Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection

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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	3.3	4.9	2011	19.2 Days	CHF 2600
Animals animals	2.7	4.9	2011	16.1 Days	CHF 2400
Dairy dairy	-	4.4	2020	27.8 Days	CHF 1200
Genes genes	2.8	5.2	2010	14.9 Days	CHF 2600
International Journal of Molecular Sciences ijms	4.9	8.1	2000	16.8 Days	CHF 2900
Veterinary Sciences vetsci	2.0	2.9	2014	21.2 Days	CHF 2100

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Published Papers (26 papers)

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17 pages, 1372 KiB  

Open AccessReview

Genetic Strategies for Enhancing Rooster Fertility in Tropical and Humid Climates: Challenges and Opportunities

by Jiraporn Juiputta, Vibuntita Chankitisakul and Wuttigrai Boonkum

Animals 2025, 15(8), 1096; https://doi.org/10.3390/ani15081096 - 10 Apr 2025

Viewed by 397

Abstract

Native chickens are important both economically and for the preservation of genetic diversity, especially for optimizing the reproductive performance of male chickens, which plays an important role in genetic propagation. However, hot and humid weather affects the quality of semen and the breeding [...] Read more.

Native chickens are important both economically and for the preservation of genetic diversity, especially for optimizing the reproductive performance of male chickens, which plays an important role in genetic propagation. However, hot and humid weather affects the quality of semen and the breeding ability of male chickens. One method used to solve this problem is genetic selection using genomic technology, which improves accuracy and shortens the breed selection time. Therefore, we collected and analyzed data from relevant research to review the genetic improvement approach for male chickens using genomic technology. We compared popular genomic selection models, such as GBLUP, ssGBLUP, Bayesian approaches, RR-GBLUP, WGBLUP, and MTGBLUP, as well as genome-wide association studies (GWASs), to identify genes associated with semen quality and heat tolerance. The results of this analysis suggested that the use of genomic data can enhance genetic selection and enable breeding to occur more quickly and accurately. We addressed the trends and scientific developments in male chicken genetic selection, together with the benefits and constraints of each method. This will help breeders and researchers to create the most successful genetic selection plans for the next generation of chickens. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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13 pages, 1503 KiB  

Open AccessArticle

Variants in BMP15 Gene Affect Promoter Activity and Litter Size in Gobi Short Tail and Ujimqin Sheep

by Shenyuan Wang, Yanyu Bai, Daqing Wang, Ming Zhang, Suhe Alatan, Ming Cang, Hai Jin, Changqing Li, Guangchen Du, Guifang Cao and Bin Tong

Vet. Sci. 2025, 12(3), 222; https://doi.org/10.3390/vetsci12030222 - 2 Mar 2025

Viewed by 670

Abstract

Reproductive performance in sheep plays a crucial role in determining the economic efficiency of the industry, with increasing litter size being a key focus for genetic improvement. The BMP15 gene is widely recognized as a major gene influencing sheep fertility. In this study, [...] Read more.

Reproductive performance in sheep plays a crucial role in determining the economic efficiency of the industry, with increasing litter size being a key focus for genetic improvement. The BMP15 gene is widely recognized as a major gene influencing sheep fertility. In this study, specific mutations in the BMP15 gene of Gobi short tail sheep were identified through direct sequencing, and these mutations were genotyped using the MassARRAY system. The g.54285159_54285161TTA indel was significantly associated with litter size in Gobi short tail sheep (p < 0.05). Three mutations, including g.54291460G>A, g.54288671C>T, and the g.54285159_54285161TTA indel, were significantly associated with litter size in Ujimqin sheep (p < 0.05). Furthermore, the promoter activity analysis demonstrated that the A allele exhibited significantly higher promoter activity compared to the G allele of the g.54291460G>A mutation. These findings highlight valuable genetic markers for improving sheep litter size and provide a robust theoretical foundation for further research on the BMP15 gene’s role in reproduction. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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13 pages, 997 KiB  

Open AccessArticle

Weighted Kernel Ridge Regression to Improve Genomic Prediction

by Chenguang Diao, Yue Zhuo, Ruihan Mao, Weining Li, Heng Du, Lei Zhou and Jianfeng Liu

Agriculture 2025, 15(5), 445; https://doi.org/10.3390/agriculture15050445 - 20 Feb 2025

Cited by 1 | Viewed by 513

Abstract

Nonparametric models have recently been receiving increased attention due to their effectiveness in genomic prediction for complex traits. However, regular nonparametric models cannot effectively differentiate the relative importance of various SNPs, which significantly impedes the further application of these methods for genomic prediction. [...] Read more.

