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Genetics and Genomics of Sheep and Goat
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Genetics and Genomics of Sheep and Goat

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

Deadline for manuscript submissions: closed (20 December 2024) | Viewed by 19288

Special Issue Editors

Dr. Yan Xiong

E-Mail Website
Guest Editor
1. Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China
2. Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu 610041, China
3. College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
Interests: sheep; goat; genetics; breeding; genome; genomics; gene regulation; agricultural traits; animal reproduction; muscle development; fat deposition
Prof. Dr. Yaqiu Lin

E-Mail Website
Guest Editor
1. Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu 610041, China
2. Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu 610041, China
3. College of Animal &Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
Interests: sheep; goat; genetics; breeding; genome; genomics; gene regulation; agricultural traits; muscle development; fat deposition

Special Issue Information

Dear Colleagues,

Sheep and goat species diverged about 4 million years ago, and were the earliest domesticated animals with economic and nutritional value. As a result of natural and artificial selection over a long period of time, there are now nearly 2,000 species of sheep and goats in the world. Before the 19th century, wool sales were the main income of the sheep industry. Since then, sheep or goat production has gradually changed from wool to both wool and meat, and then to meat, which resulted in changes in their breeding direction and a corresponding hybrid utilization system. Nevertheless, sheep and goats show their own characteristics in regard to reproductive rate, cashmere yield, meat yield, meat quality and other production performances, as well as different degrees of stimulation in their germplasm resources, providing excellent opportunities to explore the evolution and heredity of sheep and goats. In recent years, with the development of the sheep and goat genome, the most important questions related to the promotion of biological research and breeding of these important animals are highly relevant topics of inquiry; this includes the exploration of the genetic basis of important production traits in sheep and goats, and the functional anatomy of key genes.

To this end, this Special Issue invites research articles, reviews, and short communications that include, but are not limited to, the following: genetics analysis and improvements in breeding the important traits of sheep and goats, molecular function dissection, gene regulation mechanisms, gene family evolution, expression regulation networks, and other studies of sheep and goats using high-throughput data.

Dr. Yan Xiong
Prof. Dr. Yaqiu Lin
Guest Editors

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Keywords

  • goat
  • sheep
  • genetics
  • muscle development
  • fat deposition
  • regulatory
  • network
  • sequencing
  • function
  • co-expression
  • transcriptomics
  • physiological regulation of animal reproduction
  • mechanism
  • QTL
  • reproduction trait
  • cashmere production trait

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Published Papers (12 papers)

