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Genetic Regulation and Molecular Phylogeny in Goat and Sheep Breeding
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Genetic Regulation and Molecular Phylogeny in Goat and Sheep Breeding

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

Deadline for manuscript submissions: closed (25 October 2023) | Viewed by 8344

Special Issue Editor

Prof. Dr. Linjie Wang

E-Mail Website
Guest Editor
College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
Interests: molecular and cellular basis of some important economic traits of sheep and goats; identify the functional genes and regulatory elements for the meat quality, muscle development and adipose deposition in sheep and goats

Special Issue Information

Dear Colleagues,

This Special Issue is focused on the recent advances in goat and sheep molecular genetics and breeding. This includes analysis of the molecular regulatory mechanisms and molecular genetic basis for economically important traits (including but not limited to growth, reproduction, milk, wool, and disease resistance, etc.). Submissions describing genetic analysis of complex production traits using multiomics approaches (for GWAS, epigenomics, transcriptomics, proteomics, and metabolomics) to identify genetic mechanisms underlying important and complex traits are encouraged. With the help of your contribution, we hope to provide a better theoretical basis for the genetic breeding of goats and sheep.

Prof. Dr. Linjie Wang
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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

  • goats
  • sheep
  • breeding
  • traits
  • GWAS
  • multi-omics
  • epigenome
  • transcriptome

Published Papers (6 papers)