Nonparametric models have recently been receiving increased attention due to their effectiveness in genomic prediction for complex traits. However, regular nonparametric models cannot effectively differentiate the relative importance of various SNPs, which significantly impedes the further application of these methods for genomic prediction. To enhance the fitting ability of nonparametric models and improve genomic prediction accuracy, a weighted kernel ridge regression model (WKRR) was proposed in this study. For this new method, different weights were assigned to different SNPs according to the p-values from GWAS, and then a KRR model based on these weighted SNPs was constructed for genomic prediction. Cross-validation was further adopted to choose appropriate hyper-parameters during the weighting and prediction process for generalization. We compared the predictive accuracy of WKRR with the genomic best linear unbiased prediction (GBLUP), BayesR, and unweighted KRR using both simulated and real datasets. The results showed that WKRR outperformed unweighted KRR in all simulated scenarios. Additionally, WKRR achieved an average improvement of 1.70% in accuracies across all traits in a mice dataset and 2.17% for three lactation-related traits in a cattle dataset compared to GBLUP, and yielded competitive results compared to BayesR. These findings demonstrated the great potential of weighted nonparametric models for genomic prediction. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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19 pages, 1283 KiB  

Open AccessArticle

The Performance, Ingestive Behavior, Nutrient Digestibility, Ruminal Fermentation Profile, Health Status, and Gene Expression of Does Fed a Phytochemical–Lactobacilli Blend in Late Pregnancy

by Amr A. Gabr, Fayek Farrag, Mohamed Ahmed, Yosra A. Soltan, Ahmed Ateya and Umar Mafindi

Animals 2025, 15(4), 598; https://doi.org/10.3390/ani15040598 - 19 Feb 2025

Viewed by 613

Abstract

This study investigated the effects of a phytochemical–Lactobacilli blend (PEL) on the performance and health of late-pregnant does. Thirty Zaraibi does (30.9 ± 0.37 kg body weight, 3–3.5 years old, 90 days pregnant) were randomly assigned to three experimental groups, ensuring equal distribution [...] Read more.

This study investigated the effects of a phytochemical–Lactobacilli blend (PEL) on the performance and health of late-pregnant does. Thirty Zaraibi does (30.9 ± 0.37 kg body weight, 3–3.5 years old, 90 days pregnant) were randomly assigned to three experimental groups, ensuring equal distribution based on body weight, parity, litter size, and previous lactation milk production. The does were fed either a control diet (no supplementation) or a PEL-supplemented diet (control diet plus 2 g or 4 g of PEL per day) for 60 days. PEL supplementation linearly improved (p < 0.05) feed intake, nutrient digestibility, and ruminal concentrations of acetic and propionic acids, while significantly reducing (p < 0.05) ruminal ammonia-N concentrations. PEL supplementation linearly reduced (p < 0.05) feeding and rumination times while increasing idling time. Blood hematological parameters improved (p < 0.05) with PEL supplementation. Serum protein, liver and kidney function indicators, lipid metabolism, cortisol, and thyroid hormone levels were significantly improved (p < 0.01) in a linear manner with PEL supplementation. Antioxidant status, pro-inflammatory cytokines, and immune response were enhanced both linearly and quadratically (p < 0.05) with PEL treatment. Gene expression analysis revealed a linear upregulation (p < 0.05) of growth, immune, and antioxidant-related genes with PEL supplementation. These findings suggest that supplementing pregnant does with 4 g of PEL per day can effectively enhance their performance, health, and metabolic status. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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25 pages, 5873 KiB  

