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Wei T, Mo L, Wu Z, Zou T, Huang J. Gonadal transcriptome analysis of genes related to sex differentiation and sex development in the Pomacea canaliculata. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101235. [PMID: 38631127 DOI: 10.1016/j.cbd.2024.101235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
As an invasive alien animal, Pomacea canaliculata poses a great danger to the ecology and human beings. Recently, there has been a gradual shift towards bio-friendly control. Based on the development of RNA interference and CRISPR technology as molecular regulatory techniques for pest control, it was determined if the knockout of genes related to sex differentiation in P. canaliculata could induce sterility, thereby helping in population control. However, the knowledge of sex differentiation- and development-related genes in P. canaliculata is currently lacking. Here, transcriptomic approaches were used to study the genes expressed in the two genders of P. canaliculata at various developmental stages. Gonad transcriptomes of immature or mature males and females were compared, revealing 12,063 genes with sex-specific expression, of which 6066 were male- and 5997 were female-specific. Among the latter, 581 and 235 genes were up-regulated in immature and mature females, respectively. The sex-specific expressed genes identified included GnRHR2 and TSSK3 in males and ZAR1 and WNT4 in females. Of the genes, six were involved in reproduction: CCNBLIP1, MND1, DMC1, DLC1, MRE11, and E(sev)2B. Compared to immature snail gonads, the expression of HSP90 and CDK1 was markedly reduced in gonadal. It was hypothesized that the two were associated with the development of females. These findings provided new insights into crucial genetic information on sex differentiation and development in P. canaliculata. Additionally, some candidate genes were explored, which can contribute to future studies on controlling P. canaliculata using molecular regulatory techniques.
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Affiliation(s)
- Tingting Wei
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, Guangxi 541006, China; Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi 541006, China; College of Life Sciences, Guangxi Normal University, Guilin, Guangxi 541006, China
| | - Lili Mo
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, Guangxi 541006, China; Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi 541006, China; College of Life Sciences, Guangxi Normal University, Guilin, Guangxi 541006, China
| | - Zhengjun Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, Guangxi 541006, China; Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi 541006, China; College of Life Sciences, Guangxi Normal University, Guilin, Guangxi 541006, China
| | - Tongxiang Zou
- College of Life Sciences, Guangxi Normal University, Guilin, Guangxi 541006, China.
| | - Jinlong Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, Guangxi 541006, China; Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi 541006, China; College of Life Sciences, Guangxi Normal University, Guilin, Guangxi 541006, China.
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Lü Z, Liu T, Liu Y, Wang Y, Liu J, Liu B, Gong L, Liu L. Climate Adaptation and Drift Shape the Genomes of Two Eel-Goby Sister Species Endemic to Contrasting Latitude. Animals (Basel) 2023; 13:3240. [PMID: 37893964 PMCID: PMC10603712 DOI: 10.3390/ani13203240] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Deciphering the role of climate adaptation in generating genetic divergence and hence speciation is a central question in evolution. Comparisons of genomes of closely related species spanning selective climate gradients are particularly informative in discerning the signatures of selection and thereby providing valuable information concerning the role of climate adaptation in speciation. Here we re-sequenced 99 genomes of the two sister eel-goby species Odontamblyopus lacepedii and O. rebecca, which are endemic to tidal mudflats spanning contrasting latitude gradients, to estimate the influence of divergent climate selection on shaping genome-wide patterns of divergence. The results indicated that genome-wide differentiation between the two species was evident (genome-wide FST = 0.313). Against a background of high baseline genomic divergence, 588 and 1202 elevated divergent loci were detected to be widespread throughout their genomes, as opposed to focused within small islands of genomic regions. These patterns of divergence may arise from divergent climate selection in addition to genetic drift acting through past glacial segregation (1.46 million years ago). We identified several candidate genes that exhibited elevated divergence between the two species, including genes associated with substance metabolism, energy production, and response to environmental cues, all putative candidates closely linked to thermal adaptation expected from the latitude gradient. Interestingly, several candidates related to gamete recognition and time of puberty, and also exhibited elevated divergence, indicating their possible role in pre-zygote isolation and speciation of the two species. Our results would expand our knowledge on the roles of latitude climate adaptation and genetic drift in generating and maintaining biodiversity in marine teleosts.
