1
|
Liu K, Liu Y, Chu M. Detection of polymorphisms in six genes and their association analysis with litter size in sheep. Anim Biotechnol 2024; 35:2309954. [PMID: 38294691 DOI: 10.1080/10495398.2024.2309954] [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: 02/01/2024]
Abstract
Litter size in sheep is a complex trait controlled by micro-effective polygenes. APAF1, CLSTN2, CTH, PLCB1, PLCB4, and CHST11 are all involved in mammalian reproduction. However, the effects of these genes on litter size in sheep are still unclear. Therefore, in this study, we used Sequenom MassARRAY® SNP assay technology to type the single nucleotide polymorphisms (SNPs) loci of six genes in five sheep breeds. The results showed that most sheep breeds contain three genotypes at each locus. Then, we conducted population genetic analysis on the SNPs of six genes and found that the polymorphic information content in all sheep breeds ranged from 0 to 0.37, and most sheep breeds were in Hardy-Weinberg equilibrium (p > 0.05). In addition, association analysis in Small Tail Han sheep indicated that the rs399534524 locus in CLSTN2 was highly associated with first parity litter size, and litter size in ewes with CT genotype was higher than that in ewes with CC genotype or TT genotype. Furthermore, the rs407142552 locus in CTH was highly associated with second parity litter size in Small Tail Han sheep, and litter size in ewes with CT genotype was higher than that in ewes with TT genotype. Finally, we predicted the CTH and CLSTN2 protein interaction network and found that HTR1E, NOM1, CCDC174 and ALPK3 interact with CLSTN2 and have been reported as candidate genes related to litter size in sheep. These results suggest that they may be useful genetic markers for increasing litter size in sheep.
Collapse
Affiliation(s)
- Kai Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yufang Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| |
Collapse
|
2
|
Yang J, Wang DF, Huang JH, Zhu QH, Luo LY, Lu R, Xie XL, Salehian-Dehkordi H, Esmailizadeh A, Liu GE, Li MH. Structural variant landscapes reveal convergent signatures of evolution in sheep and goats. Genome Biol 2024; 25:148. [PMID: 38845023 PMCID: PMC11155191 DOI: 10.1186/s13059-024-03288-6] [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] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution. RESULTS We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats. CONCLUSIONS Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.
Collapse
Affiliation(s)
- Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qiang-Hui Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ling-Yun Luo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ran Lu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, Iran
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
3
|
Blaj I, Tetens J, Bennewitz J, Thaller G, Falker-Gieske C. Structural variants and tandem repeats in the founder individuals of four F 2 pig crosses and implications to F 2 GWAS results. BMC Genomics 2022; 23:631. [PMID: 36057580 PMCID: PMC9440560 DOI: 10.1186/s12864-022-08716-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/23/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Structural variants and tandem repeats are relevant sources of genomic variation that are not routinely analyzed in genome wide association studies mainly due to challenging identification and genotyping. Here, we profiled these variants via state-of-the-art strategies in the founder animals of four F2 pig crosses using whole-genome sequence data (20x coverage). The variants were compared at a founder level with the commonly screened SNPs and small indels. At the F2 level, we carried out an association study using imputed structural variants and tandem repeats with four growth and carcass traits followed by a comparison with a previously conducted SNPs and small indels based association study. RESULTS A total of 13,201 high confidence structural variants and 103,730 polymorphic tandem repeats (with a repeat length of 2-20 bp) were profiled in the founders. We observed a moderate to high (r from 0.48 to 0.57) level of co-localization between SNPs or small indels and structural variants or tandem repeats. In the association step 56.56% of the significant variants were not in high LD with significantly associated SNPs and small indels identified for the same traits in the earlier study and thus presumably not tagged in case of a standard association study. For the four growth and carcass traits investigated, many of the already proposed candidate genes in our previous studies were confirmed and additional ones were identified. Interestingly, a common pattern on how structural variants or tandem repeats regulate the phenotypic traits emerged. Many of the significant variants were embedded or nearby long non-coding RNAs drawing attention to their functional importance. Through which specific mechanisms the identified long non-coding RNAs and their associated structural variants or tandem repeats contribute to quantitative trait variation will need further investigation. CONCLUSIONS The current study provides insights into the characteristics of structural variants and tandem repeats and their role in association studies. A systematic incorporation of these variants into genome wide association studies is advised. While not of immediate interest for genomic prediction purposes, this will be particularly beneficial for elucidating biological mechanisms driving the complex trait variation.