Open AccessArticle

Genome-Wide Association Study on Body Conformation Traits in Xinjiang Brown Cattle

by Menghua Zhang, Yachun Wang, Qiuming Chen, Dan Wang, Xiaoxue Zhang, Xixia Huang and Lei Xu

Int. J. Mol. Sci. 2024, 25(19), 10557; https://doi.org/10.3390/ijms251910557 - 30 Sep 2024

Viewed by 1197

Abstract

Body conformation traits are linked to the health, longevity, reproductivity, and production performance of cattle. These traits are also crucial for herd selection and developing new breeds. This study utilized pedigree information and phenotypic (1185 records) and genomic (The resequencing of 496 Xinjiang [...] Read more.

Body conformation traits are linked to the health, longevity, reproductivity, and production performance of cattle. These traits are also crucial for herd selection and developing new breeds. This study utilized pedigree information and phenotypic (1185 records) and genomic (The resequencing of 496 Xinjiang Brown cattle generated approximately 74.9 billion reads.) data of Xinjiang Brown cattle to estimate the genetic parameters, perform factor analysis, and conduct a genome-wide association study (GWAS) for these traits. Our results indicated that most traits exhibit moderate to high heritability. The principal factors, which explained 59.12% of the total variance, effectively represented body frame, muscularity, rump, feet and legs, and mammary system traits. Their heritability estimates range from 0.17 to 0.73, with genetic correlations ranging from −0.53 to 0.33. The GWAS identified 102 significant SNPs associated with 12 body conformation traits. A few of the SNPs were located near previously reported genes and quantitative trait loci (QTLs), while others were novel. The key candidate genes such as LCORL, NCAPG, and FAM184B were annotated within 500 Kb upstream and downstream of the significant SNPs. Therefore, factor analysis can be used to simplify multidimensional conformation traits into new variables, thus reducing the computational burden. The identified candidate genes from GWAS can be incorporated into the genomic selection of Xinjiang Brown cattle, enhancing the reliability of breeding programs. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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16 pages, 293 KiB  

Open AccessArticle

Estimate of Genetic Parameters for Pre-Weaning Growth Traits and Kleiber Ratio in Palestinian Sheep Breeds

by Muayad Salman, Ikram Ben Souf, Samia Khnissi, Wael Halaweh and Naceur M’Hamdi

Agriculture 2024, 14(10), 1697; https://doi.org/10.3390/agriculture14101697 - 27 Sep 2024

Cited by 1 | Viewed by 1134

Abstract

Data on 1440 Awassi (AW), 2114 Assaf (AF), 261 Crossbred (XB), and 439 Improved Awassi (IA) lamb genotypes from 689 AW, 1009 AF, 105 XB, and 195 IA dams, and 152 sires, obtained from three geographical districts in the West Bank and collected [...] Read more.

Data on 1440 Awassi (AW), 2114 Assaf (AF), 261 Crossbred (XB), and 439 Improved Awassi (IA) lamb genotypes from 689 AW, 1009 AF, 105 XB, and 195 IA dams, and 152 sires, obtained from three geographical districts in the West Bank and collected between 2010 and 2015, were analyzed to estimate (co)variance components and genetic parameters for pre-weaning growth traits, including birth weight (BW), weaning weight (WW), pre-weaning average daily gain (PADG), and Kleiber ratio (KR). Explanatory statistical analyses employed the least squares method of the following factors: lamb genotype, mating type (natural mating or artificial insemination), lamb sex, and birth type, on lamb pre-weaning growth traits. The estimation of genetic parameters was performed by an animal model in Restricted Maximum Likelihood (REML) The heritability estimates for lamb traits showed that AF lambs had the highest heritability for KR 0.62, while IA lambs had a relatively high heritability for PADG 0.42. In terms of genetic correlations, the correlation between birth weight and PADG was strongest in AW 0.80, and IA lambs had a negative genetic correlation between BW and WW −0.28. For maternal genetic correlations, AF lambs exhibited a high maternal correlation between BW and WW 0.78, and AW lambs had a strong maternal correlation between PADG and KR 0.57. Phenotypic correlations were particularly strong in XB lambs between BW and KR 0.79. It was concluded that IA lambs had higher BW, and AF lambs excelled in WW and PADG. These results indicated the potential for genetic improvement in feed efficiency among AF lambs, whereas AW lambs exhibited a stronger environmental influence on growth traits. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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15 pages, 1035 KiB  