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Affiliation(s)
- Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (Z.L.); (T.L.); (Y.L.); (J.L.); (B.L.); (L.G.)
| | - Tianwei Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (Z.L.); (T.L.); (Y.L.); (J.L.); (B.L.); (L.G.)
| | - Yantao Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (Z.L.); (T.L.); (Y.L.); (J.L.); (B.L.); (L.G.)
| | - Yuzhen Wang
- National Engineering Research Center for Facilitated Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Jing Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (Z.L.); (T.L.); (Y.L.); (J.L.); (B.L.); (L.G.)
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (Z.L.); (T.L.); (Y.L.); (J.L.); (B.L.); (L.G.)
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (Z.L.); (T.L.); (Y.L.); (J.L.); (B.L.); (L.G.)
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (Z.L.); (T.L.); (Y.L.); (J.L.); (B.L.); (L.G.)
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Guo Z, Lv L, Liu D, Ma H, Radovic C. A meta-analysis: Effect of androgens on reproduction in sows. Front Endocrinol (Lausanne) 2023; 14:1094466. [PMID: 36843577 PMCID: PMC9950266 DOI: 10.3389/fendo.2023.1094466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/27/2023] [Indexed: 02/12/2023] Open
Abstract
INTRODUCTION The mechanisms by which male hormones affect the development of ovaries and follicles has been studied by injecting exogenous androgens into sows. This may provide a reference for human polycystic ovary syndrome (PCOS), and can also provide guidance for improving the litter size of sows. METHODS We present a meta-analysis of studies published in the past 30 years on the effect of androgens on the ovulation rate of sows. A total of 517 papers were analyzed. RESULTS The results showed that both testosterone (T) and dihydrotestosterone (DHT) injected into sows were positively related to the ovulation rate. T did not have a relevant effect on swine in vivo blastocyst survival rate. DHT had a negative phase with respect to blastocyst survival rate. Pig T-androgen receiver affinity was higher than the analogous affinity for DHT; this is different in humans. This suggests that sows are not suitable as human PCOS experimental animal models. DISCUSSION To improve the litter size of sows, future research should focus on the mixed use of T and DHT, and the timing of use should be consistent with the periodic changes in androgen levels in sows. In addition, the welfare of experimental sows should be considered with reference to the clinical symptoms of PCOS.
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Affiliation(s)
- Zhenhua Guo
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin, China
- *Correspondence: Di Liu, ; Zhenhua Guo,
| | - Lei Lv
- Wood Science Research Institute of Heilongjiang Academy of Forestry, Harbin, China
- Harbin University, Harbin, China
| | - Di Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin, China
- *Correspondence: Di Liu, ; Zhenhua Guo,
| | - Hong Ma
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Cedomir Radovic
- Department of Pig Breeding and Genetics, Institute for Animal Husbandry, Belgrade, Serbia
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Zhou C, Zhang L, Xu D, Ding H, Zheng S, Liu M. MeDIP-seq and RNA-seq analysis during porcine testis development reveals functional DMRs at the promoter of LDHC. Genomics 2022; 114:110467. [PMID: 36041633 DOI: 10.1016/j.ygeno.2022.110467] [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: 04/22/2022] [Revised: 08/09/2022] [Accepted: 08/26/2022] [Indexed: 11/04/2022]
Abstract
Testis development requires tight regulation of gene expression programmed by epigenetic modifiers. However, their mechanism remains to be elucidated. Here, we investigated the genome-wide DNA methylation landscape in the Duroc and Meishan boar testes using methylated DNA immunoprecipitation sequencing (MeDIP-seq). We identified over 1100 promoter differential methylation genes (DMGs) before and after puberty, most of which are associated with testis development. Furthermore, we discovered that the expression of lactate dehydrogenase C (LDHC) gene during testis development is regulated by DNA methylation. The promoter of LDHC in pre-pubertal testes is substantially methylated, whereas considerably demethylated in post-pubertal testes. Artificial demethylation with the demethylating agent 5-Aza-CdR induced LDHC expression in immature Sertoli cells (SCs). Mechanistically, we confirmed the transcription factor SP1 was recruited to bind in hypomethylated differentially methylated regions (DMRs) in LDHC promoter, which upregulated the expression of LDHC. Functionally, we demonstrated that LDHC gene was activated in mature SCs (mSCs) and its overexpression significantly increases lactate secretion in SCs. In conclusion, our results highlight the function and regulation of dynamic DNA methylation in testis development.
