1
|
Novák K, Valčíková T, Samaké K, Bjelka M. Association of Variants in Innate Immune Genes TLR4 and TLR5 with Reproductive and Milk Production Traits in Czech Simmental Cattle. Genes (Basel) 2023; 15:24. [PMID: 38254914 PMCID: PMC10815032 DOI: 10.3390/genes15010024] [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: 11/08/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Bovine genes TLR4 and TLR5, which encode antibacterial toll-like receptors, were screened for polymorphisms in Czech Red Pied (Czech Simmental) cattle to identify variants associated with reproduction, udder health, and milk production traits. Variants were discovered by hybrid resequencing of 164 bulls using HiSeq X-Ten and PacBio technologies and then individually genotyped. Nominal p-values < 0.05 for associations were detected in 18 combinations between 14 polymorphisms and 15 traits using one-way analysis of variance (ANOVA). The TLR4 variants g.610C>T (rs43578094) and g.10310T>G (rs8193072) in reference AC000135.1 were strictly associated with the index of early reproductive disorders and maternal calving ease, respectively, at false discovery rate (FDR) < 0.05. A highly permissive false discovery rate cutoff of 0.6 separated seventeen combinations in both genes comprising eight positives. In the case of the TLR4 variant g.9422T>C (rs8193060), indications were obtained for the association with as many as four reproductive traits: incidence of cystic ovaries, early reproductive disorders, calving ease, and production longevity. The permissive FDR interpretation for the TLR5 data indicated associations with cyst incidence and early reproduction disorders with maternal calving ease. Moreover, three TLR5 polymorphisms correlated with milk production traits. The discrepancy of the observed associations with the predicted impacts of the SNPs on protein function points to the role of haplotypes. Nevertheless, this question should be resolved on a larger scale. The observed associations are endorsed by independent evidence from the published functional roles in other species and by the published QTL mapping data.
Collapse
Affiliation(s)
- Karel Novák
- Department of Genetics and Breeding, Institute of Animal Science, Přátelství 815, 104 00 Prague-Uhříněves, Czech Republic
| | - Terezie Valčíková
- Department of Genetics, Czech University of Life Sciences, Kamýcká 129, 165 06 Prague, Czech Republic;
| | - Kalifa Samaké
- Department of Genetics and Microbiology, Viničná 7, Charles University, 128 43 Prague, Czech Republic;
| | - Marek Bjelka
- Breeding Company CHD Impuls, 592 55 Bohdalec, Czech Republic;
| |
Collapse
|
2
|
Wu X, Ayalew W, Chu M, Pei J, Liang C, Bao P, Guo X, Yan P. Characterization of RNA Editome in the Mammary Gland of Yaks during the Lactation and Dry Periods. Animals (Basel) 2022; 12:ani12020207. [PMID: 35049829 PMCID: PMC8773173 DOI: 10.3390/ani12020207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/01/2022] [Accepted: 01/14/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary In order to study the influence of RNA editing sites on lactation and mammary gland development process in yaks, we comprehensively characterized the RNA editome of the yak mammary gland during the lactation period and dry period by using the transcriptome and genome sequencing data. The results revealed 82,872 nonredundant RNA editing sites, 14,159 of which were differentially edited between the lactation period and dry period. Enrichment analysis showed that the genes harboring differential editing sites were mainly associated with mammary gland development-related pathways, such as MAPK pathway, PI3K-Akt pathway, FoxO signaling pathway, GnRH signaling pathway, and focal adhesion pathway. Our findings offer some novel insights into the RNA editing function in the mammary gland of yaks. Abstract The mammary gland is a complicated organ comprising several types of cells, and it undergoes extensive morphogenetic and metabolic changes during the female reproductive cycle. RNA editing is a posttranscriptional modification event occurring at the RNA nucleotide level, and it drives transcriptomic and proteomic diversities, with potential functional consequences. RNA editing in the mammary gland of yaks, however, remains poorly understood. Here, we used REDItools to identify RNA editing sites in mammary gland tissues in yaks during the lactation period (LP, n = 2) and dry period (DP, n = 3). Totally, 82,872 unique RNA editing sites were identified, most of which were detected in the noncoding regions with a low editing degree. In the coding regions (CDS), we detected 5235 editing sites, among which 1884 caused nonsynonymous amino acid changes. Of these RNA editing sites, 486 were found to generate novel possible miRNA target sites or interfere with the initial miRNA binding sites, indicating that RNA editing was related to gene regulation mediated by miRNA. A total of 14,159 RNA editing sites (involving 3238 common genes) showed a significant differential editing level in the LP when compared with that in the DP through Tukey’s Honest Significant Difference method (p < 0.05). According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, genes that showed different RNA editing levels mainly participated in pathways highly related to mammary gland development, including MAPK, PI3K-Akt, FoxO, and GnRH signaling pathways. Collectively, this work demonstrated for the first time the dynamic RNA editome profiles in the mammary gland of yaks and shed more light on the mechanism that regulates lactation together with mammary gland development.
Collapse
Affiliation(s)
- Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (W.A.); (M.C.); (J.P.); (C.L.); (P.B.)
| | - Wondossen Ayalew
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (W.A.); (M.C.); (J.P.); (C.L.); (P.B.)