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Research

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11 pages, 1291 KiB  
Article
Accuracy of Genomic Predictions for Resistance to Gastrointestinal Parasites in Australian Merino Sheep
by Brenda Vera, Elly A. Navajas, Elize Van Lier, Beatriz Carracelas, Pablo Peraza and Gabriel Ciappesoni
Genes 2025, 16(2), 159; https://doi.org/10.3390/genes16020159 - 26 Jan 2025
Viewed by 1227
Abstract
Infection by gastrointestinal nematodes (GINs) in sheep is a significant health issue that affects animal welfare and leads to economic losses in the production sector. Genetic selection for parasite resistance has shown promise in improving animal health and productivity. This study aimed to [...] Read more.
Infection by gastrointestinal nematodes (GINs) in sheep is a significant health issue that affects animal welfare and leads to economic losses in the production sector. Genetic selection for parasite resistance has shown promise in improving animal health and productivity. This study aimed to determine if incorporating genomic data into genetic prediction models currently used in Uruguay could improve the accuracy of breeding value estimations for GIN resistance in the Australian Merino breed. This study compared the accuracy of breeding value predictions using the BLUP (Best Linear Unbiased Prediction) and ssGBLUP (single-step genomic BLUP) models on partial and complete data sets, including 32,713 phenotyped and 3238 genotyped animals. The quality of predictions was evaluated using a linear regression method, focusing on 145 rams. The inclusion of genomic data increased the average individual accuracies by 4% for genotyped and phenotyped animals. For animals with genomic and non-phenotyped data, the accuracy improvement reached 8%. Of these, one group of animals that benefited from an ssGBLUP evaluation came from a facility with a strong connection to the informative nucleus and showed an average increase of 20% in their individual accuracy. Additionally, ssGBLUP slightly outperformed BLUP in terms of prediction quality. These findings demonstrate the potential of genomic information to improve the accuracy of breeding value predictions for parasite resistance in sheep. The integration of genomic data, particularly in non-phenotyped animals, offers a promising tool for enhancing genetic selection in Australian Merino sheep to improve resistance to gastrointestinal parasites. Full article
(This article belongs to the Special Issue Genetics and Genomics of Sheep and Goat)
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17 pages, 2526 KiB  
Article
Genome-Wide Patterns of Homozygosity and Heterozygosity and Candidate Genes in Greek Insular and Mainland Native Goats
by Valentina Tsartsianidou, Antonis Otapasidis, Spiros Papakostas, Nikoleta Karaiskou, Sotiria Vouraki and Alexandros Triantafyllidis
Genes 2025, 16(1), 27; https://doi.org/10.3390/genes16010027 - 27 Dec 2024
Viewed by 1035
Abstract
Background: Runs of homozygosity (ROHs) and heterozygosity (ROHets) serve for the identification of genomic regions as candidates of selection, local adaptation, and population history. Methods: The present study aimed to comprehensively explore the ROH and ROHet patterns and hotspots in Greek native dairy [...] Read more.
Background: Runs of homozygosity (ROHs) and heterozygosity (ROHets) serve for the identification of genomic regions as candidates of selection, local adaptation, and population history. Methods: The present study aimed to comprehensively explore the ROH and ROHet patterns and hotspots in Greek native dairy goats, Eghoria and Skopelos, genotyped with the Illumina Goat SNP50 BeadChip. SNP and functional enrichment analyses were conducted to further characterize hotspots and the candidate genes located within these genomic regions. Genetic relationships between and within breeds and inbreeding coefficients were also evaluated. Results: Clear genetic differentiation and diversified management practices were depicted between the two native populations. The ROH and ROHet average genome coverage for Skopelos (65.35 and 35 Mb) and Eghoria (47.64 and 43 Mb) indicated differences in mainland and insular goats, with Skopelos showing more long ROH fragments, reflecting its geographic isolation and small population size. An ROH hotspot (CHR12: 43.59–44.61 Mb) detected in the Skopelos population has been also reported across European goats and co-localizes with a selection signal detected in the Egyptian Barki goats and sheep adapted to hot–arid conditions. A novel ROH hotspot (CHR18: 60.12–61.81 Mb), shared among the Greek breeds, harbors candidate genes enriched in biosynthesis, metabolism, and immune response. Two well-conserved ROHet islands were detected in Greek goats on chromosomes 1 and 18, with genes participating in development and embryogenesis. The Eghoria population showed the highest number of ROHet islands, potentially reflecting its adaptability to diverse environments. Conclusions: These findings offer new insights into the environmental adaptation and artificial selection in Greek goats and could be utilized in future breeding strategies for sustainable goat farming. Full article