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Affiliation(s)
- Changfan Zhou
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Long Zhang
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Dequan Xu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Haisheng Ding
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Shuailong Zheng
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Min Liu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
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Batorek-Lukač N, Kress K, Čandek-Potokar M, Fazarinc G, Škrlep M, Poklukar K, Wesoly R, Stefanski V, Vrecl M. Immunocastration in adult boars as a model for late-onset hypogonadism. Andrology 2022; 10:1217-1232. [PMID: 35752946 PMCID: PMC9545940 DOI: 10.1111/andr.13219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/02/2022]
Abstract
Background While immunocastration has been studied in male pre‐pubertal pigs, data on older, sexually mature animals are limited. To understand the physiological effects of androgen deprivation in the late sexual development phase, we compared mature immunocastrated boars (n = 19; average age = 480 days) to young male immunocastrated pigs (n = 6; average age = 183 days) and young entire males (n = 6; average age = 186 days) as positive and negative controls, respectively. Objectives We hypothesized that the timing of gonadotropin‐releasing hormone suppression (early or late sexual development phases) influences the extent of reproductive function inhibition, histological structure of testicular tissue, and expression levels of selected genes related to steroid metabolism. Materials and methods Antibody titer, hormonal status, and histomorphometric analysis of testicular tissue were subjected to principal component analysis followed by hierarchical clustering to evaluate the immunocastration effectiveness in mature boars. Results Hierarchical clustering differentiated mature immunocastrated boars clustered with young immunocastrated pigs from those clustered with entire males. Although all mature immunocastrated boars responded to vaccination, as evidenced by the increased gonadotropin‐releasing hormone antibody titers (p < 0.001), decreased serum luteinizing hormone concentrations (p = 0.002), and changes in testicular tissue vascularization (lighter and less red testicular parenchyma; p ≤ 0.001), the responses were variable. Sharp decreases in testes index (p < 0.001), Leydig cell volume density (p < 0.001), Leydig cell nucleus‐to‐cytoplasm ratio (p < 0.001), and testosterone concentration (p < 0.001) were observed in mature immunocastrated boars clustered with young immunocastrated pigs compared with those that clustered with entire males. Additionally, mature immunocastrated boars clustered with young immunocastrated pigs showed lower hydroxysteroid 17‐beta dehydrogenase 7 expression than entire males (p < 0.05). The young immunocastrated pigs group showed higher follicle‐stimulating hormone receptors than the entire males and mature immunocastrated boars, lower steroidogenic acute regulatory protein expression levels compared with entire males, and mature immunocastrated boars clustered with entire males (p < 0.01). Conclusion The two‐dose vaccination regime resulted in progressive but variable regression of testicular function in adult (post‐pubertal) pigs; however, it was insufficient to induce a complete immunocastration response in all animals.
