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Liu J, Feng G, Guo C, Li Z, Liu D, Liu G, Zou X, Sun B, Guo Y, Deng M, Li Y. Identification of functional circRNAs regulating ovarian follicle development in goats. BMC Genomics 2024; 25:893. [PMID: 39342142 PMCID: PMC11439210 DOI: 10.1186/s12864-024-10834-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 09/25/2024] [Indexed: 10/01/2024] Open
Abstract
BARKGROUND Circular RNAs (circRNAs) play important regulatory roles in a variety of biological processes in mammals. Multiple birth-traits in goats are affected by several factors, but the expression and function of circRNAs in follicular development of goats are not clear. In this study, we aimed to investigate the possible regulatory mechanisms of circRNA and collected five groups of large follicles (Follicle diameter > 6 mm) and small follicles (1 mm < Follicle diameter < 3 mm) from Leizhou goats in estrus for RNA sequencing. RESULTS RNA sequencing showed that 152 circRNAs were differentially expressed in small and large follicles. Among them, 101 circRNAs were up-regulated in large follicles and 51 circRNAs were up-regulated in small follicles. GO and KEGG enrichment analyses showed that parental genes of the differential circRNAs were significantly enriched in important pathways, such as ovarian steroidogenesis, GnRH signaling pathway, animal autophagy and oxytocin signalling pathway. BioSignal analysis revealed that 152 differentially expressed circRNAs could target 91 differential miRNAs including miR-101 family (chi-miR-101-3p, chi-miR-101-5p), miR-202 family (chi-miR-202-5p, chi-miR-202-3p),60 circRNAs with translation potential. Based on the predicted sequencing results, the ceRNA networks chicirc_008762/chi-miR-338-3p/ARHGAP18 and chicirc_040444/chi-miR-338-3p/STAR were constructed in this study. Importantly, the new gene circCFAP20DC was first discovered in goats. The EDU assay and flow cytometry results indicated that circCFAP20DC enhanced the proliferation of follicular granulosa cells(GCs). Real-time quantitative PCR and western blotting assays showed that circCFAP20DC activated the Retinoblastoma(RB) pathway and promoted the progression of granulosa cells from G1 to S phase. CONCLUSION Differential circRNAs in goat size follicles may have important biological functions for follicular development. The novel gene circCFAP20DC activates the RB pathway, promoting the progression of GCs from G1 to S phase. This, in turn, enhances the proliferation of follicular GCs in goats.
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Affiliation(s)
- Jie Liu
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Guanghang Feng
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Conghui Guo
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Zhihan Li
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Dewu Liu
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Guangbin Liu
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Xian Zou
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Baoli Sun
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Yongqing Guo
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Ming Deng
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Yaokun Li
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.
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Cui W, Wang H, Li J, Lv D, Xu J, Liu M, Yin G. Sheep litter size heredity basis using genome-wide selective analysis. Reprod Domest Anim 2024; 59:e14689. [PMID: 39044628 DOI: 10.1111/rda.14689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/19/2024] [Accepted: 07/12/2024] [Indexed: 07/25/2024]
Abstract
Sheep are important herbivorous domestic animal globally, and the Chinese indigenous sheep breed has a multitude of economically significant variations due to the diverse geographical and ecological conditions. In particular, certain native breeds exhibit a visible high litter size phenotype due to the selection pressure of natural and artificial for thousands of years, offering an ideal animal model for investigating sheep's fecundity. In this study, selective signal analysis was performed on public whole-genome sequencing data from 60 sheep across eight breeds to identify candidate genes related to litter size. Results revealed that a total of 34,065,017 single-nucleotide polymorphisms (SNPs) were identified from all sheep, and 65 candidate genes (CDGs) were pinpointed from the top 1% of interacted windows and SNPs between the pairwise fixation index (FST, >0.149543) and cross-population extended haplotype homozygosity (XP-EHH, >0.701551). A total of 41 CDGs (e.g. VRTN, EYA2 and MCPH1) were annotated to 576 GO terms, of which seven terms were directly linked to follicular and embryonic development (e.g. TBXT, BMPR1B, and BMP2). In addition, 73 KEGG pathways were enriched by 21 CDGs (e.g. ENTPD5, ABCD4 and RXFP2), mainly related to Hippo (TCF4, BMPR1B and BMP2), TGF-β (BMPR1B and BMP2), PI3K-Akt (ITGB4, IL4R and PPP2R5A) and Jak-STAT signalling pathways (IL20RA and IL4R). Notably, a series of CDGs was under strong selection in sheep with high litter size traits. These findings result could improve the comprehension of the genetic underpinnings of sheep litter size. Furthermore, it provides valuable CDGS for future molecular breeding.