Collapse
Affiliation(s)
- Iulia Blaj
- Institute of Animal Breeding and Husbandry, Kiel University, Kiel, Germany.
| | - Jens Tetens
- Department of Animal Sciences, Georg-August-University, Göttingen, Germany
- Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany
| | - Jörn Bennewitz
- Institute of Animal Husbandry and Breeding, University of Hohenheim, Stuttgart, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Kiel University, Kiel, Germany
| | | |
Collapse
|
4
|
Nguyen LT, Lau LY, Fortes MRS. Proteomic Analysis of Hypothalamus and Pituitary Gland in Pre and Postpubertal Brahman Heifers. Front Genet 2022; 13:935433. [PMID: 35774501 PMCID: PMC9237413 DOI: 10.3389/fgene.2022.935433] [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: 05/03/2022] [Accepted: 05/25/2022] [Indexed: 11/28/2022] Open
Abstract
The hypothalamus and the pituitary gland are directly involved in the complex systemic changes that drive the onset of puberty in cattle. Here, we applied integrated bioinformatics to elucidate the critical proteins underlying puberty and uncover potential molecular mechanisms from the hypothalamus and pituitary gland of prepubertal (n = 6) and postpubertal (n = 6) cattle. Proteomic analysis in the hypothalamus and pituitary gland revealed 275 and 186 differentially abundant (DA) proteins, respectively (adjusted p-value < 0.01). The proteome profiles found herein were integrated with previously acquired transcriptome profiles. These transcriptomic studies used the same tissues harvested from the same heifers at pre- and post-puberty. This comparison detected a small number of matched transcripts and protein changes at puberty in each tissue, suggesting the need for multiple omics analyses for interpreting complex biological systems. In the hypothalamus, upregulated DA proteins at post-puberty were enriched in pathways related to puberty, including GnRH, calcium and oxytocin signalling pathways, whereas downregulated proteins were observed in the estrogen signalling pathway, axon guidance and GABAergic synapse. Additionally, this study revealed that ribosomal pathway proteins in the pituitary were involved in the pubertal development of mammals. The reported molecules and derived protein-protein networks are a starting point for future experimental approaches that might dissect with more detail the role of each molecule to provide new insights into the mechanisms of puberty onset in cattle.
Collapse
Affiliation(s)
- Loan To Nguyen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
- *Correspondence: Loan To Nguyen,
| | - Li Yieng Lau
- Agency of Science, Technology and Research, Singapore, Singapore
| | | |
Collapse
|
5
|
Carroll PA, Freie BW, Cheng PF, Kasinathan S, Gu H, Hedrich T, Dowdle JA, Venkataramani V, Ramani V, Wu X, Raftery D, Shendure J, Ayer DE, Muller CH, Eisenman RN. The glucose-sensing transcription factor MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis. PLoS Biol 2021; 19:e3001085. [PMID: 34669700 PMCID: PMC8528285 DOI: 10.1371/journal.pbio.3001085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 09/24/2021] [Indexed: 01/02/2023] Open
Abstract
Male germ cell (GC) production is a metabolically driven and apoptosis-prone process. Here, we show that the glucose-sensing transcription factor (TF) MAX-Like protein X (MLX) and its binding partner MondoA are both required for male fertility in the mouse, as well as survival of human tumor cells derived from the male germ line. Loss of Mlx results in altered metabolism as well as activation of multiple stress pathways and GC apoptosis in the testes. This is concomitant with dysregulation of the expression of male-specific GC transcripts and proteins. Our genomic and functional analyses identify loci directly bound by MLX involved in these processes, including metabolic targets, obligate components of male-specific GC development, and apoptotic effectors. These in vivo and in vitro studies implicate MLX and other members of the proximal MYC network, such as MNT, in regulation of metabolism and differentiation, as well as in suppression of intrinsic and extrinsic death signaling pathways in both spermatogenesis and male germ cell tumors (MGCTs).