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Affiliation(s)
- Nina Batorek-Lukač
- Agricultural Institute of Slovenia, Hacquetova ulica 17, Ljubljana, SI-1000, Slovenia
| | - Kevin Kress
- University of Hohenheim, Garbenstraße 17, Stuttgart, 70599, Germany.,Schweinezuchtverband Baden-Württemberg e.V., Im Wolfer 10, Stuttgart, 70599, Germany
| | - Marjeta Čandek-Potokar
- Agricultural Institute of Slovenia, Hacquetova ulica 17, Ljubljana, SI-1000, Slovenia.,Faculty of Agriculture and Life Sciences, University of Maribor, Pivola 10, Hoče, SI-2311, Slovenia
| | - Gregor Fazarinc
- Veterinary Faculty, University of Ljubljana, Gerbičeva ulica 60, Ljubljana, SI-1000, Slovenia
| | - Martin Škrlep
- Agricultural Institute of Slovenia, Hacquetova ulica 17, Ljubljana, SI-1000, Slovenia
| | - Klavdija Poklukar
- Agricultural Institute of Slovenia, Hacquetova ulica 17, Ljubljana, SI-1000, Slovenia
| | - Raffael Wesoly
- Schweinezuchtverband Baden-Württemberg e.V., Im Wolfer 10, Stuttgart, 70599, Germany
| | - Volker Stefanski
- University of Hohenheim, Garbenstraße 17, Stuttgart, 70599, Germany
| | - Milka Vrecl
- Veterinary Faculty, University of Ljubljana, Gerbičeva ulica 60, Ljubljana, SI-1000, Slovenia
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Correlation Networks Provide New Insights into the Architecture of Testicular Steroid Pathways in Pigs. Genes (Basel) 2021; 12:genes12040551. [PMID: 33918852 PMCID: PMC8069258 DOI: 10.3390/genes12040551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/19/2022] Open
Abstract
Steroid metabolism is a fundamental process in the porcine testis to provide testosterone but also estrogens and androstenone, which are essential for the physiology of the boar. This study concerns boars at an early stage of puberty. Using a RT-qPCR approach, we showed that the transcriptional activities of several genes providing key enzymes involved in this metabolism (such as CYP11A1) are correlated. Surprisingly, HSD17B3, a key gene for testosterone production, was absent from this group. An additional weighted gene co-expression network analysis was performed on two large sets of mRNA-seq to identify co-expression modules. Of these modules, two containing either CYP11A1 or HSD17B3 were further analyzed. This comprehensive correlation meta-analysis identified a group of 85 genes with CYP11A1 as hub gene, but did not allow the characterization of a robust correlation network around HSD17B3. As the CYP11A1-group includes most of the genes involved in steroid synthesis pathways (including LHCGR encoding for the LH receptor), it may control the synthesis of most of the testicular steroids. The independent expression of HSD17B3 probably allows part of the production of testosterone to escape this control. This CYP11A1-group contained also INSL3 and AGT genes encoding a peptide hormone and an angiotensin peptide precursor, respectively.
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You X, Qu Y, Zhang Y, Huang J, Gao X, Huang C, Luo G, Liu Q, Liu M, Xu D. Mir-331-3p Inhibits PRRSV-2 Replication and Lung Injury by Targeting PRRSV-2 ORF1b and Porcine TNF-α. Front Immunol 2020; 11:547144. [PMID: 33072088 PMCID: PMC7544944 DOI: 10.3389/fimmu.2020.547144] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/18/2020] [Indexed: 12/27/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) caused by a single-stranded RNA virus (PRRSV) is a highly infectious respiratory disease and leads to huge economic losses to the swine industry worldwide. To investigate the role of miRNAs in the infection and lung injury induced by PRRSV, the differentially expressed miRNAs (DE-miRs) were isolated from PRRSV-2 infected/mock-infected PAMs of Meishan, Landrace, Pietrain, and Qingping pigs at 9, 36, and 60 hpi. Mir-331-3p was the only common DE-miR in each set of miRNA expression profile at 36 hpi. Mir-210 was one of 7 common DE-miRs between PRRSV infected and mock-infected PAMs of Meishan, Pietrain, and Qingping pigs at 60 hpi. Mir-331-3p/mir-210 could target PRRSV-2 ORF1b, bind and downregulate porcine TNF-α/STAT1 expression, and inhibit PRRSV-2 replication, respectively. Furthermore, STAT1 and TNF-α could mediate the transcriptional activation of MCP-1, VCAM-1, and ICAM-1. STAT1 could also upregulate the expression of TNF-α by binding to its promoter region. In vivo, pEGFP-N1-mir-331-3p could significantly reduce viral replication and pathological changes in PRRSV-2 infected piglets. Taken together, Mir-331-3p/mir-210 have significant roles in the infection and lung injury caused by PRRSV-2, and they may be promising therapeutic targets for PRRS and lung injury/inflammation.
