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Published Papers (11 papers)

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16 pages, 12078 KiB  
Article
Transcriptome Profiling Unveils Key Genes Regulating the Growth and Development of Yangzhou Goose Knob
by Xinlei Xu, Suyu Fan, Wangyang Ji, Shangzong Qi, Linyu Liu, Zhi Cao, Qiang Bao, Yang Zhang, Qi Xu and Guohong Chen
Int. J. Mol. Sci. 2024, 25(8), 4166; https://doi.org/10.3390/ijms25084166 - 10 Apr 2024
Viewed by 542
Abstract
Goose is one of the most economically valuable poultry species and has a distinct appearance due to its possession of a knob. A knob is a hallmark of sexual maturity in goose (Anser cygnoides) and plays crucial roles in artificial selection, [...] Read more.
Goose is one of the most economically valuable poultry species and has a distinct appearance due to its possession of a knob. A knob is a hallmark of sexual maturity in goose (Anser cygnoides) and plays crucial roles in artificial selection, health status, social signaling, and body temperature regulation. However, the genetic mechanisms influencing the growth and development of goose knobs remain completely unclear. In this study, histomorphological and transcriptomic analyses of goose knobs in D70, D120, and D300 Yangzhou geese revealed differential changes in tissue morphology during the growth and development of goose knobs and the key core genes that regulate goose knob traits. Observation of tissue sections revealed that as age increased, the thickness of the knob epidermis, cuticle, and spinous cells gradually decreased. Additionally, fat cells in the dermis and subcutaneous connective tissue transitioned from loose to dense. Transcriptome sequencing results, analyzed through differential expression, Weighted Gene Co-expression Network Analysis (WGCNA), and pattern expression analysis methods, showed D70-vs.-D120 (up-regulated: 192; down-regulated: 423), D70-vs.-D300 (up-regulated: 1394; down-regulated: 1893), and D120-vs.-D300 (up-regulated: 1017; down-regulated: 1324). A total of 6243 differentially expressed genes (DEGs) were identified, indicating varied expression levels across the three groups in the knob tissues of D70, D120, and D300 Yangzhou geese. These DEGs are significantly enriched in biological processes (BP) such as skin morphogenesis, the regulation of keratinocyte proliferation, and epidermal cell differentiation. Furthermore, they demonstrate enrichment in pathways related to goose knob development, including ECM–receptor interaction, NF-kappa B, and PPAR signaling. Through pattern expression analysis, three gene expression clusters related to goose knob traits were identified. The joint analysis of candidate genes associated with goose knob development and WGCNA led to the identification of key core genes influencing goose knob development. These core genes comprise WNT4, WNT10A, TCF7L2, GATA3, ADRA2A, CASP3, SFN, KDF1, ERRFI1, SPRY1, and EVPL. In summary, this study provides a reference for understanding the molecular mechanisms of goose knob growth and development and provides effective ideas and methods for the genetic improvement of goose knob traits. Full article
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17 pages, 334 KiB  
Review
Progress in Research and Prospects for Application of Precision Gene-Editing Technology Based on CRISPR–Cas9 in the Genetic Improvement of Sheep and Goats
by Zeyu Lu, Lingtian Zhang, Qing Mu, Junyang Liu, Yu Chen, Haoyuan Wang, Yanjun Zhang, Rui Su, Ruijun Wang, Zhiying Wang, Qi Lv, Zhihong Liu, Jiasen Liu, Yunhua Li and Yanhong Zhao
Agriculture 2024, 14(3), 487; https://doi.org/10.3390/agriculture14030487 - 18 Mar 2024
Viewed by 1340
Abstract
Due to recent innovations in gene editing technology, great progress has been made in livestock breeding, with researchers rearing gene-edited pigs, cattle, sheep, and other livestock. Gene-editing technology involves knocking in, knocking out, deleting, inhibiting, activating, or replacing specific bases of DNA or [...] Read more.