Collapse
Affiliation(s)
- Patrick A. Carroll
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Brian W. Freie
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Pei Feng Cheng
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Sivakanthan Kasinathan
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Haiwei Gu
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington, United States of America
| | - Theresa Hedrich
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - James A. Dowdle
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Vivek Venkataramani
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Vijay Ramani
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Xiaoying Wu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Daniel Raftery
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington, United States of America
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, United States of America
| | - Donald E. Ayer
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Charles H. Muller
- Male Fertility Lab, Department of Urology, University of Washington, Seattle, Washington, United States of America
| | - Robert N. Eisenman
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| |
Collapse
|
6
|
IP3R Channels in Male Reproduction. Int J Mol Sci 2020; 21:ijms21239179. [PMID: 33276427 PMCID: PMC7730405 DOI: 10.3390/ijms21239179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
As a second messenger in cellular signal transduction, calcium signaling extensively participates in various physiological activities, including spermatogenesis and the regulation of sperm function. Abnormal calcium signaling is highly correlated with male infertility. Calcium signaling is mainly regulated by both extracellular calcium influx and the release of calcium stores. Inositol 1,4,5-trisphosphate receptor (IP3R) is a widely expressed channel for calcium stores. After being activated by inositol 1,4,5-trisphosphate (IP3) and calcium signaling at a lower concentration, IP3R can regulate the release of Ca2+ from stores into cytoplasm, and eventually trigger downstream events. The closure of the IP3R channel caused by a rise in intracellular calcium signals and the activation of the calcium pump jointly restores the calcium store to a normal level. In this review, we aim to discuss structural features of IP3R channels and the underlying mechanism of IP3R channel-mediated calcium signaling and further focus on the research progress of IP3R expression and function in the male reproductive system. Finally, we propose key directions and strategies for research of IP3R in spermatogenesis and the regulation of sperm function to provide more understanding of the function and mechanism of IP3R channel actions in male reproduction.
Collapse
|
7
|
Ding H, Liu M, Zhou C, You X, Su T, Yang Y, Xu D. Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars. BMC Genomics 2020; 21:686. [PMID: 33008286 PMCID: PMC7531090 DOI: 10.1186/s12864-020-07096-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 09/23/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis. RESULTS In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 (PLCβ1) gene was verified to be a target of ssc-mir-423-5p. CONCLUSIONS This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.
Collapse
Affiliation(s)
- Haisheng Ding
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, and Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, People's Republic of China
| | - Min Liu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, and Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Changfan Zhou
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, and Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Xiangbin You
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, and Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Tao Su
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, and Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Youbing Yang
- College of Animal Science and Technology, Henan University of Science & Technology, Luoyang, 471023, People's Republic of China
| | - Dequan Xu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, and Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
| |
Collapse
|
8
|
Galliou JM, Kiser JN, Oliver KF, Seabury CM, Moraes JGN, Burns GW, Spencer TE, Dalton J, Neibergs HL. Identification of Loci and Pathways Associated with Heifer Conception Rate in U.S. Holsteins. Genes (Basel) 2020; 11:genes11070767. [PMID: 32650431 PMCID: PMC7397161 DOI: 10.3390/genes11070767] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/27/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022] Open
Abstract
Heifer conception rate (HCR) is defined as the percentage of inseminated heifers that become pregnant at each service. The genome-wide association analyses in this study focused on identifying the loci associated with Holstein heifer (n = 2013) conception rate at first service (HCR1) and the number of times bred (TBRD) to achieve a pregnancy. There were 348 unique loci associated (p < 5 × 10−8) with HCR1 and 615 unique loci associated (p < 5 × 10−8) with TBRD. The two phenotypes shared 302 loci, and 56 loci were validated in independent cattle populations. There were 52 transcription factor binding sites (TFBS) and 552 positional candidate genes identified in the HCR1- and TBRD-associated loci. The positional candidate genes and the TFBS associated with HCR1 and TBRD were used in the ingenuity pathway analysis (IPA). In the IPA, 11 pathways, 207 master regulators and 11 upstream regulators were associated (p < 1.23 × 10−5) with HCR1 and TBRD. The validated loci associated with both HCR1 and TBRD make good candidates for genomic selection and further investigations to elucidate the mechanisms associated with subfertility and infertility.