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Affiliation(s)
- Weiguo Cui
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Hechuan Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jingchun Li
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Dongyu Lv
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jiayi Xu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Mengyu Liu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Guoan Yin
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
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Fountas S, Petinaki E, Bolaris S, Kargakou M, Dafopoulos S, Zikopoulos A, Moustakli E, Sotiriou S, Dafopoulos K. The Roles of GDF-9, BMP-15, BMP-4 and EMMPRIN in Folliculogenesis and In Vitro Fertilization. J Clin Med 2024; 13:3775. [PMID: 38999341 PMCID: PMC11242125 DOI: 10.3390/jcm13133775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/09/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024] Open
Abstract
Growth differentiation factor 9 (GDF-9) contributes to early ovarian development and oocyte survival. Higher concentrations of GDF-9 in follicular fluid (FF) are associated with oocyte nuclear maturation and optimal embryo development. In in vitro fertilization (IVF), GDF-9 affects the ability of the oocyte to fertilize and subsequent embryonic development. Bone morphogenetic protein 15 (BMP-15) is involved in the regulation of ovarian function and affects oocyte development. During IVF, BMP-15 contributes to the formation of competent blastocysts. BMP-15 may play a role in embryo implantation by affecting endometrial receptivity. Bone morphogenetic protein 4 (BMP-4) is involved in the regulation of follicle growth and development and affects granulosa cell (GC) differentiation. In relation to IVF, BMP-4 is important for embryonic development, influences cell fate and differentiation, and plays a role in facilitating embryo-endometrial interactions during the implantation process. Extracellular matrix metalloproteinase inducer (EMMPRIN) is associated with ovulation and follicle rupture, promotes the release of mature eggs, and affects the modification of the extracellular matrix of the follicular environment. In IVF, EMMPRIN is involved in embryo implantation by modulating the adhesive properties of endometrial cells and promotes trophoblastic invasion, which is essential for pregnancy to occur. The purpose of the current article is to review the studies and recent findings of GDF-9, BMP-15, BMP-4 and EMMPRIN as fundamental factors in normal follicular development and in vitro fertilization.
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Affiliation(s)
- Serafeim Fountas
- Fertility and Sterility Unit, Elena Venizelou General-Maternity District Hospital, 11521 Athens, Greece
| | - Efthymia Petinaki
- Department of Microbiology, University Hospital of Larissa, 41110 Larissa, Greece
| | - Stamatis Bolaris
- Fertility and Sterility Unit, Elena Venizelou General-Maternity District Hospital, 11521 Athens, Greece
| | - Magdalini Kargakou
- Fertility and Sterility Unit, Elena Venizelou General-Maternity District Hospital, 11521 Athens, Greece
| | - Stefanos Dafopoulos
- Department of Health Sciences, European University Cyprus, 2404 Nicosia, Cyprus
| | | | - Efthalia Moustakli
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Sotirios Sotiriou
- Department of Embryology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece
| | - Konstantinos Dafopoulos
- ART Unit, Department of Obstetrics and Gynecology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece
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Ren Y, Li X, He J, Zhang M, Liu G, Wei C, Zhang G, Zhang W, Nie F, Wang M, Tian K, Huang X. Estimation of Genetic Parameters for Early Growth Traits in Luzhong Mutton Sheep. Animals (Basel) 2024; 14:1754. [PMID: 38929373 PMCID: PMC11200940 DOI: 10.3390/ani14121754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/25/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
In this study, six different animal models were fitted, and the constrained maximum likelihood method was used to assess the genetic parameters and genetic trends of early growth traits in Luzhong mutton sheep. The experimental data of this study included the newborn weight (BWT, N = 2464), weaning weight (WWT, N = 2923), weight at 6 months of age (6WT, N = 2428), average daily weight gain from birth to weaning (ADG1, N = 2424), and average daily weight gain from weaning to 6 months of age (ADG2, N = 1836) in Luzhong mutton sheep (2015~2019). The best model for the genetic parameters of the five traits in Luzhong mutton sheep was identified as Model 4 using the Akaike information criterion (AIC) and likelihood ratio test (LRT) methods, in which the estimated values of direct heritability for the BWT, WWT, 6WT, ADG1, and ADG2 were 0.156 ± 0.057, 0.547 ± 0.031, 0.653 ± 0.031, 0.531 ± 0.035, and 0.052 ± 0.046, respectively, and the values for maternal heritability were 0.201 ± 0.100, 0.280 ± 0.047, 0.197 ± 0.053, 0.275 ± 0.052, and 0.081 ± 0.092, respectively. The genetic correlation between the ADG2 and WWT was negative, and the genetic and phenotypic correlations among the remaining traits were positive. In this study, maternal effects had a more significant influence on early growth traits in Luzhong mutton sheep. In conclusion, to effectively improve the accuracy of genetic parameter estimation, maternal effects must be fully considered to ensure more accurate and better breeding planning.
