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Peng W, Fu C, Shu S, Wang G, Wang H, Yue B, Zhang M, Liu X, Liu Y, Zhang J, Zhong J, Wang J. Whole-genome resequencing of major populations revealed domestication-related genes in yaks. BMC Genomics 2024; 25:69. [PMID: 38233755 PMCID: PMC10795378 DOI: 10.1186/s12864-024-09993-7] [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: 05/04/2023] [Accepted: 01/08/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND The yak is a symbol of the Qinghai-Tibet Plateau and provides important basic resources for human life on the plateau. Domestic yaks have been subjected to strong artificial selection and environmental pressures over the long-term. Understanding the molecular mechanisms of phenotypic differences in yak populations can reveal key functional genes involved in the domestication process and improve genetic breeding. MATERIAL AND METHOD Here, we re-sequenced 80 yaks (Maiwa, Yushu, and Huanhu populations) to identify single-nucleotide polymorphisms (SNPs) as genetic variants. After filtering and quality control, remaining SNPs were kept to identify the genome-wide regions of selective sweeps associated with domestic traits. The four methods (π, XPEHH, iHS, and XP-nSL) were used to detect the population genetic separation. RESULTS By comparing the differences in the population stratification, linkage disequilibrium decay rate, and characteristic selective sweep signals, we identified 203 putative selective regions of domestic traits, 45 of which were mapped to 27 known genes. They were clustered into 4 major GO biological process terms. All known genes were associated with seven major domestication traits, such as dwarfism (ANKRD28), milk (HECW1, HECW2, and OSBPL2), meat (SPATA5 and GRHL2), fertility (BTBD11 and ARFIP1), adaptation (NCKAP5, ANTXR1, LAMA5, OSBPL2, AOC2, and RYR2), growth (GRHL2, GRID2, SMARCAL1, and EPHB2), and the immune system (INPP5D and ADCYAP1R1). CONCLUSIONS We provided there is an obvious genetic different among domestic progress in these three yak populations. Our findings improve the understanding of the major genetic switches and domestic processes among yak populations.
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Affiliation(s)
- Wei Peng
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, 810016, China
| | - Changqi Fu
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, 810016, China
| | - Shi Shu
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, 810016, China
| | - Guowen Wang
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, 810016, China
| | - Hui Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Sichuan Province and Ministry of Education), Southwest Minzu University, Chengdu, 610041, China
| | - Binglin Yue
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Sichuan Province and Ministry of Education), Southwest Minzu University, Chengdu, 610041, China
| | - Ming Zhang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Sichuan Province and Ministry of Education), Southwest Minzu University, Chengdu, 610041, China
| | - Xinrui Liu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Sichuan Province and Ministry of Education), Southwest Minzu University, Chengdu, 610041, China
| | - Yaxin Liu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Sichuan Province and Ministry of Education), Southwest Minzu University, Chengdu, 610041, China
| | - Jun Zhang
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, 810016, China.
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Sichuan Province and Ministry of Education), Southwest Minzu University, Chengdu, 610041, China.
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Sichuan Province and Ministry of Education), Southwest Minzu University, Chengdu, 610041, China.