(This article belongs to the Special Issue Genetics and Genomics of Sheep and Goat)
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14 pages, 15679 KiB  
Article
Transcriptome Analysis Reveals Sertoli Cells Adapting Through Redox and Metabolic Pathways Under Heat Stress in Goats
by Guang Yang, Yiwei Wang, Pengyun Ji, Bingyuan Wang and Guoshi Liu
Genes 2024, 15(12), 1582; https://doi.org/10.3390/genes15121582 - 9 Dec 2024
Viewed by 1072
Abstract
Background/Objectives: Climate change-induced temperature elevations pose significant challenges to livestock reproduction, particularly affecting testicular function in small ruminants. This study investigates the acute heat-stress response in goat Sertoli cells (SCs), aiming to elucidate the molecular mechanisms underlying heat-induced damage to male reproductive tissues. [...] Read more.
Background/Objectives: Climate change-induced temperature elevations pose significant challenges to livestock reproduction, particularly affecting testicular function in small ruminants. This study investigates the acute heat-stress response in goat Sertoli cells (SCs), aiming to elucidate the molecular mechanisms underlying heat-induced damage to male reproductive tissues. Methods: SCs were isolated from testes of 4-month-old black goats and exposed to heat stress (44 °C for 2.5 h). We employed transcriptome sequencing, CCK-8 assay, electron microscopy, ROS measurement, autophagy detection, Western blot analysis, and lactate concentration measurement. Bioinformatics analyses including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein–protein interaction network analyses were performed on the transcriptome data. Results: Heat stress significantly reduced SC viability, induced oxidative stress and autophagy, and altered gene expression profiles. We identified 1231 significantly differentially expressed genes, with significant enrichment in membrane-related processes and metabolic pathways. Metabolism-related genes, including PKLR, ACOT11, and LPCT12, were significantly downregulated. Protein–protein interaction network analysis revealed ten hub genes potentially crucial in the heat-stress response: HSP90AA1, HSPA5, BAG3, IGF1, HSPH1, IL1A, CCL2, CXCL10, ALB, and CALML4. Conclusions: This study provides comprehensive insights into the molecular mechanisms underlying goat SC response to heat stress. The identified genes and pathways, particularly those related to metabolism and stress response, offer potential targets for developing strategies to mitigate heat-stress effects on livestock reproduction. These findings contribute to our understanding of climate change impacts on animal husbandry and may inform the development of heat-stress resistant livestock lines. Full article
(This article belongs to the Special Issue Genetics and Genomics of Sheep and Goat)
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12 pages, 1022 KiB  
Article
Genome-Wide Association Studies Revealed Several Candidate Genes of Meat Productivity in Saryarka Fat-Tailed Coarse-Wool Sheep Breed
by Kairat Dossybayev, Makpal Amandykova, Ainur Orakbayeva, Sholpan Adylkanova, Altynay Kozhakhmet, Kanagat Yergali, Temirlan Kulboldin, Beibit Kulataev and Aibyn Torekhanov
Genes 2024, 15(12), 1549; https://doi.org/10.3390/genes15121549 - 29 Nov 2024
Viewed by 1136
Abstract
Background: Saryarka sheep belong to fat-tailed coarse-wool sheep breed. This breed is distinguished by increased meat productivity while being competitive in young lamb production. Live weight and body indices are relevant data for assessing sheep body constitution, which directly affects the breeding characteristics [...] Read more.
Background: Saryarka sheep belong to fat-tailed coarse-wool sheep breed. This breed is distinguished by increased meat productivity while being competitive in young lamb production. Live weight and body indices are relevant data for assessing sheep body constitution, which directly affects the breeding characteristics and meat productivity of animals. Objectives: This study aimed to find associations with SNPs and nine phenotypic characteristics of the Saryarka fat-tailed coarse-wool sheep breed including live weight and eight body indices (wither height, rump height, bicoastal diameter, body depth, body length, rump width, heart girth, and cannon bone circumference), and find candidate genes related to these characteristics. Methods: A total of 100 animals from the Karaganda region of Kazakhstan were used in this study. Live weight and eight