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Affiliation(s)
- Yifan Ren
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Y.R.); (X.L.); (J.H.); (G.L.); (C.W.); (G.Z.); (W.Z.); (F.N.)
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (M.Z.); (M.W.)
| | - Xue Li
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Y.R.); (X.L.); (J.H.); (G.L.); (C.W.); (G.Z.); (W.Z.); (F.N.)
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (M.Z.); (M.W.)
| | - Junmin He
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Y.R.); (X.L.); (J.H.); (G.L.); (C.W.); (G.Z.); (W.Z.); (F.N.)
| | - Menghua Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (M.Z.); (M.W.)
| | - Guifen Liu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Y.R.); (X.L.); (J.H.); (G.L.); (C.W.); (G.Z.); (W.Z.); (F.N.)
| | - Chen Wei
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Y.R.); (X.L.); (J.H.); (G.L.); (C.W.); (G.Z.); (W.Z.); (F.N.)
| | - Guoping Zhang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Y.R.); (X.L.); (J.H.); (G.L.); (C.W.); (G.Z.); (W.Z.); (F.N.)
| | - Wenhao Zhang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Y.R.); (X.L.); (J.H.); (G.L.); (C.W.); (G.Z.); (W.Z.); (F.N.)
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (M.Z.); (M.W.)
| | - Fumei Nie
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Y.R.); (X.L.); (J.H.); (G.L.); (C.W.); (G.Z.); (W.Z.); (F.N.)
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (M.Z.); (M.W.)
| | - Ming Wang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (M.Z.); (M.W.)
| | - Kechuan Tian
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Y.R.); (X.L.); (J.H.); (G.L.); (C.W.); (G.Z.); (W.Z.); (F.N.)
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (M.Z.); (M.W.)
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Ma Z, Wang W, Zhang D, Zhang Y, Zhao Y, Li X, Zhao L, Cheng J, Xu D, Yang X, Liu J, He L, Chen Z, Gong P, Zhang X. Polymorphisms of PLIN1 and MOGAT1 genes and their association with feed efficiency in Hu sheep. Gene 2024; 897:148072. [PMID: 38081333 DOI: 10.1016/j.gene.2023.148072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/22/2023] [Accepted: 12/08/2023] [Indexed: 12/21/2023]
Abstract
Feed cost accounts for a high proportion of sheep production, and improving sheep's utilization of feed will reduce production costs and improve economic benefits. The purpose of this study was to investigate the expression characteristics of PLIN1 and MOGAT1 genes and the relationship between their polymorphisms and feed efficiency traits in Hu sheep, and to find molecular Genetic marker that can be used in breeding. The expression levels of PLIN1 and MOGAT1 genes in various tissues were determined using quantitative real-time PCR (qRT-PCR). The results showed that PLIN1 and MOGAT1 genes were widely expressed in heart, liver, spleen, lungs, kidneys, rumen, duodenum, muscle, lymph, and tail fat. The PLIN1 gene had the highest expression level in in the tail fat compared to the other nine tissues. The expression levels of MOGAT1 gene in liver, tail fat, lung and heart was significantly higher than in kidney, muscle and lymph. The expression level of MOGAT1 was lowest in muscle compared to the other tissues (heart, liver, spleen, lung, rumen and tail fat). We recorded the body weight (BW80 and BW180) and feed intake (FI) information of 985 male Hu sheep at 80 and 180 days of age, and calculated the daily average feed intake (ADFI), average daily gain (ADG), and feed conversion rate (FCR) from 80 to 180 days of age. Two intronic mutations, g.18517910 A > G and g.224856118 G > C, were identified in PLIN1 and MOGAT1 genes by PCR amplification and Sanger sequencing. MassARRAY ® SNP detection technology was used to genotype the DNA of 985 Hu sheep and analyze its association with feed efficiency traits. The results showed that the SNP g.18517910 A > G was significantly associated with BW80, BW180, FI, ADFI and FCR (P < 0.05), while SNP g.2248561118 G > C was significantly associated with FCR (P < 0.05). Meanwhile, significant differences were also observed in different combinations of genotypes (P < 0.05). Therefore, these two polymorphic loci can serve as candidate molecular markers for improving feed utilization efficiency in Hu sheep.
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Affiliation(s)
- Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Yukun Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Yuan Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Xiaolong Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Liming Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Jiangbo Cheng
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Lijuan He
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Zhanyu Chen
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Ping Gong
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Science, Urumqi, 830057, China.