Due to recent innovations in gene editing technology, great progress has been made in livestock breeding, with researchers rearing gene-edited pigs, cattle, sheep, and other livestock. Gene-editing technology involves knocking in, knocking out, deleting, inhibiting, activating, or replacing specific bases of DNA or RNA sequences at the genome level for accurate modification, and such processes can edit genes at a fixed point without needing DNA templates. In recent years, although clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system-mediated gene-editing technology has been widely used in research into the genetic breeding of animals, the system’s efficiency at inserting foreign genes is not high enough, and there are certain off-target effects; thus, it is not appropriate for use in the genome editing of large livestock such as cashmere goats. In this study, the development status, associated challenges, application prospects, and future prospects of CRISPR/Cas9-mediated precision gene-editing technology for use in livestock breeding were reviewed to provide a theoretical reference for livestock gene function analysis, genetic improvement, and livestock breeding that account for characteristics of local economies. Full article
17 pages, 4804 KiB  
Article
Massively Parallel CRISPR-Cas9 Knockout Screening in Sheep Granulosa Cells for FSH Response Genes
by Zaixia Liu, Lingli Dai, Tianhao Sun, Yongbin Liu, Yanchun Bao, Mingjuan Gu, Shaoyin Fu, Xiaolong He, Caixia Shi, Yu Wang, Lili Guo, Le Zhou, Fengying Ma, Risu Na and Wenguang Zhang
Animals 2024, 14(6), 898; https://doi.org/10.3390/ani14060898 - 14 Mar 2024
Viewed by 837
Abstract
Follicle-stimulating hormone (FSH) regulates ovarian follicle development through specific gene expression programs. Granulosa cells (GCs) are somatic cells surrounding the oocytes, secreting gonadotropins to regulate ovulation and promote follicular development. By analyzing the effects of different doses of FSH on the proliferation of [...] Read more.
Follicle-stimulating hormone (FSH) regulates ovarian follicle development through specific gene expression programs. Granulosa cells (GCs) are somatic cells surrounding the oocytes, secreting gonadotropins to regulate ovulation and promote follicular development. By analyzing the effects of different doses of FSH on the proliferation of GCs, we found that adding 10 ng/mL of FSH, as the optimal concentration, could promote the growth of GCs. Furthermore, we have successfully constructed the first CRISPR-Cas9 knockout library targeting the genes on chromosomes 2 and 3 and the X chromosomes of the sheep massively parallel coding gene, as well as an ovarian GCs knockout cell library. For the first time, we have exposed the knockout cell library to a concentration of 10 ng/mL FSH to explore the underlying mechanisms. Through this screening, we have identified 836 positive–negative screening genes that are responsive to FSH, thereby revealing the regulatory mechanisms and screening the functionality of candidate genes. Next, RNA-Seq of control (0 ng/mL), low (10 ng/mL), and high (100 ng/mL) doses of FSH revealed 1708 differentially expressed genes, and combined with 836 genes, we obtained 129 FSH dose-dependent genes with extremely significant differences. This enables us to delve deeper into investigating and identifying the mechanisms by which FSH regulates GCs. More generally, we have discovered new regulatory factors and identified reproductivity-associated major effectors. These findings provide novel research directions for further studies on sheep reproduction. Full article
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14 pages, 2609 KiB  
Article
The Establishment and Optimization of a Chicken Primordial Germ Cell Induction Model Using Small-Molecule Compounds
by Wei Gong, Juanjuan Zhao, Zeling Yao, Yani Zhang, Yingjie Niu, Kai Jin, Bichun Li and Qisheng Zuo
Animals 2024, 14(2), 302; https://doi.org/10.3390/ani14020302 - 18 Jan 2024
Viewed by 820
Abstract
In recent years, inducing pluripotent stem cells to differentiate into functional primordial germ cells (PGCs) in vitro has become an important method of obtaining a large number of PGCs. However, the instability and low induction efficiency of the in vitro PGC induction system [...] Read more.