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Research

14 pages, 1041 KiB  
Article
Identification of Key Functional Genes and LncRNAs Influencing Muscle Growth and Development in Leizhou Black Goats
by Xiuhui Zhao, Junning Ye, Xunkai Lin, Huiwen Xue, Xian Zou, Guangbin Liu, Ming Deng, Baoli Sun, Yongqing Guo, Dewu Liu and Yaokun Li
Genes 2023, 14(4), 881; https://doi.org/10.3390/genes14040881 - 08 Apr 2023
Cited by 1 | Viewed by 1202
Abstract
Meat yield and quality are important economic traits of livestock. Herein, longissimus dorsi (LD) muscles of Leizhou black goats aged 0, 3, and 6 months were used to identify differentially expressed messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) by high-throughput RNA sequencing. [...] Read more.
Meat yield and quality are important economic traits of livestock. Herein, longissimus dorsi (LD) muscles of Leizhou black goats aged 0, 3, and 6 months were used to identify differentially expressed messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) by high-throughput RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to analyze differentially expressed genes. Expression levels of regulator of calcineurin 1 (RCAN1) and olfactory receptor 2AP1 (OR2AP1) were significantly different in LD muscles of goats aged 0, 3, and 6 months, indicating potentially important roles in postnatal muscle development. Differentially expressed lncRNAs and mRNAs were mainly enriched in biological processes and pathways related to cellular energy metabolism, consistent with previous studies. Three lncRNAs, TCONS_00074191, TCONS_00074190, and TCONS_00078361, may play a cis-acting role with methyltransferase-like 11B (METTL11B) genes and participate in the methylation of goat muscle proteins. Some of the identified genes may provide valuable resources for future studies on postnatal meat development in goat muscles. Full article
(This article belongs to the Special Issue Genetic Regulation and Molecular Phylogeny in Goat and Sheep Breeding)
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12 pages, 2448 KiB  
Article
A Novel LncRNA MSTRG.310246.1 Promotes Differentiation and Thermogenesis in Goat Brown Adipocytes
by Jing Tang, Xin Liu, Duo Su, Tingting Jiang, Siyuan Zhan, Tao Zhong, Jiazhong Guo, Jiaxue Cao, Li Li, Hongping Zhang and Linjie Wang
Genes 2023, 14(4), 833; https://doi.org/10.3390/genes14040833 - 30 Mar 2023
Cited by 1 | Viewed by 1177
Abstract
Brown adipose tissue (BAT) plays a critical role in maintaining the body temperature in newborn lamb due to its unique non-shivering thermogenesis. Previous studies have found that BAT thermogenesis is regulated by several long non-coding RNAs (lncRNAs). Here, we identified a novel lncRNA, [...] Read more.
Brown adipose tissue (BAT) plays a critical role in maintaining the body temperature in newborn lamb due to its unique non-shivering thermogenesis. Previous studies have found that BAT thermogenesis is regulated by several long non-coding RNAs (lncRNAs). Here, we identified a novel lncRNA, MSTRG.310246.1, which was enriched in BAT. MSTRG.310246.1 was localized in both the nuclear and cytoplasmic compartments. In addition, MSTRG.310246.1 expression was upregulated during brown adipocyte differentiation. Overexpression of MSTRG.310246.1 increased the differentiation and thermogenesis of goat brown adipocytes. On the contrary, the knockdown of MSTRG.310246.1 inhibited the differentiation and thermogenesis of goat brown adipocytes. However, MSTRG.310246.1 had no effect on goat white adipocyte differentiation and thermogenesis. Our results show that MSTRG.310246.1 is a BAT-enriched LncRNA that improves the differentiation and thermogenesis of goat brown adipocytes. Full article
(This article belongs to the Special Issue Genetic Regulation and Molecular Phylogeny in Goat and Sheep Breeding)
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13 pages, 2139 KiB  
Article
RNA-Seq Reveals the Roles of Long Non-Coding RNAs (lncRNAs) in Cashmere Fiber Production Performance of Cashmere Goats in China
by Xinmiao Wu, Yuanhua Gu, Shiqiang Li, Shiwei Guo, Jiqing Wang, Yuzhu Luo, Jiang Hu, Xiu Liu, Shaobin Li, Zhiyun Hao, Mingna Li and Bingang Shi
Genes 2023, 14(2), 384; https://doi.org/10.3390/genes14020384 - 01 Feb 2023
Cited by 2 | Viewed by 1286
Abstract
Long non-coding RNAs (lncRNAs) are a kind of non-coding RNA being >200 nucleotides in length, and they are found to participate in hair follicle growth and development and wool fiber traits regulation. However, there are limited studies reporting the role of lncRNAs in [...] Read more.
Long non-coding RNAs (lncRNAs) are a kind of non-coding RNA being >200 nucleotides in length, and they are found to participate in hair follicle growth and development and wool fiber traits regulation. However, there are limited studies reporting the role of lncRNAs in cashmere fiber production in cashmere goats. In this study, Liaoning cashmere (LC) goats (n = 6) and Ziwuling black (ZB) goats (n = 6) with remarkable divergences in cashmere yield, cashmere fiber diameter, and cashmere color were selected for the construction of expression profiles of lncRNAs in skin tissue using RNA sequencing (RNA-seq). According to our previous report about the expression profiles of mRNAs originated from the same skin tissue as those used in the study, the cis and trans target genes of differentially expressed lncRNAs between the two caprine breeds were screened, resulting in a lncRNA–mRNA network. A total of 129 lncRNAs were differentially expressed in caprine skin tissue samples between LC goats and ZB goats. The presence of 2 cis target genes and 48 trans target genes for the differentially expressed lncRNAs resulted in 2 lncRNA-cis target gene pairs and 93 lncRNA-trans target gene pairs. The target genes concentrated on signaling pathways that were related to fiber follicle development, cashmere fiber diameter, and cashmere fiber color, including PPAR signaling pathway, metabolic pathways, fatty acid metabolism, fatty acid biosynthesis, tyrosine metabolism, and melanogenesis. A lncRNA–mRNA network revealed 22 lncRNA-trans target gene pairs for seven differentially expressed lncRNAs selected, of which 13 trans target genes contributed to regulation of cashmere fiber diameter, while nine trans target genes were responsible for cashmere fiber color. This study brings a clear explanation about the influences of lncRNAs over cashmere fiber traits in cashmere goats. Full article
(This article belongs to the Special Issue Genetic Regulation and Molecular Phylogeny in Goat and Sheep Breeding)
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15 pages, 2489 KiB  
Article
Identification and Characterization of Circular RNAs (circRNAs) Using RNA-Seq in Two Breeds of Cashmere Goats
by Liyan Hu, Jiqing Wang, Yuzhu Luo, Xiu Liu, Shaobin Li, Zhiyun Hao, Fangfang Zhao, Mingna Li, Bingang Shi and Yuanhua Gu
Genes 2023, 14(2), 331; https://doi.org/10.3390/genes14020331 - 27 Jan 2023
Cited by 1 | Viewed by 1198