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
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Abuzahra M, Wijayanti D, Effendi MH, Mustofa I, Lamid M. Association of melatonin receptor 1 A with litter size in sheep: A review. F1000Res 2024; 12:900. [PMID: 38322310 PMCID: PMC10844802 DOI: 10.12688/f1000research.134890.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/04/2024] [Indexed: 02/08/2024] Open
Abstract
Sheep are a valuable livestock species worldwide, providing meat, milk, and various dairy products. This article aims to review the latest literature on the melatonin receptor 1A (MTNR1A) gene as a potential candidate gene associated with reproductive traits, particularly the litter size trait in sheep, by searching various databases for available literature. Studies have shown that different parts of the MTNR1A gene play various roles in sheep. By identifying marker genes associated with reproductive traits in MTNR1A polymorphisms linked to the litter size trait, breeders can achieve a faster selection response in sheep breeding by recognizing the genomic region where these genes are located and understanding their physiological functions. Therefore, highlighting the literature on these functions and their association with reproductive traits may contribute to improving the genetic makeup during sheep breeding.
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Affiliation(s)
| | - Dwi Wijayanti
- Department of Animal Science, Perjuangan University of Tasikmalaya, Tasikmalaya, West Java, 46115, Indonesia
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mustofa Helmi Effendi
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Imam Mustofa
- Department of Veterinary Reproduction, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Mirni Lamid
- Department of Animal Husbandry, Universitas Airlangga, Surabaya, East Java, Indonesia
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Gamal L, Noshy MM, Aboul-Naga AM, Sabit H, El-Shorbagy HM. DNA methylation of GDF-9 and GHR genes as epigenetic regulator of milk production in Egyptian Zaraibi goat. Genes Genomics 2024; 46:135-148. [PMID: 37985544 PMCID: PMC10781795 DOI: 10.1007/s13258-023-01464-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/01/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND DNA methylation is an epigenetic mechanism that takes place at gene promoters and a potent epigenetic marker to regulate gene expression. OBJECTIVE The study aimed to improve the milk production of Zaraibi goats by addressing the methylation pattern of two milk production-related genes: the growth hormone receptor (GHR) and the growth differentiation factor-9 (GDF-9). METHODS 54 and 46 samples of low and high milk yield groups, respectively, were collected. Detection of methylation was assessed in two CpG islands in the GDF-9 promoter via methylation-specific primer assay (MSP) and in one CpG island across the GHR promoter using combined bisulfite restriction analysis (COBRA). RESULTS A positive correlation between the methylation pattern of GDF-9 and GHR and their expression levels was reported. Breeding season was significantly effective on both peak milk yield (PMY) and total milk yield (TMY), where March reported a higher significant difference in PMY than November. Whereas single birth was highly significant on TMY than multiple births. The 3rd and 4th parities reported the highest significant difference in PMY, while the 4th parity was the most effective one on TMY. CONCLUSION These results may help improve the farm animals' milk productive efficiency and develop prospective epigenetic markers to improve milk yield by epigenetic marker-assisted selection (eMAS) in goat breeding programs.
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Affiliation(s)
- Layaly Gamal
- Sheep and Goat Research Department, Animal Production Research Institute, Agriculture Research Center (ARC), Giza, Egypt
| | - Magda M Noshy
- Zoology Department, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - A M Aboul-Naga
- Sheep and Goat Research Department, Animal Production Research Institute, Agriculture Research Center (ARC), Giza, Egypt
| | - Hussein Sabit
- Department of Medical Biotechnology, College of Biotechnology, Misr University for Science and Technology, Giza, Egypt
| | - Haidan M El-Shorbagy
- Zoology Department, Faculty of Science, Cairo University, Giza, 12613, Egypt.
- Faculty of Biotechnology, October University for Modern Science and Arts, 6th October, Giza, Egypt.
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Chang C, He X, Di R, Wang X, Han M, Liang C, Chu M. Transcriptome Analysis Reveals Differentially Expressed circRNAs Associated with Fecundity in Small-Tail Han Sheep Thyroid with Different FecB Genotypes. Animals (Basel) 2023; 14:105. [PMID: 38200837 PMCID: PMC10777913 DOI: 10.3390/ani14010105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Litter size is an economically important trait in sheep, and it is a complex trait controlled by multiple genes in multiple organs. Among them, the regulation of lamb number trait by the thyroid gland is a very important part. However, the molecular mechanisms of the thyroid gland in sheep reproduction remain unclear. Here, RNA-seq was used to detect transcriptome expression patterns in the thyroid gland between follicular phase (FP) and luteal phase (LP) in FecB BB (MM) and FecB ++ (ww) STH sheep, respectively, and to identify differentially expressed circRNAs (DECs) associated with reproduction. Bioinformatic analysis of the source genes of these DECs revealed that they can be enriched in multiple signaling pathways involved in the reproductive process of animals. We found that the source genes of these DECs, such as GNAQ, VEGFC, MAPK1, STAT1, and HSD17B7, may play important roles in the reproductive process of animals. To better understand the function of these DECs, we constructed circRNA-miRNA co-expression networks. Dual luciferase reporter assays suggested that a ceRNA regulatory mechanism between circ_0003259-oar-miR-133-TXLNA and circ_0012128-oar-miR-370-3p-FGFR1 may hold. All of these DEC expression profiles in the thyroid gland provide a novel resource for elucidating the regulatory mechanisms underlying STH sheep prolificacy.