- Department of Animal Production and Technology, Wolkite University, Wolkite P.O. Box 07, Ethiopia
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (W.A.); (M.C.); (J.P.); (C.L.); (P.B.)
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (W.A.); (M.C.); (J.P.); (C.L.); (P.B.)
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (W.A.); (M.C.); (J.P.); (C.L.); (P.B.)
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (W.A.); (M.C.); (J.P.); (C.L.); (P.B.)
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (W.A.); (M.C.); (J.P.); (C.L.); (P.B.)
- Correspondence: (X.G.); (P.Y.)
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (W.A.); (M.C.); (J.P.); (C.L.); (P.B.)
- Correspondence: (X.G.); (P.Y.)
| |
Collapse
|
3
|
Atli MO, Hitit M, Özbek M, Köse M, Bozkaya F. Cell-Specific Expression Pattern of Toll-Like Receptors and Their Roles in Animal Reproduction. Handb Exp Pharmacol 2022; 276:65-93. [PMID: 35434748 DOI: 10.1007/164_2022_584] [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] [Indexed: 06/14/2023]
Abstract
Toll-like receptors (TLRs), a part of the innate immune system, have critical roles in protection against infections and involve in basic pathology and physiology. Secreted molecules from the body or pathogens could be a ligand for induction of the TLR system. There are many immune and non-immune types of cells that express at a least single TLR on their surface or cytoplasm. Those cells may be a player in a defense system or in the physiological regulation mechanisms. Reproductive tract and organs contain different types of cells that have essential functions such as hormone production, providing an environment for embryo/fetus, germ cell production, etc. Although lower parts of reproductive organs are in a relationship with outsider contaminants (bacteria, viruses, etc.), upper parts should be sterile to provide a healthy pregnancy and germ cell production. In those areas, TLRs bear controller or regulator roles. In this chapter, we will provide current information about physiological functions of TLR in the cells of the reproductive organs and tract, and especially about their roles in follicle selection, maturation, follicular atresia, ovulation, corpus luteum (CL) formation and regression, establishment and maintenance of pregnancy, sperm production, maturation, capacitation as well as the relationship between TLR polymorphism and reproduction in domestic animals. We will also discuss pathogen-associated molecular patterns (PAMPs)-induced TLRs that involve in reproductive inflammation/pathology.
Collapse
Affiliation(s)
- Mehmet Osman Atli
- Department of Reproduction, Faculty of Veterinary Medicine, Harran University, Şanlıurfa, Turkey.
| | - Mustafa Hitit
- Department of Genetics, Faculty of Veterinary Medicine, Kastamonu University, Kastamonu, Turkey
| | - Mehmet Özbek
- Department of Histology and Embryology, Faculty of Veterinary Medicine, Mehmet Akif Ersoy University, Burdur, Turkey
| | - Mehmet Köse
- Department of Obstetrics and Gynecology, Faculty of Veterinary Medicine, Dicle University, Diyarbakır, Turkey
| | - Faruk Bozkaya
- Department of Genetics, Faculty of Veterinary Medicine, Harran University, Sanlıurfa, Turkey
| |
Collapse
|
4
|
Wu X, Zhou X, Xiong L, Pei J, Yao X, Liang C, Bao P, Chu M, Guo X, Yan P. Transcriptome Analysis Reveals the Potential Role of Long Non-coding RNAs in Mammary Gland of Yak During Lactation and Dry Period. Front Cell Dev Biol 2020; 8:579708. [PMID: 33324637 PMCID: PMC7723986 DOI: 10.3389/fcell.2020.579708] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/09/2020] [Indexed: 12/26/2022] Open
Abstract
The mammary gland is a remarkably dynamic organ of milk synthesis and secretion, and it experiences drastic structural and metabolic changes during the transition from dry periods to lactation, which involves the expression and regulation of numerous genes and regulatory factors. Long non-coding RNA (lncRNA) has considered as a novel type of regulatory factors involved in a variety of biological processes. However, their role in the lactation cycle of yak is still poorly understood. To reveal the involved mechanism, Ribo-zero RNA sequencing was employed to profile the lncRNA transcriptome in mammary tissue samples from yak at two physiological stages, namely lactation (LP) and dry period (DP). Notably, 1,599 lncRNA transcripts were identified through four rigorous steps and filtered through protein-coding ability. A total of 59 lncRNAs showed significantly different expression between two stages. Accordingly, the results of qRT-PCR were consistent with that of the transcriptome data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that target genes of differentially expressed lncRNAs (DELs) were involved in pathways related to lactation, such as ECM-receptor interaction, PI3K-Akt signaling pathway, biosynthesis of amino acids and focal adhesion etc. Finally, we constructed a lncRNA-gene regulatory network containing some well known candidate genes for milk yield and quality traits. This is the first study to demonstrate a global profile of lncRNA expression in the mammary gland of yak. These results contribute to a valuable resource for future genetic and molecular studies on improving milk yield and quality, and help us to gain a better understanding of the molecular mechanisms underlying lactogenesis and mammary gland development of yak.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Xian Guo
- Key Lab of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ping Yan
- Key Lab of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| |
Collapse
|