In recent years, inducing pluripotent stem cells to differentiate into functional primordial germ cells (PGCs) in vitro has become an important method of obtaining a large number of PGCs. However, the instability and low induction efficiency of the in vitro PGC induction system restrict the application of PGCs in transgenic animal production, germplasm resource conservation and other fields. In this study, we successfully established a two-step induction model of chicken PGCs in vitro, which significantly improved the formation efficiency of PGC-like cells (PGCLCs). To further improve the PGC formation efficiency in vitro, 5025 differentially expressed genes (DEGs) were obtained between embryonic stem cells (ESCs) and PGCs through RNA-seq. GO and KEGG enrichment analysis revealed that signaling pathways such as BMP4, Wnt and Notch were significantly activated during PGC formation, similar to other species. In addition, we noted that cAMP was activated during PGC formation, while MAPK was suppressed. Based on the results of our analysis, we found that the PGC formation efficiency was significantly improved after activating Wnt and inhibiting MAPK, and was lower than after activating cAMP. To sum up, in this study, we successfully established a two-step induction model of chicken PGCs in vitro with high PGC formation efficiency, which lays a theoretical foundation for further demonstrating the regulatory mechanism of PGCs and realizing their specific applications. Full article
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13 pages, 1632 KiB  
Article
Variation in the HSL Gene and Its Association with Carcass and Meat Quality Traits in Yak
by Xiangyan Wang, Youpeng Qi, Chune Zhu, Ruifeng Zhou, Zhoume Ruo, Zhidong Zhao, Xiu Liu, Shaobin Li, Fangfang Zhao, Jiqing Wang, Jiang Hu and Bingang Shi
Animals 2023, 13(23), 3720; https://doi.org/10.3390/ani13233720 - 1 Dec 2023
Cited by 1 | Viewed by 992
Abstract
Hormone-sensitive lipase (HSL) is involved in the breakdown of triacylglycerols in adipose tissue, which influences muscle tenderness and juiciness by affecting the intramuscular fat content (IMF). This study analyzed the association between different genotypes and haplotypes of the yak HSL gene [...] Read more.
Hormone-sensitive lipase (HSL) is involved in the breakdown of triacylglycerols in adipose tissue, which influences muscle tenderness and juiciness by affecting the intramuscular fat content (IMF). This study analyzed the association between different genotypes and haplotypes of the yak HSL gene and carcass and meat quality traits. We used hybridization pool sequencing to detect exon 2, exon 8, and intron 3 variants of the yak HSL gene and genotyped 525 Gannan yaks via KASP to analyze the effects of the HSL gene variants on the carcass and meat quality traits in yaks. According to the results, the HSL gene is highly expressed in yak adipose tissue. Three single nucleotide polymorphisms (SNPs) were identified, with 2 of them located in the coding region and one in the intron region. Variants in the 2 coding regions resulted in amino acid changes. The population had 3 genotypes of GG, AG, and AA, and individuals with the AA genotype had lower WBSF values (p < 0.05). The H3H3 haplotype combinations could improve meat tenderness by reducing the WBSF values and the cooking loss rate (CLR) (p < 0.05). H1H1 haplotype combinations were associated with the increased drip loss rate (DLR) (p < 0.05). The presence of the H1 haplotype was associated the increased CLR in yaks, while that of the H2 haplotype was associated with the decreased DLR in yaks (p < 0.05). These results demonstrated that the HSL gene may influence the meat quality traits in yaks by affecting the IMF content in muscle tissues. Consequently, the HSL gene can possibly be used as a biomarker for improving the meat quality traits in yaks in the future. Full article
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12 pages, 494 KiB  
Article
Creation of a Biobank of the Sperm of the Honey Bee Drones of Different Subspecies of Apis mellifera L.
by Alexey N. Gulov, Andrey S. Berezin, Elena O. Larkina, Elena S. Saltykova and Milyausha D. Kaskinova
Animals 2023, 13(23), 3684; https://doi.org/10.3390/ani13233684 - 28 Nov 2023
Viewed by 1048
Abstract
The cryopreservation of gametes and embryos is an important element of biodiversity conservation. One species in need of conservation is the honey bee Apis mellifera L. Changing environmental factors, especially the anthropogenic factor, have led to a reduction in the numbers of this [...] Read more.