Open AccessArticle

Effects of Resveratrol-Loaded Cyclodextrin on the Quality Characteristics of Ram Spermatozoa Following Cryopreservation

by Ahmet Eser, Selin Yağcıoğlu, Ramazan Arıcı, Kamber Demir and Kemal Ak

Animals 2024, 14(18), 2745; https://doi.org/10.3390/ani14182745 - 23 Sep 2024

Cited by 2 | Viewed by 1207

Abstract

This study investigated the effects of pure and methyl-β-cyclodextrin loaded forms of resveratrol (10 µg/mL, 20 µg/mL, and 40 µg/mL) on ram sperm functions post-thawing. Semen samples were pooled and divided into ten groups: Control, RES10, RES20, RES40, CD10, CD20, CD40, RLC10, RLC20, [...] Read more.

This study investigated the effects of pure and methyl-β-cyclodextrin loaded forms of resveratrol (10 µg/mL, 20 µg/mL, and 40 µg/mL) on ram sperm functions post-thawing. Semen samples were pooled and divided into ten groups: Control, RES10, RES20, RES40, CD10, CD20, CD40, RLC10, RLC20, and RLC40. The groups were pre-diluted with media containing the group-specific chemicals, followed by 15 min of incubation, dilution, and freezing. To assess the effects of the chemicals, a post-thaw sperm quality assessment was conducted. Motility and other velocity parameters were evaluated using computer-assisted semen analysis. The functional integrity of spermatozoa membranes was assessed with the hypo-osmotic swelling test, and the capacitation status of spermatozoa was determined through fluorescent microscopic evaluation. Additionally, flow cytometry was used to evaluate mitochondrial activity, oxidative stress, and the integrity of the sperm membrane and acrosome. The results indicated that cyclodextrin adversely affected sperm functions following freezing–thawing, notably increasing the rate of spermatozoa exhibiting pre-capacitation and mitochondrial activity by approximately 34% and 16%, respectively (p < 0.05). It was found that 20 µg/mL resveratrol prevented pre-capacitation (p < 0.05). Both resveratrol and resveratrol-loaded cyclodextrin groups improved post-thaw sperm qualities overall, demonstrating their utility for freezing ram semen. However, higher concentrations of resveratrol were found to negatively impact sperm functions. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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13 pages, 3483 KiB  

Open AccessArticle

Expression of GLOD4 in the Testis of the Qianbei Ma Goat and Its Effect on Leydig Cells

by Jinqian Wang, Xiang Chen, Wei Sun, Wen Tang, Jiajing Chen, Yuan Zhang, Ruiyang Li and Yanfei Wang

Animals 2024, 14(17), 2611; https://doi.org/10.3390/ani14172611 - 8 Sep 2024

Viewed by 1386

Abstract

The expression pattern of GLOD4 in the testis and its regulatory effect on testicular cells was explored in goats to enhance our understanding of spermatogenesis and improve reproduction in breeding rams. In this study, we demonstrated the localization of GLOD4 in testicular cells [...] Read more.