body indices of sheep were measured using tape and electronic scales. The blood samples of the animals were used for DNA extraction. DNA samples were genotyped with the OvineSNP50 Genotyping BeadChip and analyzed using GWAS. Statistically significant SNPs were identified for each characteristic trait referencing the genome of Ovis aries (Oar_v3.1) using BioMart. Results: The GWAS results demonstrated a substantial chromosomal-level correlation between 32 chromosome-wide significant and suggestively significant SNPs in the studied sheep breed. Overall, seven SNPs located in seven different genes were revealed as candidates for live weight and four body indices: s20793.1 SNP in the IGFBP6 gene for live weight, OAR4_54217431.1 SNP in the ST7 gene for bicoastal diameter, s25229.1 in the SCD5 gene, and s01175.1 SNP in the DTNBP1 gene for rump width, OAR2_175574781.1 SNP in the KYNU gene for heart girth, and OAR1_209022621.1 SNP in the FGF12 gene and s15415.1 SNP in the FTO gene for cannon bone circumference. Some of these genes were previously reported to be involved in body constitution and fat deposit in other sheep breeds. Conclusions: The results of the present study open up new opportunities for targeted sheep breeding for meat and fat productivity. Full article
(This article belongs to the Special Issue Genetics and Genomics of Sheep and Goat)
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10 pages, 2514 KiB  
Article
Potential Involvement of miR-144 in the Regulation of Hair Follicle Development and Cycle Through Interaction with Lhx2
by Guangxian Zhou, Xiaolong Wang, Yulin Chen and Danju Kang
Genes 2024, 15(11), 1454; https://doi.org/10.3390/genes15111454 - 11 Nov 2024
Cited by 1 | Viewed by 1190
Abstract
Background: Cashmere, known as “soft gold”, is a highly prized fiber from Cashmere goats, produced by secondary hair follicles. Dermal papilla cells, located at the base of these follicles, regulate the proliferation and differentiation of hair matrix cells, which are essential for hair [...] Read more.
Background: Cashmere, known as “soft gold”, is a highly prized fiber from Cashmere goats, produced by secondary hair follicles. Dermal papilla cells, located at the base of these follicles, regulate the proliferation and differentiation of hair matrix cells, which are essential for hair growth and cashmere formation. Recent studies emphasize the role of microRNAs (miRNAs) in controlling gene expression within these processes. Methods: This study centered on exploring the targeted regulatory interaction between miR-144 and the Lhx2 gene. Utilizing methodologies like miRNA target prediction, luciferase reporter assays, and quantitative PCR, they assessed the interplay between miR-144 and Lhx2. Dermal papilla cells derived from Cashmere goats were cultured and transfected with either miR-144 mimics or inhibitors to observe the subsequent effects on Lhx2 expression. Results: The results demonstrated that miR-144 directly targets the Lhx2 gene by binding to its mRNA, leading to a decrease in Lhx2 expression. This modulation of Lhx2 levels influenced the behavior of dermal papilla cells, affecting their ability to regulate hair matrix cell proliferation and differentiation. Consequently, the manipulation of miR-144 levels had a significant impact on the growth cycle of cashmere wool. Conclusions: The findings suggest miR-144 regulates hair follicle dynamics by targeting Lhx2, offering insights into hair growth mechanisms. This could lead to innovations in enhancing cashmere production, fleece quality, and addressing hair growth disorders. Future research may focus on adjusting miR-144 levels to optimize Lhx2 expression and promote hair follicle activity. Full article
(This article belongs to the Special Issue Genetics and Genomics of Sheep and Goat)
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22 pages, 3101 KiB  
Article
Characterization of the Hepatic Transcriptome for Divergent Immune-Responding Sheep Following Natural Exposure to Gastrointestinal Nematodes
by Olivia Willoughby, Niel A. Karrow, Samla Marques Freire Cunha, Victoria Asselstine, Bonnie A. Mallard and Ángela Cánovas
Genes 2024, 15(6), 713; https://doi.org/10.3390/genes15060713 - 30 May 2024
Viewed by 1291
Abstract
Infections with gastrointestinal nematodes (GINs) reduce the economic efficiency of sheep operations and compromise animal welfare. Understanding the host’s response to GIN infection can help producers identify animals that are naturally resistant to infection. The objective of this study was to characterize the [...] Read more.