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Zeng J, Liu N, Yang Y, Cheng Y, Li Y, Guo X, Luo Q, Zhu L, Guan H, Song B, Sun X. Pak2 reduction induces a failure of early embryonic development in mice. Reprod Biol Endocrinol 2021; 19:181. [PMID: 34879863 PMCID: PMC8656077 DOI: 10.1186/s12958-021-00865-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/28/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The quality of the early embryo is vital to embryonic development and implantation. As a highly conserved serine/threonine kinase, p21-activated kinase 2 (Pak2) participates in diverse biologic processes, especially in cytoskeleton remodeling and cell apoptosis. In mice, Pak2 knock out and endothelial depletion of Pak2 showed embryonic lethality. However, the role of Pak2 in preimplantation embryos remains unelucidated. METHODS In the present work, Pak2 was reduced using a specific small interfering RNA in early mouse embryos, validating the unique roles of Pak2 in spindle assembly and DNA repair during mice early embryonic development. We also employed immunoblotting, immunostaining, in vitro fertilization (IVF) and image quantification analyses to test the Pak2 knockdown on the embryonic development progression, spindle assembly, chromosome alignment, oxidative stress, DNA lesions and blastocyst cell apoptosis. Areas in chromatin with γH2AX were detected by immunofluorescence microscopy and serve as a biomarker of DNA damages. RESULTS We found that Pak2 knockdown significantly reduced blastocyst formation of early embryos. In addition, Pak2 reduction led to dramatically increased abnormal spindle assembly and chromosomal aberrations in the embryos. We noted the overproduction of reactive oxygen species (ROS) with Pak2 knockdown in embryos. In response to DNA double strand breaks (DSBs), the histone protein H2AX is specifically phosphorylated at serine139 to generate γH2AX, which is used to quantitative DSBs. In this research, Pak2 knockdown also resulted in the accumulation of phosphorylated γH2AX, indicative of increased embryonic DNA damage. Commensurate with this, a significantly augmented rate of blastocyst cell apoptosis was detected in Pak2-KD embryos compared to their controls. CONCLUSIONS Collectively, our data suggest that Pak2 may serve as an important regulator of spindle assembly and DNA repair, and thus participate in the development of early mouse embryos.
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Affiliation(s)
- Juan Zeng
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
| | - Nengqing Liu
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
| | - Yinghong Yang
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
| | - Yi Cheng
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
| | - Yuanshuai Li
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
| | - Xiaoxia Guo
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
| | - Qian Luo
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
| | - Lifen Zhu
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
| | - Hongmei Guan
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
| | - Bing Song
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China
| | - Xiaofang Sun
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, Guangdong, China.
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Dolebo AT, Khayatzadeh N, Melesse A, Wragg D, Rekik M, Haile A, Rischkowsky B, Rothschild MF, Mwacharo JM. Genome-wide scans identify known and novel regions associated with prolificacy and reproduction traits in a sub-Saharan African indigenous sheep (Ovis aries). Mamm Genome 2019; 30:339-352. [PMID: 31758253 PMCID: PMC6884434 DOI: 10.1007/s00335-019-09820-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/12/2019] [Indexed: 02/05/2023]
Abstract
Maximizing the number of offspring born per female is a key functionality trait in commercial- and/or subsistence-oriented livestock enterprises. Although the number of offspring born is closely associated with female fertility and reproductive success, the genetic control of these traits remains poorly understood in sub-Saharan Africa livestock. Using selection signature analysis performed on Ovine HD BeadChip data from the prolific Bonga sheep in Ethiopia, 41 candidate regions under selection were identified. The analysis revealed one strong selection signature on a candidate region on chromosome X spanning BMP15, suggesting this to be the primary candidate prolificacy gene in the breed. The analysis also identified several candidate regions spanning genes not reported before in prolific sheep but underlying fertility and reproduction in other species. The genes associated with female reproduction traits included SPOCK1 (age at first oestrus), GPR173 (mediator of ovarian cyclicity), HB-EGF (signalling early pregnancy success) and SMARCAL1 and HMGN3a (regulate gene expression during embryogenesis). The genes involved in male reproduction were FOXJ1 (sperm function and successful fertilization) and NME5 (spermatogenesis). We also observed genes such as PKD2L2, MAGED1 and KDM3B, which have been associated with diverse fertility traits in both sexes of other species. The results confirm the complexity of the genetic mechanisms underlying reproduction while suggesting that prolificacy in the Bonga sheep, and possibly African indigenous sheep is partly under the control of BMP15 while other genes that enhance male and female fertility are essential for reproductive fitness.