The expression pattern of GLOD4 in the testis and its regulatory effect on testicular cells was explored in goats to enhance our understanding of spermatogenesis and improve reproduction in breeding rams. In this study, we demonstrated the localization of GLOD4 in testicular cells using immunohistochemistry and subcellular localization analyses. Subsequently, we analyzed the GLOD4 expression pattern in four age-based groups (0, 6, 12, and 18 months old) using real-time quantitative polymerase chain reaction (qRT-PCR) and protein blotting. Finally, we performed GLOD4 silencing and overexpression studies in Leydig cells (LCs) and explored the effects on cell proliferation, the cell cycle, steroid hormone secretion and the expression of candidate testosterone hormone-regulated genes. GLOD4 was mainly expressed in Leydig cells, and the subcellular localization results showed that the GLOD4 protein was mainly localized in the cytoplasm and nucleus. Silencing of GLOD4 significantly suppressed the mRNA expression levels of the testosterone secretion-related genes CYP11A1, 3β-HSD, and CYP17A1 and the mRNA expression levels of cell cycle-related genes CDK6, PCNA, and Cyclin E. Moreover, the cell cycle was blocked at the G2/M phase after GLOD4 silencing, which significantly suppressed testosterone secretion. In contrast, GLOD4 overexpression significantly increased the mRNA expression levels of the testosterone secretion-related genes CYP11A1, 3β-HSD, and CYP17A1 and increased the expression of the cell cycle-related genes CDK6, PCNA, and Cyclin E. Moreover, GLOD4 overexpression promoted the cell cycle from G0/G1 phases to enter the S phase and G2/M phases, promoted the secretion of testosterone. Taken together, our experimental results indicate that GLOD4 may affect the development of cells in Qianbei Ma goats of different ages by influencing the cell cycle, cell proliferation, and testosterone hormone synthesis. These findings enhance our understanding of the functions of GLOD4 in goats. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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10 pages, 2001 KiB  

Open AccessArticle

Identification of Site in the UTY Gene as Safe Harbor Locus on the Y Chromosome of Pig

by Xiaomei Chen, Guang Yang, Pengyun Ji, Guoshi Liu and Lu Zhang

Genes 2024, 15(8), 1005; https://doi.org/10.3390/genes15081005 - 1 Aug 2024

Cited by 1 | Viewed by 1370

Abstract

Genomic Safe Harbors (GSH) are loci used for the insertion of exogenous genetic elements, enabling exogenous gene expressing predictably without alterations of the host genome. These sites are becoming increasingly important as the gene editing technologies advance rapidly. Currently, only a few GSHs [...] Read more.

Genomic Safe Harbors (GSH) are loci used for the insertion of exogenous genetic elements, enabling exogenous gene expressing predictably without alterations of the host genome. These sites are becoming increasingly important as the gene editing technologies advance rapidly. Currently, only a few GSHs have been identified in the pig genome. In this study, a novel strategy was demonstrated for the efficient insertion of exogenous genetic material into the third exon of the UTY gene on the Y chromosome using CRISPR/Cas9-mediated homology arm-mediated end joining. The safety of the locus was verified according to the proper expression of the inserted EGFP gene without altering the expression of UTY. This approach enables the integration and expression of the exogenous gene at this locus, indicating that the UTY locus serves as a genomic safe harbor site for gene editing in the pig genome. Located on the Y chromosome, this site can be utilized for sex-biased pig breeding and developing biomedical models. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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12 pages, 4602 KiB  

Open AccessArticle

The Impact of Novel BMPR1B Mutations on Litter Size in Short-Tailed Gobi Sheep and Larger-Tailed Ujimqin Sheep

by Yanyu Bai, Shenyuan Wang, Kaifeng Wu, Ming Zhang, Suhe Alatan, Ming Cang, Guifang Cao, Hai Jin, Changqing Li and Bin Tong

Vet. Sci. 2024, 11(7), 297; https://doi.org/10.3390/vetsci11070297 - 1 Jul 2024

Cited by 1 | Viewed by 1378

Abstract

The significant deposition of tail fat in sheep has a profound impact on the economic benefits of animal husbandry. Furthermore, increasing the litter size is a crucial means of enhancing economic benefits. The BMPR1B and T/Brachyury genes are considered major functional [...] Read more.