Infections with gastrointestinal nematodes (GINs) reduce the economic efficiency of sheep operations and compromise animal welfare. Understanding the host’s response to GIN infection can help producers identify animals that are naturally resistant to infection. The objective of this study was to characterize the hepatic transcriptome of sheep that had been naturally exposed to GIN parasites. The hepatic transcriptome was studied using RNA-Sequencing technology in animals characterized as high (n = 5) or medium (n = 6) based on their innate immune acute-phase (AP) response phenotype compared with uninfected controls (n = 4), and with biased antibody-mediated (AbMR, n = 5) or cell-mediated (CMR, n = 5) adaptive immune responsiveness compared to uninfected controls (n = 3). Following the assessment of sheep selected for innate responses, 0, 136, and 167 genes were differentially expressed (DE) between high- and medium-responding animals, high-responding and uninfected control animals, and medium-responding and uninfected control animals, respectively (false discovery rate (FDR) < 0.05, and fold change |FC| > 2). When adaptive immune responses were assessed, 0, 53, and 57 genes were DE between antibody- and cell-biased animals, antibody-biased and uninfected control animals, and cell-biased and uninfected control animals, respectively (FDR < 0.05, |FC| > 2). Functional analyses identified enriched gene ontology (GO) terms and metabolic pathways related to the innate immune response and energy metabolism. Six functional candidate genes were identified for further functional and validation studies to better understand the underlying biological mechanisms of host responses to GINs. These, in turn, can potentially help improve decision making and management practices to increase the overall host immune response to GIN infection. Full article
(This article belongs to the Special Issue Genetics and Genomics of Sheep and Goat)
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10 pages, 235 KiB  
Article
Fitting of Growth Curves and Estimation of Genetic Relationship between Growth Parameters of Qianhua Mutton Merino
by Jiarong Li, Xuesong Shan, Yang Chen, Chongshun Xu, Lin Tang and Huaizhi Jiang
Genes 2024, 15(3), 390; https://doi.org/10.3390/genes15030390 - 21 Mar 2024
Cited by 2 | Viewed by 1470
Abstract
Qianhua Mutton Merino is a dual-purpose (meat and wool) breed of sheep that has been newly developed in China. In this study, we assessed the growth and development of the Qianhua Mutton Merino sheep breed under house feeding conditions by measuring the body [...] Read more.
Qianhua Mutton Merino is a dual-purpose (meat and wool) breed of sheep that has been newly developed in China. In this study, we assessed the growth and development of the Qianhua Mutton Merino sheep breed under house feeding conditions by measuring the body weight and chest circumference of 2300 rams and ewes of this breed aged 0–24 months. Based on the fitting results of three nonlinear growth models, namely Logistic, Gompertz, and von Bertalanffy, in Qianhua Mutton Merino, we selected the von Bertalanffy model because of its highest fitting degree among all models (R2 > 0.977). The significant analysis of the combined fixation of each sheep body’s weight and bust took place (A: mature body weight, B: adjustment parameter, K: instant relative growth rate). The results revealed that parameters A, B, and K of body weight and chest circumference have high heritability and thus could be used as target traits for genetic improvement. Moreover, the correlation strength among A, B, and K suggested that these parameters can be used as a reference to adjust the genetic parameters in the growth model to genetically improve the body size of Qianhua Mutton Merino during breeding. Full article
(This article belongs to the Special Issue Genetics and Genomics of Sheep and Goat)
17 pages, 4861 KiB  
Article
Goat miR-92a-3p Targets APOL6 Gene to Regulate the Differentiation of Intramuscular Precursor Adipocytes
by Wuqie Qubi, Jianying Zheng, Youli Wang, Guishan Xu, Yanyan Li, Yan Xiong, Yong Wang, Wei Liu and Yaqiu Lin
Genes 2024, 15(1), 57; https://doi.org/10.3390/genes15010057 - 30 Dec 2023
Cited by 1 | Viewed by 1660
Abstract
The quality of lamb meat is positively correlated with intramuscular fat content. In recent years, a large number of studies have shown that miRNAs play an important role in the proliferation and differentiation of adipocytes. In this study, we aimed to explore the [...] Read more.
The quality of lamb meat is positively correlated with intramuscular fat content. In recent years, a large number of studies have shown that miRNAs play an important role in the proliferation and differentiation of adipocytes. In this study, we aimed to explore the effect of miR-92a-3p on the differentiation of goat intramuscular preadipocytes. The results showed that the expression level of miR-92a-3p was low in the early stage of differentiation, reached the highest level on the third day of differentiation, and then decreased. And miR-92a-3p can inhibit the accumulation of lipid droplets and down-regulate the determinants of adipogenic differentiation. Mechanistically, by predicting target genes, we found that miR-92a-3p affects the differentiation of goat intramuscular preadipocytes and the accumulation of lipid droplets by regulating the expression of goat gene APOL6. This study provides important new information to better understand the relationship between miRNAs and the differentiation of goat intramuscular preadipocytes, thus providing a new reference for goat intramuscular adipogenesis. Full article