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Affiliation(s)
- Cheng Chang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China;
| | - Xiaoyun He
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Ran Di
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Xiangyu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Miaoceng Han
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China;
| | - Chen Liang
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China;
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
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9
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Budiyanto A, Hartanto S, Widayanti R, Setyawan EMN, Wardono HP, Gustari S. The relationship between G1 (c.260 G>A) and G4 (c.721 G>A) polymorphisms in the GDF9 gene and the litter size of sheep: A meta-analysis study. J Adv Vet Anim Res 2023; 10:599-607. [PMID: 38370904 PMCID: PMC10868705 DOI: 10.5455/javar.2023.j715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/21/2023] [Accepted: 08/20/2023] [Indexed: 02/20/2024] Open
Abstract
Objective The results of G1 and G4 polymorphisms as litter-size (LS) markers of ewes remain contradictory. The aim was to evaluate the impact of G1 (c.260 G>A) and G4 (c.721 G>A) polymorphisms on the LS of sheep by synthesizing data from multiple previous studies. Methods Data were extracted from 14 eligible articles. The genotypes of G1 and G4 polymorphisms were homozygous wild-type (WW), heterozygous (WM), and homozygous mutant-type (MM). The standardized mean difference (SMD) method using random effect models was employed to determine the effect size of G1 and G4 polymorphisms on LS under dominant, recessive, additive, and co-dominant genetic models. Heterogeneity was analyzed with the I2 statistic index. Publication bias was depicted with funnel plots and tested by Egger's and Begg's tests. Results The study showed that the correlation between G1 polymorphism and LS in sheep was not significant (p > 0.05) under all genetic models. The influence of G4 polymorphism on the LS of sheep was found significantly (p < 0.05) under dominant [SMD = 0.28, I2 = 0% (no heterogeneity)] and co-dominant [SMD = -0.14, I2 = 36% (moderate heterogeneity)] genetic models. The WM genotype of G4 polymorphism increased LS, while the MM genotype reduced LS in sheep. Publication bias among G1 and G4 polymorphism studies was absent in all genetic models. Conclusion Thus, the study revealed that G4 polymorphism could be a potential genetic marker for LS in ewes. On the contrary, G1 polymorphism has no association with the LS of ewes.
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Affiliation(s)
- Agung Budiyanto
- Department of Reproduction, Obstetrics and Gynecology, Faculty of Veterinary Medicine, Gadjah Mada University, Yogyakarta, Indonesia
| | - Slamet Hartanto
- National Research and Innovation Agency (BRIN), Jakarta, Indonesia
| | - Rini Widayanti
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Erif Maha Nugraha Setyawan
- Department of Reproduction, Obstetrics and Gynecology, Faculty of Veterinary Medicine, Gadjah Mada University, Yogyakarta, Indonesia
| | | | - Sri Gustari
- Department of Reproduction, Obstetrics and Gynecology, Faculty of Veterinary Medicine, Gadjah Mada University, Yogyakarta, Indonesia
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Zhang L, Zhang S, Yuan M, Zhan F, Song M, Shang P, Yang F, Li X, Qiao R, Han X, Li X, Fang M, Wang K. Genome-Wide Association Studies and Runs of Homozygosity to Identify Reproduction-Related Genes in Yorkshire Pig Population. Genes (Basel) 2023; 14:2133. [PMID: 38136955 PMCID: PMC10742578 DOI: 10.3390/genes14122133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/10/2023] [Accepted: 11/19/2023] [Indexed: 12/24/2023] Open
Abstract
Reproductive traits hold considerable economic importance in pig breeding and production. However, candidate genes underpinning the reproductive traits are still poorly identified. In the present study, we executed a genome-wide association study (GWAS) and runs of homozygosity (ROH) analysis using the PorcineSNP50 BeadChip array for 585 Yorkshire pigs. Results from the GWAS identified two genome-wide significant and eighteen suggestive significant single nucleotide polymorphisms (SNPs) associated with seven reproductive traits. Furthermore, we identified candidate genes, including ELMO1, AOAH, INSIG2, NUP205, LYPLAL1, RPL34, LIPH, RNF7, GRK7, ETV5, FYN, and SLC30A5, which were chosen due to adjoining significant SNPs and their functions in immunity, fertilization, embryonic development, and sperm quality. Several genes were found in ROH islands associated with spermatozoa, development of the fetus, mature eggs, and litter size, including INSL6, TAF4B, E2F7, RTL1, CDKN1C, and GDF9. This study will provide insight into the genetic basis for pig reproductive traits, facilitating reproduction improvement using the marker-based selection methods.