The cryopreservation of gametes and embryos is an important element of biodiversity conservation. One species in need of conservation is the honey bee Apis mellifera L. Changing environmental factors, especially the anthropogenic factor, have led to a reduction in the numbers of this insect species. In this study, we provide an example of the creation of a biobank of honey bee drone sperm. For sperm cryopreservation, drones of the most common subspecies of honey bees common in Russia were selected. These were the dark forest bee, Apis mellifera mellifera, from the Republic of Bashkortostan, with three subspecies (A. m. carnica, A. m. carpatica, and A. m. caucasica) from the southern regions of Russia, as well as two breeding stocks, the Far Eastern bee and Prioksky bee. For subspecies identification, morphometric and genetic methods were used. The subspecies of the studied samples were confirmed via the analysis of the tRNAleu-COII locus of mitochondrial DNA and nine microsatellite markers of nuclear DNA. It was shown that bees of the Prioksky breeding stock belong to the subspecies A. m. caucasica based on phylogenetic analysis, and the Far Eastern breeding stock is a stable hybrid, descending on the maternal line from the evolutionary lineage C or O. The results of the morphometric analysis are consistent with the results of the genetic analysis. For the cryopreservation of sperm, we used a cryoprotectant solution with honey. As a result, the viability of frozen–thawed sperm decreased by 20.3% compared to fresh sperm, and overall motility decreased 25-fold. The measurement of the sperm concentration in the spermatheca of artificially inseminated queens showed that it varied from 0.22 to 4.4 million/μL. Therefore, the use of honey in sperm cryopreservation has great potential. Full article
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12 pages, 1728 KiB  
Article
Insertion of 643bp Retrotransposon Upstream of PPARγ CDS Is Associated with Backfat of Large White Pigs
by Jia He, Miao Yu, Chenglin Chi, Zhanyu Du, Yao Zheng, Cai Chen, Ali Shoaib Moawad, Chengyi Song and Xiaoyan Wang
Animals 2023, 13(14), 2355; https://doi.org/10.3390/ani13142355 - 19 Jul 2023
Viewed by 989
Abstract
PPARs are essential regulators of mammalian fatty acid and lipid metabolism. Although the effects of genetic variations, including single nucleotide polymorphisms (SNPs) in PPARs genes on the phenotype of domestic animals have been investigated, there is limited information on the impact of retrotransposon [...] Read more.
PPARs are essential regulators of mammalian fatty acid and lipid metabolism. Although the effects of genetic variations, including single nucleotide polymorphisms (SNPs) in PPARs genes on the phenotype of domestic animals have been investigated, there is limited information on the impact of retrotransposon insertion polymorphisms (RIPs). In this study, a combined comparative genome and polymerase chain reaction (PCR) was used to excavate the RIPs in porcine PPARs. We also investigated the potential effects of retrotransposon insertion on phenotype and expression patterns. This study identified the two RIPs in PPARs genes, namely an ERV in intron 1 of PPARα and a combined retrotransposon in intron 2 of PPARγ, designated as PPARα-ERV-RIP and PPARγ-COM-RIP, respectively. These RIPs exhibited different distribution patterns among Chinese indigenous breeds and Western commercial breeds. Individuals with the PPARα-ERV-RIP+/+ genotype (+/+ indicated homozygous with insertion) among Large White pigs had significantly higher (p < 0.05) corrected backfat thickness compared to those with the other two genotypes. Similarly, those with the PPARγ-COM-RIP−/− genotype had significantly higher (p < 0.05) corrected backfat thickness than those with the other two genotypes in Large White pigs. Moreover, in 30-day-old Sujiang piglets, the PPARγ gene expression in the backfat of those with the PPARγ-COM-RIP−/− genotype (−/− indicated homozygous without insertion) was significantly greater (p < 0.01) than those with other genotypes. The dual luciferase reporter gene assay demonstrated that the combined retrotransposon insertion significantly reduced the activity of the MYC promoter in both C2C12 and 3T3-L1 cells (p < 0.01). Therefore, the combined retrotransposon insertion could function as a repressor to decrease the expression of PPARγ, making PPARγ-COM-RIP a valuable molecular marker for assisted selection of backfat thickness in pig breeding. Full article
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12 pages, 1163 KiB  
Article
Phenotypic Characterization of Creole Cattle in the Andean Highlands Using Bio-Morphometric Measures and Zoometric Indices
by Rolando Rojas-Espinoza, Rassiel Macedo, Alex Suaña, Alfredo Delgado, Yan P. Manrique, Halley Rodríguez, Yesenia M. Quispe, Uri H. Perez-Guerra, Manuel G. Pérez-Durand and Manuel García-Herreros
Animals 2023, 13(11), 1843; https://doi.org/10.3390/ani13111843 - 1 Jun 2023
Cited by 1 | Viewed by 1960
Abstract
Several Creole cattle biotypes can be found in the Andean highlands, and most of them are considered as being in risk of extinction. The main aim of the present study was to perform a phenotypic characterization of the Creole cattle in the Andean [...] Read more.