(This article belongs to the Special Issue Genetics and Genomics of Sheep and Goat)
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14 pages, 3345 KiB  
Article
FOS Inhibits the Differentiation of Intramuscular Adipocytes in Goats
by Tingting Hu, Zhibin Li, Chengsi Gong, Yan Xiong, Shiyu Sun, Jiani Xing, Yanyan Li, Ruiwen Li, Youli Wang, Yong Wang and Yaqiu Lin
Genes 2023, 14(11), 2088; https://doi.org/10.3390/genes14112088 - 17 Nov 2023
Cited by 2 | Viewed by 1636
Abstract
Goat intramuscular fat (IMF) deposition is precisely regulated by many key genes as well as transcription factors. Nevertheless, the potential of the regulators of goat IMF deposition remains undefined. In this work, we reported that the transcription factor FOS is expressed at a [...] Read more.
Goat intramuscular fat (IMF) deposition is precisely regulated by many key genes as well as transcription factors. Nevertheless, the potential of the regulators of goat IMF deposition remains undefined. In this work, we reported that the transcription factor FOS is expressed at a low level at the early differentiation stage and at a high level in late differentiation. The overexpression of FOS inhibited intramuscular adipocyte lipid accumulation and significantly downregulated the expressions of PPARγ, C/EBPβ, C/EBPα, AP2, SREBP1, FASN, ACC, HSL, and ATGL. Consistently, the knockdown of FOS, facilitated by two distinct siRNAs, significantly promoted intramuscular adipocyte lipid accumulation. Moreover, our analysis revealed multiple potential binding sites for FOS on the promoters of PPARγ, C/EBPβ, and C/EBPα. The expression changes in PPARγ, C/EBPβ, and C/EBPα during intramuscular adipogenesis were opposite to that of FOS. In summary, FOS inhibits intramuscular lipogenesis in goats and potentially negatively regulates the expressions of PPARγ, C/EBPβ, and C/EBPα genes. Our research will provide valuable data for the underlying molecular mechanism of the FOS regulation network of intramuscular lipogenesis. Full article
(This article belongs to the Special Issue Genetics and Genomics of Sheep and Goat)
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16 pages, 5183 KiB  
Article
Integrated Transcriptome Analysis of miRNAs and mRNAs in the Skeletal Muscle of Wuranke Sheep
by Yueying Yun, Rihan Wu, Xige He, Xia Qin, Lu Chen, Lina Sha, Xueyan Yun, Tadayuki Nishiumi and Gerelt Borjigin
Genes 2023, 14(11), 2034; https://doi.org/10.3390/genes14112034 - 31 Oct 2023
Cited by 3 | Viewed by 1989
Abstract
MicroRNAs (miRNAs) are regarded as important regulators in skeletal muscle development. To reveal the regulatory roles of miRNAs and their target mRNAs underlying the skeletal muscle development of Wuranke sheep, we investigated the miRNA and mRNA expression profiles in the biceps femoris [...] Read more.
MicroRNAs (miRNAs) are regarded as important regulators in skeletal muscle development. To reveal the regulatory roles of miRNAs and their target mRNAs underlying the skeletal muscle development of Wuranke sheep, we investigated the miRNA and mRNA expression profiles in the biceps femoris of these sheep at the fetal (3 months of gestation) and 3- and 15-month-old postnatal stages. Consequently, a total of 1195 miRNAs and 24,959 genes were identified. Furthermore, 474, 461, and 54 differentially expressed miRNAs (DEMs) and 6783, 7407, and 78 differentially expressed genes (DEGs) were detected among three comparative groups. Functional analysis demonstrated that the target mRNAs of the DEMs were enriched in multiple pathways related to muscle development. Moreover, the interactions among several predicted miRNA–mRNA pairs (oar-miR-133-HDAC1, oar-miR-1185-5p-MYH1/HADHA/OXCT1, and PC-5p-3703_578-INSR/ACTG1) that potentially affect skeletal muscle development were verified using dual-luciferase reporter assays. In this study, we identified the miRNA and mRNA differences in the skeletal muscle of Wuranke sheep at different developmental stages and revealed that a series of candidate miRNA–mRNA pairs may act as modulators of muscle development. These results will contribute to future studies on the function of miRNAs and their target mRNAs during skeletal muscle development in Wuranke sheep. Full article
(This article belongs to the Special Issue Genetics and Genomics of Sheep and Goat)
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Review