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Affiliation(s)
- Lige Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Songyuan Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Meng Yuan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Fengting Zhan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Mingkun Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Peng Shang
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China;
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
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11
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Hussen Ali O, Hassan Al- Azzawi S. Detection of polymorphism in growth differentiation factor 9 gene (GDF9) Exon1 and its association with litter size in local Iraqi goats. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.04.49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Litter size is one of the most important economic traits in goats. Growth Differential Factor 9 (GDF9) Gene is suggested as a functional candidate for fertility, fecundity and twining rate. This study was performed to identify SNPs in exon1 of the GDF9 gene and their association with fertility traits in local Iraqi goats. The exon 1 of GDF9 was sequenced, and the SNP (Single nucleotide polymorphism ) was determined in 36 local Iraqi goats. Then the association analyses between polymorphic locals of GDF9 and litter size were performed using the chi-square analysis procedure. The result shows that mutation (C 1902 G) was significantly associated with litter size in local Iraqi goats and the location of C1902 G mutation with three genotypes CC, CG and GG. A significant effect was found for birth weight, weaning weight and twin ratio, where the homozygous dominant genotype outperformed CC. A significant impact was seen for fertility and mortality, where CC topped CG and GG in fertility percentage and superiority of CG over CC and GG in mortality rate. The results preliminarily demonstrated that GDF9 was a critical gene affecting the fecundity of local Iraqi goats and that (C 1902 G) could be a potential genetic marker.
Keywords: GDF9 gene, litter size, polymorphism, Iraqi goats
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Affiliation(s)
- Ola Hussen Ali
- Department of Animal Production - College of Agriculture – University of Diyala. Iraq
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12
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Ajafar MH, Kadhim AH, Al-Thuwaini TM, Al-Shuhaib MBS, Hussein TH. Dr Association of bone morphogenetic protein 15 and growth differentiation factor 9 with litter size in livestock: a review study. ACTA SCIENTIARUM: ANIMAL SCIENCES 2022. [DOI: 10.4025/actascianimsci.v45i1.57927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
. Litter size is one of the crucial factors in livestock production and is of high economic value, which is affected by ovulation rate, hormones, and growth factors. Growth factors play a multifaceted role in reproductive physiology. This review aims to investigate the association of bone morphogenetic protein 15 (BMP15) and growth differentiation factor 9 (GDF9) with litter size in livestock. The transforming growth factor β (TGF- β) superfamily includes more than 34 members; GDF9 and BMP15 are among the most significant factors for regulating fertility and litter size in most livestock species. Ovarian follicles release BMP15 and GDF9 that are involved in the maturation of primary follicles into the basal form, proliferation of granulosa and theca cells, steroidogenesis, ovulation, and formation of the corpus luteum. Besides, these factors are highly expressed in oocytes and are necessary for female fertility and multiple ovulation in several livestock species. Animals with two inactive copies of these factors are sterile, while those with one inactive copy are fertile. Thus, the present review provides valuable information on the association of BMP15 and GDF9 with litter size in livestock that can be used as biological markers of multiple ovulation or for improving fertility in livestock.
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Polymorphism and phylogenetic analysis of FecB and FecG genes in native sheep of Meghalaya, India. Trop Anim Health Prod 2022; 54:367. [DOI: 10.1007/s11250-022-03366-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 10/24/2022] [Indexed: 12/13/2022]
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14
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Ma Z, Wang W, Zhang D, Zhang Y, Zhao Y, Li X, Zhao L, Lin C, Wang J, Zhou B, Cheng J, Xu D, Li W, Yang X, Huang Y, Cui P, Liu J, Zeng X, Zhai R, Zhang X. Ovine RAP1GAP and rBAT gene polymorphisms and their association with tail fat deposition in Hu sheep. Front Vet Sci 2022; 9:974513. [PMID: 36090178 PMCID: PMC9453205 DOI: 10.3389/fvets.2022.974513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Excessive fat deposition in the tail of sheep will affect its feed efficiency, which will increase the feeding cost. The purpose of this study was to identify the single nucleotide polymorphisms (SNPs) of RAP1GAP and rBAT genes by PCR amplification and Sanger sequencing, the SNPs were genotyped by KASP genotyping assays to evaluate their association with tail fat deposition traits. The results showed that two intronic mutations of g.13561 G > A and g.1460 T > C were found in RAP1GAP and rBAT, respectively. There were three genotypes of GG, AG, AA and CC, CT and TT at these two loci, respectively. Association analysis showed that g.13561 G > A of RAP1GAP was associated with tail width, tail fat weight and relative tail fat weight (P < 0.05). The g.1460 T > C of rBAT was associated with tail width and tail fat weight (P < 0.05). Different combinations of genotypes also differed significantly with tail fat deposition traits. In the tail fat tissue, the expression levels of RAP1GAP gene was significantly higher in small-tailed sheep than in big-tailed sheep, and the expression levels of rBAT gene was significantly higher in big-tailed sheep than in small-tailed sheep. In the liver, the expression levels of RAP1GAP and rBAT gene was significantly higher at 6 months than at 0 and 3 months. In conclusion, RAP1GAP and rBAT polymorphisms can be used as a candidate molecular marker to reduce tail fat deposition in sheep.