The significant deposition of tail fat in sheep has a profound impact on the economic benefits of animal husbandry. Furthermore, increasing the litter size is a crucial means of enhancing economic benefits. The BMPR1B and T/Brachyury genes are considered major functional genes that could affect sheep litter size and tail bone number, respectively. In this study, we employed direct sequencing to identify specific mutations of the BMPR1B gene in Gobi short tail sheep and carried out genotyping using MassARRAY technology for each variant of both the BMPR1B and T genes. Significant associations were demonstrated between the c.687G>A mutation of BMPR1B and the litter size in both the Gobi short tail sheep and Ujimqin sheep breeds. Meanwhile, the g.30058882_30058873GCAGATTAAAIndel mutation was significantly associated with the litter size in Gobi short tail sheep. These findings may provide valuable genetic markers for expanding sheep litter size. In addition, we also confirmed that the frequency of tail-bone-number-related T alleles was significantly higher in Gobi short tail sheep than in longer-tailed Ujimqin sheep. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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12 pages, 1837 KiB  

Open AccessArticle

The Value of Genetic Improvement Evaluated Using a Whole of Enterprise Market Model

by Nicolas Lopez-Villalobos, Peter Wiles and Garry Udy

Dairy 2024, 5(3), 372-383; https://doi.org/10.3390/dairy5030030 - 28 Jun 2024

Viewed by 1566

Abstract

The net return from milk to the producers is defined as the aggregate market income from dairy products, after deducting all processing and marketing costs. The way to distribute this net return is through the payment system, which is usually based on multiple [...] Read more.

The net return from milk to the producers is defined as the aggregate market income from dairy products, after deducting all processing and marketing costs. The way to distribute this net return is through the payment system, which is usually based on multiple components, mainly with a reward for fat and protein and, in the case of the New Zealand dairy industry, a penalty for milk volume. Traditionally, the value of genetic improvement is evaluated using selection index theory assuming that there is an unlimited market where all dairy products can be sold in unlimited amounts at a fixed price and therefore economic values for fat and protein are assumed to be independent of demand. The objective of this study was to estimate the value of continuous genetic improvement evaluated using a model encompassing all the dairy producers in the industry where prices of the dairy products were determined by product specific supply-demand curves. Over 10 years of genetic improvement, the present value of the benefit (10% discount rate) was estimated to be $123,000 per farm. The corresponding benefit when the markets were assumed to have fixed commodity prices was $183,000 per farm. The model revealed that systematic genetic gains had a finite duration during which incremental benefits progressively declined and would be exhausted eventually. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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13 pages, 2507 KiB  

Open AccessArticle

Genomic Selection for Weaning Weight in Alpine Merino Sheep Based on GWAS Prior Marker Information

by Haifeng Wang, Chenglan Li, Jianye Li, Rui Zhang, Xuejiao An, Chao Yuan, Tingting Guo and Yaojing Yue

Animals 2024, 14(13), 1904; https://doi.org/10.3390/ani14131904 - 27 Jun 2024

Cited by 2 | Viewed by 1383

Abstract

This study aims to compare the accuracy of genomic estimated breeding values (GEBV) estimated using a genomic best linear unbiased prediction (GBLUP) method and GEBV estimates incorporating prior marker information from a genome-wide association study (GWAS) for the weaning weight trait in highland [...] Read more.

This study aims to compare the accuracy of genomic estimated breeding values (GEBV) estimated using a genomic best linear unbiased prediction (GBLUP) method and GEBV estimates incorporating prior marker information from a genome-wide association study (GWAS) for the weaning weight trait in highland Merino sheep. The objective is to provide theoretical and technical support for improving the accuracy of genomic selection. The study used a population of 1007 highland Merino ewes, with the weaning weight at 3 months as the target trait. The population was randomly divided into two groups. The first group was used for GWAS analysis to identify significant markers, and the top 5%, top 10%, top 15%, and top 20% markers were selected as prior marker information. The second group was used to estimate genetic parameters and compare the accuracy of GEBV predictions using different prior marker information. The accuracy was obtained using a five-fold cross-validation. Finally, both groups were subjected to cross-validation. The study’s findings revealed that the heritability of the weaning weight trait, as calculated using the GBLUP model, ranged from 0.122 to 0.394, with corresponding prediction accuracies falling between 0.075 and 0.228. By incorporating prior marker information from GWAS, the heritability was enhanced to a range of 0.125 to 0.407. The inclusion of the top 5% to top 20% significant SNPs from GWAS results as prior information into GS showed potential for improving the accuracy of predicting genomic breeding value. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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14 pages, 2467 KiB  