Several Creole cattle biotypes can be found in the Andean highlands, and most of them are considered as being in risk of extinction. The main aim of the present study was to perform a phenotypic characterization of the Creole cattle in the Andean highlands using bio-morphometric measures and zoometric indices. Individuals from three different biotypes (Black ‘Negro’ (n = 57), Colour-Sided ‘Callejón’ (n = 20), and Brindle ‘Atigrado’ (n = 18)) from an experimental research center located in the Peruvian highlands were enrolled in the study. In total, seventeen morphometric parameters were evaluated and ten zoometric indices were calculated in each biotype. To test the relationship between biometric traits, correlation analyses were carried out between morphometric parameters. Differences were observed regarding different morphometric variables such as head length (HL) and rump length (RL) among cattle biotypes (p ≤ 0.05). The coefficient of variation (CV; %) regarding different morphometric parameters ranged between 11.32 for neck length (NL) and 3.63 for height at withers (HaW), which indicated low–moderate variability among morphometric variables. Differences were observed in the longitudinal pelvic index (LPI) when different zoometric indices were compared among biotypes (p ≤ 0.05). The CV regarding different zoometric indices, which ranged between 10.78 for the cephalic index (CEI) and 5.05 for LPI, indicated low variability among indices. No differences were observed in any other morphometric parameter or zoometric index among cattle biotypes or genders (p > 0.05). Finally, multiple correlations were observed between morphometric variables (p ≤ 0.05). In conclusion, it was determined that Peruvian Andean Creole cattle can be considered as a dairy-related biotype with a slight tendency for beef production (dual-purpose). The great homogeneity regarding zoometric characteristics among biotypes and genders may indicate that the Andean Creole cattle have been maintained quite isolated, avoiding the genetic influence of other foreign breeds. Finally, the phenotypic characterization including bio-morphometric measurements and zoometric indices obtained from the different Creole bovine biotypes is crucial in order to begin different conservation programs to preserve cattle breeds in the Peruvian Andean highlands. Full article
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12 pages, 2969 KiB  
Review
ADAMTS Proteases: Importance in Animal Reproduction
by Pamela Hernández-Delgado, Monserrath Felix-Portillo and José A. Martínez-Quintana
Genes 2023, 14(6), 1181; https://doi.org/10.3390/genes14061181 - 29 May 2023
Cited by 2 | Viewed by 1688
Abstract
Many reproductive physiological processes, such as folliculogenesis, ovulation, implantation, and fertilization, require the synthesis, remodeling, and degradation of the extracellular matrix (ECM). The ADAMTS (A Disintegrin and Metalloproteinase with Thrombospondin Motifs) family genes code for key metalloproteinases in the remodeling process of different [...] Read more.
Many reproductive physiological processes, such as folliculogenesis, ovulation, implantation, and fertilization, require the synthesis, remodeling, and degradation of the extracellular matrix (ECM). The ADAMTS (A Disintegrin and Metalloproteinase with Thrombospondin Motifs) family genes code for key metalloproteinases in the remodeling process of different ECM. Several genes of this family encode for proteins with important functions in reproductive processes; in particular, ADAMTS1, 4, 5 and 9 are genes that are differentially expressed in cell types and the physiological stages of reproductive tissues. ADAMTS enzymes degrade proteoglycans in the ECM of the follicles so that the oocytes can be released and regulate follicle development during folliculogenesis, favoring the action of essential growth factors, such as FGF-2, FGF-7 and GDF-9. The transcriptional regulation of ADAMTS1 and 9 in preovulatory follicles occurs because of the gonadotropin surge in preovulatory follicles, via the progesterone/progesterone receptor complex. In addition, in the case of ADAMTS1, pathways involving protein kinase A (PKA), extracellular signal regulated protein kinase (ERK1/2) and the epidermal growth factor receptor (EGFR) might contribute to ECM regulation. Different Omic studies indicate the importance of genes of the ADAMTS family from a reproductive aspect. ADAMTS genes could serve as biomarkers for genetic improvement and contribute to enhance fertility and animal reproduction; however, more research related to these genes, the synthesis of proteins encoded by these genes, and regulation in farm animals is needed. Full article
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19 pages, 6979 KiB  
Article
Overexpression of DGAT2 Regulates the Differentiation of Bovine Preadipocytes
by Pan-Pan Guo, Xin Jin, Jun-Fang Zhang, Qiang Li, Chang-Guo Yan and Xiang-Zi Li
Animals 2023, 13(7), 1195; https://doi.org/10.3390/ani13071195 - 29 Mar 2023
Viewed by 1502
Abstract
Triacylglycerols (TAGs) are a major component of intramuscular fat. Diacylglycerol O-acyltransferase 2(DGAT2) expression determines the rate of TAG synthesis. The purpose of this study was to investigate the role of DGAT2 in the differentiation of Yanbian cattle preadipocytes and lipid metabolism-related [...] Read more.