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Affiliation(s)
- Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yongliang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Rui Zhai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Xiaoxue Zhang
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15
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Zhao Y, Zhang D, Zhang X, Li F, Xu D, Zhao L, Li X, Zhang Y, Wang J, Yang X, Wang W. Expression features of the ovine FTO gene and association between FTO polymorphism and tail fat deposition related-traits in Hu sheep. Gene X 2022; 826:146451. [PMID: 35358654 DOI: 10.1016/j.gene.2022.146451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/24/2022] [Accepted: 03/18/2022] [Indexed: 11/25/2022] Open
Abstract
Fat mass and obesity associated (FTO) gene is a famous dominant predictor of obesity, and plays pivotal roles in the regulating fatty acid transport and fat metabolism. In the current study, the quantitative real-time PCR (qRT-PCR), DNA-pooled sequencing and KAspar assay were performed to detect the expression features of FTO and the polymorphisms of FTO associated with the tail fat weight related-traits of Hu sheep. The results indicated that the expression of FTO gene is widely expressed in the tissues tested, and the expression level of FTO in tail fat tissue was evidently higher compared with that in the other tissues. In addition, FTO showed the highest expression level in tail fat tissue at three months. The expression of FTO mRNA was lower in the large-tail fat group compared with that in the small-tail fat group in 6 months old. Subsequently, the polymorphism loci g. 23704451C > A detected in the FTO gene was confirmed to be significantly related to the tail length and the weight of tail fat. These results suggested that the polymorphism might be regarded as novel molecular marker for the breeding of small tail sheep.
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Affiliation(s)
- Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin 733300, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiaobing Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weiming Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
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Liu Y, Zhou Z, He X, Jiang Y, Ouyang Y, Hong Q, Chu M. Differentially Expressed Circular RNA Profile Signatures Identified in Prolificacy Trait of Yunshang Black Goat Ovary at Estrus Cycle. Front Physiol 2022; 13:820459. [PMID: 35492611 PMCID: PMC9049588 DOI: 10.3389/fphys.2022.820459] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/10/2022] [Indexed: 01/10/2023] Open
Abstract
CircRNAs acting as miRNA sponges play important roles in the growth process of animal individuals. The prolificacy trait of goats is involved in many pathways, however, the variation of circRNA expression profiles in the different phases of the estrus cycle at high and low fecundity groups is still unknown. Here, we analyzed the circRNA profiles of ovarian tissues among high and low fecundity groups in the follicular phase (HF vs LF), high and low fecundity groups in the luteal phase (HL vs LL), and high and low fecundity in the whole estrus cycle (HF vs HL and LF vs LL) using RNA-seq. A total of 283 (114 upregulated and 169 downregulated), 559 (299 upregulated and 260 downregulated), 449 (254 upregulated and 195 downregulated), and 314 (210 upregulated and 104 downregulated) differentially expressed (DE) circRNAs were screened in HF vs LF, HF vs HL, HL vs LL, and LF vs LL groups, respectively. Enrichment analysis suggested that the targeting of DE circRNAs was mainly enriched in oocyte meiosis, the GnRH signaling pathway, and estrogen signaling pathway. After integrating our previous study of miRNA-seq, there were 56 miRNAs that could target to 192 DE circRNAs, including the miR-133 family (including miR-133a-3p and miR-133b), miR-129-3p, and miR-21, which also had important influence on the prolificacy trait of goats. Then, 18 circRNAs with coding potential were obtained by four software predictions, and 9 circRNAs were validated by RT-qPCR. Together, circRNAs play a key role in the prolificacy trait and the transformation of the follicular phase to the luteal phase in the estrus cycle of goats.