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Affiliation(s)
- Xiangbin You
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Colleges of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yilin Qu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Colleges of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yue Zhang
- Colleges of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jingshu Huang
- Agricultural Development Center of Hubei Province, Wuhan, China
| | - Xiaoxiao Gao
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Colleges of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Chengyu Huang
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Colleges of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Gan Luo
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Colleges of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Qian Liu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Colleges of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Min Liu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Colleges of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Dequan Xu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Colleges of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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Shi L, Wang L, Liu J, Deng T, Yan H, Zhang L, Liu X, Gao H, Hou X, Wang L, Zhao F. Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population. J Anim Sci Biotechnol 2020; 11:46. [PMID: 32355558 PMCID: PMC7187514 DOI: 10.1186/s40104-020-00447-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/12/2020] [Indexed: 01/24/2023] Open
Abstract
Background Runs of homozygosity (ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms (SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here, we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs (FROH), homozygosity (FHOM), genomic relationship matrix (FGRM) and pedigree (FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes. Results In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes (SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between FROH_total and FHOM, while the lowest was − 0.083 between FGRM and FPED. The correlations between FPED and FROH using four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes (SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4. Conclusion FROH can be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, FROH can provide an alternative to inbreeding estimates. Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection.
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Affiliation(s)
- Liangyu Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Ligang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Jiaxin Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Tianyu Deng
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Hua Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Longchao Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xin Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Hongmei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xinhua Hou
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Lixian Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Fuping Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
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Fallah HP, Rodrigues MS, Corchuelo S, Nóbrega RH, Habibi HR. Role of GnRH Isoforms in Paracrine/Autocrine Control of Zebrafish (Danio rerio) Spermatogenesis. Endocrinology 2020; 161:5701481. [PMID: 31930304 DOI: 10.1210/endocr/bqaa004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/10/2020] [Indexed: 12/25/2022]
Abstract
Abstract
It is well established that hypothalamic GnRH (gonadotropin-releasing hormone) is one of the key peptides involved in the neuroendocrine control of testicular development and spermatogenesis. However, the role of GnRH as a paracrine regulator of testicular function has not been fully investigated. The present study demonstrates the presence of GnRH and its receptors in the zebrafish (Danio rerio) testis, and provides information on direct action of native GnRH isoforms (GnRH2 and GnRH3) on different stages of spermatogenesis in this model. Both GnRH2 and GnRH3 stimulated basal spermatogenesis by increasing numbers of type Aund spermatogonia, spermatozoa, and testosterone release, and in this study GnRH2 exerted higher relative activity than GnRH3. Next, we evaluated the effects of GnRH isoforms on human chorionic gonadotropin (hCG)- and follicle-stimulating hormone (Fsh)-induced spermatogenesis. The 2 GnRH isoforms were found to have different effects on Fsh- and hCG-induced response depending on the stage of spermatogenesis and concentration of the peptides. The results provide strong support for the hypothesis that locally produced GnRH2 and GnRH3 are important components of the complex multifactorial system that regulates testicular germinal cell development and function in adult zebrafish.
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Affiliation(s)
- Hamideh P Fallah
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Maira S Rodrigues
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Morphology, Reproductive and Molecular Biology Group, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Sheryll Corchuelo
- Department of Morphology, Reproductive and Molecular Biology Group, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Rafael H Nóbrega
- Department of Morphology, Reproductive and Molecular Biology Group, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Hamid R Habibi
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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