Open AccessArticle

Application of RNA-Seq Technology for Screening Reproduction-Related Differentially Expressed Genes in Tibetan and Yorkshire Pig Ovarian Tissue

by Yikai Yin, Jian Zhang, Xindi Li, Mengqi Duan, Mingxuan Zhao, Feifan Zhang, Yangzom Chamba and Peng Shang

Vet. Sci. 2024, 11(7), 283; https://doi.org/10.3390/vetsci11070283 - 21 Jun 2024

Cited by 1 | Viewed by 1782

Abstract

The purpose of this study was to explore and verify genes that regulate the reproductive traits of Tibetan pigs at the mRNA level. The ovarian tissues of Tibetan pigs (TPs) and Yorkshire pigs (YPs) were selected as research objects, and cDNA libraries of [...] Read more.

The purpose of this study was to explore and verify genes that regulate the reproductive traits of Tibetan pigs at the mRNA level. The ovarian tissues of Tibetan pigs (TPs) and Yorkshire pigs (YPs) were selected as research objects, and cDNA libraries of the ovarian tissue transcripts of Tibetan pigs and Yorkshire pigs were successfully constructed by the RNA-Seq technique. A total of 651 differentially expressed genes (DEGs) were screened, including 414 up-regulated genes and 237 down-regulated genes. Through GO and KEGG enrichment analysis, it was found that these differentially expressed genes were significantly enriched in cell process, reproductive process, reproduction, cell proliferation, binding, and catalytic activity, as well as oxidative phosphorylation, endocrine resistance, thyroid hormone, Notch, and other signal transduction pathways. Genes significantly enriched in pathways closely related to reproductive regulation were analyzed and selected, and the AR, CYP11A1, CYP17A1, INHBA, ARRB2, EGFR, ETS1, HSD17B1, IGF1R, MIF, SCARB1, and SMAD4 genes were identified as important candidate genes. Twelve differentially expressed genes related to reproduction were verified by RT-qPCR. The results showed that the expression of the AR, CYP17A1, EGFR, ETS1, IGF1R, and SMAD4 genes was significantly higher in Tibetan pigs than in Yorkshire pigs, while the expression of the CYP11A1, INHBA, ARRB2, HSD17B, MIF, and SCARB1 genes in Tibetan pigs was significantly lower than in Yorkshire pigs. The purpose of this study is to provide a theoretical basis for exploring the molecular mechanism of reproductive trait effect genes and the application of molecular breeding in Tibetan pigs. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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11 pages, 583 KiB  

Open AccessArticle

Machine Learning to Predict Pregnancy in Dairy Cows: An Approach Integrating Automated Activity Monitoring and On-Farm Data

by Thaisa Campos Marques, Letícia Ribeiro Marques, Patrick Bezerra Fernandes, Fabio Soares de Lima, Tiago do Prado Paim and Karen Martins Leão

Animals 2024, 14(11), 1567; https://doi.org/10.3390/ani14111567 - 25 May 2024

Cited by 3 | Viewed by 2381

Abstract

Automated activity monitoring (AAM) systems are critical in the dairy industry for detecting estrus and optimizing the timing of artificial insemination (AI), thus enhancing pregnancy success rates in cows. This study developed a predictive model to improve pregnancy success by integrating AAM data [...] Read more.

Automated activity monitoring (AAM) systems are critical in the dairy industry for detecting estrus and optimizing the timing of artificial insemination (AI), thus enhancing pregnancy success rates in cows. This study developed a predictive model to improve pregnancy success by integrating AAM data with cow-specific and environmental factors. Utilizing data from 1,054 cows, this study compared the pregnancy outcomes between two AI timings—8 or 10 h post-AAM alarm. Variables such as age, parity, body condition, locomotion, and vaginal discharge scores, peripartum diseases, the breeding program, the bull used for AI, milk production at the time of AI, and environmental conditions (season, relative humidity, and temperature–humidity index) were considered alongside the AAM data on rumination, activity, and estrus intensity. Six predictive models were assessed to determine their efficacy in predicting pregnancy success: logistic regression, Bagged AdaBoost algorithm, linear discriminant, random forest, support vector machine, and Bagged Classification Tree. Integrating the on-farm data with AAM significantly enhanced the pregnancy prediction accuracy at AI compared to using AAM data alone. The random forest models showed a superior performance, with the highest Kappa statistic and lowest false positive rates. The linear discriminant and logistic regression models demonstrated the best accuracy, minimal false negatives, and the highest area under the curve. These findings suggest that combining on-farm and AAM data can significantly improve reproductive management in the dairy industry. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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12 pages, 4483 KiB  