Collapse
Affiliation(s)
- Justine M. Galliou
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA; (J.M.G.); (J.N.K.); (K.F.O.)
| | - Jennifer N. Kiser
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA; (J.M.G.); (J.N.K.); (K.F.O.)
| | - Kayleen F. Oliver
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA; (J.M.G.); (J.N.K.); (K.F.O.)
| | - Christopher M. Seabury
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA;
| | - Joao G. N. Moraes
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA; (J.G.N.M.); (G.W.B.); (T.E.S.)
| | - Gregory W. Burns
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA; (J.G.N.M.); (G.W.B.); (T.E.S.)
| | - Thomas E. Spencer
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA; (J.G.N.M.); (G.W.B.); (T.E.S.)
| | - Joseph Dalton
- Department of Animal and Veterinary Sciences, University of Idaho, Caldwell, ID 83844, USA;
| | - Holly L. Neibergs
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA; (J.M.G.); (J.N.K.); (K.F.O.)
- Correspondence:
| |
Collapse
|
9
|
Varón-González C, Pallares LF, Debat V, Navarro N. Mouse Skull Mean Shape and Shape Robustness Rely on Different Genetic Architectures and Different Loci. Front Genet 2019; 10:64. [PMID: 30809244 PMCID: PMC6379267 DOI: 10.3389/fgene.2019.00064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/24/2019] [Indexed: 12/20/2022] Open
Abstract
The genetic architecture of skull shape has been extensively studied in mice and the results suggest a highly polygenic and additive basis. In contrast few studies have explored the genetic basis of the skull variability. Canalization and developmental stability are the two components of phenotypic robustness. They have been proposed to be emergent properties of the genetic networks underlying the development of the trait itself, but this hypothesis has been rarely tested empirically. Here we use outbred mice to investigate the genetic architecture of canalization of the skull shape by implementing a genome-wide marginal epistatic test on 3D geometric morphometric data. The same data set had been used previously to explore the genetic architecture of the skull mean shape and its developmental stability. Here, we address two questions: (1) Are changes in mean shape and changes in shape variance associated with the same genomic regions? and (2) Do canalization and developmental stability rely on the same loci and genetic architecture and do they involve the same patterns of shape variation? We found that unlike skull mean shape, among-individual shape variance and fluctuating asymmetry (FA) show a total lack of additive effects. They are both associated with complex networks of epistatic interactions involving many genes (protein-coding and regulatory elements). Remarkably, none of the genomic loci affecting mean shape contribute these networks despite their enrichment for genes involved in craniofacial variation and diseases. We also found that the patterns of shape FA and individual variation are largely similar and rely on similar multilocus epistatic genetic networks, suggesting that the processes channeling variation within and among individuals are largely common. However, the loci involved in these two networks are completely different. This in turn underlines the difference in the origin of the variation at these two levels, and points at buffering processes that may be specific to each level.