Abstract
Circular RNA (circRNA) is a type of non-coding RNA generated from back-splicing the reactions of linear RNA. It plays an important role in various cellular and biological processes. However, there are few studies about the regulatory effect of circRNAs on cashmere fiber traits [...] Read more.
Circular RNA (circRNA) is a type of non-coding RNA generated from back-splicing the reactions of linear RNA. It plays an important role in various cellular and biological processes. However, there are few studies about the regulatory effect of circRNAs on cashmere fiber traits in cashmere goats. In this study, the expression profiles of circRNAs in skin tissue were compared between Liaoning cashmere (LC) goats and Ziwuling black (ZB) goats, with a significant difference in cashmere fiber yield, cashmere fiber diameter, and cashmere fiber color, using RNA-seq. A total of 11,613 circRNAs were expressed in the caprine skin tissue, and their type, chromosomal distribution, and length distribution were characterized. A total of 115 up-regulated circRNAs and 146 down-regulated circRNAs in LC goats were screened compared to ZB goats. The authenticity of 10 differentially expressed circRNAs was validated by detecting their expression levels and the head-to-tail splice junction using RT-PCR and DNA sequencing, respectively. The parent genes of differentially expressed circRNA were mainly enriched in some Gene Ontology (GO) terms and pathways related to cashmere fiber traits, such as the canonical Wnt signaling pathway, which is involved in the regulation of cell promotion, stem cell proliferation, Wnt signaling pathway regulation, epithelial morphogenesis, MAPK signaling pathway, and cell adhesion molecules pathway. Eight differentially expressed circRNAs were further selected to construct a circRNA-miRNA network, and some miRNAs that were previously reported as related to fiber traits were found in the network. This study provides a deep understanding of the roles of circRNAs in the regulation of cashmere fiber traits in cashmere goats and the involvement of differential splicing in phenotypic expression according to breed and region. Full article
(This article belongs to the Special Issue Genetic Regulation and Molecular Phylogeny in Goat and Sheep Breeding)
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13 pages, 1180 KiB  
Article
Impact of FecB Mutation on Ovarian DNA Methylome in Small-Tail Han Sheep
by Lingli Xie, Xiangyang Miao, Qingmiao Luo, Huijing Zhao and Xiaoyu Qin
Genes 2023, 14(1), 203; https://doi.org/10.3390/genes14010203 - 12 Jan 2023
Cited by 2 | Viewed by 1343
Abstract
Booroola fecundity (FecB) gene, a mutant of bone morphogenetic protein 1B (BMPR-1B) that was discovered in Booroola Merino, was the first prolificacy gene identified in sheep related to increased ovulation rate and litter size. The mechanism of FecB impact on reproduction is unclear. [...] Read more.
Booroola fecundity (FecB) gene, a mutant of bone morphogenetic protein 1B (BMPR-1B) that was discovered in Booroola Merino, was the first prolificacy gene identified in sheep related to increased ovulation rate and litter size. The mechanism of FecB impact on reproduction is unclear. Methods: In this study, adult Han ewes with homozygous FecB(B)/FecB(B) mutations (Han BB group) and ewes with FecB(+)/FecB(+) wildtype (Han ++ group) were selected. Methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) was used to identify differences in methylated genes in ovary tissue. Results: We examined differences in DNA methylation patterns between HanBB and Han ++ sheep. In both sheep, methylated reads were mainly distributed at the gene body regions, CpG islands and introns. The differentially methylated genes were enriched in neurotrophy in signaling pathway, Gonadotropin Releasing Hormone (GnRH) signaling pathway, Wnt signaling pathway, oocyte meiosis, vascular endothelial growth factor (VEGF) signaling pathway, etc. Differentially-methylated genes were co-analyzed with differentially-expressed mRNAs. Several genes which could be associated with female reproduction were identified, such as FOXP3 (forkhead box P3), TMEFF2 (Transmembrane Protein with EGF Like and Two Follistatin Like Domains 2) and ADAT2 (Adenosine Deaminase TRNA Specific 2). Conclusions: We constructed a MeDIP-seq based methylomic study to investigate the ovarian DNA methylation differences between Small-Tail Han sheep with homozygous FecB mutant and wildtype, and successfully identified FecB gene-associated differentially-methylated genes. This study has provided information with which to understand the mechanisms of FecB gene-induced hyperprolificacy in sheep. Full article
(This article belongs to the Special Issue Genetic Regulation and Molecular Phylogeny in Goat and Sheep Breeding)
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13 pages, 3685 KiB  
Article
Lef1 and Dlx3 May Facilitate the Maturation of Secondary Hair Follicles in the Skin of Gansu Alpine Merino
by Hongxian Sun, Zhaohua He, Qiming Xi, Fangfang Zhao, Jiang Hu, Jiqing Wang, Xiu Liu, Zhidong Zhao, Mingna Li, Yuzhu Luo and Shaobin Li
Genes 2022, 13(8), 1326; https://doi.org/10.3390/genes13081326 - 25 Jul 2022
Cited by 8 | Viewed by 1585
Abstract
Lymphatic enhancer factor 1 (Lef1) and distal-less homeobox 3 (Dlx3) are the transcription factors involved in regulating hair follicle development in mice, goats, and other animals. Their deletion can lead to hair follicle deficiency. In this study, hematoxylin–eosin staining [...] Read more.
Lymphatic enhancer factor 1 (Lef1) and distal-less homeobox 3 (Dlx3) are the transcription factors involved in regulating hair follicle development in mice, goats, and other animals. Their deletion can lead to hair follicle deficiency. In this study, hematoxylin–eosin staining (HE), real-time quantitative PCR (RT-qPCR), immunohistochemistry, and immunofluorescence were used to analyze the expression, location, and biological functions of Lef1 and Dlx3 in the lateral skin of Gansu Alpine Merino aged 1, 30, 60, and 90 days. The results revealed that the number of hair follicles decreased with age and was significantly higher at 1 day than in the other three age groups (p < 0.05). The mRNA levels of Lef1 and Dlx3 in the skin of 30-day old Gansu Alpine Merino were significantly higher than those in the other three age groups (p < 0.05). Protein expression of Lef1 and Dlx3 was lowest at 1 day (p < 0.05) and peaked at 60 days. Lef1 and Dlx3 exhibited a high density and strong positive expression in the dermal papillae; additionally, Dlx3 exhibited a high density and strong positive expression in the inner and outer root sheaths. Collectively, Lef1 and Dlx3 may facilitate the maturation of secondary hair follicles, which is mainly achieved through the dermal papillae and inner and outer root sheaths. Full article
(This article belongs to the Special Issue Genetic Regulation and Molecular Phylogeny in Goat and Sheep Breeding)
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