Triacylglycerols (TAGs) are a major component of intramuscular fat. Diacylglycerol O-acyltransferase 2(DGAT2) expression determines the rate of TAG synthesis. The purpose of this study was to investigate the role of DGAT2 in the differentiation of Yanbian cattle preadipocytes and lipid metabolism-related signalling pathways. Bovine preadipocytes were infected with overexpression and interfering adenovirus vectors of DGAT2. The effects on the differentiation of Yanbian cattle preadipocytes were examined using molecular and transcriptomic techniques, including differentially expressed genes (DEGs) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. DGAT2 overexpression significantly increased (p < 0.05) intracellular TAG, adiponectin, and lipid droplet (LD) contents. Moreover, it upregulated (p < 0.05) peroxisome proliferator-activated receptor γ (PPARγ), CCAAT/enhancer binding protein α, and fatty acid binding protein 4 mRNA expression. In contrast, DGAT2 knockdown reduced intracellular TAG and LD content and downregulated (p < 0.05) C/EBPβ, mannosyl (alpha-1,3-)-glycoproteinbeta-1,2-N-acetylglucosaminyltransferase, lipin 1,1-acylglycerol-3-phosphate O-acyltransferase 4, and acetyl-CoA carboxylase alpha mRNA expression. Between DGAT2-overexpressing preadipocytes and normal cells, 208 DEGs were identified, including 106 upregulated and 102 downregulated genes. KEGG pathway analysis revealed DEGs mainly enriched in PPAR signalling and AMP-activated protein kinase pathways, cholesterol metabolism, and fatty acid biosynthesis. These results demonstrated that DGAT2 regulated preadipocyte differentiation and LD and TAG accumulation by mediating the expression of adipose differentiation-, lipid metabolism-, and fatty acid synthesis-related genes. Full article
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11 pages, 2229 KiB  
Communication
A Comprehensive Strategy Combining Feature Selection and Local Optimization Algorithm to Optimize the Design of Low-Density Chip for Genomic Selection
by Ruihan Mao, Lei Zhou, Zhaojun Wang, Jianliang Wu and Jianfeng Liu
Agriculture 2023, 13(3), 614; https://doi.org/10.3390/agriculture13030614 - 3 Mar 2023
Viewed by 1518
Abstract
Design of low-density SNP chips provides an opportunity for wide application of genomic selection at lower cost. A novel strategy referred to as the “block-free” method is proposed in this study to select a subset of SNPs from a high-density chip to form [...] Read more.
Design of low-density SNP chips provides an opportunity for wide application of genomic selection at lower cost. A novel strategy referred to as the “block-free” method is proposed in this study to select a subset of SNPs from a high-density chip to form a low-density panel. In this method, Feature Selection using a Feature Similarity (FSFS) algorithm was first performed to remove highly correlated SNPs, and then a Multiple-Objective, Local-Optimization (MOLO) algorithm was used to pick SNPs for the low-density panel. Two other commonly used methods called the “uniform” method and the “block-based” method were also implemented for comparison purposes. A real pig dataset with 7967 individuals from three breeds containing 43,832 SNPs was used for comparison of the methods. In terms of genotype imputation accuracy and genomic prediction accuracy, our strategy was superior in most cases when the densities were lower than 1K. The genotype imputation accuracy from the low-density chip compared to the original high-density chip was higher than 90% in all pig breeds as the density increased to 1K. In addition, the accuracies of predicted genomic breeding values (GEBV) calculated using the imputed panel were nearly 90% of estimates from the original chip for all traits and breeds. Our strategy is effective to design low-density chips by making full use of information of close relationships for genomic selection in animals and plants. Full article
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