Collapse
Affiliation(s)
- Ceferino Varón-González
- Institut de Systématique, Évolution, Biodiversité, ISYEB – UMR 7205 – CNRS, MNHN, UPMC, EPHE, UA, Muséum National d’Histoire Naturelle, Sorbonne Universités, Paris, France
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, Dijon, France
| | - Luisa F. Pallares
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, United States
| | - Vincent Debat
- Institut de Systématique, Évolution, Biodiversité, ISYEB – UMR 7205 – CNRS, MNHN, UPMC, EPHE, UA, Muséum National d’Histoire Naturelle, Sorbonne Universités, Paris, France
| | - Nicolas Navarro
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, Dijon, France
- EPHE, PSL University, Dijon, France
| |
Collapse
|
10
|
Wang GB, Zheng Q, Shen YW, Wu XF. Shotgun proteomic analysis of Bombyx mori brain: emphasis on regulation of behavior and development of the nervous system. INSECT SCIENCE 2016; 23:15-27. [PMID: 25504592 DOI: 10.1111/1744-7917.12195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/13/2014] [Indexed: 06/04/2023]
Abstract
The insect brain plays crucial roles in the regulation of growth and development and in all types of behavior. We used sodium dodecyl sulfate polyacrylamide gel electrophoresis and high-performance liquid chromatography - electron spray ionization tandem mass spectrometry (ESI-MS/MS) shotgun to identify the proteome of the silkworm brain, to investigate its protein composition and to understand their biological functions. A total of 2210 proteins with molecular weights in the range of 5.64-1539.82 kDa and isoelectric points in the range of 3.78-12.55 were identified. These proteins were annotated according to Gene Ontology Annotation into the categories of molecular function, biological process and cellular component. We characterized two categories of proteins: one includes behavior-related proteins involved in the regulation of behaviors, such as locomotion, reproduction and learning; the other consists of proteins related to the development or function of the nervous system. The identified proteins were classified into 283 different pathways according to KEGG analysis, including the PI3K-Akt signaling pathway which plays a crucial role in mediating survival signals in a wide range of neuronal cell types. This extensive protein profile provides a basis for further understanding of the physiological functions in the silkworm brain.
Collapse
Affiliation(s)
- Guo-Bao Wang
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Qin Zheng
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yun-Wang Shen
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Xiao-Feng Wu
- College of Animal Science, Zhejiang University, Hangzhou, China
| |
Collapse
|
11
|
Filis P, Kind PC, Spears N. Implantation failure in mice with a disruption in Phospholipase C beta 1 gene: lack of embryonic attachment, aberrant steroid hormone signalling and defective endocannabinoid metabolism. Mol Hum Reprod 2013; 19:290-301. [PMID: 23295235 DOI: 10.1093/molehr/gas067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Phospholipase C beta 1 (PLCβ1) is a downstream effector of G-protein-coupled receptor signalling and holds central roles in reproductive physiology. Mice with a disruption in the Plcβ1 gene are infertile with pleiotropic reproductive defects, the major reproductive block in females being implantation failure. Here, PLCβ1 was demonstrated at the luminal and glandular epithelia throughout the pre- and peri-implantation period, with transient stromal expression during 0.5-1.5 days post coitum (dpc). Examination of implantation sites at 4.5 dpc showed that in females lacking functional PLCβ1 (knock-out (KO) females), embryos failed to establish proper contact with the uterine epithelium. Proliferating luminal epithelial cells were evident in KO implantation sites, indicating failure to establish a receptive uterus. Real-time PCR demonstrated that KO implantation sites had aberrant ovarian steroid signalling, with high levels of estrogen receptor α, lactoferrin and amphiregulin mRNA, while immunohistochemistry revealed very low levels of estrogen receptor α protein, possibly due to rapid receptor turnover. KO implantation sites expressed markedly less fatty acid amide hydrolase and monoacylglycerol lipase, indicating that endocannabinoid metabolism was also affected. Collectively, our results show that PLCβ1 is essential for uterine preparation for implantation, and that defective PLCβ1-mediated signalling during implantation is associated with aberrant ovarian steroid signalling and endocannabinoid metabolism.
Collapse
Affiliation(s)
- Panayiotis Filis
- Centre for Integrative Physiology, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | | | | |
Collapse
|
12
|
O'Donnell L, Nicholls PK, O'Bryan MK, McLachlan RI, Stanton PG. Spermiation: The process of sperm release. SPERMATOGENESIS 2011; 1:14-35. [PMID: 21866274 DOI: 10.4161/spmg.1.1.14525] [Citation(s) in RCA: 244] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 12/16/2010] [Accepted: 12/17/2010] [Indexed: 02/06/2023]
Abstract
Spermiation is the process by which mature spermatids are released from Sertoli cells into the seminiferous tubule lumen prior to their passage to the epididymis. It takes place over several days at the apical edge of the seminiferous epithelium, and involves several discrete steps including remodelling of the spermatid head and cytoplasm, removal of specialized adhesion structures and the final disengagement of the spermatid from the Sertoli cell. Spermiation is accomplished by the co-ordinated interactions of various structures, cellular processes and adhesion complexes which make up the "spermiation machinery". This review addresses the morphological, ultrastructural and functional aspects of mammalian spermiation. The molecular composition of the spermiation machinery, its dynamic changes and regulatory factors are examined. The causes of spermiation failure and their impact on sperm morphology and function are assessed in an effort to understand how this process may contribute to sperm count suppression during contraception and to phenotypes of male infertility.