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Affiliation(s)
- Asrat Tera Dolebo
- Southern Agricultural Research Institute (SARI), P.O. Box 06, Hawassa, Ethiopia
- Department of Animal and Range Sciences, Hawassa University, P.O Box 5, Hawassa, Ethiopia
| | - Negar Khayatzadeh
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences (BOKU), Gregor-Mendel-Strasse, 1180, Vienna, Austria
| | - Aberra Melesse
- Department of Animal and Range Sciences, Hawassa University, P.O Box 5, Hawassa, Ethiopia
| | - David Wragg
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, UK
| | - Mourad Rekik
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Aynalem Haile
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Barbara Rischkowsky
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011-3150, USA
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia.
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The effect of ovine oocyte vitrification on expression of subset of genes involved in epigenetic modifications during oocyte maturation and early embryo development. Theriogenology 2016; 86:2136-2146. [DOI: 10.1016/j.theriogenology.2016.07.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 07/05/2016] [Accepted: 07/05/2016] [Indexed: 11/20/2022]
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Li DD, Guo CH, Yue L, Duan CC, Yang ZQ, Cao H, Guo B, Yue ZP. Expression, regulation and function of Hmgn3 during decidualization in mice. Mol Cell Endocrinol 2015; 413:13-25. [PMID: 26112184 DOI: 10.1016/j.mce.2015.05.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 01/12/2023]
Abstract
Although Hmgn3 is involved in the regulation of development and cellular differentiation, its physiological roles on decidualization are still unknown. Here we showed that Hmgn3 was highly expressed in the decidua and decidualizing stromal cells. Overexpression of Hmgn3 variants, Hmgn3a or Hmgn3b, enhanced the expression of decidualization markers Prl8a2 and Prl3c1, whereas inhibition of Hmgn3 reduced their expression. Hmgn3 could mediate the effects of Hoxa10 and cAMP on the expression of Prl8a2 and Prl3c1. Further study found that Hmgn3 directed the process of decidualization through influencing the expression of Hand2. Progesterone could induce the expression of Hmgn3 in the ovariectomized mouse uterus, uterine epithelial cells and stromal cells. Knockdown of Hoxa10 with siRNA alleviated the induction of progesterone and cAMP on Hmgn3 expression. Simultaneously, siRNA-mediated down-regulation of Hmgn3 in the uterine stromal cells could attenuate the effects of progesterone, cAMP and Hoxa10 on the expression of Hand2. Collectively, Hmgn3 may play an important role during mouse decidualization.
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Affiliation(s)
- Dang-Dang Li
- College of Veterinary Medicine, Jilin University, Changchun, PR China
| | - Chuan-Hui Guo
- College of Veterinary Medicine, Jilin University, Changchun, PR China
| | - Liang Yue
- College of Clinical Medicine, Jilin University, Changchun, PR China
| | - Cui-Cui Duan
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, PR China
| | - Zhan-Qing Yang
- College of Veterinary Medicine, Jilin University, Changchun, PR China
| | - Hang Cao
- College of Veterinary Medicine, Jilin University, Changchun, PR China
| | - Bin Guo
- College of Veterinary Medicine, Jilin University, Changchun, PR China.
| | - Zhan-Peng Yue
- College of Veterinary Medicine, Jilin University, Changchun, PR China
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Sylvestre EL, Robert C, Pennetier S, Labrecque R, Gilbert I, Dufort I, Léveillé MC, Sirard MA. Evolutionary conservation of the oocyte transcriptome among vertebrates and its implications for understanding human reproductive function. Mol Hum Reprod 2013; 19:369-79. [PMID: 23340479 DOI: 10.1093/molehr/gat006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Cross-phylum and cross-species comparative transcriptomic analyses provide an evolutionary perspective on how specific tissues use genomic information. A significant mRNA subset present in the oocytes of most vertebrates is stabilized or stored for post-LH surge use. Since transcription is arrested in the oocyte before ovulation, this RNA is important for completing maturation and sustaining embryo development until zygotic genome activation. We compared the human oocyte transcriptome with an oocyte-enriched subset of mouse, bovine and frog (Xenopus laevis) genes in order to evaluate similarities between species. Graded temperature stringency hybridization on a multi-species oocyte cDNA array was used to measure the similarity of preferentially expressed sequences to the human oocyte library. Identity analysis of 679 human orthologs compared with each identified official gene symbol found in the subtractive (somatic-oocyte) libraries comprising our array revealed that bovine/human similarity was greater than mouse/human or frog/human similarity. However, based on protein sequence, mouse/human similarity was greater than bovine/human similarity. Among the genes over-expressed in oocytes relative to somatic tissue in Xenopus, Mus and Bos, a high level of conservation was found relative to humans, especially for genes involved in early embryonic development.