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Affiliation(s)
- Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Zuyang Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanting Jiang
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Yina Ouyang
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Qionghua Hong
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Comparative Transcriptomic Analysis of Hu Sheep Pituitary Gland Prolificacy at the Follicular and Luteal Phases. Genes (Basel) 2022; 13:genes13030440. [PMID: 35327994 PMCID: PMC8949571 DOI: 10.3390/genes13030440] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/20/2022] [Accepted: 02/25/2022] [Indexed: 11/17/2022] Open
Abstract
The pituitary gland directly regulates the reproduction of domestic animals. Research has increasingly focused on the potential regulatory mechanism of non-coding RNA in pituitary development. Little is known about the differential expression pattern of lncRNAs in Hu sheep, a famous sheep breed with high fecundity, and its role in the pituitary gland between the follicular phase and luteal phase. Herein, to identify the transcriptomic differences of the sheep pituitary gland during the estrus cycle, RNA sequencing (RNA-Seq) was performed. The results showed that 3529 lncRNAs and 16,651 mRNAs were identified in the pituitary gland. Among of them, 144 differentially expressed (DE) lncRNA transcripts and 557 DE mRNA transcripts were screened in the follicular and luteal phases. Moreover, GO and KEGG analyses demonstrated that 39 downregulated and 22 upregulated genes interacted with pituitary functions and reproduction. Lastly, the interaction of the candidate lncRNA XR_001039544.4 and its targeted gene LHB were validated in sheep pituitary cells in vitro. LncRNA XR_001039544.4 and LHB showed high expression levels in the luteal phase in Hu sheep. LncRNA XR_001039544.4 is mainly located in the cytoplasm, as determined by FISH analysis, indicating that XR_001039544.4 might act as competing endogenous RNAs for miRNAs to regulate LHB. LncRNA XR_001039544.4 knockdown significantly inhibited LH secretion and cell proliferation. LncRNA XR_001039544.4 may regulate the secretion of LH in the luteal-phase pituitary gland via affecting cell proliferation. Taken together, these findings provided genome-wide lncRNA- and mRNA-expression profiles for the sheep pituitary gland between the follicular and luteal phases, thereby contributing to the elucidation of the molecular mechanisms of pituitary function.
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18
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Di R, Wang F, Yu P, Wang X, He X, Mwacharo JM, Pan L, Chu M. Detection of Novel Variations Related to Litter Size in BMP15 Gene of Luzhong Mutton Sheep ( Ovis aries). Animals (Basel) 2021; 11:ani11123528. [PMID: 34944305 PMCID: PMC8698048 DOI: 10.3390/ani11123528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/02/2021] [Accepted: 12/05/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary BMP15 is a critical gene in sheep reproduction. Most of its variations have been reported in European sheep. In this study, the entire open reading frame (ORF) region of BMP15 was sequenced in 154 Luzhong mutton sheep. Among 13 identified variations, six were novel. Four SNPs (ENSOART00000010201.1:c.352+342C>A, c.352+1232T>C, c.352+1165A>G and c.353-2036T>A) were significantly associated with litter size, and could be used as candidate genetic markers for improving litter size. The results also suggested possible interaction between BMP15 and FecB/GDF9. Abstract Litter size is an important economic trait in the mutton sheep industry. BMP15 is one of the key candidate genes for litter size in sheep. In this study, the entire ORF region of BMP15 was sequenced in 154 Luzhong mutton ewes, and the novel variations were determined. The association between polymorphism in BMP15 and litter size was analyzed using a general linear model. Six out of a total of thirteen variations were identified to be novel. Association analysis indicated that four (SNPs ENSOART00000010201.1:c.352+342C>A, c.352+1232T>C, c.352+1165A>G and c.353-2036T>A) were significantly associated with litter size. The joint analysis among three major genes (BMP15, BMPR1B and GDF9) exhibited significant interaction effects in three combinations (FecB and c.352+1232T>C of BMP15; FecB and c.352+1165A>G of BMP15; c.352+342C>A of BMP15 and ENSOART00000014382.1:c.994G>A of GDF9). For the SNPs c.352+1232T>C and c.352+342C>A, the global distribution of allele frequencies showed that the highest variation frequency occurs in Western Europe. In conclusion, the results demonstrated that BMP15 is a major gene for litter size in Luzhong mutton sheep and candidate SNPs associated with litter size were identified.
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Affiliation(s)
- Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (R.D.); (F.W.); (P.Y.); (X.W.); (X.H.)
| | - Fengyan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (R.D.); (F.W.); (P.Y.); (X.W.); (X.H.)
| | - Ping Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (R.D.); (F.W.); (P.Y.); (X.W.); (X.H.)
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (R.D.); (F.W.); (P.Y.); (X.W.); (X.H.)
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (R.D.); (F.W.); (P.Y.); (X.W.); (X.H.)
| | - Joram Mwashigadi Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa P.O. Box 5689, Ethiopia;
- Animal and Veterinary Sciences, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute Building, Midlothian EH25 9RG, UK
| | - Linxiang Pan
- Shandong Yingtai Agriculture and Animal Husbandry Technology Co., Ltd., Jinan 271114, China;
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (R.D.); (F.W.); (P.Y.); (X.W.); (X.H.)
- Correspondence: ; Tel.: +86-010-6281-9850
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