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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: 20 December 2024 | Viewed by 11390

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

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

 

Keywords

  • 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 (9 papers)

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Research

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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 314
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
Viewed by 615
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 969
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
Viewed by 1119
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
Viewed by 1350
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 1 | Viewed by 1314
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 1 | Viewed by 1638
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 952
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 3 | Viewed by 2088
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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