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17 pages, 822 KiB  
Review
Research Progress on Genomic Regions and Candidate Genes Related to Milk Composition Traits of Dairy Goats Based on Functional Genomics: A Narrative Review
by Xu Yang, Qing Li, Yanyan Wang, Jianmin Wang, Jiaqing Hu, Zhibin Ji and Tianle Chao
Genes 2024, 15(10), 1341; https://doi.org/10.3390/genes15101341 - 19 Oct 2024
Viewed by 1681
Abstract
Background: Goat milk has gained global attention for its unique nutritional properties and potential health benefits. Advancements in functional genomic technologies have significantly progressed genetic research on milk composition traits in dairy goats. Results: This review summarizes various research methodologies applied in this [...] Read more.
Background: Goat milk has gained global attention for its unique nutritional properties and potential health benefits. Advancements in functional genomic technologies have significantly progressed genetic research on milk composition traits in dairy goats. Results: This review summarizes various research methodologies applied in this field. Genome-wide association studies (GWAS) have identified genomic regions associated with major milk components, with the diacylglycerol acyltransferase 1 (DGAT1) gene and casein gene cluster consistently linked to milk composition traits. Transcriptomics has revealed gene expression patterns in mammary tissue across lactation stages, while the role of non-coding RNAs (such as miRNAs and circRNAs) in regulating milk composition has been confirmed. Proteomic and metabolomic studies have not only helped us gain a more comprehensive understanding of goat milk composition characteristics but have also provided crucial support for the functional validation of genes related to milk components. The integration of multi-omics data has emerged as an effective strategy for elucidating complex regulatory networks from a systems biology perspective. Conclusions: Despite progress, challenges remain, including refining reference genomes, collecting large-scale phenotypic data, and conducting functional validations. Future research should focus on improving reference genomes, expanding study populations, investigating functional milk components, exploring epigenetic regulation and non-coding RNAs, and studying microbiome–host genome interactions. These efforts will inform more precise genomic and marker-assisted selection strategies, advancing genetic improvements in milk composition traits in dairy goats. Full article
(This article belongs to the Special Issue Genetics and Genomics of Sheep and Goat)
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35 pages, 1318 KiB  
Review
Genomic Regions Associated with Resistance to Gastrointestinal Nematode Parasites in Sheep—A Review
by Samla Marques Freire Cunha, Stephanie Lam, Bonnie Mallard, Niel A. Karrow and Ángela Cánovas
Genes 2024, 15(2), 187; https://doi.org/10.3390/genes15020187 - 30 Jan 2024
Cited by 4 | Viewed by 2558
Abstract
Gastrointestinal nematodes (GINs) can be a major constraint and global challenge to the sheep industry. These nematodes infect the small intestine and abomasum of grazing sheep, causing symptoms such as weight loss, diarrhea, hypoproteinemia, and anemia, which can lead to death. The use [...] Read more.
Gastrointestinal nematodes (GINs) can be a major constraint and global challenge to the sheep industry. These nematodes infect the small intestine and abomasum of grazing sheep, causing symptoms such as weight loss, diarrhea, hypoproteinemia, and anemia, which can lead to death. The use of anthelmintics to treat infected animals has led to GIN resistance, and excessive use of these drugs has resulted in residue traced in food and the environment. Resistance to GINs can be measured using multiple traits, including fecal egg count (FEC), Faffa Malan Chart scores, hematocrit, packed cell volume, eosinophilia, immunoglobulin (Ig), and dagginess scores. Genetic variation among animals exists, and understanding these differences can help identify genomic regions associated with resistance to GINs in sheep. Genes playing important roles in the immune system were identified in several studies in this review, such as the CFI and MUC15 genes. Results from several studies showed overlapping quantitative trait loci (QTLs) associated with multiple traits measuring resistance to GINs, mainly FEC. The discovery of genomic regions, positional candidate genes, and QTLs associated with resistance to GINs can help increase and accelerate genetic gains in sheep breeding programs and reveal the genetic basis and biological mechanisms underlying this trait. Full article
(This article belongs to the Special Issue Genetics and Genomics of Sheep and Goat)
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