Open AccessArticle

Transcriptional Regulation Analysis Provides Insight into the Function of GSK3β Gene in Diannan Small-Ear Pig Spermatogenesis

by Xia Zhang, Guiying Zhao, Fuhua Yang, Changyao Li, Wan Lin, Hongmei Dai, Lan Zhai, Xuemin Xi, Qingting Yuan and Jinlong Huo

Genes 2024, 15(6), 655; https://doi.org/10.3390/genes15060655 - 22 May 2024

Viewed by 1685

Abstract

Glycogen synthase kinase-3β (GSK3β) not only plays a crucial role in regulating sperm maturation but also is pivotal in orchestrating the acrosome reaction. Here, we integrated single-molecule long-read and short-read sequencing to comprehensively examine GSK3β expression patterns in adult Diannan small-ear pig (DSE) [...] Read more.

Glycogen synthase kinase-3β (GSK3β) not only plays a crucial role in regulating sperm maturation but also is pivotal in orchestrating the acrosome reaction. Here, we integrated single-molecule long-read and short-read sequencing to comprehensively examine GSK3β expression patterns in adult Diannan small-ear pig (DSE) testes. We identified the most important transcript ENSSSCT00000039364 of GSK3β, obtaining its full-length coding sequence (CDS) spanning 1263 bp. Gene structure analysis located GSK3β on pig chromosome 13 with 12 exons. Protein structure analysis reflected that GSK3β consisted of 420 amino acids containing PKc-like conserved domains. Phylogenetic analysis underscored the evolutionary conservation and homology of GSK3β across different mammalian species. The evaluation of the protein interaction network, KEGG, and GO pathways implied that GSK3β interacted with 50 proteins, predominantly involved in the Wnt signaling pathway, papillomavirus infection, hippo signaling pathway, hepatocellular carcinoma, gastric cancer, colorectal cancer, breast cancer, endometrial cancer, basal cell carcinoma, and Alzheimer’s disease. Functional annotation identified that GSK3β was involved in thirteen GOs, including six molecular functions and seven biological processes. ceRNA network analysis suggested that DSE GSK3β was regulated by 11 miRNA targets. Furthermore, qPCR expression analysis across 15 tissues highlighted that GSK3β was highly expressed in the testis. Subcellular localization analysis indicated that the majority of the GSK3β protein was located in the cytoplasm of ST (swine testis) cells, with a small amount detected in the nucleus. Overall, our findings shed new light on GSK3β’s role in DSE reproduction, providing a foundation for further functional studies of GSK3β function. Full article

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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Open AccessArticle

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 1959

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

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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17 pages, 334 KiB  

Open AccessReview

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

Cited by 4 | Viewed by 6921

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

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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Open AccessArticle

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

Cited by 1 | Viewed by 1930

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

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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Open AccessArticle

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

Cited by 5 | Viewed by 1949

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

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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13 pages, 1632 KiB  

Open AccessArticle

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 2 | Viewed by 1790

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

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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12 pages, 494 KiB  

Open AccessArticle

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

Cited by 4 | Viewed by 2317

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

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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12 pages, 1728 KiB  

Open AccessArticle

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 1571

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

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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Open AccessArticle

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 4 | Viewed by 3064

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

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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12 pages, 2969 KiB  

Open AccessReview

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 10 | Viewed by 2949

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

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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Open AccessArticle

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

Cited by 4 | Viewed by 2497

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

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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Open AccessCommunication

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

Cited by 2 | Viewed by 2326

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

(This article belongs to the Topic Application of Reproductive and Genomic Biotechnologies for Livestock Breeding and Selection)

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