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Affiliation(s)
- Eve-Lyne Sylvestre
- Centre de Recherche en Biologie de la Reproduction, Département des Sciences Animales, Université Laval, Québec, QC, Canada G1V 0A6
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Rodriguez-Osorio N, Urrego R, Cibelli JB, Eilertsen K, Memili E. Reprogramming mammalian somatic cells. Theriogenology 2012; 78:1869-86. [PMID: 22979962 DOI: 10.1016/j.theriogenology.2012.05.030] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 05/20/2012] [Accepted: 05/31/2012] [Indexed: 01/23/2023]
Abstract
Somatic cell nuclear transfer (SCNT), the technique commonly known as cloning, permits transformation of a somatic cell into an undifferentiated zygote with the potential to develop into a newborn animal (i.e., a clone). In somatic cells, chromatin is programmed to repress most genes and express some, depending on the tissue. It is evident that the enucleated oocyte provides the environment in which embryonic genes in a somatic cell can be expressed. This process is controlled by a series of epigenetic modifications, generally referred to as "nuclear reprogramming," which are thought to involve the removal of reversible epigenetic changes acquired during cell differentiation. A similar process is thought to occur by overexpression of key transcription factors to generate induced pluripotent stem cells (iPSCs), bypassing the need for SCNT. Despite its obvious scientific and medical importance, and the great number of studies addressing the subject, the molecular basis of reprogramming in both reprogramming strategies is largely unknown. The present review focuses on the cellular and molecular events that occur during nuclear reprogramming in the context of SCNT and the various approaches currently being used to improve nuclear reprogramming. A better understanding of the reprogramming mechanism will have a direct impact on the efficiency of current SCNT procedures, as well as iPSC derivation.
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WANG H, CAMARGO RODRIGUEZ O, MEMILI E. Mycotoxin Alpha-Zearalenol Impairs the Quality of Preimplantation Porcine Embryos. J Reprod Dev 2012; 58:338-43. [DOI: 10.1262/jrd.11-113h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Hongfeng WANG
- Department of Animal and Dairy Sciences, Mississippi State University, MS, USA
- Present: College of Engineering, Marquette University, Wisconsin, USA
- Department of Animal and Dairy Sciences, Mississippi State University, MS, USA
- Present: College of Engineering, Marquette University, Wisconsin, USA
| | - Omar CAMARGO RODRIGUEZ
- Department of Animal and Dairy Sciences, Mississippi State University, MS, USA
- Present: Department of Animal Production, National University of Colombia, Medellín, Colombia
- Department of Animal and Dairy Sciences, Mississippi State University, MS, USA
- Present: Department of Animal Production, National University of Colombia, Medellín, Colombia
| | - Erdogan MEMILI
- Department of Animal and Dairy Sciences, Mississippi State University, MS, USA
- Department of Animal and Dairy Sciences, Mississippi State University, MS, USA
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Tellam RL, Lemay DG, Van Tassell CP, Lewin HA, Worley KC, Elsik CG. Unlocking the bovine genome. BMC Genomics 2009; 10:193. [PMID: 19393070 PMCID: PMC2680899 DOI: 10.1186/1471-2164-10-193] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Accepted: 04/24/2009] [Indexed: 02/06/2023] Open
Abstract
The draft genome sequence of cattle (Bos taurus) has now been analyzed by the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium, which together represent an extensive collaboration involving more than 300 scientists from 25 different countries.
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Affiliation(s)
- Ross L Tellam
- CSIRO Livestock Industries, St Lucia, QLD, Australia.
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