Collapse
Affiliation(s)
- Liza O'Donnell
- Prince Henry's Institute of Medical Research; Clayton, VIC Australia
| | | | | | | | | |
Collapse
|
13
|
Filis P, Lannagan T, Thomson A, Murray AA, Kind PC, Spears N. Phospholipase C-beta1 signaling affects reproductive behavior, ovulation, and implantation. Endocrinology 2009; 150:3259-66. [PMID: 19342451 PMCID: PMC2703520 DOI: 10.1210/en.2009-0214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Infertility can result from a wide range of defects, from behavioral, through germ cell development and maturation, to fertilization or embryo development. Many of the hormones regulating these processes signal via G protein-coupled receptors, which in turn activate a range of plasma membrane enzymes including phospholipase C (PLC)-beta isoforms. Transgenic mice lacking functional Plc-beta1 (Plc-beta1 KO mice) have been noted to have severely impaired fertility, but there has been little study of the reproductive processes affected by lack of this enzyme. This study examined reproductive behavior, gonadal development, fertilization, and implantation in Plc-beta1 KO mice. Male and female Plc-beta1 KO mice exhibited impaired reproductive behavior. No other defect in reproduction was noted in males, raising the possibility that the reduced fertility of Plc-beta1 KO males could be due solely to impaired behavior. In contrast, female Plc-beta1 KO mice exhibited both behavioral and nonbehavioral defects. Plc-beta1 KO females ovulated only in response to exogenous hormones, with a large proportion of in vivo embryos recovered on embryonic d 4.5 exhibiting abnormal morphology. In addition, uteri of pregnant Plc-beta1 KO females exhibited an implantation defect, with poor embryo attachment and a failure to up-regulate cyclooxygenase-2 mRNA.
Collapse
Affiliation(s)
- Panayiotis Filis
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom
| | | | | | | | | | | |
Collapse
|
14
|
|
15
|
Pesty A, Broca O, Poirot C, Lefèvre B. The Role of PLCβ1 in the Control of Oocyte Meiosis During Folliculogenesis. Reprod Sci 2008; 15:661-72. [DOI: 10.1177/1933719108322434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Arlette Pesty
- UMR-S 566, CEA, DSV/iRCM/SCSR/LGAG; INSERM, Unité 566; Université Denis Diderot-Paris 7; Université Paris-Sud F-92260, Fontenay aux Roses, France
| | - Ophélie Broca
- AP-HP, Groupe hospitalier Pitié Salpêtrière, UF Biologie de la Reproduction, Université Pierre et Marie Curie-Paris 6, Paris, F-75013 France
| | - Catherine Poirot
- AP-HP, Groupe hospitalier Pitié Salpêtrière, UF Biologie de la Reproduction, Université Pierre et Marie Curie-Paris 6, Paris, F-75013 France
| | - Brigitte Lefèvre
- UMR-S 566, CEA, DSV/iRCM/SCSR/LGAG; INSERM, Unité 566; Université Denis Diderot-Paris 7; Université Paris-Sud F-92260, Fontenay aux Roses, France, , AP-HP, Groupe hospitalier Pitié Salpêtrière, UF Biologie de la Reproduction, Université Pierre et Marie Curie-Paris 6, Paris, F-75013 France
| |
Collapse
|
16
|
Ballester M, Sánchez A, Folch JM. Assignment of the phospholipase Cbeta1 (PLCB1) gene to porcine chromosome 17. Anim Genet 2006; 36:516-7. [PMID: 16293129 DOI: 10.1111/j.1365-2052.2005.01354.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M Ballester
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
| | | | | |
Collapse
|